| ▼ src | |
| ► core | |
| ► chemical | |
| ► carbohydrates | |
| CarbohydrateInfo.cc | Method definitions for CarbohydrateInfo |
| CarbohydrateInfo.fwd.hh | Forward declarations for CarbohydrateInfo |
| CarbohydrateInfo.hh | Declarations and simple accessor/mutator definitions for CarbohydrateInfo |
| CarbohydrateInfoManager.cc | Method definitions for CarbohydrateInfoManager |
| CarbohydrateInfoManager.fwd.hh | Forward declaration for CarbohydrateInfoManager |
| CarbohydrateInfoManager.hh | Method declarations for CarbohydrateInfoManager |
| database_io.cc | Database input/output function definitions for carbohydrate-specific data |
| database_io.hh | Database input/output function declarations for carbohydrate-specific data |
| LinkageConformers.hh | Data structure declarations for glycosydic linkage conformers |
| SugarModificationsNomenclatureTable.hh | Definitions for SugarModificationsNomenclatureTable |
| ► gasteiger | |
| GasteigerAtomTypeData.cc | The data for the gasteiger atom types |
| GasteigerAtomTypeData.fwd.hh | |
| GasteigerAtomTypeData.hh | The data for the gasteiger atom types |
| GasteigerAtomTyper.cc | The type assigner for gasteiger type data |
| GasteigerAtomTyper.hh | The type assigner for gasteiger type data |
| GasteigerAtomTypeSet.cc | |
| GasteigerAtomTypeSet.fwd.hh | |
| GasteigerAtomTypeSet.hh | |
| util.hh | Utilities for dealing with gasteiger things |
| ► mainchain_potential | |
| MainchainScoreTable.cc | A general class for storing a torsional potential for mainchain resiudes |
| MainchainScoreTable.fwd.hh | |
| MainchainScoreTable.hh | Forward declarations for a general class for storing a torsional potential for mainchain resiudes |
| util.cc | Utility functions for mainchain torsional potentials |
| util.hh | Headers for utility functions for mainchain torsional potentials |
| ► mmCIF | |
| mmCIFParser.cc | |
| mmCIFParser.fwd.hh | |
| mmCIFParser.hh | |
| ► orbitals | |
| AssignOrbitals.cc | |
| AssignOrbitals.hh | |
| ICoorOrbitalData.cc | |
| ICoorOrbitalData.fwd.hh | |
| ICoorOrbitalData.hh | |
| OrbitalType.cc | |
| OrbitalType.fwd.hh | |
| OrbitalType.hh | |
| OrbitalTypeMapper.cc | |
| OrbitalTypeMapper.fwd.hh | |
| OrbitalTypeMapper.hh | |
| OrbitalTypeSet.cc | |
| OrbitalTypeSet.fwd.hh | |
| OrbitalTypeSet.hh | |
| ► residue_properties | |
| update_ResidueType_enum_files.py | |
| ► rings | |
| AxEqDesignation.hh | Enumeration definition for AxEqDesignation |
| ring_conformer_io.cc | Database input/output function definitions for ring-conformer-specific data |
| ring_conformer_io.hh | Database input/output function declarations for ring-conformer-specific data |
| RingConformer.fwd.hh | RingConformer forward declarations header |
| RingConformer.hh | Definitions for RingConformer |
| RingConformerManager.cc | Method definitions for RingConformerManager |
| RingConformerManager.fwd.hh | Forward declaration for RingConformerManager |
| RingConformerManager.hh | Declarations and simple accessor/mutator definitions for RingConformerManager |
| RingConformerSet.cc | Method definitions for RingConformerSet |
| RingConformerSet.fwd.hh | Forward declarations for RingConformerSet |
| RingConformerSet.hh | Declarations and simple accessor/mutator definitions for RingConformerSet |
| RingSaturationType.hh | Enumeration definition for RingSaturationType |
| util.cc | Definitions for ring-related utility functions |
| util.hh | |
| ► rna | |
| RNA_FittedTorsionInfo.cc | Statistically derived torsion information for RNA |
| RNA_FittedTorsionInfo.fwd.hh | |
| RNA_FittedTorsionInfo.hh | Statistically derived torsion information for RNA |
| RNA_Info.cc | |
| RNA_Info.fwd.hh | |
| RNA_Info.hh | |
| RNA_SamplerUtil.cc | |
| RNA_SamplerUtil.hh | |
| util.cc | |
| util.hh | |
| ► rotamers | |
| BasicRotamerLibrarySpecification.cc | The BasicRotamerLibrarySpecification class says to build simple rotamer libraries |
| BasicRotamerLibrarySpecification.fwd.hh | Forward declaration of a class that says to build simple rotamer libraries |
| BasicRotamerLibrarySpecification.hh | The BasicRotamerLibrarySpecification class says to do simple rotamer libraries |
| BasicRotamerLibrarySpecificationCreator.hh | Class for instantiating a particular BasicRotamerLibrarySpecification |
| CenrotRotamerLibrarySpecification.cc | The CenrotRotamerLibrarySpecification class specifies building centroid rotamers |
| CenrotRotamerLibrarySpecification.fwd.hh | Forward declaration of a class that specifies to build centroid rotamers |
| CenrotRotamerLibrarySpecification.hh | The CenrotRotamerLibrarySpecification class tells how to build CenrotRotamers |
| CenrotRotamerLibrarySpecificationCreator.hh | Class for instantiating a particular CenrotRotamerLibrarySpecification |
| DunbrackRotamerLibrarySpecification.cc | The DunbrackRotamerLibrarySpecification class specifies building DunbrackRotamers |
| DunbrackRotamerLibrarySpecification.fwd.hh | Forward declaration of a class that specifies to build Dunbrack rotamers |
| DunbrackRotamerLibrarySpecification.hh | The DunbrackRotamerLibrarySpecification class tells how to build DunbrackRotamers |
| DunbrackRotamerLibrarySpecificationCreator.hh | Class for instantiating a particular DunbrackRotamerLibrarySpecification |
| NCAARotamerLibrarySpecification.cc | The NCAARotamerLibrarySpecification class specifies building NCAARotamers |
| NCAARotamerLibrarySpecification.fwd.hh | Forward declaration of a class that specifies how to build a rotamer library from an NCAA rotlib |
| NCAARotamerLibrarySpecification.hh | The NCAARotamerLibrarySpecification class says to build a rotamer library from a NCAA rotlib |
| NCAARotamerLibrarySpecificationCreator.hh | Class for instantiating a particular NCAARotamerLibrarySpecification |
| PDBRotamerLibrarySpecification.cc | The PDBRotamerLibrarySpecification class specifies building PDBRotamers |
| PDBRotamerLibrarySpecification.fwd.hh | Forward declaration of a class that specifies how to build a rotamer library from a PDB listing |
| PDBRotamerLibrarySpecification.hh | The PDBRotamerLibrarySpecification class says to build a rotamer library from a PDB file |
| PDBRotamerLibrarySpecificationCreator.hh | Class for instantiating a particular PDBRotamerLibrarySpecification |
| RotamerLibrarySpecification.cc | The RotamerLibrarySpecification class tells how to build a rotamer library for a ResidueType |
| RotamerLibrarySpecification.fwd.hh | Forward declaration of a class that specifies how to build a rotamer library from a Restype |
| RotamerLibrarySpecification.hh | The RotamerLibrarySpecification class tells how to build a Rotamer library for a ResidueType |
| RotamerLibrarySpecificationCreator.hh | Class for instantiating a particular RotamerLibrarySpecification |
| RotamerLibrarySpecificationFactory.cc | Implementation of the class for instantiating arbitrary RotamerLibrarySpecifications from a string –> RotamerLibrarySpecificationCreator map |
| RotamerLibrarySpecificationFactory.hh | |
| RotamerLibrarySpecificationRegistrator.hh | Declaration of the template class for registrating RotamerLibrarySpecificationCreators with the RotamerLibrarySpecificationFactory |
| StoredRotamerLibrarySpecification.cc | The StoredRotamerLibrarySpecification class specifies building PDBRotamers |
| StoredRotamerLibrarySpecification.fwd.hh | Forward declaration of a class that specifies how to build a rotamer library from a stored set of coordinates |
| StoredRotamerLibrarySpecification.hh | The StoredRotamerLibrarySpecification class says to build a rotamer library from a set of stored coordinates |
| StoredRotamerLibrarySpecificationCreator.hh | Class for instantiating a particular StoredRotamerLibrarySpecification |
| ► sdf | |
| CtabParserBase.fwd.hh | |
| CtabParserBase.hh | |
| CtabV2000Parser.cc | |
| CtabV2000Parser.fwd.hh | Forward declarations for ctab_parser |
| CtabV2000Parser.hh | Parse the CTAB table into a residue object |
| CtabV3000Parser.cc | |
| CtabV3000Parser.fwd.hh | Forward declarations for ctab_parser |
| CtabV3000Parser.hh | Parse the CTAB table into a residue object |
| mol_util.cc | |
| mol_util.fwd.hh | |
| mol_util.hh | |
| mol_writer.cc | |
| mol_writer.fwd.hh | |
| mol_writer.hh | |
| MolFileIOData.cc | |
| MolFileIOData.fwd.hh | |
| MolFileIOData.hh | |
| MolFileIOReader.cc | |
| MolFileIOReader.fwd.hh | |
| MolFileIOReader.hh | |
| SDFParser.cc | |
| SDFParser.fwd.hh | |
| SDFParser.hh | |
| AA.cc | Translation between amino acid enum and string name/one letter char codes |
| AA.hh | |
| Adduct.cc | Definition of residue adduct class |
| Adduct.fwd.hh | Declaration of class for adducts on residues |
| Adduct.hh | Declaration of implementation class for residue adducts |
| adduct_util.cc | |
| adduct_util.hh | |
| Atom.cc | |
| Atom.fwd.hh | Class declaration for chemical::Atom |
| Atom.hh | Method definitions for chemical::Atom |
| AtomICoor.cc | Declaration of implementation class for abstract class Residue |
| AtomICoor.fwd.hh | Declaration of implementation class for abstract class Residue |
| AtomICoor.hh | Declaration of implementation class for abstract class Residue |
| AtomProperties.cc | Method definitions for AtomProperties |
| AtomProperties.fwd.hh | Forward declarations for AtomProperties |
| AtomProperties.hh | Declarations and simple accessor/mutator definitions for AtomProperties |
| AtomPropertiesManager.cc | Method definitions for AtomPropertiesManager |
| AtomPropertiesManager.fwd.hh | Forward declaration for AtomPropertiesManager |
| AtomPropertiesManager.hh | Method declarations for AtomPropertiesManager |
| AtomProperty.hh | Enumeration definitions for AtomProperties |
| AtomProperty_mappings.cc | |
| AtomType.cc | A class for defining atom parameters, known as atom_types |
| AtomType.fwd.hh | |
| AtomType.hh | A class for defining atom parameters, known as atom_types |
| atomtype_support.cc | |
| atomtype_support.hh | |
| AtomTypeDatabaseIO.cc | Write chemical information associated with atom types to a database |
| AtomTypeDatabaseIO.fwd.hh | |
| AtomTypeDatabaseIO.hh | |
| AtomTypeSet.cc | |
| AtomTypeSet.fwd.hh | |
| AtomTypeSet.hh | |
| automorphism.cc | |
| automorphism.hh | |
| Bond.cc | |
| Bond.fwd.hh | |
| Bond.hh | |
| bond_support.cc | |
| bond_support.hh | Support functions for class Bond; functions that should not be included as part of the class |
| CacheableResidueTypeSets.cc | A (Pose-cacheable) container for ResidueTypeSets |
| CacheableResidueTypeSets.fwd.hh | A (Pose-cacheable) container for ResidueTypeSets |
| CacheableResidueTypeSets.hh | A (Pose-cacheable) container for ResidueTypeSets |
| ChemicalManager.cc | |
| ChemicalManager.fwd.hh | |
| ChemicalManager.hh | Chemical manager class header |
| ElectronConfiguration.cc | |
| ElectronConfiguration.fwd.hh | |
| ElectronConfiguration.hh | |
| Element.cc | The data for the element types |
| Element.fwd.hh | |
| Element.hh | The data for the element types |
| Elements.cc | |
| Elements.hh | All the elements known to mankind (me)...as of4/18/2014 |
| ElementSet.cc | |
| ElementSet.fwd.hh | |
| ElementSet.hh | |
| GlobalResidueTypeSet.cc | GlobalResidueTypeSet class |
| GlobalResidueTypeSet.fwd.hh | |
| GlobalResidueTypeSet.hh | |
| GreekDistance.hh | Enumeration definitions for GreekDistance |
| icoor_support.cc | External support for manipulating the ResidueType's icoor/ideal_xyz |
| icoor_support.hh | |
| IdealBondLengthSet.cc | |
| IdealBondLengthSet.fwd.hh | |
| IdealBondLengthSet.hh | |
| MergeBehaviorManager.cc | |
| MergeBehaviorManager.fwd.hh | |
| MergeBehaviorManager.hh | |
| Metapatch.cc | A structure for applying multiple Patches procedurally |
| Metapatch.fwd.hh | |
| Metapatch.hh | |
| MMAtomType.cc | Molecular mechanics atom type class |
| MMAtomType.fwd.hh | |
| MMAtomType.hh | Molecular mechanics atom type class |
| MMAtomTypeSet.cc | |
| MMAtomTypeSet.fwd.hh | |
| MMAtomTypeSet.hh | |
| MutableChiRecord.cc | A Chi record object for a MutableResidueType |
| MutableChiRecord.fwd.hh | A Chi record object for a MutableResidueType |
| MutableChiRecord.hh | A Chi record object for a MutableResidueType |
| MutableICoorRecord.cc | A ICoord record object for a MutableResidueType |
| MutableICoorRecord.fwd.hh | A ICoord record object for a MutableResidueType |
| MutableICoorRecord.hh | A ICoord record object for a MutableResidueType |
| MutableResidueConnection.cc | A class representing a connection point to another residue for a MutableResidueType |
| MutableResidueConnection.fwd.hh | A version of ResidueConnection used with MutableResidueType |
| MutableResidueConnection.hh | Inter-residue chemical bond connection point class declaration |
| MutableResidueType.cc | Method definitions for MutableResidueType |
| MutableResidueType.fwd.hh | Declaration of MutableResidueType class |
| MutableResidueType.hh | Method declarations and simple accessors/getters for MutableResidueType |
| NucleotideTools.cc | |
| NucleotideTools.hh | |
| Orbital.cc | |
| Orbital.fwd.hh | |
| Orbital.hh | |
| Patch.cc | Implementation class for abstract class Residue |
| Patch.fwd.hh | |
| Patch.hh | |
| PatchOperation.cc | Polymorphic classes representing the contents of a residue-type patch file |
| PatchOperation.fwd.hh | |
| PatchOperation.hh | Polymorphic classes representing the contents of a residue-type patch file |
| PoseResidueTypeSet.cc | A ResidueTypeSet which can be cached in the Pose |
| PoseResidueTypeSet.fwd.hh | A ResidueTypeSet which can be cached in the Pose |
| PoseResidueTypeSet.hh | A ResidueTypeSet which can be cached in the Pose |
| ResConnID.cc | |
| ResConnID.fwd.hh | |
| ResConnID.hh | |
| residue_io.cc | Helper methods for ResidueType input/output |
| residue_io.hh | |
| residue_support.cc | |
| residue_support.hh | Support functions for class residue; functions that should not be included as part of the class |
| ResidueConnection.cc | Auto-generated serialization template functions |
| ResidueConnection.fwd.hh | Declaration of implementation class for abstract class Residue |
| ResidueConnection.hh | Inter-residue chemical bond connection point class declaration |
| ResidueDatabaseIO.cc | |
| ResidueDatabaseIO.fwd.hh | |
| ResidueDatabaseIO.hh | |
| ResidueGraphTypes.hh | Graph structure for ResidueType |
| ResidueGraphTypes.srlz.hh | Helper functions for serializing objects in ResidueGraphTypes.hh and associated |
| ResidueProperties.cc | Method definitions for ResidueProperties |
| ResidueProperties.fwd.hh | Forward declarations for ResidueProperties |
| ResidueProperties.hh | Declarations and simple accessor/mutator definitions for ResidueProperties |
| ResidueProperty.hh | Enumeration definition for ResidueProperty |
| ResidueProperty_mappings.cc | Method definitions for private singleton methods declared in AtomPropertiesManager.hh |
| ResidueSubGraphTypes.cc | |
| ResidueSubGraphTypes.hh | Filtered subgraphs |
| ResidueType.cc | Method definitions for ResidueType |
| ResidueType.fwd.hh | Declaration of implementation class for abstract class Residue |
| ResidueType.hh | Method declarations and simple accessors/getters for ResidueType |
| ResidueType.srlz.cc | Serialization and deserialization routines for when working with globally-accessible ResidueTypes |
| ResidueType.srlz.hh | Serialization and deserialization routines for when working with globally-accessible ResidueTypes |
| ResidueTypeBase.cc | Method definitions for ResidueTypeBase |
| ResidueTypeBase.fwd.hh | Declaration of implementation class for abstract class Residue |
| ResidueTypeBase.hh | Method declarations and simple accessors/getters for ResidueTypeBase |
| ResidueTypeFinder.cc | |
| ResidueTypeFinder.fwd.hh | |
| ResidueTypeFinder.hh | Functions to find residue_type(s) from ResidueTypeSet without requiring instantiation of all rsd_types |
| ResidueTypeKinWriter.cc | Class to write kinemage-formatted output for Residue and chemical |
| ResidueTypeKinWriter.fwd.hh | |
| ResidueTypeKinWriter.hh | Class to write kinemage-formatted output for ResidueType |
| ResidueTypeSelector.cc | |
| ResidueTypeSelector.fwd.hh | |
| ResidueTypeSelector.hh | |
| ResidueTypeSet.cc | ResidueTypeSet class |
| ResidueTypeSet.fwd.hh | |
| ResidueTypeSet.hh | |
| ResidueTypeSet.srlz.cc | Serialization and deserialization routines for when working with ResidueTypeSets |
| ResidueTypeSet.srlz.hh | Serialization and deserialization routines for when working with ResidueTypeSets |
| ResidueTypeSetCache.cc | |
| ResidueTypeSetCache.fwd.hh | |
| ResidueTypeSetCache.hh | |
| RestypeDestructionEvent.fwd.hh | Forward declaration for core::chemical::RestypeDestructionEvent |
| RestypeDestructionEvent.hh | |
| types.hh | Rosetta project type declarations |
| util.cc | Utilities for modifying and utilizing ResidueTypes and other core::chemical classes |
| util.hh | Utilities for modifying and utilizing Residues and other core::chemical classes |
| VariantType.hh | Enumeration definition for VariantType |
| VariantType_mappings.cc | Method definitions for private static methods declared in ResidueProperties.hh |
| ► conformation | |
| ► carbohydrates | |
| GlycanNode.cc | |
| GlycanNode.fwd.hh | |
| GlycanNode.hh | |
| GlycanTree.cc | |
| GlycanTree.fwd.hh | |
| GlycanTree.hh | |
| GlycanTreeSet.cc | |
| GlycanTreeSet.fwd.hh | |
| GlycanTreeSet.hh | |
| GlycanTreeSetObserver.cc | |
| GlycanTreeSetObserver.fwd.hh | The CacheablePoseObserver version of GlycanTreeSet that will react to pose length changes. |
| GlycanTreeSetObserver.hh | The CacheablePoseObserver version of GlycanTreeSet that will react to pose length changes. |
| util.cc | Utility functions that DO NOT require a pose |
| util.hh | Utility functions that DO NOT require a pose |
| ► membrane | |
| AqueousPoreParameters.cc | A class for defining an aqueous pore |
| AqueousPoreParameters.fwd.hh | A class for defining an aqueous pore |
| AqueousPoreParameters.hh | A class for defining an aqueous pore |
| Exceptions.hh | Exception Hierarchy for Membrane framework Code |
| ImplicitLipidInfo.cc | |
| ImplicitLipidInfo.fwd.hh | |
| ImplicitLipidInfo.hh | An Implicit Lipid Membrane Model |
| MembraneInfo.cc | Data describing the relationship between protein(s) and a membrane environment |
| MembraneInfo.fwd.hh | Data describing the relationship between protein(s) and a membrane environment |
| MembraneInfo.hh | Data describing the relationship between protein(s) and a membrane environment |
| MembraneParams.hh | Membrane Params Enum - map Atom indices to atom types |
| Span.cc | |
| Span.fwd.hh | Object for describing start and end of a transmembrane span |
| Span.hh | |
| SpanningTopology.cc | Transmembrane Spans Object |
| SpanningTopology.fwd.hh | Membrane Spanning Topology Data |
| SpanningTopology.hh | Transmembrane Spans Object |
| util.cc | |
| util.hh | |
| ► orbitals | |
| OrbitalXYZCoords.cc | Created on: Jun 30, 2011 |
| OrbitalXYZCoords.fwd.hh | |
| OrbitalXYZCoords.hh | Created on: Jun 30, 2011 |
| ► parametric | |
| BooleanValuedParameter.cc | A class for holding a single Boolean-valued parameter for parametric backbone generation |
| BooleanValuedParameter.fwd.hh | Owning pointers and whatnot for the class for holding a Boolean-valued parameter for parametric backbone generation |
| BooleanValuedParameter.hh | |
| Parameter.cc | A class for holding a single parameter for parametric backbone generation |
| Parameter.fwd.hh | Owning pointers and whatnot for the class for holding a parameter for parametric backbone generation |
| Parameter.hh | |
| Parameters.cc | A class for holding sets of parameters for parametric backbone generation |
| Parameters.fwd.hh | Owning pointers and whatnot for the class for holding parameters for parametric backbone generation |
| Parameters.hh | |
| ParametersSet.cc | A class for holding sets of parameters for parametric backbone generation |
| ParametersSet.fwd.hh | Owning pointers and whatnot for the class for holding sets of parameters for parametric backbone generation |
| ParametersSet.hh | |
| ParametrizationCalculator.cc | Function definitions for the ParametrizationCalculator class, a base class from which classes that calculate particular parametrizations will be derived |
| ParametrizationCalculator.fwd.hh | Forward declarations for the ParametrizationCalculator base class, from which classes that calculate particular parametrizations will be derived |
| ParametrizationCalculator.hh | |
| RealValuedParameter.cc | A class for holding a single real-valued parameter for parametric backbone generation |
| RealValuedParameter.fwd.hh | Owning pointers and whatnot for the class for holding a real-valued parameter for parametric backbone generation |
| RealValuedParameter.hh | |
| RealVectorValuedParameter.cc | A class for holding a single vector-valued parameter for parametric backbone generation |
| RealVectorValuedParameter.fwd.hh | Owning pointers and whatnot for the class for holding a vector-valued parameter for parametric backbone generation |
| RealVectorValuedParameter.hh | |
| SizeValuedParameter.cc | A class for holding a single core::Size-valued parameter for parametric backbone generation |
| SizeValuedParameter.fwd.hh | Owning pointers and whatnot for the class for holding a core::Size-valued parameter for parametric backbone generation |
| SizeValuedParameter.hh | |
| SizeVectorValuedParameter.cc | A class for holding a single utility::vector1<core::Size>-valued parameter for parametric backbone generation |
| SizeVectorValuedParameter.fwd.hh | Owning pointers and whatnot for the class for holding a utility::vector1<core::Size>-valued parameter for parametric backbone generation |
| SizeVectorValuedParameter.hh | |
| ► signals | |
| ConnectionEvent.fwd.hh | Forward declaration for core::conformation::signals::ConnectionEvent |
| ConnectionEvent.hh | Signal a change in the connection with a Conformation object, e.g. destruction or transfer |
| GeneralEvent.fwd.hh | Forward declaration for core::conformation::signals::GeneralEvent |
| GeneralEvent.hh | Signal for a general change in a Conformation |
| IdentityEvent.fwd.hh | Forward declaration for core::conformation::signals::IdentityEvent |
| IdentityEvent.hh | Signal a residue identity change in a Conformation (e.g. residue identity change) |
| LengthEvent.cc | |
| LengthEvent.fwd.hh | Forward declaration for core::conformation::signals::LengthEvent |
| LengthEvent.hh | Signal for a change in length of residues in a Conformation |
| XYZEvent.fwd.hh | Forward declaration for core::conformation::signals::XYZEvent |
| XYZEvent.hh | Signal for a change in XYZ coordinates in a Conformation |
| ► symmetry | |
| MirrorSymmetricConformation.cc | Symmetry conformation container |
| MirrorSymmetricConformation.fwd.hh | |
| MirrorSymmetricConformation.hh | Symmetry conformation container |
| SymDof.cc | Class to store ingformation about symmetrical dofs |
| SymDof.fwd.hh | |
| SymDof.hh | SymDof data container |
| SymmData.cc | Class to store symmetry data specified from input files |
| SymmData.fwd.hh | |
| SymmData.hh | Symmetry data container |
| SymmDataLoader.cc | Load the SymmData data-structure, which is used to configure symmetric poses |
| SymmDataLoader.fwd.hh | Load the SymmData data-structure, which is used to configure symmetric poses |
| SymmDataLoader.hh | Load the SymmData data-structure, which is used to configure symmetric poses |
| SymmDataLoaderCreator.hh | Load the SymmData data-structure, which is used to configure symmetric poses |
| SymmDataOptions.fwd.hh | Load the SymmData data-structure, which is used to configure symmetric poses |
| SymmetricConformation.cc | |
| SymmetricConformation.fwd.hh | |
| SymmetricConformation.hh | Symmetry conformation container |
| SymmetryInfo.cc | |
| SymmetryInfo.fwd.hh | |
| SymmetryInfo.hh | |
| SymmetryTransform.cc | Stores information about a transform between two symmetry subunits |
| SymmetryTransform.fwd.hh | Forward declarations and owning pointer declarations for the SymmetryTransform class, which stores information about a transform between two symmetry subunits |
| SymmetryTransform.hh | |
| SymSlideInfo.cc | Class to store ingformation about symmetrical dofs |
| SymSlideInfo.fwd.hh | |
| SymSlideInfo.hh | SymSlideInfo data container |
| util.cc | |
| util.hh | Utility functions for handling of symmetric conformations |
| VirtualCoordinate.cc | VirtualCoordinate container |
| VirtualCoordinate.fwd.hh | |
| VirtualCoordinate.hh | |
| AbstractRotamerTrie.cc | Auto-generated serialization template functions |
| AbstractRotamerTrie.fwd.hh | Forward declaration of the AbstractRotamerTrie class, defined in the conformation layer |
| AbstractRotamerTrie.hh | Base class from which all Tries will derive; this class is a handle for the tries that will be defined in core/scoring, but which have to be stored by the RotamerSetBase class defined in core/conformation |
| Atom.cc | Method definitions for conformation::Atom |
| Atom.fwd.hh | Class declaration for conformation::Atom |
| Atom.hh | Class definitions for conformation::Atom |
| AtomGraph.cc | |
| AtomGraph.fwd.hh | |
| AtomGraph.hh | |
| AtomGraphData.fwd.hh | |
| AtomGraphData.hh | |
| Conformation.cc | Method definitions for the Conformation class |
| Conformation.fwd.hh | Forward declaration for Conformation.hh |
| Conformation.hh | Conformation container |
| ConformationTests.fwd.hh | |
| find_neighbors.fwd.hh | |
| find_neighbors.hh | |
| PointGraph.cc | Graph for detecting neighbors; vertices store points, edges store square distances |
| PointGraph.fwd.hh | Graph for detecting neighbors; vertices store points, edges store square distances |
| PointGraph.hh | Graph for detecting neighbors; vertices store points, edges store square distances |
| PointGraphData.cc | Serlialization routines for the two types templated upon to define the PointGraph |
| PointGraphData.fwd.hh | |
| PointGraphData.hh | Classes to work with UpperEdgeGraph for fast neighbor detection |
| ppo_torsion_bin.cc | |
| ppo_torsion_bin.fwd.hh | An enumeration to represent a binning of the phi/psi/omega torsions |
| ppo_torsion_bin.hh | Functions for assigning and manipulating the phi/psi/omega torsion bins |
| PseudoBond.cc | |
| PseudoBond.fwd.hh | |
| PseudoBond.hh | |
| Residue.cc | Method definitions for the Residue class |
| Residue.functions.cc | Implementation of non-member functions that operate on Residue objects |
| Residue.functions.hh | Header file for non-member functions that operate on Residue objects |
| Residue.fwd.hh | |
| Residue.hh | Method declarations and simple accessor definitions for the Residue class |
| residue_datacache.hh | Enum for storing data in the Residue's datacache |
| ResidueFactory.cc | |
| ResidueFactory.hh | |
| ResidueKinWriter.cc | Class to write kinemage-formatted output for Residue and Conformation |
| ResidueKinWriter.fwd.hh | |
| ResidueKinWriter.hh | Class to write kinemage-formatted output for Residue and Conformation |
| ResidueMatcher.cc | |
| ResidueMatcher.fwd.hh | |
| ResidueMatcher.hh | |
| RotamerSetBase.cc | RotamerSetBase class implementation |
| RotamerSetBase.fwd.hh | |
| RotamerSetBase.hh | Abstract base class for a class that holds disembodied Residues (ie not contained within a Pose) as Rotamers |
| RotamerSetCacheableDataType.hh | Enum for the DataCache within the RotamerSet class; EnergyMethods in core/scoring forward-declare themselves here if they intend to cache data within the the RotamerSet |
| UltraLightResidue.cc | |
| UltraLightResidue.fwd.hh | |
| UltraLightResidue.hh | Extremely light residue class used for fast direct cartesian space transforms on ligands |
| util.cc | |
| util.hh | |
| ► energy_methods | |
| AACompositionEnergy.cc | |
| AACompositionEnergy.fwd.hh | |
| AACompositionEnergy.hh | |
| AACompositionEnergyCreator.hh | |
| AARepeatEnergy.cc | |
| AARepeatEnergy.fwd.hh | |
| AARepeatEnergy.hh | |
| AARepeatEnergyCreator.hh | |
| AbegoEnergy.cc | ABEGO energy method class implementation |
| AbegoEnergy.fwd.hh | ABEGO energy method class forward declaration |
| AbegoEnergy.hh | |
| AbegoEnergyCreator.hh | |
| ArgCationPiEnergy.cc | Cation pi term that specializes in bringing Arginine and rings together |
| ArgCationPiEnergy.fwd.hh | Cation pi term that specializes in bringing Arginine and rings together |
| ArgCationPiEnergy.hh | Cation pi term that specializes in bringing Arginine and rings together |
| ArgCationPiEnergyCreator.hh | |
| AromaticBackboneRestraintEnergy.cc | Aramid backbone restraint energy method class implementation |
| AromaticBackboneRestraintEnergy.fwd.hh | Noncanonical ring closure energy method class forward declaration |
| AromaticBackboneRestraintEnergy.hh | Aromatic backbone restraint energy method class headers |
| AromaticBackboneRestraintEnergyCreator.hh | Declaration for the class that connects AromaticBackboneRestraintEnergy with the ScoringManager |
| AspartimidePenaltyEnergy.cc | |
| AspartimidePenaltyEnergy.fwd.hh | Forward declarations for the AspartimidePenaltyEnergy |
| AspartimidePenaltyEnergy.hh | This is a score term that penalizes sequences that are likely to result in aspartimide formation during peptide synthesis |
| AspartimidePenaltyEnergyCreator.hh | Declaration for the class that connects AspartimidePenaltyEnergy with the ScoringManager |
| BranchEnergy.cc | Method definitions for BranchEnergyCreator and BranchEnergy classes |
| BranchEnergy.fwd.hh | |
| BranchEnergy.hh | Method declarations and typedefs for BranchEnergy |
| BranchEnergyCreator.hh | Declaration for the class that connects BranchEnergy with the ScoringManager |
| Burial_v2Energy.cc | |
| Burial_v2Energy.hh | Energy term use for score burial of a specific residue |
| Burial_v2EnergyCreator.hh | Declaration for the class that connects Burial_v2Energy with the ScoringManager |
| BurialEnergy.cc | |
| BurialEnergy.hh | Energy term use for scoring predicted burial |
| BurialEnergyCreator.hh | Declaration for the class that connects BurialEnergy with the ScoringManager |
| CartesianBondedEnergy.cc | Harmonic bondangle/bondlength/torsion constraints |
| CartesianBondedEnergy.fwd.hh | |
| CartesianBondedEnergy.hh | |
| CartesianBondedEnergyCreator.hh | Declaration for the class that connects CartesianBondedEnergy with the ScoringManager |
| CenHBEnergy.cc | Smooth, differentiable version of centroid hbond term |
| CenHBEnergy.fwd.hh | |
| CenHBEnergy.hh | Smooth, differentiable version of centroid hbond term |
| CenHBEnergyCreator.hh | Declaration for the class that connects CenHBEnergy with the ScoringManager |
| CenPairEnergy.cc | Statistically derived rotamer pair potential class implementation |
| CenPairEnergy.hh | Statistically derived rotamer pair potential class declaration |
| CenPairEnergyCreator.hh | |
| CenPairMotifDegreeEnergy.cc | |
| CenPairMotifDegreeEnergy.hh | |
| CenPairMotifDegreeEnergyCreator.hh | |
| CenPairMotifEnergy.cc | |
| CenPairMotifEnergy.hh | |
| CenPairMotifEnergyCreator.hh | |
| CenRotEnvEnergy.cc | CenRot version of centroid env |
| CenRotEnvEnergy.hh | |
| CenRotEnvEnergyCreator.hh | |
| CenRotPairEnergy.cc | CenRot version of cen pair |
| CenRotPairEnergy.hh | |
| CenRotPairEnergyCreator.hh | |
| CentroidDisulfideEnergy.cc | Centroid Disulfide Energy class implementation |
| CentroidDisulfideEnergy.fwd.hh | Centroid Disulfide Energy class forward declaration |
| CentroidDisulfideEnergy.hh | Centroid Disulfide Energy class declaration |
| CentroidDisulfideEnergyCreator.hh | Declaration for the class that connects CentroidDisulfideEnergy with the ScoringManager |
| ChainbreakEnergy.cc | Method definitions for ChainbreakEnergyCreator and ChainbreakEnergy classes |
| ChainbreakEnergy.fwd.hh | |
| ChainbreakEnergy.hh | Method declarations and typedefs for ChainbreakEnergy |
| ChainbreakEnergyCreator.hh | Declaration for the class that connects ChainbreakEnergy with the ScoringManager |
| ChemicalShiftAnisotropyEnergy.cc | CSA energy - Orientation dependent chemical shift |
| ChemicalShiftAnisotropyEnergy.fwd.hh | |
| ChemicalShiftAnisotropyEnergy.hh | CSP energy |
| ChemicalShiftAnisotropyEnergyCreator.hh | Declaration for the class that connects ChemicalShiftAnisotropyEnergy with the ScoringManager |
| ContactOrderEnergy.cc | Calculates the contact order of a given conformation average sequence |
| ContactOrderEnergy.hh | Statistically derived rotamer pair potential class declaration |
| ContactOrderEnergyCreator.hh | Declaration for the class that connects ContactOrderEnergy with the ScoringManager |
| ContextDependentGeometricSolEnergy.cc | |
| ContextDependentGeometricSolEnergy.fwd.hh | |
| ContextDependentGeometricSolEnergy.hh | |
| ContextDependentGeometricSolEnergyCreator.hh | |
| ContextIndependentGeometricSolEnergy.cc | |
| ContextIndependentGeometricSolEnergy.fwd.hh | |
| ContextIndependentGeometricSolEnergy.hh | |
| ContextIndependentGeometricSolEnergyCreator.hh | |
| CovalentLabelingEnergy.cc | |
| CovalentLabelingEnergy.fwd.hh | |
| CovalentLabelingEnergy.hh | Energy term use for scoring predicted CovalentLabeling |
| CovalentLabelingEnergyCreator.hh | Declaration for the class that connects CovalentLabelingEnergy with the ScoringManager |
| CovalentLabelingFAEnergy.cc | |
| CovalentLabelingFAEnergy.fwd.hh | |
| CovalentLabelingFAEnergy.hh | Energy term use for scoring predicted CovalentLabelingFA |
| CovalentLabelingFAEnergyCreator.hh | Declaration for the class that connects CovalentLabelingFAEnergy with the ScoringManager |
| CustomAtomPairEnergy.cc | Simple EnergyMethod for calculating residue-residue constraints under some interaction cutoff |
| CustomAtomPairEnergy.fwd.hh | Statistically derived rotamer pair potential class forward declaration |
| CustomAtomPairEnergy.hh | |
| CustomAtomPairEnergyCreator.hh | Declaration for the class that connects CustomAtomPairEnergy with the ScoringManager |
| D2H_SA_Energy.cc | Sa energy function definition |
| D2H_SA_Energy.hh | Statistically derived rotamer pair potential class declaration |
| D2H_SA_EnergyCreator.hh | Declaration for the class that connects D2H_SA_Energy with the ScoringManager |
| DEEREnergy.cc | Score term for data obtained with double electron-electron resonance (DEER) |
| DEEREnergy.fwd.hh | |
| DEEREnergy.hh | Score term for data obtained with double electron-electron resonance (DEER) |
| DEEREnergyCreator.hh | Parent class for DEEREnergy structure |
| DFIRE_Energy.cc | |
| DFIRE_Energy.fwd.hh | |
| DFIRE_Energy.hh | |
| DFIRE_EnergyCreator.hh | |
| DipolarCouplingEnergy.cc | DC energy - Orientation dependent chemical shift |
| DipolarCouplingEnergy.fwd.hh | |
| DipolarCouplingEnergy.hh | CSP energy |
| DipolarCouplingEnergyCreator.hh | Declaration for the class that connects DipolarCouplingEnergy with the ScoringManager |
| DirectReadoutEnergy.cc | Statistically derived DNA contact potential class implementation |
| DirectReadoutEnergy.fwd.hh | |
| DirectReadoutEnergy.hh | Statistically derived DNA contact potential class declaration |
| DirectReadoutEnergyCreator.hh | Declaration for the class that connects DirectReadoutEnergy with the ScoringManager |
| DistanceChainbreakEnergy.cc | |
| DistanceChainbreakEnergy.fwd.hh | |
| DistanceChainbreakEnergy.hh | |
| DistanceChainbreakEnergyCreator.hh | Declaration for the class that connects DistanceChainbreakEnergy with the ScoringManager |
| DisulfideMatchingEnergy.cc | Centroid Disulfide Energy class implementation |
| DisulfideMatchingEnergy.fwd.hh | Centroid Disulfide Energy class forward declaration |
| DisulfideMatchingEnergy.hh | Centroid Disulfide Energy class declaration |
| DisulfideMatchingEnergyCreator.hh | Declaration for the class that connects DisulfideMatchingEnergy with the ScoringManager |
| DNA_BaseEnergy.cc | |
| DNA_BaseEnergy.fwd.hh | |
| DNA_BaseEnergy.hh | Statistically derived rotamer pair potential class declaration |
| DNA_BaseEnergyCreator.hh | Declaration for the class that connects DNA_BaseEnergy with the ScoringManager |
| DNA_DihedralEnergy.cc | Dna scoring |
| DNA_DihedralEnergy.fwd.hh | Dna scoring |
| DNA_DihedralEnergy.hh | Dna scoring |
| DNA_DihedralEnergyCreator.hh | Dna scoring |
| DNA_EnvPairEnergy.cc | Dna scoring |
| DNA_EnvPairEnergy.fwd.hh | Dna scoring |
| DNA_EnvPairEnergy.hh | Dna scoring |
| DNA_EnvPairEnergyCreator.hh | Dna scoring |
| DNA_ReferenceEnergy.cc | Dna scoring |
| DNA_ReferenceEnergy.fwd.hh | Dna scoring |
| DNA_ReferenceEnergy.hh | Dna scoring |
| DNA_ReferenceEnergyCreator.hh | Dna scoring |
| DNAChiEnergy.cc | |
| DNAChiEnergy.fwd.hh | |
| DNAChiEnergy.hh | |
| DNAChiEnergyCreator.hh | Declaration for the class that connects DNAChiEnergy with the ScoringManager |
| DNATorsionEnergy.cc | DNATorsion energy method class implementation |
| DNATorsionEnergy.fwd.hh | |
| DNATorsionEnergy.hh | Statistically derived rotamer pair potential class declaration |
| DNATorsionEnergyCreator.hh | Declaration for the class that connects DNATorsionEnergy with the ScoringManager |
| DumpTrajectoryEnergy.cc | An EnergyMethod that dumps trajectories to file |
| DumpTrajectoryEnergy.fwd.hh | Forward declarations for an EnergyMethod that dumps trajectories to file |
| DumpTrajectoryEnergy.hh | Headers for an EnergyMethod that dumps trajectories to file |
| DumpTrajectoryEnergyCreator.hh | Creator for an EnergyMethod that dump trajectories to file |
| ElecDensAllAtomCenEnergy.cc | |
| ElecDensAllAtomCenEnergy.hh | |
| ElecDensAllAtomCenEnergyCreator.hh | |
| ElecDensAtomwiseEnergy.cc | |
| ElecDensAtomwiseEnergy.fwd.hh | |
| ElecDensAtomwiseEnergy.hh | |
| ElecDensAtomwiseEnergyCreator.hh | |
| ElecDensCenEnergy.cc | |
| ElecDensCenEnergy.hh | |
| ElecDensCenEnergyCreator.hh | |
| ElecDensEnergy.cc | |
| ElecDensEnergy.hh | |
| ElecDensEnergyCreator.hh | |
| EnvEnergy.cc | |
| EnvEnergy.hh | EnergyMethod that evaluates env and cbeta energies |
| EnvEnergyCreator.hh | Declaration for the class that connects EnvEnergy with the ScoringManager |
| EnvSmoothEnergy.cc | Statistically derived rotamer pair potential class implementation |
| EnvSmoothEnergy.fwd.hh | |
| EnvSmoothEnergy.hh | Statistically derived rotamer pair potential class declaration |
| EnvSmoothEnergyCreator.hh | Declaration for the class that connects EnvSmoothEnergy with the ScoringManager |
| ExactOccludedHbondSolEnergy.cc | |
| ExactOccludedHbondSolEnergy.fwd.hh | |
| ExactOccludedHbondSolEnergy.hh | |
| ExactOccludedHbondSolEnergyCreator.hh | |
| FA_ElecEnergyAroAll.cc | Electrostatics energy method for aromatic side chain (stand-in for pi/pi interactions) |
| FA_ElecEnergyAroAll.fwd.hh | Electrostatics for RNA class forward declaration |
| FA_ElecEnergyAroAll.hh | |
| FA_ElecEnergyAroAllCreator.hh | Declaration for the class that connects FA_ElecEnergyAroAll with the ScoringManager |
| FA_ElecEnergyAroAro.cc | Electrostatics energy method for aromatic side chain (stand-in for pi/pi interactions) |
| FA_ElecEnergyAroAro.fwd.hh | Electrostatics for RNA class forward declaration |
| FA_ElecEnergyAroAro.hh | |
| FA_ElecEnergyAroAroCreator.hh | Declaration for the class that connects FA_ElecEnergyAroAro with the ScoringManager |
| FA_GrpElecEnergy.cc | |
| FA_GrpElecEnergy.fwd.hh | |
| FA_GrpElecEnergy.hh | |
| FA_GrpElecEnergyCreator.hh | Declaration for the class that connects FA_ElecEnergy with the ScoringManager |
| Fa_MbenvEnergy.cc | |
| Fa_MbenvEnergy.fwd.hh | Probability of observing an amino acid (NOT conditional on phi/psi), energy method forward declaration |
| Fa_MbenvEnergy.hh | |
| Fa_MbenvEnergyCreator.hh | Declaration for the class that connects Fa_MbenvEnergy with the ScoringManager |
| Fa_MbsolvEnergy.cc | |
| Fa_MbsolvEnergy.fwd.hh | |
| Fa_MbsolvEnergy.hh | LK Solvation using hemisphere culling class forward declaration |
| Fa_MbsolvEnergyCreator.hh | Declaration for the class that connects Fa_MbsolvEnergy with the ScoringManager |
| FACTSEnergy.cc | |
| FACTSEnergy.fwd.hh | |
| FACTSEnergy.hh | |
| FACTSEnergyCreator.hh | |
| FaMPEnvEnergy.cc | |
| FaMPEnvEnergy.fwd.hh | |
| FaMPEnvEnergy.hh | LK-Type Membrane Environment Energy |
| FaMPEnvEnergyCreator.hh | |
| FaMPEnvSmoothEnergy.cc | |
| FaMPEnvSmoothEnergy.fwd.hh | |
| FaMPEnvSmoothEnergy.hh | Fullatom Smoothed Membrane Environment Energy |
| FaMPEnvSmoothEnergyCreator.hh | |
| FaMPSolvEnergy.cc | LK-Type Membrane Solvation Energy |
| FaMPSolvEnergy.fwd.hh | |
| FaMPSolvEnergy.hh | LK-Type Membrane Solvation Energy |
| FaMPSolvEnergyCreator.hh | |
| FastDensEnergy.cc | |
| FastDensEnergy.hh | |
| FastDensEnergyCreator.hh | |
| FastSAXSEnergy.cc | |
| FastSAXSEnergy.hh | |
| FastSAXSEnergyCreator.hh | |
| FiberDiffractionEnergy.cc | |
| FiberDiffractionEnergy.hh | |
| FiberDiffractionEnergyCreator.hh | |
| FiberDiffractionEnergyDens.cc | |
| FiberDiffractionEnergyDens.hh | |
| FiberDiffractionEnergyDensCreator.hh | |
| FiberDiffractionEnergyGpu.cc | |
| FiberDiffractionEnergyGpu.hh | |
| FiberDiffractionEnergyGpuCreator.hh | |
| FreeDOF_Energy.cc | FreeMoiety energy method implementation |
| FreeDOF_Energy.fwd.hh | FreeMoiety energy method forward declaration |
| FreeDOF_Energy.hh | Score function class |
| FreeDOF_EnergyCreator.hh | Declaration for the class that connects FreeDOF_Energy with the ScoringManager |
| FullatomDisulfideEnergy.cc | |
| FullatomDisulfideEnergy.fwd.hh | |
| FullatomDisulfideEnergy.hh | |
| FullatomDisulfideEnergyCreator.hh | Declaration for the class that connects FullatomDisulfideEnergy with the ScoringManager |
| GaussianOverlapEnergy.cc | Gaussian Overlap Energy |
| GaussianOverlapEnergy.fwd.hh | Golap |
| GaussianOverlapEnergy.hh | Energy of overlaps |
| GaussianOverlapEnergyCreator.hh | Declaration for the class that connects GaussianOverlapEnergy with the ScoringManager |
| GenBornEnergy.cc | Statistically derived rotamer pair potential class implementation |
| GenBornEnergy.fwd.hh | |
| GenBornEnergy.hh | Statistically derived rotamer pair potential class declaration |
| GenBornEnergyCreator.hh | Declaration for the class that connects GenBornEnergy with the ScoringManager |
| GenericBondedEnergy.cc | A "generic" (atom-type-only-based) torsional potential |
| GenericBondedEnergy.fwd.hh | |
| GenericBondedEnergy.hh | A "generic" (atom-type-only-based) torsional potential |
| GenericBondedEnergyCreator.hh | Declaration for the class that connects GenericBondedEnergy with the ScoringManager |
| GoapEnergy.cc | C++ implementaion of GOAP(Generalized Orientation-dependent, All-atom statistical Potential) by Zhou H & Skolnick J, Biophys J 2011, 101(8):2043-52 |
| GoapEnergy.fwd.hh | |
| GoapEnergy.hh | |
| GoapEnergyCreator.hh | |
| HackAroEnergy.cc | |
| HackAroEnergy.fwd.hh | |
| HackAroEnergy.hh | |
| HackAroEnergyCreator.hh | |
| HolesEnergy.cc | |
| HolesEnergy.hh | |
| HolesEnergyCreator.hh | |
| HRF_MSLabelingEnergy.cc | |
| HRF_MSLabelingEnergy.fwd.hh | |
| HRF_MSLabelingEnergy.hh | Energy term use for scoring predicted HRF_MSLabeling |
| HRF_MSLabelingEnergyCreator.hh | Declaration for the class that connects HRF_MSLabelingEnergy with the ScoringManager |
| HRFDynamicsEnergy.cc | Score term calculated based upon neighbor count agreement with hydroxyl radical footprinting labeling data. In a manuscript to be published in 2020 |
| HRFDynamicsEnergy.fwd.hh | |
| HRFDynamicsEnergy.hh | Score term based off mass spectrometry HRF data |
| HRFDynamicsEnergyCreator.hh | Declaration for the class that connects HRFDynamicsEnergy with the ScoringManager |
| HybridVDW_Energy.cc | Statistically derived rotamer pair potential class implementation |
| HybridVDW_Energy.fwd.hh | |
| HybridVDW_Energy.hh | Statistically derived rotamer pair potential class declaration |
| HybridVDW_EnergyCreator.hh | Declaration for the class that connects HybridVDW_Energy with the ScoringManager |
| HydroxylTorsionEnergy.cc | |
| HydroxylTorsionEnergy.fwd.hh | |
| HydroxylTorsionEnergy.hh | Term for proton_chi on Ser/Thr/Tyr residues |
| HydroxylTorsionEnergyCreator.hh | |
| IntermolEnergy.cc | Cost of bringing two chains together |
| IntermolEnergy.hh | Radius of gyration score for METHODS, to match Rosetta++ |
| IntermolEnergyCreator.hh | Declaration for the class that connects IntermolEnergy with the ScoringManager |
| LinearBranchEnergy.cc | Atom pair energy functions |
| LinearBranchEnergy.fwd.hh | |
| LinearBranchEnergy.hh | |
| LinearBranchEnergyCreator.cc | LinearBranchEnergyCreator implementation |
| LinearBranchEnergyCreator.hh | Declaration for the class that connects LinearBranchEnergy with the ScoringManager |
| LinearChainbreakEnergy.cc | Atom pair energy functions |
| LinearChainbreakEnergy.fwd.hh | |
| LinearChainbreakEnergy.hh | |
| LinearChainbreakEnergyCreator.cc | LinearChainbreakEnergyCreator implementation |
| LinearChainbreakEnergyCreator.hh | Declaration for the class that connects LinearChainbreakEnergy with the ScoringManager |
| LK_hack.cc | |
| LK_hack.fwd.hh | |
| LK_hack.hh | LK Solvation using hemisphere culling class declaration |
| LK_hackCreator.hh | Declaration for the class that connects LK_hack with the ScoringManager |
| LK_PolarNonPolarEnergy.cc | |
| LK_PolarNonPolarEnergy.fwd.hh | |
| LK_PolarNonPolarEnergy.hh | LK Solvation using hemisphere culling class forward declaration |
| LK_PolarNonPolarEnergyCreator.hh | Declaration for the class that connects LK_PolarNonPolarEnergy with the ScoringManager |
| LoopCloseEnergy.cc | Cost of bringing two chains together |
| LoopCloseEnergy.hh | |
| LoopCloseEnergyCreator.hh | Declaration for the class that connects LoopCloseEnergy with the ScoringManager |
| MembraneCbetaEnergy.cc | |
| MembraneCbetaEnergy.fwd.hh | |
| MembraneCbetaEnergy.hh | Membrane Environment Cbeta Energy |
| MembraneCbetaEnergyCreator.hh | Declaration for the class that connects MembraneCbetaEnergy with the ScoringManager |
| MembraneCenPairEnergy.cc | Statistically derived rotamer pair potential class implementation |
| MembraneCenPairEnergy.fwd.hh | |
| MembraneCenPairEnergy.hh | Statistically derived rotamer pair potential class declaration |
| MembraneCenPairEnergyCreator.hh | Declaration for the class that connects MembraneCenPairEnergy with the ScoringManager |
| MembraneEnvEnergy.cc | |
| MembraneEnvEnergy.fwd.hh | |
| MembraneEnvEnergy.hh | Membrane Environment Cbeta Energy |
| MembraneEnvEnergyCreator.hh | Declaration for the class that connects MembraneEnvEnergy with the ScoringManager |
| MembraneEnvPenalties.cc | |
| MembraneEnvPenalties.fwd.hh | |
| MembraneEnvPenalties.hh | RMS Energy function. Used to optimize the RMSD between two structures |
| MembraneEnvPenaltiesCreator.hh | Declaration for the class that connects MembraneEnvPenalties with the ScoringManager |
| MembraneEnvSmoothEnergy.cc | Statistically derived smooth membrane environment potential class implementation |
| MembraneEnvSmoothEnergy.fwd.hh | |
| MembraneEnvSmoothEnergy.hh | Statistically derived smooth membrane environment potential class declaration |
| MembraneEnvSmoothEnergyCreator.hh | Declaration for the class that connects MembraneEnvSmoothEnergy with the ScoringManager |
| MembraneLipo.cc | |
| MembraneLipo.fwd.hh | |
| MembraneLipo.hh | RMS Energy function. Used to optimize the RMSD between two structures |
| MembraneLipoCreator.hh | Declaration for the class that connects MembraneLipo with the ScoringManager |
| MgEnergy.cc | |
| MgEnergy.fwd.hh | |
| MgEnergy.hh | |
| MgEnergyCreator.hh | Declaration for the class that connects MgEnergy with the ScoringManager |
| MHCEpitopeEnergy.cc | |
| MHCEpitopeEnergy.fwd.hh | |
| MHCEpitopeEnergy.hh | |
| MHCEpitopeEnergyCreator.hh | |
| MissingEnergy.cc | Cost of failing to close loops |
| MissingEnergy.hh | Cost of failing to close loops |
| MissingEnergyCreator.hh | Declaration for the class that connects MissingEnergy with the ScoringManager |
| MotifDockEnergy.cc | Adaptation of Motif score for Docking |
| MotifDockEnergy.fwd.hh | |
| MotifDockEnergy.hh | Adaptation of Motif score for Docking |
| MotifDockEnergyCreator.hh | Adaptation of Motif score for Docking |
| MPCBetaEnergy.cc | |
| MPCBetaEnergy.fwd.hh | |
| MPCBetaEnergy.hh | |
| MPCBetaEnergyCreator.hh | |
| MPEnvEnergy.cc | Membrane Environemnt Energy |
| MPEnvEnergy.fwd.hh | Membrane Environemnt Energy |
| MPEnvEnergy.hh | Membrane Environemnt Energy |
| MPEnvEnergyCreator.hh | |
| MPHelicalityEnergy.cc | Fullatom and centroid level smooth membrane non-helicality penalty |
| MPHelicalityEnergy.fwd.hh | |
| MPHelicalityEnergy.hh | Fullatom and centroid level smooth membrane non-helicality penalty |
| MPHelicalityEnergyCreator.hh | |
| MPPairEnergy.cc | Membrane Residue Pair Energy Term |
| MPPairEnergy.fwd.hh | |
| MPPairEnergy.hh | Membrane Residue Pair Energy Term |
| MPPairEnergyCreator.hh | |
| MPResidueLipophilicityEnergy.cc | Fullatom Smoothed Membrane Environment Energy |
| MPResidueLipophilicityEnergy.fwd.hh | |
| MPResidueLipophilicityEnergy.hh | Fullatom Smoothed Membrane Environment Energy |
| MPResidueLipophilicityEnergyCreator.hh | |
| MPSpanAngleEnergy.cc | Penalize spans with unnatural dG of insertion |
| MPSpanAngleEnergy.hh | |
| MPSpanAngleEnergyCreator.hh | |
| MPSpanInsertionEnergy.cc | Penalize spans with unnatural dG of insertion |
| MPSpanInsertionEnergy.hh | |
| MPSpanInsertionEnergyCreator.hh | |
| MultipoleElecEnergy.cc | Fixed multipole electrostatics using Jay Ponder's approach in Tinker/Amoeba |
| MultipoleElecEnergy.fwd.hh | |
| MultipoleElecEnergy.hh | Fixed multipole electrostatics using Jay Ponder's approach in Tinker/Amoeba |
| MultipoleElecEnergyCreator.hh | Declaration for the class that connects MultipoleElecEnergy with the ScoringManager |
| NetChargeEnergy.cc | |
| NetChargeEnergy.fwd.hh | |
| NetChargeEnergy.hh | |
| NetChargeEnergyCreator.hh | |
| non_scorefxn_exact_model.cc | |
| non_scorefxn_exact_model.hh | |
| NPDHBondEnergy.cc | |
| NPDHBondEnergy.fwd.hh | |
| NPDHBondEnergy.hh | |
| NPDHBondEnergyCreator.hh | Declaration for the class that connects NPDHBondEnergy with the ScoringManager |
| OccludedHbondSolEnergy.cc | |
| OccludedHbondSolEnergy.fwd.hh | |
| OccludedHbondSolEnergy.hh | |
| OccludedHbondSolEnergy_onebody.cc | |
| OccludedHbondSolEnergy_onebody.fwd.hh | |
| OccludedHbondSolEnergy_onebody.hh | |
| OccludedHbondSolEnergy_onebodyCreator.hh | |
| OccludedHbondSolEnergyCreator.hh | |
| OmegaTetherEnergy.cc | OmegaTether energy method class implementation |
| OmegaTetherEnergy.fwd.hh | OmegaTether energy method class forward declaration |
| OmegaTetherEnergy.hh | OmegaTether energy method class declaration |
| OmegaTetherEnergyCreator.hh | Declaration for the class that connects OmegaTetherEnergy with the ScoringManager |
| OtherPoseEnergy.cc | Way to handle scoring of a collection of poses, allowing shift of focus between poses |
| OtherPoseEnergy.fwd.hh | |
| OtherPoseEnergy.hh | |
| OtherPoseEnergyCreator.hh | Declaration for the class that connects OtherPoseEnergy with the ScoringManager |
| P_AA_Energy.cc | Probability of observing an amino acid (NOT conditional on phi/psi), energy method implementation |
| P_AA_Energy.fwd.hh | Probability of observing an amino acid (NOT conditional on phi/psi), energy method forward declaration |
| P_AA_Energy.hh | Probability of observing an amino acid (NOT conditional on phi/psi), energy method declaration |
| P_AA_EnergyCreator.hh | Declaration for the class that connects P_AA_Energy with the ScoringManager |
| P_AA_pp_Energy.cc | Probability of observing an amino acid, given its phi/psi energy method declaration |
| P_AA_pp_Energy.fwd.hh | |
| P_AA_pp_Energy.hh | Probability of observing an amino acid, given its phi/psi energy method forward declaration |
| P_AA_pp_EnergyCreator.hh | Declaration for the class that connects P_AA_pp_Energy with the ScoringManager |
| P_AA_ss_Energy.cc | Probability of observing an amino acid (NOT conditional on phi/psi), energy method implementation |
| P_AA_ss_Energy.fwd.hh | Probability of observing an amino acid (NOT conditional on phi/psi), energy method forward declaration |
| P_AA_ss_Energy.hh | Probability of observing an amino acid (NOT conditional on phi/psi), energy method declaration |
| P_AA_ss_EnergyCreator.hh | Declaration for the class that connects P_AA_ss_Energy with the ScoringManager |
| PackStatEnergy.cc | Radius of gyration energy function definition. Returns -1 * RG for a given Pose |
| PackStatEnergy.hh | |
| PackStatEnergyCreator.hh | Declaration for the class that connects PackStatEnergy with the ScoringManager |
| PairEnergy.cc | Statistically derived rotamer pair potential class implementation |
| PairEnergy.fwd.hh | Statistically derived rotamer pair potential class forward declaration |
| PairEnergy.hh | Statistically derived rotamer pair potential class declaration |
| PairEnergyCreator.hh | Declaration for the class that connects PairEnergy with the ScoringManager |
| PeptideBondEnergy.cc | |
| PeptideBondEnergy.fwd.hh | |
| PeptideBondEnergy.hh | Scoring method that defines ideal bond lengths between carbonyl carbon of residue N and nitrogen of residue N+1 |
| PeptideBondEnergyCreator.hh | Declaration for the class that connects PeptideBondEnergy with the ScoringManager |
| pHEnergy.cc | Energy due to ionization state of the residue at a particular pH (see pHEnergy.hh for a detailed description) |
| pHEnergy.fwd.hh | PH energy forward declaration |
| pHEnergy.hh | |
| pHEnergyCreator.hh | |
| PointWaterEnergy.cc | |
| PointWaterEnergy.fwd.hh | |
| PointWaterEnergy.hh | Statistical point water energy function |
| PointWaterEnergyCreator.hh | |
| PoissonBoltzmannEnergy.cc | Ramachandran energy method class implementation |
| PoissonBoltzmannEnergy.fwd.hh | Ramachandran energy method class forward declaration |
| PoissonBoltzmannEnergy.hh | Membrane Environment Cbeta Energy |
| PoissonBoltzmannEnergyCreator.hh | |
| ProClosureEnergy.cc | Proline ring closure energy method class implementation |
| ProClosureEnergy.fwd.hh | Proline ring closure energy method class forward declaration |
| ProClosureEnergy.hh | Proline ring closure energy method class declaration |
| ProClosureEnergyCreator.hh | Declaration for the class that connects ProClosureEnergy with the ScoringManager |
| ProQ_Energy.cc | ProQ energy function definition |
| ProQ_Energy.hh | Statistically derived rotamer pair potential class declaration |
| ProQ_EnergyCreator.hh | Declaration for the class that connects ProQ_Energy with the ScoringManager |
| PyEnergy.hh | Various Energy classes for subclassing in PyRosetta |
| RamachandranEnergy.cc | Ramachandran energy method class implementation |
| RamachandranEnergy.fwd.hh | Ramachandran energy method class forward declaration |
| RamachandranEnergy.hh | Ramachandran energy method class declaration |
| RamachandranEnergy2B.cc | |
| RamachandranEnergy2B.fwd.hh | |
| RamachandranEnergy2B.hh | Ramachandran energy method class declaration |
| RamachandranEnergy2BCreator.hh | Declaration for the class that connects RamachandranEnergy2B with the ScoringManager |
| RamachandranEnergyCreator.hh | Declaration for the class that connects RamachandranEnergy with the ScoringManager |
| RamaPreProEnergy.cc | A variation on the Ramachandran scorefunction that has separate probability tables for residues that precede prolines |
| RamaPreProEnergy.fwd.hh | |
| RamaPreProEnergy.hh | A variation on the Ramachandran scorefunction that has separate probability tables for residues that precede prolines |
| RamaPreProEnergyCreator.hh | Declaration for the class that connects RamaPreProEnergy with the ScoringManager |
| ReferenceEnergy.cc | |
| ReferenceEnergy.fwd.hh | Reference energy method forward declaration |
| ReferenceEnergy.hh | Reference energy method implementation |
| ReferenceEnergyCreator.hh | Declaration for the class that connects ReferenceEnergy with the ScoringManager |
| ReferenceEnergyNoncanonical.cc | Reference energy method implementation |
| ReferenceEnergyNoncanonical.fwd.hh | Reference energy method forward declaration |
| ReferenceEnergyNoncanonical.hh | Reference energy method declaration |
| ReferenceEnergyNoncanonicalCreator.hh | Declaration for the class that connects ReferenceEnergyNoncanonical with the ScoringManager |
| ResidualDipolarCouplingEnergy.cc | RDC energy - comparing experimental RDC values to calculated values |
| ResidualDipolarCouplingEnergy.fwd.hh | |
| ResidualDipolarCouplingEnergy.hh | RDC energy - comparing experimental RDC values to calculated values |
| ResidualDipolarCouplingEnergy_Rohl.cc | RDC energy - comparing experimental RDC values to calculated values |
| ResidualDipolarCouplingEnergy_Rohl.hh | |
| ResidualDipolarCouplingEnergy_RohlCreator.hh | Declaration for the class that connects ResidualDipolarCouplingEnergy_Rohl with the ScoringManager |
| ResidualDipolarCouplingEnergyCreator.hh | Declaration for the class that connects ResidualDipolarCouplingEnergy with the ScoringManager |
| RG_Energy_Fast.cc | Radius of gyration energy function definition |
| RG_Energy_Fast.hh | Statistically derived rotamer pair potential class declaration |
| RG_Energy_FastCreator.hh | Declaration for the class that connects RG_Energy_Fast with the ScoringManager |
| RG_Energy_RNA.cc | |
| RG_Energy_RNA.hh | |
| RG_Energy_RNACreator.hh | |
| RG_LocalEnergy.cc | Radius of gyration for local region |
| RG_LocalEnergy.hh | Only calculates RG the length of the repeat. Uses code from RG_Energy_fast |
| RG_LocalEnergyCreator.hh | |
| RingClosureEnergy.cc | Noncanonical ring closure energy method class implementation |
| RingClosureEnergy.fwd.hh | Noncanonical ring closure energy method class forward declaration |
| RingClosureEnergy.hh | Noncanonical ring closure energy method class headers |
| RingClosureEnergyCreator.hh | Declaration for the class that connects RingClosureEnergy with the ScoringManager |
| RMS_Energy.cc | RMS Energy function. Used to optimize the RMSD between two structures |
| RMS_Energy.hh | RMS Energy function. Used to optimize the RMSD between two structures |
| RMS_EnergyCreator.hh | Declaration for the class that connects RMS_Energy with the ScoringManager |
| RNA_BulgeEnergy.cc | |
| RNA_BulgeEnergy.fwd.hh | |
| RNA_BulgeEnergy.hh | |
| RNA_BulgeEnergyCreator.hh | |
| RNA_ChemicalMappingEnergy.cc | |
| RNA_ChemicalMappingEnergy.fwd.hh | |
| RNA_ChemicalMappingEnergy.hh | |
| RNA_ChemicalMappingEnergyCreator.hh | |
| RNA_ChemicalShiftEnergy.cc | Energy score based on the agreement between experimentally determined and theoretically calculated NMR chemical_shift |
| RNA_ChemicalShiftEnergy.hh | Energy score based on the agreement between experimentally determined and theoretically calculated NMR chemical_shift |
| RNA_ChemicalShiftEnergyCreator.hh | |
| RNA_DataBackboneEnergy.cc | Statistically derived rotamer pair potential class implementation |
| RNA_DataBackboneEnergy.fwd.hh | |
| RNA_DataBackboneEnergy.hh | Statistically derived rotamer pair potential class declaration |
| RNA_DataBackboneEnergyCreator.hh | |
| RNA_FA_ElecEnergy.cc | Electrostatics energy method for RNA class implementation |
| RNA_FA_ElecEnergy.fwd.hh | Electrostatics for RNA class forward declaration |
| RNA_FA_ElecEnergy.hh | |
| RNA_FA_ElecEnergyCreator.hh | Declaration for the class that connects RNA_FA_ElecEnergy with the ScoringManager |
| RNA_FullAtomStackingEnergy.cc | |
| RNA_FullAtomStackingEnergy.fwd.hh | |
| RNA_FullAtomStackingEnergy.hh | |
| RNA_FullAtomStackingEnergyCreator.hh | |
| RNA_FullAtomVDW_BasePhosphate.cc | |
| RNA_FullAtomVDW_BasePhosphate.fwd.hh | |
| RNA_FullAtomVDW_BasePhosphate.hh | FullAtom VDW energy between the base and phosphate group in the same (intra) nucleotide |
| RNA_FullAtomVDW_BasePhosphateCreator.fwd.hh | |
| RNA_FullAtomVDW_BasePhosphateCreator.hh | |
| RNA_JR_SuiteEnergy.cc | |
| RNA_JR_SuiteEnergy.fwd.hh | |
| RNA_JR_SuiteEnergy.hh | |
| RNA_JR_SuiteEnergyCreator.hh | |
| RNA_LJ_BaseEnergy.cc | |
| RNA_LJ_BaseEnergy.fwd.hh | |
| RNA_LJ_BaseEnergy.hh | |
| RNA_LJ_BaseEnergyCreator.hh | |
| RNA_MgPointEnergy.cc | Statistically derived Mg(2+) binding potential for RNA |
| RNA_MgPointEnergy.hh | Statistically derived Mg(2+) binding potential for RNA |
| RNA_MgPointEnergyCreator.hh | Declaration for the class that connects RNA_MgPointEnergy with the ScoringManager |
| RNA_PairwiseLowResolutionEnergy.cc | |
| RNA_PairwiseLowResolutionEnergy.fwd.hh | |
| RNA_PairwiseLowResolutionEnergy.hh | |
| RNA_PairwiseLowResolutionEnergyCreator.hh | |
| RNA_PartitionEnergy.cc | |
| RNA_PartitionEnergy.hh | |
| RNA_PartitionEnergyCreator.hh | |
| RNA_StubCoordinateEnergy.cc | |
| RNA_StubCoordinateEnergy.fwd.hh | |
| RNA_StubCoordinateEnergy.hh | |
| RNA_StubCoordinateEnergyCreator.hh | |
| RNA_SugarCloseEnergy.cc | |
| RNA_SugarCloseEnergy.fwd.hh | |
| RNA_SugarCloseEnergy.hh | |
| RNA_SugarCloseEnergyCreator.hh | |
| RNA_SuiteEnergy.cc | |
| RNA_SuiteEnergy.fwd.hh | |
| RNA_SuiteEnergy.hh | |
| RNA_SuiteEnergyCreator.hh | |
| RNA_TorsionEnergy.cc | |
| RNA_TorsionEnergy.fwd.hh | |
| RNA_TorsionEnergy.hh | |
| RNA_TorsionEnergyCreator.hh | |
| RNA_VDW_Energy.cc | |
| RNA_VDW_Energy.fwd.hh | |
| RNA_VDW_Energy.hh | |
| RNA_VDW_EnergyCreator.hh | |
| RNP_LowResEnergy.cc | |
| RNP_LowResEnergy.fwd.hh | |
| RNP_LowResEnergy.hh | |
| RNP_LowResEnergyCreator.hh | |
| RNP_LowResPairDistEnergy.cc | |
| RNP_LowResPairDistEnergy.fwd.hh | |
| RNP_LowResPairDistEnergy.hh | |
| RNP_LowResPairDistEnergyCreator.hh | |
| RNP_LowResStackEnergy.cc | |
| RNP_LowResStackEnergy.fwd.hh | |
| RNP_LowResStackEnergy.hh | |
| RNP_LowResStackEnergyCreator.hh | |
| SA_Energy.cc | Sa energy function definition |
| SA_Energy.hh | Statistically derived rotamer pair potential class declaration |
| SA_EnergyCreator.hh | |
| SASAEnergy.cc | Power Diagram-derived solvent-accessible surface area energy |
| SASAEnergy.fwd.hh | Power Diagram-derived solvent-accessible surface area energy |
| SASAEnergy.hh | Power Diagram-derived solvent-accessible surface area energy |
| SASAEnergyCreator.hh | Declaration for the class that connects SASAEnergy with the ScoringManager |
| SAXSEnergy.cc | FastSAX scoring of Stovgaard et al (BMC Bioinf. 2010) |
| SAXSEnergy.hh | |
| SAXSEnergyCEN.hh | |
| SAXSEnergyCreator.hh | |
| SAXSEnergyCreatorCEN.cc | |
| SAXSEnergyCreatorCEN.hh | Declaration for the class that connects SAXSEnergyCreatorCEN with the ScoringManager |
| SAXSEnergyCreatorFA.cc | |
| SAXSEnergyCreatorFA.hh | Declaration for the class that connects SAXSEnergyCreatorFA with the ScoringManager |
| SAXSEnergyFA.hh | |
| SecondaryStructureEnergy.cc | Statistically derived rotamer pair potential class implementation |
| SecondaryStructureEnergy.fwd.hh | |
| SecondaryStructureEnergy.hh | Statistically derived rotamer pair potential class declaration |
| SecondaryStructureEnergyCreator.hh | Declaration for the class that connects SecondaryStructureEnergy with the ScoringManager |
| SequenceDependentRefEnergy.cc | |
| SequenceDependentRefEnergy.fwd.hh | Reference energy method forward declaration |
| SequenceDependentRefEnergy.hh | Reference energy method implementation |
| SequenceDependentRefEnergyCreator.hh | Declaration for the class that connects SequenceDependentRefEnergy with the ScoringManager |
| SmoothCenPairEnergy.cc | Smooth, differentiable, version of cenpair |
| SmoothCenPairEnergy.hh | |
| SmoothCenPairEnergyCreator.hh | |
| SmoothEnvEnergy.cc | Smooth, differentiable, version of centroid env |
| SmoothEnvEnergy.hh | |
| SmoothEnvEnergyCreator.hh | |
| SplitUnfoldedTwoBodyEnergy.cc | Split unfolded energy two body energy method |
| SplitUnfoldedTwoBodyEnergy.fwd.hh | Forward header for energy method for the two body portion of the split unfolded energy |
| SplitUnfoldedTwoBodyEnergy.hh | Header for the split unfolded energy two body component energy method |
| SplitUnfoldedTwoBodyEnergyCreator.cc | |
| SplitUnfoldedTwoBodyEnergyCreator.hh | Energy creator for the split unfolded two body energy method |
| SSElementMotifContactEnergy.cc | |
| SSElementMotifContactEnergy.h | |
| SSElementMotifContactEnergy.hh | Will's motif score to determine how well packed the protein core is |
| SSElementMotifContactEnergyCreator.hh | |
| StackElecEnergy.cc | |
| StackElecEnergy.fwd.hh | |
| StackElecEnergy.hh | |
| StackElecEnergyCreator.hh | |
| SuckerEnergy.cc | Statistically derived rotamer pair potential class implementation |
| SuckerEnergy.fwd.hh | Statistically derived rotamer pair potential class forward declaration |
| SuckerEnergy.hh | Energy attracting atoms to sucker atoms |
| SuckerEnergyCreator.hh | Declaration for the class that connects SuckerEnergy with the ScoringManager |
| SugarBackboneEnergy.cc | |
| SugarBackboneEnergy.fwd.hh | Forward declarations for SugarBackboneEnergy |
| SugarBackboneEnergy.hh | Method definitions for SugarBackboneEnergy and SugarBackboneEnergyCreator |
| SugarBackboneEnergyCreator.hh | |
| SurfEnergy.cc | Packing Score |
| SurfEnergy.hh | Packing Score |
| SurfEnergyCreator.hh | |
| SurfVolEnergy.cc | Packing Score |
| SurfVolEnergy.hh | |
| SurfVolEnergyCreator.hh | |
| SymmetricLigandEnergy.cc | Dunbrack energy method implementation |
| SymmetricLigandEnergy.fwd.hh | Dunbrack energy method forward declaration |
| SymmetricLigandEnergy.hh | Score for implicit ligand interactions from symmetric geometry |
| SymmetricLigandEnergyCreator.hh | |
| TNA_SuiteEnergy.cc | |
| TNA_SuiteEnergy.fwd.hh | |
| TNA_SuiteEnergy.hh | |
| TNA_SuiteEnergyCreator.hh | |
| UnfoldedStateEnergy.cc | Unfolded state energy method implementation; energies based on eneriges of residues in fragments |
| UnfoldedStateEnergy.fwd.hh | Unfolded state energy method, forward declaration |
| UnfoldedStateEnergy.hh | Unfolded state energy declaration header file |
| UnfoldedStateEnergyCreator.hh | Declaration for the class that connects UnfoldedStateEnergy with the ScoringManager |
| VdWTinkerEnergy.cc | VdW treatment using buffered 14-7 approach in Tinker/Amoeba |
| VdWTinkerEnergy.fwd.hh | |
| VdWTinkerEnergy.hh | |
| VdWTinkerEnergyCreator.hh | |
| WaterAdductHBondEnergy.cc | |
| WaterAdductHBondEnergy.fwd.hh | |
| WaterAdductHBondEnergy.hh | |
| WaterAdductHBondEnergyCreator.hh | |
| WaterAdductIntraEnergy.cc | |
| WaterAdductIntraEnergy.fwd.hh | |
| WaterAdductIntraEnergy.hh | Energetic offset/cost for placing a water adduct on an amino or nucleic acid |
| WaterAdductIntraEnergyCreator.hh | |
| WaterSpecificEnergy.cc | |
| WaterSpecificEnergy.fwd.hh | |
| WaterSpecificEnergy.hh | Energetic considerations for explicit water molecules, |
| WaterSpecificEnergyCreator.hh | |
| XtalMLEnergy.cc | |
| XtalMLEnergy.hh | |
| XtalMLEnergyCreator.hh | |
| YHHPlanarityEnergy.cc | |
| YHHPlanarityEnergy.fwd.hh | |
| YHHPlanarityEnergy.hh | Term for chi3 on tyrosine residues to prefer the hydrogen lie in the plane of the ring |
| YHHPlanarityEnergyCreator.hh | |
| ► environment | |
| DofPassport.cc | |
| DofPassport.fwd.hh | Definition of the DofPassport class |
| DofPassport.hh | |
| EnvCore.cc | |
| EnvCore.fwd.hh | Definition of the EnvCore class |
| EnvCore.hh | Low compile-level functions of Environment |
| EnvExcnBase.hh | |
| FoldTreeSketch.cc | |
| FoldTreeSketch.fwd.hh | Definition of the FoldTreeSketch class |
| FoldTreeSketch.hh | A temporary "sketch" of a fold tree that keeps track of everything as a graph and doesn't mind invalid states (cycles, detached bits, etc.) |
| LocalPosition.cc | |
| LocalPosition.fwd.hh | Definition of the LocalPosition class |
| LocalPosition.hh | |
| SequenceAnnotation.cc | |
| SequenceAnnotation.fwd.hh | Definition of the SequenceAnnotation class |
| SequenceAnnotation.hh | An object to store, mainipulate and manage the different labels that might be attached to a ProtectedConformation |
| ► enzymes | |
| consensus_sequence_parsers.cc | Definitions for helper functions for the parsing of enzyme consensus sequences |
| consensus_sequence_parsers.hh | Declarations for helper functions for the parsing of enzyme consensus sequences |
| database_io.cc | |
| database_io.hh | Database input/output function definitions for enzyme data |
| EnzymeData.hh | Definitions for EnzymeData |
| EnzymeManager.cc | |
| EnzymeManager.fwd.hh | Forward declaration for EnzymeManager |
| EnzymeManager.hh | Method definitions for EnzymeManager |
| ► fragment | |
| ► picking_old | |
| ► concepts | |
| Book.fwd.hh | Forward declaration for core::fragment::picking_old::concepts |
| Book.hh | Wrapper class demonstrating the Book concept |
| Extent.fwd.hh | Forward declaration for Extent |
| Extent.hh | Class demonstrating the Extent concept |
| Librarian.fwd.hh | |
| Librarian.hh | Librarian template for sorting through and extracting desired fragments |
| Library.fwd.hh | Forward declaration for core::fragment::concepts::Library |
| Library.hh | Class demonstrating the Library concept |
| ► vall | |
| ► eval | |
| ABEGOEval.cc | Scores a fragment based on abego identity |
| ABEGOEval.fwd.hh | Forward declaration of core::fragment::picking_old::vall::eval::ABEGOEval |
| ABEGOEval.hh | Scores a fragment based on ABEGO |
| EnergyEval.cc | Scores a fragment by inserting its backbone angles into a Pose and evaluating its energy using a given ScoreFunction |
| EnergyEval.fwd.hh | Forward declaration of core::fragment::picking_old::vall::eval::EnergyEval |
| EnergyEval.hh | Scores a fragment by inserting its backbone angles into a Pose and evaluating its energy using a given ScoreFunction |
| IdentityEval.cc | Scores a fragment based on secondary structure identity and sequence identity |
| IdentityEval.fwd.hh | Forward declaration of core::fragment::picking_old::vall::eval::IdentityEval |
| IdentityEval.hh | Scores a fragment based on secondary structure identity and sequence identity |
| VallFragmentEval.cc | Base class for Vall ExtentEvaluator |
| VallFragmentEval.fwd.hh | Forward declaration of core::fragment::picking_old::vall::eval::VallFragmentEval |
| VallFragmentEval.hh | Base class for Vall ExtentEvaluator |
| ► gen | |
| LengthGen.cc | Default constant length fragment VallExtentGenerator |
| LengthGen.fwd.hh | Forward declaration for core::fragment::picking_old::vall::gen::LengthGen |
| LengthGen.hh | Default constant length fragment VallExtentGenerator |
| SecStructGen.cc | Default constant length fragment VallExtentGenerator |
| SecStructGen.fwd.hh | Forward declaration for core::fragment::picking_old::vall::gen::SecStructGen |
| SecStructGen.hh | Generator that requires fragments to have a specific secondary structure string |
| VallFragmentGen.cc | Base class Vall ExtentGenerator |
| VallFragmentGen.fwd.hh | Forward declaration for core::fragment::picking_old::vall::gen::VallFragmentGen |
| VallFragmentGen.hh | Base class Vall ExtentGenerator |
| ► scores | |
| VallFragmentScore.fwd.hh | Forward declaration for core::fragment::picking_old::vall::scores::VallFragmentScore |
| VallFragmentScore.hh | Base Vall FragmentScore struct |
| util.cc | Utility functions for interacting with VallLibrary |
| util.hh | Utility functions for interacting with VallLibrary |
| vall_io.cc | |
| vall_io.hh | Reading/writing of Vall libraries |
| VallLibrarian.cc | Librarian that picks fragments from the Vall |
| VallLibrarian.fwd.hh | Forward declaration for core::fragment::picking_old::vall::VallLibrarian |
| VallLibrarian.hh | Librarian that picks fragments from the Vall |
| VallLibrary.fwd.hh | Forward declaration for VallLibrary |
| VallLibrary.hh | Vall fragment library |
| VallResidue.cc | Class for managing a line of the Vall fragment library |
| VallResidue.fwd.hh | Forward declaration for core::fragment::picking_old::vall:VallResidue |
| VallResidue.hh | Class for managing a line of the Vall fragment library |
| VallSection.fwd.hh | Forward declaration for VallSection |
| VallSection.hh | Class implementing the Book concept for a continuous section of lines in the Vall library |
| FragmentLibraryManager.cc | Singleton class for accessing fragment libraries |
| FragmentLibraryManager.fwd.hh | Forward declaration for FragmentLibraryManager |
| FragmentLibraryManager.hh | Singleton class for accessing fragment libraries |
| ► rna | |
| FragmentLibrary.cc | |
| FragmentLibrary.fwd.hh | |
| FragmentLibrary.hh | |
| FullAtomRNA_Fragments.cc | |
| FullAtomRNA_Fragments.fwd.hh | |
| FullAtomRNA_Fragments.hh | |
| RNA_FragmentHomologyExclusion.cc | |
| RNA_FragmentHomologyExclusion.fwd.hh | |
| RNA_FragmentHomologyExclusion.hh | |
| RNA_Fragments.cc | |
| RNA_Fragments.fwd.hh | |
| RNA_Fragments.hh | |
| RNA_FragmentsClasses.fwd.hh | |
| RNA_MatchType.hh | |
| TorsionSet.cc | |
| TorsionSet.fwd.hh | |
| TorsionSet.hh | |
| BaseCacheUnit.hh | |
| BBTorsionAndAnglesSRFD.cc | |
| BBTorsionAndAnglesSRFD.hh | |
| BBTorsionSRFD.cc | |
| BBTorsionSRFD.fwd.hh | |
| BBTorsionSRFD.hh | |
| ConstantLengthFragSet.cc | |
| ConstantLengthFragSet.fwd.hh | |
| ConstantLengthFragSet.hh | |
| ConstantLengthFragSetIterator_.hh | |
| FragCache.fwd.hh | |
| FragCache.hh | |
| FragData.cc | |
| FragData.fwd.hh | |
| FragData.hh | |
| FragID.cc | |
| FragID.fwd.hh | |
| FragID.hh | |
| FragID_Iterator.cc | |
| FragID_Iterator.fwd.hh | |
| FragID_Iterator.hh | |
| FragmentIO.cc | |
| FragmentIO.hh | |
| FragmentRmsd.cc | |
| FragmentRmsd.fwd.hh | |
| FragmentRmsd.hh | |
| FragmentSetLoader.cc | |
| FragmentSetLoader.fwd.hh | |
| FragmentSetLoader.hh | |
| FragmentSetLoaderCreator.hh | |
| FragSet.cc | |
| FragSet.fwd.hh | |
| FragSet.hh | |
| FragSetCollection.cc | |
| FragSetCollection.fwd.hh | |
| FragSetCollection.hh | |
| Frame.cc | |
| Frame.fwd.hh | |
| Frame.hh | |
| FrameIterator.cc | |
| FrameIterator.fwd.hh | |
| FrameIterator.hh | |
| FrameIteratorWorker_.fwd.hh | |
| FrameIteratorWorker_.hh | |
| FrameList.cc | |
| FrameList.fwd.hh | |
| FrameList.hh | |
| FrameListIterator_.hh | |
| IndependentBBTorsionSRFD.cc | A version of BBTorsionSRFD that considers each torsion independently during is_applicable() and apply() calls when passed a MoveMap (vs the all-torsions-must-be-moveable-or-nothing-is behavior in the original BBTorsionSRFD) |
| IndependentBBTorsionSRFD.fwd.hh | Forward declaration for IndependentBBTorsionSRFD |
| IndependentBBTorsionSRFD.hh | A version of BBTorsionSRFD that considers each torsion independently during is_applicable() and apply() calls when passed a MoveMap (vs the all-torsions-must-be-moveable-or-nothing-is behavior in the original BBTorsionSRFD) |
| JumpingFrame.cc | |
| JumpingFrame.fwd.hh | |
| JumpingFrame.hh | |
| JumpSRFD.cc | |
| JumpSRFD.fwd.hh | |
| JumpSRFD.hh | |
| MinimalFragSet.cc | |
| MinimalFragSet.fwd.hh | |
| MinimalFragSet.hh | |
| MinimalFragSetIterator_.hh | |
| OrderedFragSet.cc | |
| OrderedFragSet.fwd.hh | |
| OrderedFragSet.hh | |
| OrderedFragSetIterator_.hh | |
| SecondaryStructure.cc | Secondary structure will hold statistics about secondary structure predictions sources can be from |
| SecondaryStructure.fwd.hh | |
| SecondaryStructure.hh | Secondary structure will hold statistics about secondary structure predictions sources can be from |
| SecstructSRFD.cc | |
| SecstructSRFD.hh | |
| SingleResidueFragData.cc | |
| SingleResidueFragData.fwd.hh | |
| SingleResidueFragData.hh | |
| util.cc | |
| util.hh | |
| ► grid | |
| CartGrid.fwd.hh | |
| CartGrid.hh | |
| ► id | |
| AtomID.cc | Kinematics Atom identifier |
| AtomID.fwd.hh | Kinematics AtomID forward declarations header |
| AtomID.hh | Declarations for the TorsionID class |
| AtomID_Map.fwd.hh | Core::id::AtomID_Map forward declarations |
| AtomID_Map.hh | Map from Atom identifiers to contained values class |
| AtomID_Map.srlz.hh | Serialization routines for AtomID_Map |
| AtomID_Mask.fwd.hh | Id::AtomID_Mask forward declarations header |
| AtomID_Mask.hh | Map from Atom identifiers to booleans |
| bogus.cc | |
| bogus.hh | |
| CacheableAtomID_MapVector.cc | Serialization routines for the CacheableAtomID_MapVector class |
| CacheableAtomID_MapVector.fwd.hh | |
| CacheableAtomID_MapVector.hh | |
| DOF_ID.cc | Kinematics DOF identifier class |
| DOF_ID.fwd.hh | Kinematics DOF_ID forward declarations header |
| DOF_ID.hh | |
| DOF_ID_Map.fwd.hh | Core::id::DOF_ID_Map forward declarations |
| DOF_ID_Map.hh | Map from Atom DOF identifiers to contained values class |
| DOF_ID_Mask.fwd.hh | Id::DOF_ID_Mask forward declarations header |
| DOF_ID_Range.cc | Kinematics DOF identifier class |
| DOF_ID_Range.fwd.hh | Kinematics DOF_ID_Range forward declarations header |
| DOF_ID_Range.hh | |
| Exceptions.cc | |
| Exceptions.hh | |
| JumpID.cc | Jump identifier |
| JumpID.fwd.hh | Kinematics JumpID forward declarations header |
| JumpID.hh | |
| NamedAtomID.cc | Kinematics Atom identifier |
| NamedAtomID.fwd.hh | |
| NamedAtomID.hh | |
| NamedAtomID_Map.fwd.hh | Core::id::NamedAtomID_Map forward declarations |
| NamedAtomID_Map.hh | Map from named Atom identifiers to contained values class |
| NamedStubID.cc | |
| NamedStubID.fwd.hh | |
| NamedStubID.hh | |
| SequenceMapping.cc | |
| SequenceMapping.fwd.hh | |
| SequenceMapping.hh | |
| TorsionID.cc | Kinematics Atom identifier |
| TorsionID.fwd.hh | Kinematics TorsionID forward declarations header |
| TorsionID.hh | |
| TorsionID_Range.cc | Conformation torsion identifier class |
| TorsionID_Range.fwd.hh | Kinematics TorsionID_Range forward declarations header |
| TorsionID_Range.hh | |
| types.hh | Core::id package type declarations |
| ► import_pose | |
| ► atom_tree_diffs | |
| atom_tree_diff.cc | |
| atom_tree_diff.hh | |
| ► libraries | |
| BasePairStepLibrary.cc | |
| BasePairStepLibrary.fwd.hh | |
| BasePairStepLibrary.hh | |
| ChunkSet.cc | |
| ChunkSet.fwd.hh | |
| ChunkSet.hh | |
| RNA_ChunkLibrary.cc | |
| RNA_ChunkLibrary.fwd.hh | |
| RNA_ChunkLibrary.hh | Forward declarations header |
| RNA_JumpLibrary.cc | |
| RNA_JumpLibrary.fwd.hh | |
| RNA_JumpLibrary.hh | |
| RNA_LibraryManager.cc | |
| RNA_LibraryManager.fwd.hh | |
| RNA_LibraryManager.hh | |
| ► options | |
| RNA_BasicOptions.cc | |
| RNA_BasicOptions.fwd.hh | |
| RNA_BasicOptions.hh | |
| RNA_DeNovoProtocolOptions.cc | |
| RNA_DeNovoProtocolOptions.fwd.hh | |
| RNA_DeNovoProtocolOptions.hh | |
| RNA_FragmentMonteCarloOptions.cc | |
| RNA_FragmentMonteCarloOptions.fwd.hh | |
| RNA_FragmentMonteCarloOptions.hh | |
| RNA_MinimizerOptions.cc | |
| RNA_MinimizerOptions.fwd.hh | |
| RNA_MinimizerOptions.hh | |
| ► pose_stream | |
| ExtendedPoseInputStream.cc | |
| ExtendedPoseInputStream.hh | |
| LazySilentFilePoseInputStream.cc | |
| LazySilentFilePoseInputStream.fwd.hh | |
| LazySilentFilePoseInputStream.hh | |
| MetaPoseInputStream.cc | |
| MetaPoseInputStream.fwd.hh | |
| MetaPoseInputStream.hh | |
| PDBPoseInputStream.cc | |
| PDBPoseInputStream.fwd.hh | |
| PDBPoseInputStream.hh | |
| PoseInputStream.cc | |
| PoseInputStream.fwd.hh | |
| PoseInputStream.hh | |
| SilentFilePoseInputStream.cc | |
| SilentFilePoseInputStream.fwd.hh | |
| SilentFilePoseInputStream.hh | |
| util.cc | |
| util.hh | |
| FullModelPoseBuilder.cc | |
| FullModelPoseBuilder.fwd.hh | |
| FullModelPoseBuilder.hh | |
| import_pose.cc | Various functions to construct Pose object(s) from PDB(s) |
| import_pose.hh | Various functions to construct Pose object(s) from PDB(s) |
| import_pose_options.cc | |
| import_pose_options.fwd.hh | |
| import_pose_options.hh | |
| PDBSilentStruct.cc | |
| PDBSilentStruct.hh | |
| PDBSilentStructCreator.cc | |
| PDBSilentStructCreator.hh | |
| PoseFromPDBLoader.cc | |
| PoseResource.cc | |
| PoseResource.fwd.hh | Declaration for the bitwise-constant class that holds a load-once Pose in memory and protects it so that it can be shared safely between threads |
| PoseResource.hh | |
| PoseResourceLoader.cc | |
| PoseResourceLoader.fwd.hh | |
| PoseResourceLoader.hh | |
| PoseResourceLoaderCreator.hh | |
| RNA_BasePairHandler.cc | |
| RNA_BasePairHandler.fwd.hh | |
| RNA_BasePairHandler.hh | |
| RNA_DeNovoParameters.cc | |
| RNA_DeNovoParameters.fwd.hh | |
| RNA_DeNovoParameters.hh | |
| RNA_DeNovoSetup.cc | |
| RNA_DeNovoSetup.fwd.hh | |
| RNA_DeNovoSetup.hh | |
| RNA_HelixAssembler.cc | Make a helix that is low energy in Rosetta |
| RNA_HelixAssembler.fwd.hh | |
| RNA_HelixAssembler.hh | |
| RNA_JumpMover.cc | |
| RNA_JumpMover.fwd.hh | |
| RNA_JumpMover.hh | |
| ► init | |
| init.cc | Options system initialization routines |
| init.hh | Core Init functions |
| score_function_corrections.cc | Initialize Score Funciton Corrections |
| score_function_corrections.hh | Initialize score function corrections |
| ► io | |
| ► carbohydrates | |
| pose_io.cc | Pose input/output function definitions for carbohydrate-specific data formats |
| pose_io.hh | Pose input/output function declarations for carbohydrate-specific data formats |
| ► ddg | |
| PositionDdGInfo.cc | |
| PositionDdGInfo.fwd.hh | |
| PositionDdGInfo.hh | |
| ► external | |
| PsiPredInterface.cc | |
| PsiPredInterface.fwd.hh | |
| PsiPredInterface.hh | |
| ► mmcif | |
| cif_reader.cc | |
| cif_reader.hh | |
| cif_writer.cc | |
| cif_writer.hh | |
| ► mmtf | |
| ExtraDataEnum.hh | Enum definitions for pose extra data we will be storing/retrieving |
| ExtraDataEnumManager.cc | Enum string/enum functions for pose extra data we will be storing/retrieving |
| ExtraDataEnumManager.fwd.hh | Enum string/enum functions for pose extra data we will be storing/retrieving |
| ExtraDataEnumManager.hh | Enum string/enum functions for pose extra data we will be storing/retrieving |
| mmtf_reader.cc | |
| mmtf_reader.hh | |
| mmtf_writer.cc | Functions for MMTF writing |
| mmtf_writer.hh | |
| util.cc | Functions for MMTF writing/reading |
| util.hh | Functions for MMTF writing/reading |
| ► nmr | |
| AtomSelection.cc | Implementation of class AtomSelection |
| AtomSelection.fwd.hh | Forward declaration for AromSelection |
| AtomSelection.hh | Class that holds selection identifiers for a single atom. An atom list is read in from a general NMR input/assignment file |
| ParaIon.cc | Function definitions of ParaIon class |
| ParaIon.fwd.hh | Forward declaration for ParaIon |
| ParaIon.hh | Class to store properties of paramagnetic ions such as charge and spin quantum numbers |
| ParamagneticDatabaseHandler.cc | Function definitions of ParamagneticDatabaseHandler class |
| ParamagneticDatabaseHandler.fwd.hh | Forward declaration for ParamagneticDatabaseHandler |
| ParamagneticDatabaseHandler.hh | Classes to handle ion properties database file |
| SpinlabelDatabaseHandler.cc | Implementation of class SpinlabelDatabaseHandler |
| SpinlabelDatabaseHandler.fwd.hh | Forward declaration for SpinlabelDatabaseHandler |
| SpinlabelDatabaseHandler.hh | |
| util.cc | Util functions for Input and Output of NMR data |
| util.hh | Util functions for Input and Output of NMR data |
| ► pdb | |
| build_pose_as_is.cc | |
| build_pose_as_is.hh | Declarations for StructFileRep and related classes |
| Field.cc | Each line of a PDB file is a Record which is divided into Fields |
| Field.fwd.hh | Forward declaration for a .pdb record field data structure |
| Field.hh | Definitions for the Field data structures and related helper function declarations |
| pdb_reader.cc | Function definitions for reading of .pdb files |
| pdb_reader.hh | Function declarations for reading of .pdb files |
| pdb_writer.cc | Function(s) for pdb writing |
| pdb_writer.hh | Function(s) for pdb writing |
| Record.cc | Helper function definitions for Record data structures |
| Record.hh | Typedef for a .pdb file record data structure |
| record_def_io.cc | |
| record_def_io.hh | Database input/output function definitions for PDB record definition data |
| RecordCollection.cc | Method definitions for RecordCollection |
| RecordCollection.fwd.hh | Forward declaration for RecordCollection |
| RecordCollection.hh | Declarations and simple accessor/mutator definitions for RecordCollection |
| RecordType.hh | Enumeration definition for RecordType |
| ► pose_from_sfr | |
| chirality_resolution.cc | |
| chirality_resolution.fwd.hh | Various utilities to accomodated PDB input issues |
| chirality_resolution.hh | Various utilities to accomodated PDB input issues |
| PoseFromSFRBuilder.cc | |
| PoseFromSFRBuilder.fwd.hh | |
| PoseFromSFRBuilder.hh | |
| ► pose_to_sfr | |
| PoseToStructFileRepConverter.cc | A class to convert a pose to a StructFileRep |
| PoseToStructFileRepConverter.fwd.hh | Forward declarations for class to convert a pose to a StructFileRep |
| PoseToStructFileRepConverter.hh | Headers for class to convert a pose to a StructFileRep |
| PoseToStructFileRepConverterTests.fwd.hh | |
| ► raw_data | |
| DecoyFileData.cc | Write decoys in "silent" format |
| DecoyFileData.hh | |
| DecoyStruct.cc | Protein-specific "silent" file reader and writer for mini |
| DecoyStruct.hh | Silent input file reader for mini |
| DisulfideFile.cc | |
| DisulfideFile.hh | A simple wrapper for a Disulfide File suitable for the -fix_disulf option |
| Raw.fwd.hh | Forward declarations for raw data classes |
| RawFileData.cc | |
| RawFileData.hh | FileData base class |
| RawStruct.cc | Struct base class |
| RawStruct.hh | Struct base class |
| ScoreFileData.cc | Way to write out just the score using the SilentFile stuff |
| ScoreFileData.hh | Way to write out just the score using the SilentFile stuff |
| ScoreMap.cc | A place to put some common functions for score-file output |
| ScoreMap.hh | A place to put some common functions for score-file output |
| ScoreStructJSON.cc | Write out only score information in JSON format |
| ScoreStructJSON.hh | Write out only the scores in JSON format |
| ScoreStructText.cc | Write out only score information |
| ScoreStructText.hh | Write out only the scores (equivalent to a scorefile) |
| ► rcsb | |
| ExperimentalTechnique.cc | Helper function definitions for ExperimentalTechnique |
| ExperimentalTechnique.hh | Enumeration definition for ExperimentalTechnique and helper function declarations |
| ► rna | |
| RDAT.cc | |
| RDAT.fwd.hh | |
| RDAT.hh | |
| RNA_DataReader.cc | |
| RNA_DataReader.fwd.hh | |
| RNA_DataReader.hh | |
| ► sequence_comparation | |
| DesignContrast.cc | |
| DesignContrast.fwd.hh | |
| DesignContrast.hh | |
| ► serialization | |
| serialize_pose.cc | |
| serialize_pose.hh | |
| ► silent | |
| BasicSilentStructCreators.cc | |
| BasicSilentStructCreators.hh | |
| BinarySilentStruct.cc | |
| BinarySilentStruct.hh | |
| EnergyNames.fwd.hh | Silent input file reader for mini |
| EnergyNames.hh | Class representing a set of energy names used in silent-file input/output |
| ProteinSilentStruct.hh | Representation of rosetta++ protein silent-file structures |
| ProteinSilentStruct.tmpl.hh | Representation of rosetta++ protein silent-file structures |
| RigidBodySilentStruct.cc | |
| RigidBodySilentStruct.hh | |
| RNA_SilentStruct.cc | Representation of rosetta++ protein silent-file structures |
| RNA_SilentStruct.hh | Representation of rosetta++ RNA silent-file structures |
| ScoreFileSilentStruct.cc | Representation of PDB files in a silent-file format |
| ScoreFileSilentStruct.hh | Representation of rosetta++ protein silent-file structures |
| ScoreJumpFileSilentStruct.cc | Representation of PDB files in a silent-file format |
| ScoreJumpFileSilentStruct.hh | Representation of rosetta++ protein silent-file structures |
| SharedSilentData.cc | Serialization routines for shared silent data |
| SharedSilentData.hh | Silent input file reader for mini |
| silent.fwd.hh | |
| SilentEnergy.hh | Simple class for managing energies in SilentStruct objects |
| SilentFileData.cc | Silent input file reader for mini |
| SilentFileData.fwd.hh | |
| SilentFileData.hh | Silent input file reader for mini |
| SilentFileOptions.cc | |
| SilentFileOptions.fwd.hh | Forward Header for options for constructing a pose from a silent file |
| SilentFileOptions.hh | Options for constructing a pose from a silent file |
| SilentFileRMOptions.cc | |
| SilentStruct.cc | Silent input file reader for mini |
| SilentStruct.fwd.hh | |
| SilentStruct.hh | Silent input file reader for mini |
| SilentStructCreator.cc | |
| SilentStructCreator.fwd.hh | |
| SilentStructCreator.hh | Base class for SilentStructCreators for the SilentStruct load-time factory registration scheme |
| SilentStructFactory.cc | Factory for creating various types of silent |
| SilentStructFactory.fwd.hh | Silent input file reader for mini |
| SilentStructFactory.hh | Factory for creating various types of SilentStruct objects |
| util.cc | Utility functions for silent-file classes |
| util.hh | Utility functions for silent-files |
| alt_codes_io.cc | |
| alt_codes_io.hh | |
| AtomInformation.hh | |
| CrystInfo.cc | Auto-generated serialization template functions |
| CrystInfo.hh | |
| HeaderInformation.cc | Information stored in the Title Section in the PDB format |
| HeaderInformation.fwd.hh | Information stored in the HEADER record in the PDB format |
| HeaderInformation.hh | Information stored in the Title Section in the PDB format |
| NomenclatureManager.cc | |
| NomenclatureManager.fwd.hh | |
| NomenclatureManager.hh | |
| Remarks.cc | |
| Remarks.fwd.hh | |
| Remarks.hh | |
| ResidueInformation.cc | Method definitions for ResidueInformation |
| ResidueInformation.fwd.hh | Class declaration for ResidueInformation |
| ResidueInformation.hh | Structure definition for ResidueInformation |
| StructFileReaderOptions.cc | Definitions for StructFileReaderOptions |
| StructFileReaderOptions.fwd.hh | |
| StructFileReaderOptions.hh | |
| StructFileRep.cc | Class/structure method definitions for StructFileRep |
| StructFileRep.fwd.hh | Class/structure declarations for StructFileRep |
| StructFileRep.hh | Class/structure definitions for StructFileRep |
| StructFileRepOptions.cc | Definitions for StructFileRepOptions |
| StructFileRepOptions.fwd.hh | |
| StructFileRepOptions.hh | |
| util.cc | Util functions for Input and Output. Very general IO should go to utility/io. These should be related to core in a deep way or not able to be called from utility |
| util.hh | Util functions for Input and Output. Very general IO should go to utility/io. These should be related to core in a deep way |
| ► kinematics | |
| ► jacobian | |
| JacobianStructure.cc | Class that defines structure of Jacobian modules |
| JacobianStructure.fwd.hh | Class that defines structure of Jacobian modules |
| JacobianStructure.hh | Class that defines structure of Jacobian modules |
| ModuleType1.cc | Class to perform Jacobian analyses on a series of atoms with mobility in three Universal joints (collocated torsions) |
| ModuleType1.fwd.hh | Class that contains the linearized Cartesian motion/force space of a 1,2,3-amino acid module |
| ModuleType1.hh | Class that contains the linearized Cartesian motion/force space of a 1,2,3-amino acid module |
| SeriesJacobians.cc | Class that handles the Jacobian analysis of atoms connected in series |
| SeriesJacobians.fwd.hh | Class that defines series of Jacobian modules |
| SeriesJacobians.hh | Class that defines series of Jacobian modules |
| ► tree | |
| Atom.fwd.hh | Kinematics Atom forward declarations header |
| Atom.hh | Kinematics Atom interface class |
| Atom_.cc | Kinematics Atom abstract base class |
| Atom_.hh | Kinematics Atom abstract base class |
| BondedAtom.cc | Kinematics |
| BondedAtom.hh | Kinematics |
| JumpAtom.cc | Jump atom |
| JumpAtom.hh | Jump atom |
| AtomPointer.fwd.hh | Kinematics::AtomPointer2D forward declarations header |
| AtomPointer.hh | Map from Atom identifiers to Atom pointers |
| AtomTree.cc | Atom tree class |
| AtomTree.fwd.hh | Kinematics::AtomTree forward declarations header |
| AtomTree.hh | Atom tree class |
| AtomWithDOFChange.cc | |
| AtomWithDOFChange.fwd.hh | Data structure for output-sensitie refold data class forward declaration |
| AtomWithDOFChange.hh | Data structure for output-sensitie refold data class declaration |
| constants.cc | |
| constants.hh | |
| DomainMap.fwd.hh | |
| DomainMap.hh | |
| Edge.cc | Fold tree edge class |
| Edge.fwd.hh | Kinematics Edge forward declarations header |
| Edge.hh | Fold tree edge class |
| Exceptions.hh | Fold tree class |
| FoldTree.cc | Fold tree class |
| FoldTree.fwd.hh | Kinematics::FoldTree forward declarations header |
| FoldTree.hh | Fold tree class |
| Jump.cc | Kinematics Jump class |
| Jump.fwd.hh | Kinematics Jump forward declarations header |
| Jump.hh | Kinematics Jump class |
| MinimizerMapBase.cc | Kinematics |
| MinimizerMapBase.fwd.hh | Forward declaration of the minimizer-map base class for communicating between an AtomTree and the class that will use the AtomTree to perform some gradient-based minimization |
| MinimizerMapBase.hh | Deriviative classes from this base class will implement three virtual functions allowing the AtomTree to communicate with an outside Minimizer about how the degrees of freedom in the AtomTree should be minimized |
| MoveMap.cc | Method definitions for the MoveMap |
| MoveMap.fwd.hh | Kinematics MoveMap forward declarations header |
| MoveMap.hh | Declarations for the MoveMap class |
| ResidueCoordinateChangeList.cc | |
| ResidueCoordinateChangeList.fwd.hh | AtomTree/Conformation communication vector class forward declaration |
| ResidueCoordinateChangeList.hh | |
| RT.cc | Rotation + translation class |
| RT.fwd.hh | Kinematics RT forward declarations header |
| RT.hh | Rotation + translation class |
| ShortestPathInFoldTree.cc | Helper class to FoldTree: allows to measure distance in fold-trees |
| ShortestPathInFoldTree.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| ShortestPathInFoldTree.hh | Fold tree helper class |
| Stub.cc | Stub class |
| Stub.fwd.hh | Kinematics Stub forward declarations header |
| Stub.hh | Stub class |
| types.hh | Core::kinematics package type declarations |
| util.cc | Kinematics utility functions |
| util.hh | Kinematics utility functions |
| ► membrane | |
| hull.cc | Utility functions to compute 2D convex and concave hulls from a slice in a pose |
| hull.hh | Utility functions to compute 2D convex and concave hulls from a slice in a pose |
| ► optimization | |
| ► symmetry | |
| sym_atom_tree_minimize.cc | |
| sym_atom_tree_minimize.hh | |
| SymAtomTreeMinimizer.cc | High-level atom tree minimizer class for symmetrical minimization |
| SymAtomTreeMinimizer.fwd.hh | |
| SymAtomTreeMinimizer.hh | |
| SymAtomTreeMultifunc.cc | |
| SymAtomTreeMultifunc.hh | |
| SymMinimizerMap.cc | |
| SymMinimizerMap.fwd.hh | |
| SymMinimizerMap.hh | |
| atom_tree_minimize.cc | Atom tree minimization functions |
| atom_tree_minimize.hh | Atom tree minimization functions |
| AtomTreeMinimizer.cc | High-level atom tree minimizer class |
| AtomTreeMinimizer.fwd.hh | Core::optimization::AtomTreeMinimizer forward declarations |
| AtomTreeMinimizer.hh | High-level atom tree minimizer class |
| AtomTreeMultifunc.cc | |
| AtomTreeMultifunc.fwd.hh | Core::optimization::AtomTreeMultifunc forward declarations |
| AtomTreeMultifunc.hh | Atom tree multifunction class |
| cartesian_minimize.cc | Atom tree minimization functions |
| cartesian_minimize.hh | |
| CartesianMinimizer.cc | High-level Cartesian minimizer class |
| CartesianMinimizer.fwd.hh | Core::optimization::CartesianMinimizer forward declarations |
| CartesianMinimizer.hh | |
| CartesianMinimizerMap.cc | |
| CartesianMinimizerMap.fwd.hh | Forward declaration of CartesianMinimizerMap class |
| CartesianMinimizerMap.hh | Class for connecting DOFs in the atom tree to DOFs optimized by the AtomTreeMinimizer |
| CartesianMultifunc.cc | |
| CartesianMultifunc.fwd.hh | |
| CartesianMultifunc.hh | |
| DOF_Node.fwd.hh | |
| DOF_Node.hh | |
| GA_Minimizer.cc | Minimizer based on Genetic Algorithm |
| GA_Minimizer.hh | Minimizer based on Genetic Algorithm |
| LineMinimizer.cc | Line minimizer classes |
| LineMinimizer.fwd.hh | Core::optimization::LineMinimizer forward declarations |
| LineMinimizer.hh | Line minimizer classes |
| Minimizer.cc | Minimizer class |
| Minimizer.fwd.hh | Core::optimization::Minimizer forward declarations |
| Minimizer.hh | Simple low-level minimizer class |
| MinimizerMap.cc | |
| MinimizerMap.fwd.hh | Forward declaration of MinimizerMap class |
| MinimizerMap.hh | Class for connecting DOFs in the atom tree to DOFs optimized by the AtomTreeMinimizer |
| MinimizerOptions.cc | Minimizer options class implementation |
| MinimizerOptions.fwd.hh | Core::optimization::MinimizerOptions forward declarations |
| MinimizerOptions.hh | Minimizer options class |
| Multifunc.fwd.hh | Core::optimization::Multifunc forward declarations |
| Multifunc.hh | Multifunction interface class |
| NelderMeadSimplex.cc | |
| NelderMeadSimplex.hh | |
| NumericalDerivCheckResult.cc | |
| NumericalDerivCheckResult.fwd.hh | Forward declaration for nuerical derivative check results classes |
| NumericalDerivCheckResult.hh | Declaration for nuerical derivative check results classes |
| ParticleSwarmMinimizer.cc | |
| ParticleSwarmMinimizer.fwd.hh | |
| ParticleSwarmMinimizer.hh | |
| SingleResidueMultifunc.cc | |
| SingleResidueMultifunc.fwd.hh | |
| SingleResidueMultifunc.hh | |
| types.hh | Core::optimization optimization type declarations |
| ► pack | |
| ► annealer | |
| AnnealerFactory.cc | Annealer Factory class implementation |
| AnnealerFactory.fwd.hh | Annealer Factory class forward declaration |
| AnnealerFactory.hh | |
| DebuggingAnnealer.cc | Debugging annealer class implementation |
| DebuggingAnnealer.fwd.hh | Debugging annealer class forward declaration |
| DebuggingAnnealer.hh | Debugging annealer class declaration |
| FASTERAnnealer.cc | |
| FASTERAnnealer.fwd.hh | |
| FASTERAnnealer.hh | |
| FixbbCoupledRotamerSimAnnealer.cc | Packer's standard simulated annealing class implementation |
| FixbbCoupledRotamerSimAnnealer.fwd.hh | |
| FixbbCoupledRotamerSimAnnealer.hh | Packer's standard annealer class declaration |
| FixbbLinkingRotamerSimAnnealer.cc | Packer's standard simulated annealing class implementation |
| FixbbLinkingRotamerSimAnnealer.fwd.hh | |
| FixbbLinkingRotamerSimAnnealer.hh | Packer's standard annealer class declaration |
| FixbbPwatSimAnnealer.cc | Fixed temperature annealer for packing with statistical PWAT water model |
| FixbbPwatSimAnnealer.fwd.hh | Packer's standard annealer class forward declaration |
| FixbbPwatSimAnnealer.hh | |
| FixbbSimAnnealer.cc | Packer's standard simulated annealing class implementation |
| FixbbSimAnnealer.fwd.hh | Packer's standard annealer class forward declaration |
| FixbbSimAnnealer.hh | Packer's standard annealer class declaration, originally written by Brian Kuhlman and factored into base and derived classes by Jenny Hu |
| MultiCoolAnnealer.cc | Multiple low-temperature cooling cycles annealer class definition |
| MultiCoolAnnealer.fwd.hh | Multiple low-temperature cooling cycles annealer class forward declaration |
| MultiCoolAnnealer.hh | Multiple low-temperature cooling cycles annealer class declaration |
| RotamerAssigningAnnealer.cc | Annealer class that assigns rotamers implementation |
| RotamerAssigningAnnealer.fwd.hh | Residue assigning annealer class forward declaration |
| RotamerAssigningAnnealer.hh | Residue assigning annealer class declaration |
| SequenceSymmetricAnnealer.cc | |
| SequenceSymmetricAnnealer.fwd.hh | |
| SequenceSymmetricAnnealer.hh | |
| SimAnnealerBase.cc | Packer's simulated annealing base class implementation |
| SimAnnealerBase.fwd.hh | Packer's annealer base class forward declaration |
| SimAnnealerBase.hh | Packer's simulated annealing base class implementation |
| SmartFixbbSimAnnealer.cc | Derivation of the FixbbSimAnnealer with some fancy Tensorflow logic to adaptively decrease sample space during the run |
| SmartFixbbSimAnnealer.fwd.hh | |
| SmartFixbbSimAnnealer.hh | Derivation of the FixbbSimAnnealer with some fancy Tensorflow logic to adaptively decrease sample space during the run |
| ► dunbrack | |
| ► cenrot | |
| CenRotDunEnergy.cc | |
| CenRotDunEnergy.hh | |
| CenRotDunEnergyCreator.hh | |
| CenrotLibrary.cc | |
| CenrotLibrary.fwd.hh | CenrotLibrary forward declarations and typedefs |
| CenrotLibrary.hh | |
| SingleResidueCenrotLibrary.cc | |
| SingleResidueCenrotLibrary.fwd.hh | |
| SingleResidueCenrotLibrary.hh | |
| SingleResidueCenrotLibraryCreator.cc | Class for instantiating a particular SingleResidueRotamerLibrary |
| SingleResidueCenrotLibraryCreator.fwd.hh | Forward declaration of a class that instantiates a particular SingleResidueCenrotLibrary |
| SingleResidueCenrotLibraryCreator.hh | Class for instantiating a particular SingleResidueRotamerLibrary |
| ChiSet.fwd.hh | |
| ChiSet.hh | |
| DunbrackConstraint.cc | |
| DunbrackConstraint.fwd.hh | |
| DunbrackConstraint.hh | |
| DunbrackConstraintCreator.hh | Base class for ConstraintCreators for the Constraint load-time factory registration scheme |
| DunbrackEnergy.cc | Dunbrack energy method implementation |
| DunbrackEnergy.fwd.hh | |
| DunbrackEnergy.hh | |
| DunbrackEnergyCreator.hh | |
| DunbrackRotamer.cc | |
| DunbrackRotamer.fwd.hh | |
| DunbrackRotamer.hh | |
| RotamerConstraint.cc | |
| RotamerConstraint.fwd.hh | |
| RotamerConstraint.hh | |
| RotamericSingleResidueDunbrackLibrary.fwd.hh | |
| RotamericSingleResidueDunbrackLibrary.hh | |
| RotamericSingleResidueDunbrackLibrary.tmpl.hh | |
| RotamericSingleResidueDunbrackLibraryParser.cc | A helper class to assist in parsing rotamer libraries |
| RotamericSingleResidueDunbrackLibraryParser.fwd.hh | A helper class to assist in parsing rotamer libraries |
| RotamericSingleResidueDunbrackLibraryParser.hh | A helper class to assist in parsing rotamer libraries |
| RotamericSingleResidueDunbrackLibraryParser.tmpl.hh | A helper class to assist in parsing rotamer libraries. Template functions are declared here |
| RotamerLibrary.cc | |
| RotamerLibrary.fwd.hh | RotamerLibrary forward declarations and typedefs |
| RotamerLibrary.hh | |
| RotamerLibrary.inst.hh | |
| RotamerLibraryScratchSpace.cc | |
| RotamerLibraryScratchSpace.fwd.hh | |
| RotamerLibraryScratchSpace.hh | |
| SemiRotamericSingleResidueDunbrackLibrary.cc | |
| SemiRotamericSingleResidueDunbrackLibrary.fwd.hh | |
| SemiRotamericSingleResidueDunbrackLibrary.hh | |
| SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh | |
| SingleResidueDunbrackLibrary.cc | |
| SingleResidueDunbrackLibrary.fwd.hh | SingleResidueDunbrackLibrary forward declarations and typedefs |
| SingleResidueDunbrackLibrary.hh | SingleResidueDunbrackLibrary class |
| SingleResidueDunbrackLibraryCreator.cc | |
| SingleResidueDunbrackLibraryCreator.fwd.hh | Forward declaration of a class that instantiates a particular SingleResidueDunbrackLibrary |
| SingleResidueDunbrackLibraryCreator.hh | Class for instantiating a particular SingleResidueRotamerLibrary |
| ► guidance_scoreterms | |
| ► approximate_buried_unsat_penalty | |
| ApproximateBuriedUnsatPenalty.cc | Guidance term that gives a quadratic approximation to no buried unsats |
| ApproximateBuriedUnsatPenalty.fwd.hh | Forward declaration for ApproximateBuriedUnsatPenalty |
| ApproximateBuriedUnsatPenalty.hh | Guidance term that gives a quadratic approximation to no buried unsats |
| ApproximateBuriedUnsatPenaltyCreator.hh | Declaration for the class that connects ApproximateBuriedUnsatPenalty with the ScoringManager |
| util.cc | Utility functions for ApproximateBuriedUnsatPenalty |
| util.hh | Utility functions for ApproximateBuriedUnsatPenalty |
| ► buried_unsat_penalty | |
| ► graph | |
| BuriedUnsatPenaltyGraph.cc | |
| BuriedUnsatPenaltyGraph.fwd.hh | Forward declarations for the BuriedUnsatPenaltyGraph class and its related Node and Edge classes |
| BuriedUnsatPenaltyGraph.hh | The BuriedUnsatPenaltyGraph class and its related Node and Edge classes |
| BuriedUnsatPenaltyGraphContainer.cc | A container for the BuriedUnsatPenaltyGraph, to allow it to be cached in a pose while skirting multiple inheritance issues |
| BuriedUnsatPenaltyGraphContainer.fwd.hh | A container for the BuriedUnsatPenaltyGraph, to allow it to be cached in a pose while skirting multiple inheritance issues |
| BuriedUnsatPenaltyGraphContainer.hh | A container for the BuriedUnsatPenaltyGraph, to allow it to be cached in a pose while skirting multiple inheritance issues |
| BuriedUnsatPenaltyGraphOptions.cc | Options container for the BuriedUnsatPenaltyGraph. Initialized by the BuriedUnsatPenalty energy method |
| BuriedUnsatPenaltyGraphOptions.fwd.hh | Options container for the BuriedUnsatPenaltyGraph. Initialized by the BuriedUnsatPenalty energy method |
| BuriedUnsatPenaltyGraphOptions.hh | Options container for the BuriedUnsatPenaltyGraph. Initialized by the BuriedUnsatPenalty energy method |
| BuriedUnsatPenaltyGraphTests.fwd.hh | Forward declarations for the BuriedUnsatPenaltyGraphTests class to allow friendship to BuriedUnsatPenaltyGraph and BuriedUnsatPenalty classes |
| BuriedUnsatPenalty.cc | An EnergyMethod that gives a penalty for buried unsatisfied hydrogen bond donors and acceptors |
| BuriedUnsatPenalty.fwd.hh | Forward declarations for an EnergyMethod that gives a penalty for buried unsatisfied hydrogen bond donors and acceptors |
| BuriedUnsatPenalty.hh | Headers for an EnergyMethod that gives a penalty for buried unsatisfied hydrogen bond donors and acceptors |
| BuriedUnsatPenaltyCreator.hh | Creator for an EnergyMethod that gives a penalty for buried unsatisfied hydrogen bond donors and acceptors |
| BuriedUnsatPenaltyTests.fwd.hh | Forward declarations for the BuriedUnsatPenaltyTests class to allow friendship to BuriedUnsatPenalty class |
| ► hbnet_energy | |
| HBNetEnergy.cc | An EnergyMethod that gives a bonus for hydrogen bond networks, which ramps nonlinearly with the size of the networks |
| HBNetEnergy.fwd.hh | Forward declarations for an EnergyMethod that gives a bonus for hydrogen bond networks, which ramps nonlinearly with the size of the networks |
| HBNetEnergy.hh | Headers for an EnergyMethod that gives a bonus for hydrogen bond networks, which ramps nonlinearly with the size of the networks |
| HBNetEnergyCreator.hh | Creator for an EnergyMethod that gives a bonus for hydrogen bond networks, which ramps nonlinearly with the size of the networks |
| ► voids_penalty_energy | |
| VoidsPenaltyEnergy.cc | An EnergyMethod intended for packing, which penalizes solutions in which the total volume to fill differs greatly from the total volume of the current set of rotamers |
| VoidsPenaltyEnergy.fwd.hh | Forward declarations for an EnergyMethod intended for packing, which penalizes solutions in which the total volume to fill differs greatly from the total volume of the current set of rotamers |
| VoidsPenaltyEnergy.hh | Headers for an EnergyMethod intended for packing, which penalizes solutions in which the total volume to fill differs greatly from the total volume of the current set of rotamers |
| VoidsPenaltyEnergyCreator.hh | Creator for an EnergyMethod intended for packing, which penalizes solutions in which the total volume to fill differs greatly from the total volume of the current set of rotamers |
| VoidsPenaltyVoxelGrid.cc | A 3D boolean array used for identifying core voxels in the VoidsPenaltyEnergy |
| VoidsPenaltyVoxelGrid.fwd.hh | A 3D boolean array used for identifying core voxels in the VoidsPenaltyEnergy |
| VoidsPenaltyVoxelGrid.hh | A 3D boolean array used for identifying core voxels in the VoidsPenaltyEnergy |
| VoidsPenaltyVoxelGridTests.fwd.hh | |
| ► hbonds | |
| HBondGraph_util.cc | A collections of methods that are useful for dealing with HBondGraphs |
| HBondGraph_util.hh | A collections of methods that are useful for dealing with HBondGraphs. These are all methods that would normally resid in the HBondGraph itself but they need core.4 info and the HBondGraph needs to be in core.3 |
| HBondGraphInitializerIG.cc | Dervied class of PDInteractionGraph that does not save twobody energy calculations but rather passes them directly to a HBondGraph |
| HBondGraphInitializerIG.fwd.hh | Dervied class of PDInteractionGraph that does not save twobody energy calculations but rather passes them directly to a HBondGraph |
| HBondGraphInitializerIG.hh | Dervied class of PDInteractionGraph that does not save twobody energy calculations but rather passes them directly to a HBondGraph |
| ► interaction_graph | |
| AdditionalBackgroundNodesInteractionGraph.hh | Interaction graph which can handle some residues not changing during packing |
| AminoAcidNeighborSparseMatrix.fwd.hh | Sparse Matrix class for rotamer pair energy storage forward declaration |
| AminoAcidNeighborSparseMatrix.hh | Amino acid neighbor sparse matrix template class |
| AnnealableGraphBase.cc | Base interface for annealable graphs |
| AnnealableGraphBase.fwd.hh | Base interface for annealable graphs |
| AnnealableGraphBase.hh | |
| DensePDInteractionGraph.cc | Dense Edge-Matrix, Pairwise Decomposable interaction graph class implementation |
| DensePDInteractionGraph.fwd.hh | |
| DensePDInteractionGraph.hh | Dense Edge-Matrix, Pairwise Decomposable interaction graph class header This graph does not take advantage of the memory-saving AANeighborSparseMatrix for the storage of RPEs (rotamer pair energies); for this reason it's a little bit faster and weights a little less than the PDInteractionGraph for fixed-sequence repackings – memory becomes a significant issue for design simulations, and this graph should not be used for that purpose |
| DoubleDensePDInteractionGraph.cc | |
| DoubleDensePDInteractionGraph.fwd.hh | |
| DoubleDensePDInteractionGraph.hh | Double-The-Memory interaction graph which stores interaction energies for a rotamer and all of its neighbors in a single row in memory |
| DoubleLazyInteractionGraph.cc | Interaction graph that computes each rotamer pair energy at most once |
| DoubleLazyInteractionGraph.fwd.hh | Interaction graph that computes each rotamer pair energy at most once |
| DoubleLazyInteractionGraph.hh | Interaction graph that computes each rotamer pair energy at most once |
| FASTERInteractionGraph.cc | |
| FASTERInteractionGraph.fwd.hh | |
| FASTERInteractionGraph.hh | |
| FASTERInteractionGraphTests.fwd.hh | |
| FixedBBInteractionGraph.cc | Precomputed interaction graph class |
| FixedBBInteractionGraph.fwd.hh | Interaction graph base class for fixed-backbone packing |
| FixedBBInteractionGraph.hh | Interaction graph base class for fixed-backbone packing |
| HPatchEnergy.cc | |
| HPatchEnergy.fwd.hh | |
| HPatchEnergy.hh | |
| HPatchEnergyCreator.hh | |
| HPatchInteractionGraph.fwd.hh | Forward header for an IG that designs against hydrophobic area on the surface of proteins |
| HPatchInteractionGraph.hh | Interaction graph which implements a non-PD score that optimizes against surface hydrophobic patches. Computational Protein Design with Explicit Consideration of Surface Hydrophobic Patches. R. Jacak, A. Leaver-Fay, and B. Kuhlman. Proteins. 2012 Mar;80(3):825-38 |
| InteractionGraphBase.cc | Interaction graph base class |
| InteractionGraphBase.fwd.hh | InteractionGraph base class forward declaration |
| InteractionGraphBase.hh | Base interface for annealable graphs |
| InteractionGraphFactory.cc | Interation graph factory class definition |
| InteractionGraphFactory.fwd.hh | Interation graph factory class forward declaration |
| InteractionGraphFactory.hh | Interation graph factory class declaration |
| LazyInteractionGraph.cc | Interaction graph that computes each rotamer pair energy at most once |
| LazyInteractionGraph.fwd.hh | Interaction graph that computes each rotamer pair energy at most once |
| LazyInteractionGraph.hh | Interaction graph that computes each rotamer pair energy at most once |
| LinearMemoryInteractionGraph.cc | |
| LinearMemoryInteractionGraph.fwd.hh | |
| LinearMemoryInteractionGraph.hh | |
| MultiplexedAnnealableGraph.cc | Multiplexing packing graph container |
| MultiplexedAnnealableGraph.fwd.hh | |
| MultiplexedAnnealableGraph.hh | Multiplexing packing graph container |
| NPDHBondInteractionGraph.cc | Non-templated helper functions for the NPDHBondInteractionGraph |
| NPDHBondInteractionGraph.fwd.hh | Forward header for an IG that assigns hydrogen bonds a (non-pairwise-decomposable) weight |
| NPDHBondInteractionGraph.hh | Interaction graph which implements a non-PD score that optimizes against surface hydrophobic patches. Computational Protein Design with Explicit Consideration of Surface Hydrophobic Patches. R. Jacak, A. Leaver-Fay, and B. Kuhlman. Proteins. 2012 Mar;80(3):825-38 |
| NPDHBSimpleInteractionGraph.cc | |
| NPDHBSimpleInteractionGraph.fwd.hh | Data structure for representing changing energies for a Pose undergoing rotamer substitutions with the non-pairwise decomposable hydrogen bond potential |
| NPDHBSimpleInteractionGraph.hh | |
| OnTheFlyInteractionGraph.cc | |
| OnTheFlyInteractionGraph.fwd.hh | |
| OnTheFlyInteractionGraph.hh | |
| PDInteractionGraph.cc | Pairwise Decomposable interaction graph class |
| PDInteractionGraph.fwd.hh | Sparse pairwise decomposable interaction graph forward declaration |
| PDInteractionGraph.hh | Pairwise Decomposable interaction graph class header |
| PrecomputedPairEnergiesInteractionGraph.cc | Precomputed interaction graph class |
| PrecomputedPairEnergiesInteractionGraph.fwd.hh | Precomputed Pair Energies Interaction Graph forward declaration |
| PrecomputedPairEnergiesInteractionGraph.hh | Precomputed interaction graph class header |
| ResidueArrayAnnealingEvaluator.cc | |
| ResidueArrayAnnealingEvaluator.fwd.hh | |
| ResidueArrayAnnealingEvaluator.hh | Annealable interface for score terms evaluated over an array of residues |
| RotamerDots.cc | RotamerDots classes files - ported from rosetta++ |
| RotamerDots.fwd.hh | RotamerDots classes, forward declaration - ported from rosetta++ |
| RotamerDots.hh | RotamerDots classes header files - ported from rosetta++ |
| SimpleInteractionGraph.cc | |
| SimpleInteractionGraph.fwd.hh | |
| SimpleInteractionGraph.hh | |
| SparseMatrixIndex.fwd.hh | Helper class for AminoAcidNeighborSparseMatrix forward declaration |
| SparseMatrixIndex.hh | |
| SurfaceEnergy.cc | |
| SurfaceEnergy.fwd.hh | |
| SurfaceEnergy.hh | |
| SurfaceEnergyCreator.hh | |
| SurfaceInteractionGraph.fwd.hh | Forward header for an IG that designs against hydrophobic area on the surface of proteins |
| SurfaceInteractionGraph.hh | Interaction graph which implements a non-PD, environment-dependent score for surface residues |
| SurfacePotential.cc | |
| SurfacePotential.hh | |
| SymmLinMemInteractionGraph.cc | |
| SymmLinMemInteractionGraph.fwd.hh | |
| SymmLinMemInteractionGraph.hh | |
| SymmMinimalistInteractionGraph.cc | |
| SymmMinimalistInteractionGraph.fwd.hh | |
| SymmMinimalistInteractionGraph.hh | |
| SymmOnTheFlyInteractionGraph.cc | |
| SymmOnTheFlyInteractionGraph.fwd.hh | |
| SymmOnTheFlyInteractionGraph.hh | |
| util.cc | Simple utilities for interaction graphs |
| util.hh | Simple utilities for interaction graphs |
| ► palette | |
| CustomBaseTypePackerPalette.cc | CustomBaseTypePackerPalette: a PackerPalette that allows a user to define additional ResidueTypes with which to design (but not additional VariantTypes, at this time) |
| CustomBaseTypePackerPalette.fwd.hh | CustomBaseTypePackerPalette: a PackerPalette that allows a user to define additional ResidueTypes with which to design (but not additional VariantTypes, at this time) |
| CustomBaseTypePackerPalette.hh | CustomBaseTypePackerPalette: a PackerPalette that allows a user to define additional ResidueTypes with which to design (but not additional VariantTypes, at this time) |
| CustomBaseTypePackerPaletteCreator.hh | Declaration of the creator for CustomBaseTypePackerPalette |
| DefaultPackerPalette.cc | DefaultPackerPalette: a PackerPalette that just sets up default Packer behaviour (design with the canonical 20 amino acids and whatever is present at a position in a pose). This PackerPalette has no user-configurable options. was implemented as part of the 2016 Chemical XRW (eXtreme Rosetta Workshop) |
| DefaultPackerPalette.fwd.hh | DefaultPackerPalette: a PackerPalette that just sets up default Packer behaviour (design with the canonical 20 amino acids and whatever is present at a position in a pose). These are the forward declarations. was implemented as part of the 2016 Chemical XRW (eXtreme Rosetta Workshop) |
| DefaultPackerPalette.hh | DefaultPackerPalette: a PackerPalette that just sets up default Packer behaviour (design with the canonical 20 amino acids and whatever is present at a position in a pose). This PackerPalette has no user-configurable options. was implemented as part of the 2016 Chemical XRW (eXtreme Rosetta Workshop) |
| DefaultPackerPaletteCreator.hh | Declaration of the creator for DefaultPackerPalette |
| NCAADefaultPackerPalette.cc | NCAADefaultPackerPalette: a PackerPalette that just sets up default Packer behaviour (design with the canonical 20 amino acids and equivalent sets for ANY backbone.) |
| NCAADefaultPackerPalette.fwd.hh | NCAADefaultPackerPalette: a PackerPalette that just sets up default Packer behaviour (design with the canonical 20 amino acids and equivalent sets for ANY backbone.) |
| NCAADefaultPackerPalette.hh | NCAADefaultPackerPalette: a PackerPalette that just sets up default Packer behaviour (design with the canonical 20 amino acids and equivalent sets for ANY backbone.) |
| NCAADefaultPackerPaletteCreator.hh | Declaration of the creator for NCAADefaultPackerPalette |
| NoDesignPackerPalette.cc | NoDesignPackerPalette: a PackerPalette that sets up absolutely no design residues |
| NoDesignPackerPalette.fwd.hh | NoDesignPackerPalette: a PackerPalette that sets up absolutely no design residues |
| NoDesignPackerPalette.hh | NoDesignPackerPalette: a PackerPalette that sets up absolutely no design residues |
| NoDesignPackerPaletteCreator.hh | Declaration of the creator for NoDesignPackerPalette |
| PackerPalette.cc | PackerPalette: a class for storing the set of ResidueTypes and VariantTypes that the packer uses by default, in the absence of any TaskOperations that limit the set actually used |
| PackerPalette.fwd.hh | PackerPalette: a class for storing the set of ResidueTypes and VariantTypes that the packer uses by default, in the absence of any TaskOperations that limit the set actually used |
| PackerPalette.hh | PackerPalette: a class for storing the set of ResidueTypes and VariantTypes that the packer uses by default, in the absence of any TaskOperations that limit the set actually used |
| PackerPaletteCreator.fwd.hh | Base class for PackerPalette creation classes – forward declarations |
| PackerPaletteCreator.hh | Declaration of the base class for PackerPalette factory registration and creation |
| PackerPaletteFactory.cc | Factory class for creating instances of PackerPalettes (e.g. for RosettaScripts) |
| PackerPaletteFactory.fwd.hh | Forward declarations for factory class for creating instances of PackerPalettes (e.g. for RosettaScripts) |
| PackerPaletteFactory.hh | Headers for factory class for creating instances of PackerPalettes (e.g. for RosettaScripts) |
| PackerPaletteRegistrator.hh | |
| xsd_util.cc | XSD utilities for the PackerPalette class and its sub-classes |
| xsd_util.hh | |
| ► rotamer_set | |
| ► symmetry | |
| SymmetricRotamerSet_.cc | Amino acid rotamer set class implementation for symmetric packing |
| SymmetricRotamerSet_.fwd.hh | |
| SymmetricRotamerSet_.hh | Rotamer set implementation class for symmetric packing |
| SymmetricRotamerSets.cc | |
| SymmetricRotamerSets.fwd.hh | |
| SymmetricRotamerSets.hh | |
| AddResiduesRotamerSetOperation.cc | |
| AddResiduesRotamerSetOperation.hh | |
| bb_independent_rotamers.cc | Build rotamers for residue type given neutral beckbone |
| bb_independent_rotamers.hh | Bunch of utility functions used in enzdes |
| BumpSelector.cc | Bump selector class implementation |
| BumpSelector.hh | |
| ContinuousRotamerSet.cc | |
| ContinuousRotamerSet.fwd.hh | |
| ContinuousRotamerSet.hh | |
| DeleteAllRotamerSetOperation.cc | |
| DeleteAllRotamerSetOperation.fwd.hh | |
| DeleteAllRotamerSetOperation.hh | |
| FixbbRotamerSets.cc | Fixed-backbone Residue Sets interface class implementation |
| FixbbRotamerSets.fwd.hh | Fixed-backbone Residue Sets interface class foward declarations |
| FixbbRotamerSets.hh | |
| rna_rotamer_building_functions.cc | RNA nucleotide rotamer set class implementation |
| rna_rotamer_building_functions.hh | |
| rotamer_building_functions.cc | |
| rotamer_building_functions.hh | |
| RotamerCouplings.cc | Auto-generated serialization template functions |
| RotamerCouplings.fwd.hh | |
| RotamerCouplings.hh | |
| RotamerLinks.cc | Auto-generated serialization template functions |
| RotamerLinks.fwd.hh | |
| RotamerLinks.hh | |
| RotamerSet.cc | |
| RotamerSet.fwd.hh | Residue set class forward declarations |
| RotamerSet.hh | |
| RotamerSet_.cc | Amino acid rotamer set class implementation |
| RotamerSet_.fwd.hh | Rotamer set implementation class forward declarations |
| RotamerSet_.hh | Rotamer set implementation class |
| RotamerSetFactory.cc | |
| RotamerSetFactory.fwd.hh | Residue Set Facotry class forward declaration |
| RotamerSetFactory.hh | Residue Set Factory class |
| RotamerSetOperation.cc | Rotamer set operation implementation |
| RotamerSetOperation.fwd.hh | Rotamer set operation forward declaration |
| RotamerSetOperation.hh | Rotamer set operation class |
| RotamerSets.cc | |
| RotamerSets.fwd.hh | Residue Sets class foward declarations |
| RotamerSets.hh | |
| RotamerSetsFactory.cc | |
| RotamerSetsFactory.fwd.hh | |
| RotamerSetsFactory.hh | (Symmetry agnostic) factory for the RotamerSets class |
| RotamerSubset.cc | |
| RotamerSubset.fwd.hh | |
| RotamerSubset.hh | |
| RotamerSubsets.cc | |
| RotamerSubsets.fwd.hh | Residue Subsets class foward declarations |
| RotamerSubsets.hh | |
| UnboundRotamersOperation.cc | |
| UnboundRotamersOperation.fwd.hh | |
| UnboundRotamersOperation.hh | |
| water_rotamer_building_functions.cc | |
| water_rotamer_building_functions.hh | Few water rotamer building functions |
| WaterAnchorInfo.cc | |
| WaterAnchorInfo.fwd.hh | |
| WaterAnchorInfo.hh | |
| WaterPackingInfo.cc | |
| WaterPackingInfo.fwd.hh | |
| WaterPackingInfo.hh | |
| ► rotamers | |
| SingleBasicRotamerLibrary.cc | |
| SingleBasicRotamerLibrary.fwd.hh | |
| SingleBasicRotamerLibrary.hh | |
| SingleBasicRotamerLibraryCreator.hh | Class for instantiating a Basic rotlib |
| SingleLigandRotamerLibrary.cc | |
| SingleLigandRotamerLibrary.fwd.hh | |
| SingleLigandRotamerLibrary.hh | |
| SingleLigandRotamerLibraryCreator.cc | Class for instantiating a particular SingleResidueRotamerLibrary |
| SingleLigandRotamerLibraryCreator.fwd.hh | Forward declaration of a class that instantiates a particular SingleLigandRotamerLibrary |
| SingleLigandRotamerLibraryCreator.hh | Class for instantiating a particular SingleLigandRotamerLibrary |
| SingleNCAARotamerLibraryCreator.cc | |
| SingleNCAARotamerLibraryCreator.fwd.hh | Forward declaration of a class that instantiates a particular NCAA rotlib |
| SingleNCAARotamerLibraryCreator.hh | Class for instantiating a particular SingleResidueRotamerLibrary |
| SingleResidueRotamerLibrary.cc | SingleResidueRotamerLibrary class |
| SingleResidueRotamerLibrary.fwd.hh | SingleResidueRotamerLibrary forward declarations and typedefs |
| SingleResidueRotamerLibrary.hh | SingleResidueRotamerLibrary virtual base class |
| SingleResidueRotamerLibraryCreator.cc | Class for instantiating a particular SingleResidueRotamerLibrary |
| SingleResidueRotamerLibraryCreator.fwd.hh | Forward declaration of a class that instantiates a particular SingleResidueRotamerLibrary |
| SingleResidueRotamerLibraryCreator.hh | Class for instantiating a particular SingleResidueRotamerLibrary |
| SingleResidueRotamerLibraryFactory.cc | Implementation of the class for instantiating arbitrary SingleResidueRotamerLibrarys from a string –> SingleResidueRotamerLibraryCreator map |
| SingleResidueRotamerLibraryFactory.hh | |
| SingleResidueRotamerLibraryRegistrator.hh | Declaration of the template class for registrating SingleResidueRotamerLibraryCreators with the SingleResidueRotamerLibraryFactory |
| StoredRotamerLibraryCreator.cc | Class for instantiating a SingleLigandRotamerLibrary from a StoredRotamerLibrarySpecification |
| StoredRotamerLibraryCreator.hh | Class for instantiating a SingleLigandRotamerLibrary from a StoredRotamerLibrarySpecification |
| ► scmin | |
| AtomTreeCollection.cc | Implementation for the classes holding sets of AtomTrees used during variuos packing+minimizing schemes |
| AtomTreeCollection.fwd.hh | |
| AtomTreeCollection.hh | Forward declaration for the classes holding sets of AtomTrees used during variuos packing+minimizing schemes |
| AtomTreeSCMinMinimizerMap.cc | Class for identifying the sidechain DOFs in the AtomTree which are free during any particular call to the minimizer |
| AtomTreeSCMinMinimizerMap.fwd.hh | Foward declaration for the class identifying sidechain DOFs in the AtomTree which are free during any particular call to the minimizer |
| AtomTreeSCMinMinimizerMap.hh | Class for identifying the sidechain DOFs in the AtomTree which are free during any particular call to the minimizer |
| CartSCMinMinimizerMap.cc | Class for identifying the sidechain DOFs in the AtomTree which are free during any particular call to the minimizer |
| CartSCMinMinimizerMap.fwd.hh | Foward declaration for the class identifying sidechain DOFs in the AtomTree which are free during any particular call to the minimizer |
| CartSCMinMinimizerMap.hh | Class for identifying the sidechain DOFs in the AtomTree which are free during any particular call to the minimizer |
| CartSCMinMultifunc.cc | Class for interfacing with the minimizer during sidechain minimization |
| CartSCMinMultifunc.fwd.hh | Forward declaration of the interface class to the minimizer during sidechain minimization |
| CartSCMinMultifunc.hh | Class for interfacing with the minimizer during sidechain minimization |
| SCMinMinimizerMap.fwd.hh | Foward declaration for the class identifying sidechain DOFs in the AtomTree which are free during any particular call to the minimizer |
| SCMinMinimizerMap.hh | Class for identifying the sidechain DOFs in the AtomTree which are free during any particular call to the minimizer |
| SCMinMultifunc.cc | Class for interfacing with the minimizer during sidechain minimization |
| SCMinMultifunc.fwd.hh | Forward declaration of the interface class to the minimizer during sidechain minimization |
| SCMinMultifunc.hh | Class for interfacing with the minimizer during sidechain minimization |
| SidechainStateAssignment.cc | |
| SidechainStateAssignment.fwd.hh | Foward declaration for the SidechainStateAssignment class |
| SidechainStateAssignment.hh | Declaration for the class that holds a state assignment for an entire system under continuous sidechain optimization |
| ► task | |
| ► operation | |
| ClashBasedRepackShell.cc | ClashBasedRepackShell header file |
| ClashBasedRepackShell.fwd.hh | Forward declaration for ClashBasedRepackShell |
| ClashBasedRepackShell.hh | ClashBasedRepackShell header file |
| ClashBasedRepackShellCreator.hh | |
| DesignRestrictions.cc | Combine a set of ResidueSelectors and ResidueLevelTaskOperations concisely, using boolean logic to join selectors concisely |
| DesignRestrictions.fwd.hh | Combine a set of ResidueSelectors and ResidueLevelTaskOperations concisely, using boolean logic to join selectors concisely |
| DesignRestrictions.hh | |
| DesignRestrictionsCreator.hh | |
| EnableMultiCoolAnnealer.cc | Task Operation for turning on the multi-cool annealer |
| EnableMultiCoolAnnealer.fwd.hh | Task Operation for turning on the multi-cool annealer |
| EnableMultiCoolAnnealer.hh | |
| EnableMultiCoolAnnealerCreator.hh | |
| EnableSmartAnnealer.cc | |
| EnableSmartAnnealer.fwd.hh | |
| EnableSmartAnnealer.hh | The smart annealer uses tensorflow to decrease the sample space of a typical packing run |
| EnableSmartAnnealerCreator.hh | |
| FillAUTOTaskOperation.cc | Fills the AUTO behavior for all residues in Task. Useful if a protocol expects AUTO-style resfile, but no resfile present |
| FillAUTOTaskOperation.fwd.hh | Fills the AUTO behavior for all residues in Task. Useful if a protocol expects AUTO-style resfile, but no resfile present |
| FillAUTOTaskOperation.hh | |
| FillAUTOTaskOperationCreator.hh | |
| KeepSequenceSymmetry.cc | Use this when you give Rosetta a multimer to design and you want the sequences of the chains to be the same but you don't need strict physical symmetry |
| KeepSequenceSymmetry.fwd.hh | |
| KeepSequenceSymmetry.hh | Use this when you give Rosetta a multimer to design and you want the sequences of the chains to be the same but you don't need strict physical symmetry |
| KeepSequenceSymmetryCreator.hh | |
| NoRepackDisulfides.cc | Prevent disulfides from being repacked; assumes disulfide info in Pose is up-to-date |
| NoRepackDisulfides.fwd.hh | Forward declaration for NoRepackDisulfides |
| NoRepackDisulfides.hh | Prevent disulfides from being repacked; assumes disulfide info in Pose is up-to-date |
| NoRepackDisulfidesCreator.hh | |
| OperateOnCertainResidues.cc | Class to support the general case of configuring PackerTask at the ResidueLevelTask level in some way, with an optional filter to limit the effects to certain residues |
| OperateOnCertainResidues.fwd.hh | Forward declaration of a class that performs an operation on a packer task, in a configurable residue-specific manner |
| OperateOnCertainResidues.hh | Class to support the general case of configuring PackerTask at the ResidueLevelTask level in some way, with an optional filter to limit the effects to certain residues |
| OperateOnCertainResiduesCreator.hh | |
| OperateOnResidueSubset.cc | Class, much like the OperateOnResidueSubset task operation, to apply a particular residue-level task operation on the residues identified by a ResidueSelector |
| OperateOnResidueSubset.fwd.hh | Forward declaration of a class that performs an operation on a packer task, in a configurable residue-specific manner |
| OperateOnResidueSubset.hh | Class, much like the OperateOnCertainResidues task operation, to apply a particular residue-level task operation on the residues identified by a ResidueSelector (Or a pre-selected set of residues) |
| OperateOnResidueSubsetCreator.hh | |
| OptCysHG.cc | Run optH on non-disulfided bonded CYS only; meant to relieve any clashes caused by swapping of CYD->CYS after calling Conformation::detect_disulfides() |
| OptCysHG.fwd.hh | Forward declaration for OptCysHG |
| OptCysHG.hh | Run optH on non-disulfided bonded CYS only; meant to relieve any clashes caused by swapping of CYD->CYS after calling Conformation::detect_disulfides() |
| OptCysHGCreator.hh | |
| OptH.cc | Run optH |
| OptH.fwd.hh | Forward declaration for OptH |
| OptH.hh | Run optH |
| OptHCreator.hh | |
| parsing_utilities.cc | Utility functions for extracting packer-related objects out of the DataMap |
| parsing_utilities.hh | Utility functions for extracting packer-related objects out of the DataMap |
| ReplicateTask.cc | |
| ReplicateTask.fwd.hh | Forward declaration for ReplicateTask |
| ReplicateTask.hh | |
| ResFilter.fwd.hh | Forward declaration of a class that takes a pose and a residue index, and returns true or false |
| ResFilter.hh | Abstract base class that takes a pose and a residue index, and returns true or false |
| ResFilterCreator.fwd.hh | |
| ResFilterCreator.hh | |
| ResFilterCreators.hh | Declaration for the class that connects ResFilters with the ResFilterFactory |
| ResFilterFactory.cc | |
| ResFilterFactory.fwd.hh | |
| ResFilterFactory.hh | |
| ResFilterRegistrator.hh | |
| ResFilters.cc | |
| ResFilters.fwd.hh | Core-level (very general) classes that take a pose and a residue index, and returns true or false |
| ResFilters.hh | Core-level (very general) classes that take a pose and a residue index, and return true or false |
| ResLvlTaskOperation.fwd.hh | Forward declaration of a class that performs an operation on ResidueLevelTask usually by a TaskFactory right after the task's construction |
| ResLvlTaskOperation.hh | Class that performs an operation on ResidueLevelTask, usually by a PackerTaskFactory right after the task's construction |
| ResLvlTaskOperationCreator.fwd.hh | |
| ResLvlTaskOperationCreator.hh | |
| ResLvlTaskOperationCreators.hh | Declaration for the class that connects ResLvlTaskOperations with the ResLvlTaskOperationFactory |
| ResLvlTaskOperationFactory.cc | |
| ResLvlTaskOperationFactory.fwd.hh | |
| ResLvlTaskOperationFactory.hh | |
| ResLvlTaskOperationRegistrator.hh | |
| ResLvlTaskOperations.cc | |
| ResLvlTaskOperations.fwd.hh | Forward declaration for core-level (very general) derived classes that wrap widely-used methods of the ResidueLevelTask interface. These are used by higher-level TaskOperations that allow the user to configure the behavior of PackerTasks that are created by TaskFactory |
| ResLvlTaskOperations.hh | Core-level (very general) derived classes that wrap widely-used methods of the ResidueLevelTask interface. These are used by higher-level TaskOperations that allow the user to configure the behavior of PackerTasks that are created by TaskFactory |
| RestrictInteractionGraphThreadsOperation.cc | A task operation that restricts the number of threads allowed for interaction graph computation |
| RestrictInteractionGraphThreadsOperation.fwd.hh | A task operation that restricts the number of threads allowed for interaction graph computation |
| RestrictInteractionGraphThreadsOperation.hh | |
| RestrictInteractionGraphThreadsOperationCreator.hh | |
| task_op_schemas.cc | Utility functions for creating XML Schema definitions for TaskOperations |
| task_op_schemas.hh | Utility functions for creating XML Schema definitions for TaskOperations |
| TaskOperation.cc | An operation to perform on a packer task – usually, by a PackerTaskFactory right after the task's construction |
| TaskOperation.fwd.hh | Forward declaration of a class that performs an operation on a packer task, usually, by a PackerTaskFactory right after the task's construction |
| TaskOperation.hh | An operation to perform on a packer task – usually, by a PackerTaskFactory right after the task's construction |
| TaskOperationCreator.fwd.hh | |
| TaskOperationCreator.hh | |
| TaskOperationCreators.hh | Declaration for the class that connects TaskOperations with the TaskOperationFactory |
| TaskOperationFactory.cc | |
| TaskOperationFactory.fwd.hh | |
| TaskOperationFactory.hh | |
| TaskOperationRegistrator.hh | |
| TaskOperations.cc | |
| TaskOperations.fwd.hh | Forward declaration of a class that performs an operation on a packer task, usually, by a PackerTaskFactory right after the task's construction |
| TaskOperations.hh | An operation to perform on a packer task – usually, by a PackerTaskFactory right after the task's construction This is an incomplete list. Freely define your own TaskOperation and hand it to a PackerTaskFactory |
| ► residue_selector | |
| ClashBasedShellSelector.cc | The ClashBasedShellSelector identifies all residues that clash with at least one rotamer of a design position |
| ClashBasedShellSelector.fwd.hh | Forward declaration of a class that identifies all residues that clash with at least one rotamer of a design position |
| ClashBasedShellSelector.hh | The ClashBasedShellSelector identifies all residues that clash with at least one rotamer of a design position |
| ClashBasedShellSelectorCreator.hh | The ClashBasedShellSelector identifies all residues that clash with at least one rotamer of a design position |
| ► rna | |
| RNA_ResidueLevelTask.cc | |
| RNA_ResidueLevelTask.fwd.hh | |
| RNA_ResidueLevelTask.hh | |
| IGEdgeReweightContainer.cc | |
| IGEdgeReweightContainer.fwd.hh | |
| IGEdgeReweightContainer.hh | |
| PackerTask.cc | Task class to describe packer's behavior |
| PackerTask.fwd.hh | Task class to describe packer's behavior forward declaration |
| PackerTask.hh | Task class to describe packer's behavior header |
| PackerTask_.cc | |
| PackerTask_.fwd.hh | Implementation class for task class to describe packer's behavior forward declaration Almost all of rosetta needs to use packer tasks, but very little of rosetta needs to see how it behaves internally |
| PackerTask_.hh | Implementation class for task class to describe packer's behavior header Almost all of rosetta needs to use packer tasks, but very little of rosetta needs to see how it behaves internally |
| ResfileReader.cc | Implementation of resfile reader and its command classes |
| ResfileReader.fwd.hh | |
| ResfileReader.hh | Header of classes for resfile options |
| ResidueLevelTask.cc | Task class to describe packer's behavior |
| ResidueLevelTask.hh | Task class to describe packer's behavior header |
| ResidueLevelTask_.cc | |
| ResidueLevelTask_.hh | Implementation class for task class to describe packer's behavior header Almost all of rosetta needs to use packer tasks, but very little of rosetta needs to see how it behaves internally |
| RotamerSampleOptions.cc | |
| RotamerSampleOptions.hh | Class to describe rotamer construction header |
| TaskFactory.cc | |
| TaskFactory.fwd.hh | |
| TaskFactory.hh | Task class to describe packer's behavior header |
| util.cc | Utility functions for main task classes |
| util.hh | Utility functions for main task classes |
| xml_util.cc | Task operation/factory utilities useful in RosettaScripts |
| xml_util.hh | Task operation/factory utilities useful in RosettaScripts |
| make_symmetric_task.cc | |
| make_symmetric_task.hh | Utility functions for handling with symmetric conformations |
| min_pack.cc | Pack rotamers with minimization module |
| min_pack.hh | Pack and minimize sidechains |
| optimizeH.cc | Standard hydrogen optimization subroutine |
| optimizeH.hh | Declaration of standard hydrogen optimization subroutine |
| pack_missing_sidechains.cc | Function to fix missing sidechains in input PDBs (especially those surface lysines that get sidechain-backbone clashes!) |
| pack_missing_sidechains.hh | Header for subroutine to run rotamer trials on residues missing sidechain density in a PDB |
| pack_rotamers.cc | Pack rotamers module |
| pack_rotamers.hh | Pack rotamers module header |
| packer_neighbors.cc | Creates a graph that describes the possible connectivity induced by designing-in larger side chains |
| packer_neighbors.hh | Creates a graph that describes the possible connectivity induced by designing-in larger side chains |
| rotamer_trials.cc | Rotamer trials module |
| rotamer_trials.hh | Rotamer trials module header |
| rtmin.cc | Rotamer trials with minimization module header. Originally concieved of and implemented in Rosetta++ by Chu Wang |
| rtmin.hh | Rotamer trials with minimization module header |
| util.cc | Simple utilities for computing rotamer recovery between 2 poses |
| util.hh | Simple utilities for computing rotamer recovery between 2 poses |
| ► pack_basic | |
| RotamerSetsBase.cc | |
| RotamerSetsBase.fwd.hh | |
| RotamerSetsBase.hh | |
| ► pose | |
| ► carbohydrates | |
| util.cc | Utility function definitions for carbohydrate-containing poses |
| util.hh | Utility function declarations for carbohydrate-containing poses |
| ► copydofs | |
| CopyDofs.cc | |
| CopyDofs.fwd.hh | |
| CopyDofs.hh | |
| CopyDofsInfo.cc | |
| CopyDofsInfo.fwd.hh | |
| CopyDofsInfo.hh | |
| util.cc | |
| util.hh | |
| ► datacache | |
| cacheable_observers.cc | |
| cacheable_observers.fwd.hh | Forward declarations for a bunch of CacheableObserver implementations |
| cacheable_observers.hh | File that has class definitions for a bunch of general CacheableObserver implementations |
| CacheableDataType.cc | Enum indexing the data types stored in a Pose's internal DataCache |
| CacheableDataType.hh | Enum indexing the data types stored in a Pose's internal DataCache |
| CacheableObserver.cc | Base class for Pose/Conformation observers that are stored in a Pose's DataCache |
| CacheableObserver.fwd.hh | Forward declaration for CacheableObserver |
| CacheableObserver.hh | Base class for Pose/Conformation observers that are stored in a Pose's ObserverCache |
| CacheableObserverType.hh | Enum indexing the observer types stored in a Pose's internal ObserverCache |
| CacheablePoseRawPtr.cc | |
| CacheablePoseRawPtr.fwd.hh | |
| CacheablePoseRawPtr.hh | |
| ObserverCache.cc | A DataCache storing objects derived from core::pose::datacache::CacheableData |
| ObserverCache.fwd.hh | Forward declaration for ObserverCache |
| ObserverCache.hh | |
| PositionConservedResiduesStore.cc | |
| PositionConservedResiduesStore.fwd.hh | |
| PositionConservedResiduesStore.hh | |
| ► full_model_info | |
| FullModelInfo.cc | |
| FullModelInfo.fwd.hh | |
| FullModelInfo.hh | |
| FullModelParameters.cc | |
| FullModelParameters.fwd.hh | |
| FullModelParameters.hh | |
| FullModelParameterType.cc | |
| FullModelParameterType.hh | |
| SubMotifInfo.cc | Stores information about submotifs in a pose |
| SubMotifInfo.fwd.hh | Stores information about submotifs in a pose |
| SubMotifInfo.hh | Stores information about submotifs in a pose |
| util.cc | Mapping from a working pose into a bigger pose, for swa monte carlo stuff |
| util.hh | |
| ► metrics | |
| ► simple_calculators | |
| InterfaceDefinitionCalculatorBase.cc | |
| InterfaceDefinitionCalculatorBase.hh | |
| InterfaceDeltaEnergeticsCalculator.cc | |
| InterfaceDeltaEnergeticsCalculator.hh | |
| InterfaceNeighborDefinitionCalculator.cc | |
| InterfaceNeighborDefinitionCalculator.hh | |
| InterfaceSasaDefinitionCalculator.cc | SasaCalculatorLegacy class |
| InterfaceSasaDefinitionCalculator.hh | |
| SasaCalculator2.cc | |
| SasaCalculator2.hh | |
| SasaCalculatorLegacy.cc | |
| SasaCalculatorLegacy.hh | |
| CalculatorFactory.cc | CalculatorFactory class |
| CalculatorFactory.hh | |
| PoseMetricCalculatorBase.cc | Auto-generated serialization template functions |
| PoseMetricCalculatorBase.fwd.hh | |
| PoseMetricCalculatorBase.hh | |
| PoseMetricContainer.cc | PoseMetricContainer class |
| PoseMetricContainer.fwd.hh | |
| PoseMetricContainer.hh | Container for managing PoseMetricCalculators |
| ► motif | |
| reference_frames.cc | |
| reference_frames.hh | Compute motif-related reference frames for residues, chemical groups, etc |
| ► ncbb | |
| util.cc | Utility function definitions for poses with noncanonical backbones |
| util.hh | Utility function declarations for poses with noncanonical backbone |
| ► reference_pose | |
| ReferencePose.cc | Forward declarations for ReferencePose, a class for holding information relating the current pose to a reference pose |
| ReferencePose.fwd.hh | Forward declarations for ReferencePose, a class for holding information relating the current pose to a reference pose |
| ReferencePose.hh | Forward declarations for ReferencePose, a class for holding information relating the current pose to a reference pose |
| ReferencePoseSet.cc | Headers for ReferencePoseSet, a class for holding sets of reference poses |
| ReferencePoseSet.fwd.hh | Forward declarations for ReferencePoseSet, a class for holding sets of reference poses |
| ReferencePoseSet.hh | Headers for ReferencePoseSet, a class for holding sets of reference poses |
| ► rna | |
| ► secstruct_legacy | |
| RNA_SecStructLegacyInfo.cc | |
| RNA_SecStructLegacyInfo.fwd.hh | |
| RNA_SecStructLegacyInfo.hh | |
| BasePair.cc | |
| BasePair.fwd.hh | |
| BasePair.hh | |
| BasePairStep.cc | |
| BasePairStep.fwd.hh | |
| BasePairStep.hh | |
| BaseStack.cc | |
| BaseStack.fwd.hh | |
| BaseStack.hh | |
| leontis_westhof_util.cc | |
| leontis_westhof_util.hh | Implementation of Leontis/Westhof nucleic acid base-pair classification |
| RNA_BaseDoubletClasses.cc | Auto-generated serialization template functions |
| RNA_BaseDoubletClasses.hh | |
| RNA_BasePairClassifier.cc | |
| RNA_BasePairClassifier.hh | |
| RNA_DataInfo.cc | Statistically derived rotamer pair potential class implementation |
| RNA_DataInfo.fwd.hh | Statistically derived rotamer pair potential class implementation |
| RNA_DataInfo.hh | |
| RNA_FilteredBaseBaseInfo.cc | |
| RNA_FilteredBaseBaseInfo.fwd.hh | |
| RNA_FilteredBaseBaseInfo.hh | |
| RNA_IdealCoord.cc | Apply ideal RNA geometry to a residue or a pose |
| RNA_IdealCoord.fwd.hh | |
| RNA_IdealCoord.hh | Apply ideal RNA geometry to a residue or a pose |
| RNA_RawBaseBaseInfo.cc | Statistically derived rotamer pair potential class implementation |
| RNA_RawBaseBaseInfo.fwd.hh | |
| RNA_RawBaseBaseInfo.hh | Statistically derived RNA potential |
| RNA_SecStruct.cc | |
| RNA_SecStruct.fwd.hh | |
| RNA_SecStruct.hh | |
| RNA_SuiteName.cc | RNA suite assignment ported from suitename program (V 0.3.070628) |
| RNA_SuiteName.fwd.hh | RNA suite assignment ported from suitename program |
| RNA_SuiteName.hh | |
| StubStubType.fwd.hh | For computing or constrainign rotation/translation – different stub-stube conventions in use |
| util.cc | |
| util.hh | |
| VDW_Grid.cc | |
| VDW_Grid.fwd.hh | |
| VDW_Grid.hh | |
| VDW_RepScreenInfo.cc | |
| VDW_RepScreenInfo.fwd.hh | |
| VDW_RepScreenInfo.hh | |
| ► signals | |
| ConformationEvent.fwd.hh | Forward declaration for core::pose::signals::ConformationEvent |
| ConformationEvent.hh | Signal for a conformation change in a Pose |
| DestructionEvent.fwd.hh | Forward declaration for core::pose::signals::DestructionEvent |
| DestructionEvent.hh | Signal that the Pose is getting destroyed |
| EnergyEvent.fwd.hh | Forward declaration for core::pose::signals::EnergyEvent |
| EnergyEvent.hh | Signal for an energy change in a Pose |
| GeneralEvent.fwd.hh | Forward declaration for core::pose::signals::GeneralEvent |
| GeneralEvent.hh | Signal for a general change in a Pose |
| ► symmetry | |
| util.cc | |
| util.hh | Utility functions for handling with symmetric conformations |
| ► toolbox | |
| AtomID_Mapper.cc | |
| AtomID_Mapper.fwd.hh | |
| AtomID_Mapper.hh | |
| AtomLevelDomainMap.cc | Stores at the atom level information on domains in the pose (kind of like a movemap) |
| AtomLevelDomainMap.fwd.hh | AtomLevelDomainMap forward declarations header |
| AtomLevelDomainMap.hh | |
| annotated_sequence.cc | Utility functions for making poses from sequences |
| annotated_sequence.hh | |
| chains_util.cc | |
| chains_util.hh | Pose utilities |
| extra_pose_info_util.cc | |
| extra_pose_info_util.hh | Pose utilities |
| MiniPose.cc | MiniPose class |
| MiniPose.fwd.hh | MiniPose forward declarations header |
| MiniPose.hh | MiniPose class |
| PDBInfo.cc | Class to hold PDB information so it's not loose in the pose |
| PDBInfo.fwd.hh | Fwd declaration of classes defined in pose/PDBInfo |
| PDBInfo.hh | Pose information so it's not loose in the pose |
| PDBPoseMap.cc | Class to allow querying for pose resid with pdb chain/seqpos |
| PDBPoseMap.fwd.hh | Fwd declaration of classes defined in pose/PDBPoseMap |
| PDBPoseMap.hh | Class to allow querying for pose resid with pdb chain/seqpos |
| Pose.cc | Pose class |
| Pose.fwd.hh | Pose forward declarations header |
| Pose.hh | Pose class |
| ref_pose.cc | |
| ref_pose.hh | Reference Pose utilities |
| ResidueIndexDescription.cc | Classes designed to hold data neceassary to describe a residue in a Pose, which may come from a text file, e.g., and to resolve that data into an actual residue index when a Pose becomes available (which is likely not at the time that the file is read) and to throw an exception if the index cannot be resolved |
| ResidueIndexDescription.fwd.hh | Classes designed to hold data neceassary to describe a residue in a Pose, which may come from a text file, e.g., and to resolve that data into an actual residue index when a Pose becomes available (which is likely not at the time that the file is read) and to throw an exception if the index cannot be resolved |
| ResidueIndexDescription.hh | Classes designed to hold data neceassary to describe a residue in a Pose, which may come from a text file, e.g., and to resolve that data into an actual residue index when a Pose becomes available (which is likely not at the time that the file is read) and to throw an exception if the index cannot be resolved |
| selection.cc | Pose residue selections |
| selection.hh | Selcetion of pose residues |
| subpose_manipulation_util.cc | Pose class utilities |
| subpose_manipulation_util.hh | Pose subpose_manipulation_utilities |
| util.cc | Pose class utilities |
| util.hh | Pose utilities |
| util.tmpl.hh | |
| variant_util.cc | Pose class utilities |
| variant_util.hh | Pose utilities |
| xyzStripeHashPose.cc | |
| xyzStripeHashPose.fwd.hh | |
| xyzStripeHashPose.hh | |
| ► scoring | |
| ► aa_composition_energy | |
| AACompositionConstraint.cc | A constraint for constraining sequences to have a desired amino acid composition, analogous to a geometric constraint |
| AACompositionConstraint.fwd.hh | Forward declarations for a constraint for constraining sequences to have a desired amino acid composition, analogous to a geometric constraint |
| AACompositionConstraint.hh | Headers for a constraint for constraining sequences to have a desired amino acid composition, analogous to a geometric constraint |
| AACompositionEnergySetup.cc | A helper for the EnergyMethod that penalizes deviation from a desired amino acid composition |
| AACompositionEnergySetup.fwd.hh | Forward declarations for a helper class that stores the setup information for the AACompositionEnergy score term |
| AACompositionEnergySetup.hh | |
| SequenceConstraint.cc | A base class for constraining sequences, analogous to a geometric constraint |
| SequenceConstraint.fwd.hh | Forward declarations for base class for constraining sequences, analogous to a geometric constraint |
| SequenceConstraint.hh | Headers for a constraint for constraining sequences to have a desired amino acid composition, analogous to a geometric constraint |
| ► annealing | |
| ResidueArrayAnnealableEnergy.cc | Annealable method interrface for score types evaluated over explicit list of residues |
| ResidueArrayAnnealableEnergy.fwd.hh | |
| ResidueArrayAnnealableEnergy.hh | Annealable method interrface for score types evaluated over explicit list of residues |
| RotamerSets.fwd.hh | Residue Sets class foward declarations |
| ► atomic_depth | |
| AtomicDepth.cc | Calculates depth of atoms from the edge of the Sasa surface |
| AtomicDepth.fwd.hh | AtomicDepth forward declaration |
| AtomicDepth.hh | Calculates depth of atoms from the edge of the Sasa surface |
| util.cc | |
| util.hh | Util functions for atomic_depth calculations |
| ► bin_transitions | |
| BinTransitionCalculator.cc | Class member functions for BinTransitionCalculator class |
| BinTransitionCalculator.fwd.hh | Defines owning pointers for BinTransitionCalculator class |
| BinTransitionCalculator.hh | Headers for BinTransitionCalculator class |
| BinTransitionData.cc | Class member functions for BinTransitionData class |
| BinTransitionData.fwd.hh | Defines owning pointers for BinTransitionData class |
| BinTransitionData.hh | Headers for BinTransitionData class |
| ► carbohydrates | |
| CHIEnergyFunction.cc | Method definitions for CHIEnergyFunction |
| CHIEnergyFunction.fwd.hh | Forward declarations for CHIEnergyFunction |
| CHIEnergyFunction.hh | Method declarations for CHIEnergyFunction |
| CHIEnergyFunctionLinkageType.hh | |
| database_io.cc | Database input/output function definitions for carbohydrate-specific scoring data |
| database_io.hh | Database input/output function declarations for carbohydrate-specific scoring data |
| OmegaPreferencesFunction.cc | Method definitions for OmegaPreferencesFunction |
| OmegaPreferencesFunction.fwd.hh | Forward declarations for OmegaPreferencesFunction |
| OmegaPreferencesFunction.hh | Method declarations for OmegaPreferencesFunction |
| OmegaPreferenceType.hh | |
| util.cc | Utility function definitions for scoring carbohydrate-containing poses |
| util.hh | Utility function declarations for scoring carbohydrate-containing poses |
| ► carbon_hbonds | |
| CarbonHBondEnergy.cc | |
| CarbonHBondEnergy.fwd.hh | Hydrogen bond energy method forward declaration |
| CarbonHBondEnergy.hh | |
| CarbonHBondEnergyCreator.hh | Declaration for the class that connects CarbonHBondEnergy with the ScoringManager |
| CarbonHBondPotential.cc | |
| CarbonHBondPotential.fwd.hh | |
| CarbonHBondPotential.hh | Statistically derived rotamer pair potential class declaration |
| ► constraints | |
| AmbiguousConstraint.cc | Declarations for a type of constraint that holds a number of constraints |
| AmbiguousConstraint.fwd.hh | |
| AmbiguousConstraint.hh | Declarations for a type of constraint that holds multiple other |
| AmbiguousNMRConstraint.cc | Declarations for a type of constraint that holds a number of constraints |
| AmbiguousNMRConstraint.fwd.hh | |
| AmbiguousNMRConstraint.hh | Declarations for a type of constraint that holds multiple other constrains that belong to each other and are all evaluate at once |
| AmbiguousNMRDistanceConstraint.cc | |
| AmbiguousNMRDistanceConstraint.fwd.hh | |
| AmbiguousNMRDistanceConstraint.hh | |
| AngleConstraint.cc | Definition of AngularConstraints |
| AngleConstraint.fwd.hh | |
| AngleConstraint.hh | |
| AtomPairConstraint.cc | |
| AtomPairConstraint.fwd.hh | |
| AtomPairConstraint.hh | |
| BackboneStubConstraint.cc | |
| BackboneStubConstraint.fwd.hh | |
| BackboneStubConstraint.hh | |
| BackboneStubLinearConstraint.cc | |
| BackboneStubLinearConstraint.fwd.hh | |
| BackboneStubLinearConstraint.hh | |
| BasePairConstraint.cc | A wrapper for a very particular AmbiguousConstraint of MultiConstraints |
| BasePairConstraint.fwd.hh | A wrapper for a very particular AmbiguousConstraint of MultiConstraints |
| BasePairConstraint.hh | A wrapper for a very particular AmbiguousConstraint of MultiConstraints |
| BasicConstraintCreators.cc | |
| BasicConstraintCreators.hh | |
| BigBinConstraint.cc | |
| BigBinConstraint.hh | |
| BoundConstraint.cc | |
| BoundConstraint.fwd.hh | |
| BoundConstraint.hh | |
| ConstantConstraint.cc | |
| ConstantConstraint.fwd.hh | |
| ConstantConstraint.hh | |
| Constraint.cc | |
| Constraint.fwd.hh | |
| Constraint.hh | Base class definition for Constraint class hierarchy |
| ConstraintCreator.cc | |
| ConstraintCreator.fwd.hh | |
| ConstraintCreator.hh | Base class for ConstraintCreators for the Constraint load-time factory registration scheme |
| ConstraintEnergyContainer.cc | |
| ConstraintEnergyContainer.fwd.hh | |
| ConstraintEnergyContainer.hh | |
| ConstraintFactory.cc | Factory for creating various types of constraints |
| ConstraintFactory.hh | Factory for creating various types of constraints |
| ConstraintGraph.cc | |
| ConstraintGraph.fwd.hh | Constraints Energy Graph class forward declaration |
| ConstraintGraph.hh | |
| ConstraintIO.cc | |
| ConstraintIO.hh | |
| Constraints.cc | |
| Constraints.fwd.hh | |
| Constraints.hh | |
| ConstraintsEnergy.cc | |
| ConstraintsEnergy.fwd.hh | Constraints Energy Method forward declaration |
| ConstraintsEnergy.hh | Constraints Energy Method declaration |
| ConstraintsEnergyCreator.hh | Declaration for the class that connects ConstraintsEnergy with the ScoringManager |
| ConstraintSet.cc | |
| ConstraintSet.fwd.hh | |
| ConstraintSet.hh | |
| CoordinateConstraint.cc | |
| CoordinateConstraint.hh | |
| CstMinimizationData.cc | A cacheable data wrapper for ConstraintsOPs for use in minimization |
| CstMinimizationData.hh | A cacheable data wrapper for ConstraintsOPs for use in minimization |
| DihedralConstraint.cc | |
| DihedralConstraint.fwd.hh | |
| DihedralConstraint.hh | |
| DihedralPairConstraint.cc | |
| DihedralPairConstraint.hh | |
| DistancePairConstraint.cc | |
| DistancePairConstraint.hh | |
| DOF_Constraint.cc | |
| DOF_Constraint.fwd.hh | |
| DOF_Constraint.hh | |
| FabConstraint.cc | This class is specific to antibodies and penalizes presence of non-cdr residues |
| FabConstraint.fwd.hh | This class is specific to antibodies and penalizes presence of residues flanking |
| FabConstraint.hh | This class is specific to antibodies and penalizes presence of residues flanking antibody cdr residues at Antigen-Antibody interfaces (ported from Fab constraint in rosetta++ which uses a constant constraint score of 0.5/flanking residue) |
| KofNConstraint.cc | Meta constraint where N constraints declared |
| KofNConstraint.fwd.hh | Meta constraint where N constraints declared |
| KofNConstraint.hh | Meta constraint where N constraints declared |
| LocalCoordinateConstraint.cc | |
| LocalCoordinateConstraint.hh | |
| MembraneSpanConstraint.cc | Constarint the TM spans specified by user to stay in the membrane |
| MembraneSpanConstraint.fwd.hh | |
| MembraneSpanConstraint.hh | |
| MembraneSpanTermZConstraint.cc | Constraint the Z axis distance between TM span edges |
| MembraneSpanTermZConstraint.fwd.hh | |
| MembraneSpanTermZConstraint.hh | |
| MultiConstraint.cc | Declarations for a type of constraint that holds multiple other constrains that belong to each other and are all evaluate at once |
| MultiConstraint.fwd.hh | |
| MultiConstraint.hh | Declarations for a type of constraint that holds multiple other constrains that belong to each other and are all evaluate at once |
| NamedAngleConstraint.cc | Provides an angle constraint based on atom names, rather than numbers. Useful for when atom numbers change |
| NamedAngleConstraint.fwd.hh | Provides an angle constraint based on atom names, rather than numbers. Useful for when atom numbers change |
| NamedAngleConstraint.hh | |
| NamedAtomPairConstraint.cc | |
| NamedAtomPairConstraint.fwd.hh | |
| NamedAtomPairConstraint.hh | |
| NamedDihedralConstraint.cc | Provides a dihedral constraint based on atom names, rather than numbers. Useful for when atom numbers change |
| NamedDihedralConstraint.fwd.hh | Provides a dihedral constraint based on atom names, rather than numbers. Useful for when atom numbers change |
| NamedDihedralConstraint.hh | |
| NonResidueTypeConstraint.cc | |
| NonResidueTypeConstraint.fwd.hh | |
| NonResidueTypeConstraint.hh | |
| ResidueCouplingConstraint.cc | |
| ResidueCouplingConstraint.fwd.hh | Constrainting two residues to be the same type, based on |
| ResidueCouplingConstraint.hh | |
| ResidueTypeConstraint.cc | |
| ResidueTypeConstraint.fwd.hh | |
| ResidueTypeConstraint.hh | |
| ResidueTypeLinkingConstraint.cc | Implements linked constraints, where bonuses or penalties can be applied if pairs of residues match specific sequences |
| ResidueTypeLinkingConstraint.fwd.hh | Constrainting two residues to be the same type, based on |
| ResidueTypeLinkingConstraint.hh | Implements linked constraints, where bonuses or penalties can be applied if pairs of residues match specific sequences |
| RTConstraint.cc | |
| RTConstraint.fwd.hh | |
| RTConstraint.hh | Constraint definition for RT of stub pairs |
| SequenceProfileConstraint.cc | This is a constraint that refers to a core::sequence::SequenceProfile? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design). A note about the SequenceProfile::read_from_checkpoint function that is used to read in scores for amino acid types: the first line of the file will be ignored |
| SequenceProfileConstraint.fwd.hh | |
| SequenceProfileConstraint.hh | This is a constraint that refers to a core::sequence::SequenceProfile? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design) |
| SequenceProfileConstraintCreator.hh | |
| SiteConstraint.cc | This class is an AmbiguousConstraint in which the set is comprised of AtomPairConstraints |
| SiteConstraint.fwd.hh | This class is an AmbiguousConstraint in which the set is comprised of AtomPairConstraints |
| SiteConstraint.hh | This class is an AmbiguousConstraint in which the set is comprised of AtomPairConstraints |
| SiteConstraintResidues.cc | This class is an AmbiguousConstraint in which the set is comprised of AtomPairConstraints |
| SiteConstraintResidues.fwd.hh | This class is an AmbiguousConstraint in which the set is comprised of AtomPairConstraints |
| SiteConstraintResidues.hh | This class is an AmbiguousConstraint in which the set is comprised of AtomPairConstraints |
| util.cc | Utility functions for defining and using constraints |
| util.hh | Utility functions for defining and using constraints |
| ► cryst | |
| PhenixInterface.cc | |
| PhenixInterface.fwd.hh | |
| PhenixInterface.hh | Singleton class that manages interface with phenix refinement, incl. temporary storage |
| util.cc | |
| util.hh | |
| ► custom_pair_distance | |
| FullatomCustomPairDistanceEnergy.cc | |
| FullatomCustomPairDistanceEnergy.fwd.hh | Class declaration |
| FullatomCustomPairDistanceEnergy.hh | |
| FullatomCustomPairDistanceEnergyCreator.hh | Declaration for the class that connects FullatomCustomPairDistanceEnergy with the ScoringManager |
| ► disulfides | |
| CentroidDisulfideEnergyContainer.cc | |
| CentroidDisulfideEnergyContainer.fwd.hh | |
| CentroidDisulfideEnergyContainer.hh | Disulfide Energy Container class declaration |
| CentroidDisulfidePotential.cc | Centroid Disulfide Energy Potentials |
| CentroidDisulfidePotential.fwd.hh | |
| CentroidDisulfidePotential.hh | Centroid Disulfide Energy Potentials |
| DisulfideAtomIndices.cc | Disulfide Energy class implementation |
| DisulfideAtomIndices.fwd.hh | Disulfide Atom Indices class forward declaration |
| DisulfideAtomIndices.hh | Disulfide Atom Indices class declaration |
| DisulfideMatchingDatabase.cc | |
| DisulfideMatchingDatabase.hh | Centroid Disulfide Energy Databases |
| DisulfideMatchingEnergyContainer.cc | |
| DisulfideMatchingEnergyContainer.fwd.hh | |
| DisulfideMatchingEnergyContainer.hh | Disulfide Energy Container class declaration |
| DisulfideMatchingPotential.cc | |
| DisulfideMatchingPotential.fwd.hh | |
| DisulfideMatchingPotential.hh | Centroid Disulfide Energy Potentials |
| FullatomDisulfideEnergyContainer.cc | |
| FullatomDisulfideEnergyContainer.fwd.hh | |
| FullatomDisulfideEnergyContainer.hh | Disulfide Energy Container class declaration |
| FullatomDisulfidePotential.cc | Fullatom Disulfide potential class definition |
| FullatomDisulfidePotential.fwd.hh | Fullatom Disulfide Potential class forward declaration |
| FullatomDisulfidePotential.hh | Fullatom Disulfide Potential class declaration |
| ► dna | |
| base_geometry.cc | |
| base_geometry.hh | |
| BasePartner.cc | |
| BasePartner.fwd.hh | |
| BasePartner.hh | |
| DirectReadoutPotential.cc | |
| DirectReadoutPotential.fwd.hh | |
| DirectReadoutPotential.hh | |
| DNA_BasePotential.cc | |
| DNA_BasePotential.fwd.hh | |
| DNA_BasePotential.hh | |
| DNA_DihedralPotential.cc | Dna scoring |
| DNA_DihedralPotential.fwd.hh | Dna scoring |
| DNA_DihedralPotential.hh | Dna scoring |
| DNA_EnvPairPotential.cc | Dna scoring |
| DNA_EnvPairPotential.fwd.hh | Dna scoring |
| DNA_EnvPairPotential.hh | Dna scoring |
| DNABFormPotential.cc | DNA B-form specific torsion potential class implementation |
| DNABFormPotential.fwd.hh | DNA B-form specific torsion potential class forward delcaration |
| DNABFormPotential.hh | DNA B-form specific torsion potential class delcaration |
| DNATorsionPotential.cc | DNATorsionPotential potential class implementation |
| DNATorsionPotential.fwd.hh | |
| DNATorsionPotential.hh | DNATorsionPotential potential class delcaration |
| setup.cc | |
| setup.hh | |
| ► dssp | |
| Dssp.cc | |
| Dssp.fwd.hh | Fwd headers for ns dssp |
| Dssp.hh | |
| PairingsList.cc | |
| PairingsList.fwd.hh | Fwd headers for ns dssp |
| PairingsList.hh | |
| StrandPairing.cc | |
| StrandPairing.fwd.hh | |
| StrandPairing.hh | |
| util.cc | |
| util.hh | |
| ► elec | |
| ► electrie | |
| ElecAtom.cc | |
| ElecAtom.fwd.hh | |
| ElecAtom.hh | |
| ElecTrie.fwd.hh | |
| ElecTrieEvaluator.cc | |
| ElecTrieEvaluator.fwd.hh | |
| ElecTrieEvaluator.hh | |
| CountPairRepresentative.hh | Count pair function for use in initializing the NBList that uses the FA_ElecEnergy::get_countpair_representative_atom function to determine the representative for an atom, and then to ask the inner CountPairFunction whether the two representatives should have their interaction counted. Note: this count pair function is not set up to be used efficiently in the atom_pair_energy_inline functions |
| CPRepMapType.fwd.hh | |
| FA_ElecEnergy.cc | |
| FA_ElecEnergy.fwd.hh | |
| FA_ElecEnergy.hh | |
| FA_ElecEnergyCreator.hh | |
| GroupElec.cc | |
| GroupElec.hh | |
| util.cc | |
| util.hh | |
| ► electron_density | |
| ElectronDensity.cc | |
| ElectronDensity.fwd.hh | |
| ElectronDensity.hh | |
| SplineInterp.cc | |
| SplineInterp.hh | |
| util.cc | |
| util.hh | |
| xray_scattering.cc | |
| xray_scattering.hh | |
| ► electron_density_atomwise | |
| ElectronDensityAtomwise.cc | Elec_dens_atomwise scoring method implementation |
| ElectronDensityAtomwise.hh | Scoring a structure against an electron density map |
| ► epr_deer | |
| DEERData.cc | Container for DEER experimental data and dataype-specific scoring function These classes contain the base and derived types for various DEER data containers. The DEERData parent class stores generic information. The DEERDistanceBounds type stores a distance value of interest and evaluates as a harmonic function. The DEERDistanceDistribution type store the data as a probability distribution and tries to maximize overlap. The DEERDecayData type stores the raw data and tries to recapitulate it from the simulated distribution |
| DEERData.fwd.hh | |
| DEERData.hh | Container for DEER experimental data and dataype-specific scoring function These classes contain the base and derived types for various DEER data containers. The DEERData parent class stores generic information. The DEERDistanceBounds type stores a distance value of interest and evaluates as a harmonic function. The DEERDistanceDistribution type store the data as a probability distribution and tries to maximize overlap. The DEERDecayData type stores the raw data and tries to recapitulate it from the simulated distribution |
| DEERDataCache.cc | Contains data for DEER energy method, stored as DEERData objects |
| DEERDataCache.fwd.hh | |
| DEERDataCache.hh | |
| DEERIO.cc | IO class for data obtained with double electron-electron resonance (DEER) |
| DEERIO.fwd.hh | IO class for data obtained with double electron-electron resonance (DEER) |
| DEERIO.hh | IO class for data obtained with double electron-electron resonance (DEER) |
| EPRSpinLabel.cc | This is a container class specific to the use of double electron-electron resonance data |
| EPRSpinLabel.fwd.hh | This is a container class specific to the use of double electron-electron resonance data |
| EPRSpinLabel.hh | This is a container class specific to the use of double electron-electron resonance data |
| Simulated4PDEERTrace.cc | |
| Simulated4PDEERTrace.fwd.hh | |
| Simulated4PDEERTrace.hh | |
| ► etable | |
| ► coulomb | |
| Coulomb.cc | |
| Coulomb.fwd.hh | Forward header for Coulomb class |
| Coulomb.hh | Evaluate Coulombic potential |
| ► count_pair | |
| CountPair1B.fwd.hh | Count pair for residue pairs connected with one bond |
| CountPair1B.hh | Count pair for residue pairs connected with one bond, where the crossover from excluding to counting atom pair interactions is at 3 bonds |
| CountPair2B.fwd.hh | Count pair for residue pairs separated by another residue. If you need to weight interactions between atoms separated by four bonds, you could find yourself in this situation. For instance, C in residue 1 and N in residue 3 are separated by four bonds, and the other CountPair options don't handle this correctly |
| CountPair2B.hh | Count pair for residue pairs separated by another residue. If you need to weight interactions between atoms separated by four bonds, you could find yourself in this situation. For instance, C in residue 1 and N in residue 3 are separated by four bonds, and the other CountPair options don't handle this correctly |
| CountPairAll.cc | Count pair for residues where all atom pairs should be counted |
| CountPairAll.fwd.hh | Count pair for residues where all atom pairs should be counted |
| CountPairAll.hh | Count pair for residues where all atom pairs should be counted |
| CountPairCrossover3.cc | |
| CountPairCrossover3.fwd.hh | |
| CountPairCrossover3.hh | Count pair for residue pairs connected with one bond, where the crossover from excluding to counting atom pair interactions is at 3 bonds |
| CountPairCrossover34.cc | |
| CountPairCrossover34.fwd.hh | |
| CountPairCrossover34.hh | Count pair for residue pairs where the crossover from excluding to counting atom pair interactions is at 3 bonds, but where the weighting is different for 3 bonds versus 4 |
| CountPairCrossover3full.cc | |
| CountPairCrossover3full.fwd.hh | |
| CountPairCrossover3full.hh | |
| CountPairCrossover4.cc | Count pair for residue pairs where the crossover from excluding to counting atom pair interactions is at 4 bonds |
| CountPairCrossover4.fwd.hh | Count pair for residue pairs where the crossover from excluding to counting atom pair interactions is at 4 bonds |
| CountPairCrossover4.hh | Count pair for residue pairs where the crossover from excluding to counting atom pair interactions is at 4 bonds |
| CountPairFactory.cc | |
| CountPairFactory.fwd.hh | |
| CountPairFactory.hh | |
| CountPairFunction.cc | Count pair base class implementation |
| CountPairFunction.fwd.hh | Count pair base class forward declaration |
| CountPairFunction.hh | Count pair base class interface |
| CountPairGeneric.cc | |
| CountPairGeneric.fwd.hh | |
| CountPairGeneric.hh | |
| CountPairIntraRes.fwd.hh | |
| CountPairIntraRes.hh | Count pair for residue pairs connected with one bond, where the crossover from excluding to counting atom pair interactions is at 3 bonds |
| CountPairNone.cc | Count pair for residues where all atom pairs should be counted |
| CountPairNone.fwd.hh | Count pair for residues where all atom pairs should be counted |
| CountPairNone.hh | Count pair for residues where all atom pairs should be counted |
| types.hh | |
| ► etrie | |
| CountPairData_1_1.cc | CountPair Data for a residue with one connection point |
| CountPairData_1_1.fwd.hh | |
| CountPairData_1_1.hh | |
| CountPairData_1_2.cc | |
| CountPairData_1_2.fwd.hh | |
| CountPairData_1_2.hh | |
| CountPairData_1_3.cc | |
| CountPairData_1_3.fwd.hh | |
| CountPairData_1_3.hh | |
| CountPairDataGeneric.cc | |
| CountPairDataGeneric.fwd.hh | Forward declaration of generic count-pair data class for the trie |
| CountPairDataGeneric.hh | Class to hold per-atom count pair for residues with non-canonical inter-residue connections |
| EtableAtom.cc | |
| EtableAtom.fwd.hh | |
| EtableAtom.hh | |
| EtableTrie.fwd.hh | |
| TrieCountPair1BC3.cc | |
| TrieCountPair1BC3.fwd.hh | |
| TrieCountPair1BC3.hh | |
| TrieCountPair1BC4.cc | |
| TrieCountPair1BC4.fwd.hh | |
| TrieCountPair1BC4.hh | |
| TrieCountPairAll.analytic_etable.cc | |
| TrieCountPairAll.cc | File which actually instantiates the templated trie-vs-trie and trie-vs-path algorithms for the analytic etable energy |
| TrieCountPairAll.fa_elec.cc | |
| TrieCountPairAll.fwd.hh | |
| TrieCountPairAll.hbonds.cc | File which handles the (failed) dispatch to the TrieCountPairAll class' trie-vs-trie and trie-vs-path functions from the HBondEnergy. These functions should never be called |
| TrieCountPairAll.hh | |
| TrieCountPairAll.lkball.cc | |
| TrieCountPairAll.mm_inter.cc | |
| TrieCountPairAll.table_etable.cc | File which actually instantiates the templated trie-vs-trie and trie-vs-path algorithms for the table-lookup etable energy |
| TrieCountPairAll.vdw.cc | |
| TrieCountPairGeneric.cc | |
| TrieCountPairGeneric.fwd.hh | |
| TrieCountPairGeneric.hh | Implementation of count pair class to go along with the CountPairGeneric atom data |
| TrieCountPairNone.cc | |
| TrieCountPairNone.fwd.hh | |
| TrieCountPairNone.hh | |
| atom_pair_energy_inline.hh | |
| BaseEtableEnergy.hh | |
| BaseEtableEnergy.tmpl.hh | |
| Etable.cc | |
| Etable.fwd.hh | |
| Etable.hh | |
| EtableEnergy.cc | Atom pair energy functions |
| EtableEnergy.fwd.hh | |
| EtableEnergy.hh | Etable energy method class declaration |
| EtableEnergyCreator.hh | Declaration for the class that connects EtableEnergy with the ScoringManager |
| EtableOptions.cc | |
| EtableOptions.fwd.hh | Forward header for EtableOptions class |
| EtableOptions.hh | |
| ► facts | |
| FACTSPose.cc | |
| FACTSPose.hh | |
| FACTSPotential.cc | |
| FACTSPotential.fwd.hh | |
| FACTSPotential.hh | |
| FACTSResidue.cc | |
| FACTSResidue.hh | |
| ► fiber_diffraction | |
| CentroidScatter.cc | Cache for scattering factors in centroid mode |
| CentroidScatter.fwd.hh | Cache for scattering factors in centroid mode |
| CentroidScatter.hh | Cache for scattering factors in centroid mode |
| FAScatter.cc | Cache for scattering factors in all-atom mode |
| FAScatter.fwd.hh | Cache for scattering factors in all-atom mode |
| FAScatter.hh | Cache for scattering factors in all atom mode |
| FiberDiffraction.cc | |
| FiberDiffraction.fwd.hh | Fiber Diffraction forward declarations |
| FiberDiffraction.hh | Fiber diffraction data collector class |
| FiberDiffractionKernelGpu.hh | FiberDiffraction kernel module for GPU computations |
| hankel_kiss_fft.cc | |
| hankel_kiss_fft.hh | |
| util.cc | |
| util.hh | |
| util_ndft.cc | FiberDiffractionDens scoring |
| util_ndft.hh | |
| xray_scattering.cc | |
| xray_scattering.hh | |
| ► func | |
| AmberPeriodicFunc.cc | Definition for periodic functions |
| AmberPeriodicFunc.fwd.hh | Forward declaration for Mixture functions |
| AmberPeriodicFunc.hh | Definition for a periodic function used in constraints |
| CharmmPeriodicFunc.cc | Definition for periodic functions |
| CharmmPeriodicFunc.hh | Definition for a periodic function used in constraints |
| CircularGeneral1D_Func.cc | A general 1D function that can be initialized by FArray or from text file. There's stuff like this all over Rosetta |
| CircularGeneral1D_Func.fwd.hh | Forward declaration for CircularGeneral1D_Func class |
| CircularGeneral1D_Func.hh | A general 1D function that can be initialized by FArray or from text file. There's stuff like this all over Rosetta |
| CircularHarmonicFunc.cc | Definition for functions used in definition of constraints |
| CircularHarmonicFunc.fwd.hh | Forward declaration for CircularHarmonicFunc class |
| CircularHarmonicFunc.hh | |
| CircularPowerFunc.cc | |
| CircularPowerFunc.fwd.hh | Forward declaration for CircularPowerFunc class |
| CircularPowerFunc.hh | Definition for functions used in definition of constraints |
| CircularSigmoidalFunc.cc | Definition for functions used in definition of constraints |
| CircularSigmoidalFunc.fwd.hh | Forward declaration for CircularSigmoidalFunc class |
| CircularSigmoidalFunc.hh | |
| CircularSplineFunc.cc | Similar to spline func but periodic on [0,360) |
| CircularSplineFunc.fwd.hh | Similar to spline func but periodic on [0,360) |
| CircularSplineFunc.hh | Similar to spline func but periodic on [0,360) |
| ConstantFunc.cc | Definition for functions used in definition of constraints |
| ConstantFunc.fwd.hh | Forward declaration for Constant functions |
| ConstantFunc.hh | Definition for functions used in definition of constraints |
| CountViolFunc.cc | Weighted constraint function that reweights other constraints by a constant scalar value |
| CountViolFunc.hh | |
| EtableFunc.cc | |
| EtableFunc.fwd.hh | Forward declaration for Etable functions |
| EtableFunc.hh | Definition for functions used in definition of constraints |
| FadeFunc.cc | |
| FadeFunc.fwd.hh | Forward declaration for Mixture functions |
| FadeFunc.hh | Definition for functions used in definition of constraints |
| FlatHarmonicFunc.cc | |
| FlatHarmonicFunc.fwd.hh | Forward declaration for Mixture functions |
| FlatHarmonicFunc.hh | Definition for functions used in definition of constraints |
| FourPointsFunc.cc | |
| FourPointsFunc.fwd.hh | |
| FourPointsFunc.hh | |
| Func.cc | Definition for functions used in definition of constraints |
| Func.fwd.hh | |
| Func.hh | Definition for functions used in definition of constraints |
| FuncFactory.cc | Factory for creating various types of constraints |
| FuncFactory.fwd.hh | Factory for creating various types of constraints |
| FuncFactory.hh | Factory for creating various types of constraints |
| GaussianChainDoubleFunc.cc | Definition for functions used in loop closure terms |
| GaussianChainDoubleFunc.fwd.hh | Forward declaration for Mixture functions |
| GaussianChainDoubleFunc.hh | Definition for functions used in definition of loop closure energies |
| GaussianChainFunc.cc | Definition for functions used in loop closure terms |
| GaussianChainFunc.fwd.hh | Forward declaration for Mixture functions |
| GaussianChainFunc.hh | Definition for functions used in definition of loop closure energies |
| GaussianChainGeneralFunc.cc | |
| GaussianChainGeneralFunc.fwd.hh | Forward declaration for Mixture functions |
| GaussianChainGeneralFunc.hh | Definition for functions used in loop closure terms |
| GaussianChainQuadrupleFunc.cc | |
| GaussianChainQuadrupleFunc.fwd.hh | Forward declaration for Mixture functions |
| GaussianChainQuadrupleFunc.hh | Definition for functions used in loop closure terms |
| GaussianChainSingleFunc.cc | |
| GaussianChainSingleFunc.fwd.hh | Forward declaration for Mixture functions |
| GaussianChainSingleFunc.hh | Definition for functions used in loop closure terms |
| GaussianChainTripleFunc.cc | |
| GaussianChainTripleFunc.fwd.hh | Forward declaration for Mixture functions |
| GaussianChainTripleFunc.hh | Definition for functions used in loop closure terms |
| GaussianFunc.cc | |
| GaussianFunc.fwd.hh | Forward declaration for Gaussian functions |
| GaussianFunc.hh | Definition for functions used in definition of constraints |
| HarmonicFunc.cc | |
| HarmonicFunc.fwd.hh | Forward declaration for Mixture functions |
| HarmonicFunc.hh | Definition for functions used in definition of constraints |
| IdentityFunc.cc | |
| IdentityFunc.fwd.hh | Forward declaration for Identity function |
| IdentityFunc.hh | Definition for functions used in definition of constraints |
| KarplusFunc.cc | Definition for functions used in definition of constraints |
| KarplusFunc.fwd.hh | |
| KarplusFunc.hh | |
| LinearPenaltyFunction.cc | |
| LinearPenaltyFunction.hh | Linear penalty for values outside a certain range |
| MinMultiHarmonicFunc.cc | |
| MinMultiHarmonicFunc.fwd.hh | Forward declaration for Mixture functions |
| MinMultiHarmonicFunc.hh | |
| MixtureFunc.cc | Definition for functions used in definition of constraints |
| MixtureFunc.fwd.hh | Forward declaration for Mixture functions |
| MixtureFunc.hh | Definition for functions used in definition of constraints |
| PeriodicFunc.cc | Definition for periodic functions |
| PeriodicFunc.hh | Definition for a periodic function used in constraints |
| ScalarWeightedFunc.cc | Weighted constraint function that reweights other constraints by a constant scalar value |
| ScalarWeightedFunc.fwd.hh | |
| ScalarWeightedFunc.hh | Weighted constraint function that encapsulates other constraints |
| SigmoidFunc.cc | |
| SigmoidFunc.fwd.hh | Forward declaration for Mixture functions |
| SigmoidFunc.hh | Definition for functions used in definition of constraints |
| SkipViolFunc.cc | Weighted constraint function that reweights other constraints by a constant scalar value |
| SkipViolFunc.hh | |
| SmoothStepFunc.cc | |
| SmoothStepFunc.fwd.hh | Forward declaration for Smooth Step Function |
| SmoothStepFunc.hh | Definition for functions used in definition of constraints |
| SoedingFunc.cc | |
| SoedingFunc.fwd.hh | Forward declaration for SoedingFunc class |
| SoedingFunc.hh | Definition for functions used in definition of constraints |
| SOGFunc.cc | |
| SOGFunc.fwd.hh | Forward declaration for SOG functions |
| SOGFunc.hh | Definition for functions used in definition of constraints |
| SOGFunc_Impl.cc | Definition for functions used in definition of constraints |
| SOGFunc_Impl.fwd.hh | Forward declaration for SOG functions |
| SOGFunc_Impl.hh | Definition for functions used in definition of constraints |
| SplineFunc.cc | Constraint function for looking up data in a histogram over which a spline is created |
| SplineFunc.fwd.hh | Forward declaration for SplineFunc |
| SplineFunc.hh | Constraint function for looking up data in a histogram over which a spline is created |
| SquareWell2Func.cc | |
| SquareWell2Func.fwd.hh | Forward declaration for Mixture functions |
| SquareWell2Func.hh | Definition for functions used in definition of constraints |
| SquareWellFunc.cc | |
| SquareWellFunc.fwd.hh | Forward declaration for Mixture functions |
| SquareWellFunc.hh | Definition for functions used in definition of constraints |
| SumFunc.cc | Weighted constraint function that reweights other constraints by a constant scalar value |
| SumFunc.fwd.hh | |
| SumFunc.hh | Sum of several individual constraints |
| TopOutFunc.cc | |
| TopOutFunc.fwd.hh | Implementation of phenix "top-out" function |
| TopOutFunc.hh | Implementation of phenix "top-out" function Similar to Geman-McClure: harmonic near 'x0_', flat past 'limit_' |
| USOGFunc.cc | |
| USOGFunc.fwd.hh | |
| USOGFunc.hh | |
| XYZ_Func.cc | |
| XYZ_Func.fwd.hh | |
| XYZ_Func.hh | |
| ► geometric_solvation | |
| DatabaseOccSolEne.cc | Database containing params for OccludedHbondSolEnergy (i.e., for the pwSHO model) |
| DatabaseOccSolEne.fwd.hh | Database containing params for OccludedHbondSolEnergy |
| DatabaseOccSolEne.hh | Database containing params for OccludedHbondSolEnergy (i.e., for the pwSHO model) |
| GeometricSolEnergyEvaluator.cc | |
| GeometricSolEnergyEvaluator.fwd.hh | |
| GeometricSolEnergyEvaluator.hh | Geometric solvation energy |
| ► hbonds | |
| ► graph | |
| AtomInfo.hh | |
| HBondGraph.cc | HBondGraph, HBondNode, and HBondEdge classes |
| HBondGraph.fwd.hh | HBondGraph forward declarations |
| HBondGraph.hh | Class headers for HBondGraph, HBondNode, and HBondEdge |
| HBondInfo.hh | |
| ► hbtrie | |
| HBAtom.cc | |
| HBAtom.fwd.hh | |
| HBAtom.hh | |
| HBCountPairFunction.cc | |
| HBCountPairFunction.fwd.hh | |
| HBCountPairFunction.hh | |
| HBCPData.cc | |
| HBCPData.fwd.hh | |
| HBCPData.hh | This class enforces the sc/bb hbond exclusion rule for use in the trie |
| HBondsTrieVsTrieCachedDataContainer.cc | A class for passing data to the trie-vs-trie calculation for hydrogen bonds, without having to cache it in mutable data in the HBondEnergy method or whatnot |
| HBondsTrieVsTrieCachedDataContainer.fwd.hh | A class for passing data to the trie-vs-trie calculation for hydrogen bonds, without having to cache it in mutable data in the HBondEnergy method or whatnot |
| HBondsTrieVsTrieCachedDataContainer.hh | A class for passing data to the trie-vs-trie calculation for hydrogen bonds, without having to cache it in mutable data in the HBondEnergy method or whatnot |
| HBondTrie.fwd.hh | |
| constants.hh | |
| FadeInterval.cc | FadeInterval class, used a simplified cross term for the hbond score term |
| FadeInterval.fwd.hh | |
| FadeInterval.hh | FadeInterval class, used a simplified cross term for the hbond score term |
| HBEvalTuple.cc | |
| HBEvalTuple.fwd.hh | Tuple describing data about the donor and acceptor in a single hbond |
| HBEvalTuple.hh | Tuple describing data about the donor and acceptor in a single hbond |
| HBondDatabase.cc | Database containing params for HBondEnergy |
| HBondDatabase.fwd.hh | Forward header for HBondDatabase class |
| HBondDatabase.hh | |
| HBondEnergy.cc | |
| HBondEnergy.fwd.hh | |
| HBondEnergy.hh | |
| HBondEnergyCreator.hh | Declaration for the class that connects HBondEnergy with the ScoringManager |
| HBondOptions.cc | HBondOptions class, holds the options for the hbond energy function |
| HBondOptions.fwd.hh | Forward header for HBondOptions class |
| HBondOptions.hh | HBondOptions class, holds the options for the hbond energy function |
| hbonds.cc | |
| hbonds.hh | Set of utilities for detection of hydrogen bonds |
| hbonds_geom.cc | |
| hbonds_geom.hh | |
| HBondSet.cc | |
| HBondSet.fwd.hh | Hydrogen bond set for a pose forward declaration |
| HBondSet.hh | Hydrogen bond set class implementation |
| HBondTypeManager.cc | |
| HBondTypeManager.fwd.hh | Forward header for HBondTypeManager class |
| HBondTypeManager.hh | HBond enumeration type manager |
| NPDHBondSet.cc | |
| NPDHBondSet.fwd.hh | Hydrogen bond set for a pose forward declaration |
| NPDHBondSet.hh | Hydrogen bond set class implementation |
| polynomial.cc | Classes for hydrogen bond polynomial evaluation functions |
| polynomial.fwd.hh | Forward header for Polynomial class |
| polynomial.hh | Polynomial objects for hydrogen bond score term |
| types.cc | Functions for manipulating hydrogen bond types |
| types.hh | Core::scoring package type declarations |
| ► interface_ | |
| DDPlookup.cc | |
| DDPlookup.fwd.hh | |
| DDPlookup.hh | |
| DDPscore.cc | |
| DDPscore.fwd.hh | |
| DDPscore.hh | |
| DDPscoreCreator.hh | |
| ► lkball | |
| ► lkbtrie | |
| LKBAtom.cc | |
| LKBAtom.fwd.hh | |
| LKBAtom.hh | |
| LKBTrie.fwd.hh | |
| LKBTrieEvaluator.cc | |
| LKBTrieEvaluator.fwd.hh | |
| LKBTrieEvaluator.hh | |
| LK_BallEnergy.cc | |
| LK_BallEnergy.fwd.hh | |
| LK_BallEnergy.hh | |
| LK_BallEnergyCreator.hh | |
| LK_BallInfo.cc | |
| LK_BallInfo.hh | |
| ► loop_graph | |
| ► evaluator | |
| GaussianChainFuncPotentialEvaluator.cc | |
| GaussianChainFuncPotentialEvaluator.fwd.hh | |
| GaussianChainFuncPotentialEvaluator.hh | |
| LoopClosePotentialEvaluator.cc | |
| LoopClosePotentialEvaluator.fwd.hh | |
| LoopClosePotentialEvaluator.hh | |
| SixDTransRotPotential.cc | Six-dimensional potential (translations, rotations) that can be evaluated on a jump |
| SixDTransRotPotential.fwd.hh | |
| SixDTransRotPotential.hh | |
| SixDTransRotPotentialEvaluator.cc | |
| SixDTransRotPotentialEvaluator.fwd.hh | |
| SixDTransRotPotentialEvaluator.hh | |
| util.hh | |
| Loop.cc | |
| Loop.fwd.hh | |
| Loop.hh | |
| LoopCycle.cc | |
| LoopCycle.fwd.hh | |
| LoopCycle.hh | |
| LoopGraph.cc | |
| LoopGraph.fwd.hh | |
| LoopGraph.hh | |
| util.cc | |
| util.fwd.hh | |
| util.hh | |
| ► magnesium | |
| MgKnowledgeBasedPotential.cc | |
| MgKnowledgeBasedPotential.fwd.hh | |
| MgKnowledgeBasedPotential.hh | Information on which atoms to use for computing clashes |
| util.cc | |
| util.hh | |
| ► memb_etable | |
| MembEtable.cc | Table of pre-computed LK membrane solvation energies |
| MembEtable.fwd.hh | Table of pre-computed LK membrane solvation energies |
| MembEtable.hh | Table of pre-computed LK membrane solvation energies |
| ► membrane | |
| MembraneData.cc | Membrane Scorefunction Statistics Class |
| MembraneData.fwd.hh | Membrane Base Potential |
| MembraneData.hh | Membrane Scorefunction Statistics Class |
| MPNonHelixPenalty.cc | Membrane Protein Non helix in Mmebrane Penalty |
| MPNonHelixPenalty.fwd.hh | Membrane Protein Non helix in Mmebrane Penalty |
| MPNonHelixPenalty.hh | Membrane Protein Non helix in Mmebrane Penalty |
| MPNonHelixPenaltyCreator.hh | Membrane Protein Non helix in Mmebrane Penalty |
| MPTerminiPenalty.cc | Membrane Protein Termini Penalty |
| MPTerminiPenalty.fwd.hh | Membrane Protein Termini Penalty |
| MPTerminiPenalty.hh | Membrane Protein Termini Penalty |
| MPTerminiPenaltyCreator.hh | Membrane Protein Termini Penalty Creator Class |
| MPTMProjPenalty.cc | Membrane Protein TM Proj Penalty |
| MPTMProjPenalty.fwd.hh | Membrane Protein TM Proj Penalty |
| MPTMProjPenalty.hh | Membrane Protein TM Proj Penalty |
| MPTMProjPenaltyCreator.hh | Membrane Protein TM Proj Penalty |
| ► methods | |
| ► dfire | |
| DFIRE_Potential.cc | |
| DFIRE_Potential.fwd.hh | |
| DFIRE_Potential.hh | DFIRE Potential class declaration |
| branch_energy_util.cc | |
| branch_energy_util.hh | |
| CartBondedParameters.hh | |
| chainbreak_util.cc | Utility functions for scoring chainbreaks |
| chainbreak_util.hh | Utility functions for scoring chainbreaks |
| ContextDependentLRTwoBodyEnergy.cc | Context-Dependent, Long-Range, Two-Body Energy class implementation |
| ContextDependentLRTwoBodyEnergy.fwd.hh | Context-Dependent, Long-Range, Two-Body Energy Method class forward declaration |
| ContextDependentLRTwoBodyEnergy.hh | |
| ContextDependentOneBodyEnergy.cc | |
| ContextDependentOneBodyEnergy.fwd.hh | |
| ContextDependentOneBodyEnergy.hh | |
| ContextDependentTwoBodyEnergy.cc | Score function class |
| ContextDependentTwoBodyEnergy.fwd.hh | Forward declaration for the Context-Dependent (ShortRange) Two-Body EnergyMethod base class |
| ContextDependentTwoBodyEnergy.hh | |
| ContextIndependentLRTwoBodyEnergy.cc | Context-Independent, Long-Range, Two-Body Energy class implementation |
| ContextIndependentLRTwoBodyEnergy.fwd.hh | Context-Independent, Long-Range, Two-Body Energy Method class forward declaration |
| ContextIndependentLRTwoBodyEnergy.hh | Context-Dependent, Long-Range, Two-Body Energy class declaration |
| ContextIndependentOneBodyEnergy.cc | |
| ContextIndependentOneBodyEnergy.fwd.hh | |
| ContextIndependentOneBodyEnergy.hh | |
| ContextIndependentTwoBodyEnergy.cc | |
| ContextIndependentTwoBodyEnergy.fwd.hh | |
| ContextIndependentTwoBodyEnergy.hh | Short ranged, context-independent, two-body energy class declaration |
| EnergyMethod.cc | |
| EnergyMethod.fwd.hh | Energy Method class forward declaration and EnergyMethodType enum definition |
| EnergyMethod.hh | |
| EnergyMethodCreator.fwd.hh | Base class for EnergyMethod factory-registration and creation classes |
| EnergyMethodCreator.hh | Declaration of the base class for EnergyMethod factory registration and creation |
| EnergyMethodOptions.cc | |
| EnergyMethodOptions.fwd.hh | |
| EnergyMethodOptions.hh | |
| EnergyMethodRegistrator.hh | Declaration of the base class for EnergyMethod factory registration and creation |
| FreeDOF_Options.cc | |
| FreeDOF_Options.fwd.hh | |
| FreeDOF_Options.hh | |
| LongRangeTwoBodyEnergy.cc | Long-Range, Two-Body Energy class implementation |
| LongRangeTwoBodyEnergy.fwd.hh | Long range two body energy method class forward declaration |
| LongRangeTwoBodyEnergy.hh | Long range two body energy method class declaration |
| Methods.hh | Energy Method enumeration |
| MMBondAngleEnergy.cc | |
| MMBondAngleEnergy.fwd.hh | Molecular mechanics bond angle energy forward declaration |
| MMBondAngleEnergy.hh | Molecular mechanics bond angle energy |
| MMBondAngleEnergyCreator.hh | Declaration for the class that connects MMBondAngleEnergy with the ScoringManager |
| MMBondLengthEnergy.cc | |
| MMBondLengthEnergy.fwd.hh | Molecular mechanics bond length score class |
| MMBondLengthEnergy.hh | Molecular mechanics bond length score class |
| MMBondLengthEnergyCreator.hh | Molecular mechanics bond length score class |
| MMLJEnergyInter.cc | |
| MMLJEnergyInter.fwd.hh | Molecular mechanics lj energy forward declaration |
| MMLJEnergyInter.hh | Molecular mechanics lj energy |
| MMLJEnergyInterCreator.hh | Declaration for the class that connects MMLJEnergyInter with the ScoringManager |
| MMLJEnergyIntra.cc | |
| MMLJEnergyIntra.fwd.hh | Molecular mechanics lj energy forward declaration |
| MMLJEnergyIntra.hh | Molecular mechanics lj energy |
| MMLJEnergyIntraCreator.hh | Declaration for the class that connects MMLJEnergyIntra with the ScoringManager |
| MMTorsionEnergy.cc | |
| MMTorsionEnergy.fwd.hh | Molecular mechanics torsion energy forward declaration |
| MMTorsionEnergy.hh | Molecular mechanics torsion energy |
| MMTorsionEnergyCreator.hh | Declaration for the class that connects MMTorsionEnergy with the ScoringManager |
| OneBodyEnergy.cc | |
| OneBodyEnergy.fwd.hh | |
| OneBodyEnergy.hh | |
| PyEnergyMethodRegisterer.hh | EnergyMethod factory registration and creation in PyRosetta |
| ShortRangeTwoBodyEnergy.cc | Short-Range, Two-Body Energy Method base class implementation |
| ShortRangeTwoBodyEnergy.fwd.hh | Short Range Two Body Energy Method base class forward declaration |
| ShortRangeTwoBodyEnergy.hh | Short Range Two Body Energy Method base class declaration |
| TwoBodyEnergy.cc | Two Body Energy Method base class implementation |
| TwoBodyEnergy.fwd.hh | Two Body Energy Method base class forward declaration |
| TwoBodyEnergy.hh | Two Body Energy Method base class declaration |
| util.cc | Utility methods for scoring |
| util.hh | Utility functions for the distance-dependent dielectric potential |
| WholeStructureEnergy.cc | Implementation of the EnergyMethod that applies to a whole structure and not on a residue-by-residue basis |
| WholeStructureEnergy.fwd.hh | EnergyMethod that applies to a whole structure and not on a residue-by-residue basis |
| WholeStructureEnergy.hh | EnergyMethod that applies to a whole structure and not on a residue-by-residue basis |
| ► mhc_epitope_energy | |
| MHCEpitopeConstraint.cc | A constraint for MHC epitope scores Follows analogous file for Vikram K. Mulligan's NetChargeEnergy |
| MHCEpitopeConstraint.fwd.hh | Headers for a constraint for MHC epitope scores |
| MHCEpitopeConstraint.hh | Headers for a constraint for MHC epitope scores |
| MHCEpitopeEnergySetup.cc | A helper for the MHCEpitopeEnergy |
| MHCEpitopeEnergySetup.fwd.hh | Forward declarations for a helper class that stores the setup information for the MHCEpitopeEnergy score term |
| MHCEpitopeEnergySetup.hh | |
| MHCEpitopePredictor.cc | Base class for an MHC epitope predictor, which takes a peptide (string) and returns a score predicting its risk of MHC binding (lower is lower risk, with 0 being none) |
| MHCEpitopePredictor.fwd.hh | Forward declaration for class MHCEpitopePredictor |
| MHCEpitopePredictor.hh | Base class for an MHC epitope predictor, which takes a peptide (string) and returns a score predicting its risk of MHC binding (lower is lower risk, with 0 being none) |
| MHCEpitopePredictorExternal.cc | MHC epitope predictor using calculations from an external program cached in an sqlite database |
| MHCEpitopePredictorExternal.fwd.hh | Forward declaration for class MHCEpitopePredictorExternal |
| MHCEpitopePredictorExternal.hh | MHC epitope predictor using calculations from an external program cached in an sqlite database |
| MHCEpitopePredictorMatrix.cc | MHC epitope predictor using a position weight matrix, targeted to Propred though in theory generalizable to others |
| MHCEpitopePredictorMatrix.fwd.hh | Forward declaration for class MHCEpitopePredictorMatrix |
| MHCEpitopePredictorMatrix.hh | MHC epitope predictor using a position weight matrix, targeted to Propred though in theory generalizable to others |
| MHCEpitopePredictorPreLoaded.cc | MHC epitope predictor with precomputed values loaded into a peptide->score map |
| MHCEpitopePredictorPreLoaded.fwd.hh | Forward declaration for class MHCEpitopePredictorPreLoaded |
| MHCEpitopePredictorPreLoaded.hh | |
| MHCEpitopePredictorSVM.cc | Wraps NmerSVM into the mhc_epitope_energy scoreterm framework |
| MHCEpitopePredictorSVM.fwd.hh | Forward declaration for class MHCEpitopePredictorSVM |
| MHCEpitopePredictorSVM.hh | Wraps NmerSVM into the mhc_epitope_energy scoreterm framework |
| ► mm | |
| ► mmtrie | |
| MMEnergyTableAtom.cc | Implimentation for the MMEnergyTableAtom. Heavily coppied from the EtableAtom.cc |
| MMEnergyTableAtom.fwd.hh | Forward header for the MMEnergyTableAtom. Heavily coppied from the EtableAtom.fwd.hh |
| MMEnergyTableAtom.hh | Header for the MMEnergyTableAtom. Heavily coppied from the EtableAtom.hh |
| MMBondAngleLibrary.cc | |
| MMBondAngleLibrary.fwd.hh | Core::scoring::mm::MMBondAngleLibrary forward declarations |
| MMBondAngleLibrary.hh | Molecular mechanics bond angle library class |
| MMBondAngleResidueTypeParam.cc | Class to store bond angle parameters for a particular ResidueType |
| MMBondAngleResidueTypeParam.fwd.hh | Core::scoring::mm::MMBondAngleResidueTypeParam forward declarations |
| MMBondAngleResidueTypeParam.hh | Class to store bond angle parameters for a particular ResidueType |
| MMBondAngleResidueTypeParamSet.cc | |
| MMBondAngleResidueTypeParamSet.fwd.hh | Core::scoring::mm::MMBondAngleResidueTypeParamSet forward declarations |
| MMBondAngleResidueTypeParamSet.hh | Class to store bond angle parameters for a set of ResidueTypes |
| MMBondAngleScore.cc | Molecular mechanics bond angle score class |
| MMBondAngleScore.fwd.hh | Core::scoring::mm::MMBondAngleScore forward declarations |
| MMBondAngleScore.hh | Molecular mechanics bond angle score class |
| MMBondLengthLibrary.cc | |
| MMBondLengthLibrary.fwd.hh | Molecular mechanics bond length score class |
| MMBondLengthLibrary.hh | Molecular mechanics bond length score class |
| MMBondLengthScore.cc | Molecular mechanics bond length score class |
| MMBondLengthScore.fwd.hh | Molecular mechanics bond length score class |
| MMBondLengthScore.hh | Molecular mechanics bond length score class |
| MMLJEnergyTable.cc | Molecular mechanics lj energy table class |
| MMLJEnergyTable.fwd.hh | Core::scoring::mm::MMLJEnergyTable forward declarations |
| MMLJEnergyTable.hh | Molecular mechanics lj score class |
| MMLJLibrary.cc | |
| MMLJLibrary.fwd.hh | Core::scoring::mm::MMLJLibrary forward declarations |
| MMLJLibrary.hh | Molecular mechanics lj library class |
| MMLJScore.cc | Molecular mechanics lj score class |
| MMLJScore.fwd.hh | Core::scoring::mm::MMLJScore forward declarations |
| MMLJScore.hh | Molecular mechanics lj score class |
| MMTorsionLibrary.cc | |
| MMTorsionLibrary.fwd.hh | Core::scoring::mm::MMTorsionLibrary forward declarations |
| MMTorsionLibrary.hh | Molecular mechanics torsion library class |
| MMTorsionScore.cc | Molecular mechanics torsion score class |
| MMTorsionScore.fwd.hh | Core::scoring::mm::MMTorsionScore forward declarations |
| MMTorsionScore.hh | Molecular mechanics torsion score class |
| ► motif | |
| motif_hash_stuff.cc | |
| motif_hash_stuff.fwd.hh | |
| motif_hash_stuff.hh | |
| util.cc | |
| util.hh | |
| xfrags.cc | |
| xfrags.hh | |
| ► netcharge_energy | |
| NetChargeConstraint.cc | A constraint for constraining sequences to have a desired net charge, analogous to a geometric constraint |
| NetChargeConstraint.fwd.hh | Forward declarations for a constraint for constraining sequences to have a desired net charge, analogous to a geometric constraint |
| NetChargeConstraint.hh | Headers for a constraint for constraining sequences to have a desired net charge, analogous to a geometric constraint |
| NetChargeEnergySetup.cc | A helper for the EnergyMethod that penalizes deviation from a desired net charge |
| NetChargeEnergySetup.fwd.hh | Forward declarations for a helper class that stores the setup information for the NetChargeEnergy score term |
| NetChargeEnergySetup.hh | |
| ► nmer | |
| NMerPSSMEnergy.cc | |
| NMerPSSMEnergy.fwd.hh | PSSMerence energy method forward declaration |
| NMerPSSMEnergy.hh | PSSMerence energy method implementation |
| NMerPSSMEnergyCreator.hh | Declaration for the class that connects NMerPSSMEnergy with the ScoringManager |
| NMerRefEnergy.cc | |
| NMerRefEnergy.fwd.hh | Reference energy method forward declaration |
| NMerRefEnergy.hh | Reference energy method implementation |
| NMerRefEnergyCreator.hh | Declaration for the class that connects NMerRefEnergy with the ScoringManager |
| NMerSVMEnergy.cc | SVM sequence profile energy method implementation |
| NMerSVMEnergy.fwd.hh | SVMerence energy method forward declaration |
| NMerSVMEnergy.hh | SVM energy method declaration |
| NMerSVMEnergyCreator.hh | Declaration for the class that connects NMerSVMEnergy with the ScoringManager |
| ► nmr | |
| ► pcs | |
| PCSData.cc | Implementation of class PCSData |
| PCSData.fwd.hh | Forward declaration for PCSData.hh |
| PCSData.hh | Class that stores and handles all PCS data for all tagging sites and all lanthanides |
| PCSMultiSet.cc | Implementation of class PCSMultiSet |
| PCSMultiSet.fwd.hh | Forward declaration for PCSMultiSet.hh |
| PCSMultiSet.hh | Class that stores and handles data for one tagging site which can contain datasets for multiple lanthanides (i.e. multiple PCSSingleSet objects) |
| PCSSingle.cc | Implementation of class PCSSingle |
| PCSSingle.fwd.hh | Forward declaration for PCSSingle.hh |
| PCSSingle.hh | Class that stores and handles data related to one single PCS |
| PCSSingleSet.cc | Implementation of class PCSSingleSet |
| PCSSingleSet.fwd.hh | Forward declaration for PCSSingleSet.hh |
| PCSSingleSet.hh | Class that stores and handles data of one single PCS dataset (i.e. for one lanthanide ion) |
| PCSTensor.cc | |
| PCSTensor.fwd.hh | Forward declaration for PCSTensor.hh |
| PCSTensor.hh | Derived class of NMRTensor specific for the treatment of PCSs the tensor we are using here is the magnetic susceptibility anisotropy tensor (delta chi tensor) |
| ► pre | |
| PREData.cc | Implementation of class PREData |
| PREData.fwd.hh | Forward declaration for PREData.hh |
| PREData.hh | Class that stores all PRE data for all spinlabel sites |
| PREMultiSet.cc | Implementation of class PREMultiSet |
| PREMultiSet.fwd.hh | Forward declaration for PREMultiSet.hh |
| PREMultiSet.hh | Class that stores PRE data for one spinlabel site which can contain data for multiple spinlabels and metals (i.e. multiple PRESingleSet objects) |
| PRESingle.cc | Implementation of class PRESingle |
| PRESingle.fwd.hh | Forward declaration for PRESingle.hh |
| PRESingle.hh | Class that stores and handles data related to one single PRE value |
| PRESingleSet.cc | Implementation of class PRESingleSet |
| PRESingleSet.fwd.hh | Forward declaration for PRESingleSet.hh |
| PRESingleSet.hh | Class that stores and handles data for one single PRE dataset/experiment (i.e. for one spinlabel at on tagging site) |
| ► rdc | |
| parameters.hh | Utility functions that return constant values of the dipolar coupling constant or RDC scaling factor for the choice of the RDC atom type |
| RDCData.cc | Implementation of class RDCData |
| RDCData.fwd.hh | Forward declaration for RDCData.hh |
| RDCData.hh | Class that stores and handles all RDC data for all alignment media and experiments |
| RDCMultiSet.cc | Implementation of class RDCMultiSet |
| RDCMultiSet.fwd.hh | Forward declaration for RDCMultiSet.hh |
| RDCMultiSet.hh | Class that stores and handles RDC data collected for one alignment medium can contain multiple RDCSingleSets, each obtained for a different type of dipolar couplings (i.e. a different NMR experiment) |
| RDCSingle.cc | Implementation of class RDCSingle |
| RDCSingle.fwd.hh | |
| RDCSingle.hh | Class that stores and handles data related to one single RDC |
| RDCSingleSet.cc | Implementation of class RDCSingleSet |
| RDCSingleSet.fwd.hh | Forward declaration for RDCSingleSet.hh |
| RDCSingleSet.hh | Class that stores and handles data for one single RDC dataset (i.e. of one type of dipolar coupling in one alignment medium) |
| RDCTensor.cc | |
| RDCTensor.fwd.hh | Forward declaration for RDCTensor.hh |
| RDCTensor.hh | Derived class of NMRTensor specific for the treatment of RDCs the tensor we are using here is the alignment tensor A that is related to the Saupe order matrix according to S = 3/2 A |
| NMRDataFactory.cc | Implementation of class NMRDataFactory |
| NMRDataFactory.fwd.hh | Forward declaration for NMRDataFactory.hh |
| NMRDataFactory.hh | Singleton class that handles the creation of different types of NMR data through a common interface. At the moment, it supports three paramagnetic NMR interactions (i.e. PCSs, RDCs, PREs) but other NMR data types can be easily added. They should provide a constructor that takes a filename as argument and is called from inside the factory function which returns an owning pointer to the new created NMR data object |
| NMRDummySpinlabelEnsemble.cc | |
| NMRDummySpinlabelEnsemble.fwd.hh | Forward declaration for NMRDummySpinlabelEnsemble.hh |
| NMRDummySpinlabelEnsemble.hh | Implementation of classes NMRDummySpinlabelConformer and NMRDummySpinlabelEnsemble |
| NMRDummySpinlabelVoxelGrid.cc | |
| NMRDummySpinlabelVoxelGrid.fwd.hh | Forward declaration for NMRDummySpinlabelVoxelGrid.hh |
| NMRDummySpinlabelVoxelGrid.hh | Implementation of classes NMRDummySpinlabelVoxelGrid and VoxelGridPoint |
| NMRGridSearch.cc | Implementation of class NMRGridSearch |
| NMRGridSearch.fwd.hh | Forward declaration for NMRGridSearch.hh |
| NMRGridSearch.hh | Class that performs a grid search to find the metal ion position that is in best agreement with PCS and PRE data |
| NMRSpinlabel.cc | Implementation of class NMRSpinlabel |
| NMRSpinlabel.fwd.hh | Forward declaration for NMRSpinlabel.hh |
| NMRSpinlabel.hh | Class that contains data to describe an NMR spinlabel e.g. its chemical structure. The NMRSpinlabel contains the spinlabel's ResidueType, name, code and other related data. An NMRDummySpinlabelEnsemble object is used to represent the spinlabel's conformations. Filtering of NMRDummySpinlabel conformers is done either by neighbor count or bump energy calculation |
| NMRTensor.cc | Implementation of class NMRTensor |
| NMRTensor.fwd.hh | Forward declaration for NMRTensor.hh |
| NMRTensor.hh | Base tensor class for the representation of different NMR interactions like PCS, RDC or CSA |
| types.hh | Type definitions and enums for classes in core/scoring/nmr |
| util.cc | Function definitions for util.hh |
| util.hh | Utility functions for core/scoring/nmr classes |
| ► nv | |
| NVlookup.cc | Neighbor Vector algorithm lookup table processing class |
| NVlookup.fwd.hh | |
| NVlookup.hh | |
| NVscore.cc | |
| NVscore.fwd.hh | |
| NVscore.hh | |
| NVscoreCreator.hh | |
| ► orbitals | |
| OrbitalsLookup.cc | |
| OrbitalsLookup.fwd.hh | Created on: Jun 3, 2010 |
| OrbitalsLookup.hh | |
| OrbitalsScore.cc | |
| OrbitalsScore.fwd.hh | Created on: Jun 2, 2010 |
| OrbitalsScore.hh | |
| OrbitalsScoreCreator.hh | Created on: Jun 3, 2010 |
| OrbitalsStatistics.cc | |
| OrbitalsStatistics.hh | |
| ► packing | |
| Ball.hh | |
| compute_holes_score.cc | Packing Score |
| compute_holes_score.hh | Packing Score |
| compute_holes_score_res.cc | Packing Score |
| compute_holes_score_res.hh | Packing Score |
| HolesEnergyRes.cc | |
| HolesEnergyRes.hh | Packing Score |
| HolesParams.hh | |
| HolesParamsRes.hh | |
| PoseBalls.cc | |
| PoseBalls.hh | |
| PoseBallsLite.cc | |
| PoseBallsLite.hh | |
| surf_vol.cc | Packing Score |
| surf_vol.hh | |
| ► packstat | |
| AtomRadiusMap.cc | |
| AtomRadiusMap.fwd.hh | |
| AtomRadiusMap.hh | |
| CavityBall.cc | |
| CavityBall.fwd.hh | |
| CavityBall.hh | |
| compute_sasa.cc | |
| compute_sasa.hh | |
| io.cc | |
| io.hh | |
| LeeRichards.cc | |
| LeeRichards.hh | |
| packing_score_params.cc | |
| packing_score_params.hh | |
| PackingScore.cc | |
| PackingScore.hh | |
| sasa_dot_locations.hh | |
| SimplePDB.cc | |
| SimplePDB.fwd.hh | |
| SimplePDB.hh | |
| SimplePDB_Atom.cc | |
| SimplePDB_Atom.fwd.hh | |
| SimplePDB_Atom.hh | |
| types.hh | |
| util.hh | |
| ► power_diagram | |
| PowerDiagram.cc | Class for constructing and querying power diagrams |
| PowerDiagram.fwd.hh | Core::scoring::power_diagram::PowerDiagram forward declaration |
| PowerDiagram.hh | Class for PowerDiagram, including consruction and access |
| ► rna | |
| ► chemical_shift | |
| RNA_ChemicalShiftPotential.cc | The real workhorse behind RNA_ChemicalShiftEnergy.cc |
| RNA_ChemicalShiftPotential.fwd.hh | RNA_ChemicalShiftPotential potential class forward delcaration |
| RNA_ChemicalShiftPotential.hh | The real workhorse behind RNA_ChemicalShiftEnergy.cc |
| RNA_CS_MagneticAnisotropy.cc | |
| RNA_CS_MagneticAnisotropy.hh | |
| RNA_CS_Parameters.cc | |
| RNA_CS_Parameters.hh | |
| RNA_CS_RingCurrent.cc | |
| RNA_CS_RingCurrent.hh | |
| RNA_CS_Util.cc | |
| RNA_CS_Util.hh | |
| ► data | |
| RNA_DMS_LowResolutionPotential.cc | |
| RNA_DMS_LowResolutionPotential.fwd.hh | |
| RNA_DMS_LowResolutionPotential.hh | |
| RNA_DMS_Potential.cc | |
| RNA_DMS_Potential.fwd.hh | |
| RNA_DMS_Potential.hh | |
| util.cc | |
| util.hh | |
| RNA_AtomVDW.cc | |
| RNA_AtomVDW.fwd.hh | |
| RNA_AtomVDW.hh | Information on which atoms to use for computing clashes |
| RNA_CentroidInfo.cc | |
| RNA_CentroidInfo.fwd.hh | |
| RNA_CentroidInfo.hh | |
| RNA_EnergyMethodOptions.cc | |
| RNA_EnergyMethodOptions.fwd.hh | |
| RNA_EnergyMethodOptions.hh | |
| RNA_LowResolutionPotential.cc | |
| RNA_LowResolutionPotential.fwd.hh | |
| RNA_LowResolutionPotential.hh | |
| RNA_LowResolutionPotentialCreator.hh | Declaration for the class that connects RNA_LowResolutionPotential with the ScoringManager |
| RNA_Motif.cc | |
| RNA_Motif.fwd.hh | |
| RNA_Motif.hh | Find RNA motifs (u-turns, T-loops, etc.) in a pose |
| RNA_ScoringInfo.cc | |
| RNA_ScoringInfo.fwd.hh | |
| RNA_ScoringInfo.hh | |
| RNA_ScoringUtil.cc | |
| RNA_ScoringUtil.hh | |
| RNA_SuitePotential.cc | |
| RNA_SuitePotential.fwd.hh | |
| RNA_SuitePotential.hh | |
| RNA_TorsionPotential.cc | |
| RNA_TorsionPotential.fwd.hh | |
| RNA_TorsionPotential.hh | |
| RNP_LowResPairDistPotential.cc | Statistically derived RNP low-res potential, simple distance-based |
| RNP_LowResPairDistPotential.fwd.hh | |
| RNP_LowResPairDistPotential.hh | |
| RNP_LowResPotential.cc | Statistically derived rotamer pair potential class implementation |
| RNP_LowResPotential.fwd.hh | |
| RNP_LowResPotential.hh | |
| RNP_LowResStackData.cc | Statistically derived rotamer pair potential class implementation |
| RNP_LowResStackData.fwd.hh | |
| RNP_LowResStackData.hh | |
| TNA_SuitePotential.cc | |
| TNA_SuitePotential.fwd.hh | |
| TNA_SuitePotential.hh | |
| util.cc | Some useful nonmember functions |
| util.hh | Some useful nonmember functions |
| ► sasa | |
| LeGrandSasa.cc | |
| LeGrandSasa.fwd.hh | |
| LeGrandSasa.hh | Sasa Method LeGrand 1993 |
| SasaCalc.cc | |
| SasaCalc.fwd.hh | |
| SasaCalc.hh | Class based interface to original sasa functions. Should result in less incorrect uses of radii |
| SasaMethod.cc | |
| SasaMethod.fwd.hh | |
| SasaMethod.hh | Abstract class defining a 'SasaMethod' |
| SasaMethodFactory.cc | |
| SasaMethodFactory.hh | |
| util.cc | |
| util.hh | Routines which calculate solvent accessible surface area |
| ► saxs | |
| DistanceHistogram.fwd.hh | Forward declaration of a DistanceHistogram data type |
| DistanceHistogram.hh | |
| FormFactor.cc | Represents an atomic scattering form factor |
| FormFactor.fwd.hh | Forward declaration of a form factor data type |
| FormFactor.hh | Collects histogram of distances between atoms of given SAXS-types, e.g. distances between ARG-CEN and TRP-CEN |
| FormFactorManager.cc | Loads and manages atomic form factors |
| FormFactorManager.fwd.hh | Forward declaration of a form factor manager |
| FormFactorManager.hh | Loads and manages atomic form factors |
| SinXOverX.cc | |
| SinXOverX.hh | |
| ► sc | |
| ContactMolecularSurfaceCalculator.cc | Headers for the Shape Complementarity Calculator |
| ContactMolecularSurfaceCalculator.fwd.hh | Headers for the Weighted Contact Molecular Surface Calculator |
| ContactMolecularSurfaceCalculator.hh | Headers for the Weighted Contact Molecular Surface Calculator |
| ElectrostaticComplementarityCalculator.cc | Headers for the Electrostatic Complementarity Calculator |
| ElectrostaticComplementarityCalculator.fwd.hh | Headers for the Electrostatic Complementarity Calculator |
| ElectrostaticComplementarityCalculator.hh | Headers for the Electrostatic Complementarity Calculator |
| MolecularSurfaceCalculator.cc | |
| MolecularSurfaceCalculator.fwd.hh | Forward header for the Molecular Surface Calculator |
| MolecularSurfaceCalculator.hh | |
| ShapeComplementarityCalculator.cc | Implementation of molecular surface calculation for shape complementarity |
| ShapeComplementarityCalculator.fwd.hh | Headers for the Shape Complementarity Calculator |
| ShapeComplementarityCalculator.hh | Headers for the Molecular Surface Calculator |
| ShapeComplementarityCalculator_Private.hh | |
| ► solid_surface | |
| SurfaceEnergies.cc | SurfaceEnergies class avoids calculating energies between surface residues, and detecting their neighbor relationships |
| SurfaceEnergies.fwd.hh | SurfaceEnergies forward declarations header |
| SurfaceEnergies.hh | SurfaceEnergies class |
| ► sym_e | |
| symE.cc | |
| symE.fwd.hh | |
| symE.hh | |
| symECreator.hh | |
| ► symmetry | |
| SymmetricEnergies.cc | |
| SymmetricEnergies.fwd.hh | Symmetric Energies class to store cached energies and track the residue neighbor relationships |
| SymmetricEnergies.hh | Symmetric Energies class to store cached energies and track the residue neighbor relationships |
| SymmetricScoreFunction.fwd.hh | Core::scoring::symmetry::SymmetricScoreFunction forward declarations |
| SymmetricScoreFunction.hh | Symmetric Score function class |
| ► trie | |
| CPDataCorrespondence.cc | |
| CPDataCorrespondence.fwd.hh | |
| CPDataCorrespondence.hh | |
| RotamerDescriptor.fwd.hh | |
| RotamerDescriptor.hh | |
| RotamerTrie.fwd.hh | |
| RotamerTrie.hh | |
| RotamerTrie.srlz.hh | |
| RotamerTrieBase.fwd.hh | |
| RotamerTrieBase.hh | |
| trie.functions.fwd.hh | |
| trie.functions.hh | |
| trie_vs_path.cc | |
| trie_vs_path.hh | |
| trie_vs_trie.cc | |
| trie_vs_trie.fwd.hh | |
| trie_vs_trie.hh | |
| TrieCollection.cc | |
| TrieCollection.fwd.hh | |
| TrieCollection.hh | Container class for storing rotamer tries in an Energies object |
| TrieCountPairBase.cc | |
| TrieCountPairBase.fwd.hh | |
| TrieCountPairBase.hh | The functions in this file are required by the compiler, but represent paths that should never be reached. They are cases in which dynamic dispatch fails because two incompatible RotamerTrie classes are used together, e.g. an HBond trie and and Etable trie |
| TrieVsTrieCachedDataContainerBase.cc | A generic base class for passing data to the trie-vs-trie calculation, without having to cache it in mutable data in an EnergyMethod or whatnot |
| TrieVsTrieCachedDataContainerBase.fwd.hh | A generic base class for passing data to the trie-vs-trie calculation, without having to cache it in mutable data in an EnergyMethod or whatnot |
| TrieVsTrieCachedDataContainerBase.hh | A generic base class for passing data to the trie-vs-trie calculation, without having to cache it in mutable data in an EnergyMethod or whatnot |
| ► vdwaals | |
| VDW_Energy.cc | Low resolution (centroid) repulsive energy |
| VDW_Energy.fwd.hh | |
| VDW_Energy.hh | Low resolution (centroid) repulsive energy |
| VDW_EnergyCreator.hh | Declaration for the class that connects VDW_Energy with the ScoringManager |
| VDWTrie.cc | Trie data structure for the low-resolution (centroid) repulsive energy |
| VDWTrie.fwd.hh | Trie data structure for the low-resolution (centroid) repulsive energy |
| VDWTrie.hh | Trie data structure for the low-resolution (centroid) repulsive energy |
| APBSWrapper.cc | |
| APBSWrapper.fwd.hh | |
| APBSWrapper.hh | |
| AtomVDW.cc | |
| AtomVDW.fwd.hh | |
| AtomVDW.hh | |
| CenHBPotential.cc | |
| CenHBPotential.fwd.hh | |
| CenHBPotential.hh | |
| CenRotEnvPairPotential.cc | |
| CenRotEnvPairPotential.fwd.hh | |
| CenRotEnvPairPotential.hh | |
| ChemicalShiftAnisotropy.cc | Uses NMR CSA for scoring (Bertram R et al J of Magn Reson 147, 9-16) |
| ChemicalShiftAnisotropy.fwd.hh | |
| ChemicalShiftAnisotropy.hh | Uses NMR CSA for scoring |
| constants.hh | Core::scoring package constants |
| ContextGraph.cc | Context graph class |
| ContextGraph.fwd.hh | Context graph class forward declaration |
| ContextGraph.hh | Context graph class declaration |
| ContextGraphFactory.cc | Context graph class factory implementation |
| ContextGraphFactory.fwd.hh | Context graph class factory forward declaration |
| ContextGraphFactory.hh | Context graph factory class declaration |
| ContextGraphTypes.hh | |
| DenseEnergyContainer.cc | A container for storing all-against-all energies as the upper triangle of a matrix |
| DenseEnergyContainer.fwd.hh | |
| DenseEnergyContainer.hh | A container for storing all-against-all energies as the upper triangle of a matrix |
| DerivVectorPair.cc | |
| DerivVectorPair.fwd.hh | Class for storing a pair of derivative vectors, f1 and f2, used in our internal-geometry minimization algorithm |
| DerivVectorPair.hh | Serialization routines for the DerivVectorPair class |
| DipolarCoupling.cc | Uses NMR DC for scoring (Bertram R et al J of Magn Reson 147, 9-16) |
| DipolarCoupling.fwd.hh | |
| DipolarCoupling.hh | Uses NMR DC for scoring |
| DockingScoreFunction.cc | |
| DockingScoreFunction.fwd.hh | Core::scoring::DockingScoreFunction forward declarations |
| DockingScoreFunction.hh | |
| Energies.cc | Energies class to store cached energies and track the residue neighbor relationships |
| Energies.fwd.hh | Energies forward declarations header |
| Energies.hh | Energies class |
| EnergiesCacheableDataType.hh | Enum for the DataCache within the Energies class |
| EnergyGraph.cc | Energy graph class implementation |
| EnergyGraph.fwd.hh | Energy graph class forward declaration |
| EnergyGraph.hh | Energy graph class declaration |
| EnergyMap.cc | Vector of scores implementation |
| EnergyMap.fwd.hh | Vector of scores forward declaration |
| EnergyMap.hh | Vector of scores declaration |
| EnvPairPotential.cc | |
| EnvPairPotential.fwd.hh | |
| EnvPairPotential.hh | |
| GenBornPotential.cc | |
| GenBornPotential.fwd.hh | |
| GenBornPotential.hh | |
| GenericBondedPotential.cc | |
| GenericBondedPotential.fwd.hh | Probability of observing an amino acid, given its phi/psi energy method forward declaration |
| GenericBondedPotential.hh | |
| HydroxylTorsionPotential.cc | Potential for core/scoring/methods/HydroxyTorsionEnergy |
| HydroxylTorsionPotential.fwd.hh | |
| HydroxylTorsionPotential.hh | |
| interpolation_util.hh | |
| LREnergyContainer.cc | |
| LREnergyContainer.fwd.hh | |
| LREnergyContainer.hh | |
| Membrane_FAPotential.cc | Membrane FA Potential - Class for Fullatom Membrane Scoring Methods |
| Membrane_FAPotential.fwd.hh | |
| Membrane_FAPotential.hh | |
| MembranePotential.cc | Membrane Potential - Base Scoring Methods for LowRes Energy Function |
| MembranePotential.fwd.hh | Membrane Potential - Base Scoring Methods for LowRes Energy Function |
| MembranePotential.hh | Membrane Potential - Base Scoring Methods for LowRes Energy Function |
| MembraneTopology.cc | |
| MembraneTopology.fwd.hh | |
| MembraneTopology.hh | |
| MinimizationData.cc | A container class for use by certain EnergyMethods during derivative and |
| MinimizationData.fwd.hh | Forward declaration of the container class for use by certain EnergyMethods |
| MinimizationData.hh | A container class for use by certain EnergyMethods during derivative and |
| MinimizationGraph.cc | Minimization graph class implementation |
| MinimizationGraph.fwd.hh | Minimization graph class forward declaration |
| MinimizationGraph.hh | Minimization graph class declaration |
| MinScoreScoreFunction.cc | |
| MinScoreScoreFunction.fwd.hh | Core::scoring::MinScoreScoreFunction forward declarations |
| MinScoreScoreFunction.hh | |
| MultipoleElecPotential.cc | |
| MultipoleElecPotential.fwd.hh | |
| MultipoleElecPotential.hh | |
| NeighborList.cc | |
| NeighborList.fwd.hh | Foward declaration of NeighborList class and owning pointer typedefs |
| NeighborList.hh | |
| NeighborList.tmpl.hh | |
| OmegaTether.cc | OmegaTether potential class implementation |
| OmegaTether.fwd.hh | Omega Tether potential class forward delcaration |
| OmegaTether.hh | OmegaTether potential class delcaration |
| OneToAllEnergyContainer.cc | A container interface for storing and scoring long range energies |
| OneToAllEnergyContainer.fwd.hh | |
| OneToAllEnergyContainer.hh | A container interface for storing and scoring long range energies |
| P_AA.cc | Amino acid probability arrays and functions |
| P_AA.fwd.hh | |
| P_AA.hh | Amino acid probability arrays and functions |
| P_AA_ABEGO3.cc | Amino acid probability given an ABEGO (ramachandran bins) triplet/sequence, arrays and functions |
| P_AA_ABEGO3.fwd.hh | Amino acid probability given an ABEGO (ramachandran bins) triplet/sequence, arrays and functions |
| P_AA_ABEGO3.hh | Amino acid probability given an ABEGO (ramachandran bins) triplet/sequence, arrays and functions |
| P_AA_ss.cc | Amino acid probability arrays and functions |
| P_AA_ss.fwd.hh | |
| P_AA_ss.hh | |
| PairEPotential.cc | PairE knowledge-based potential class |
| PairEPotential.fwd.hh | PairE knowledge-based potential class forward delcaration |
| PairEPotential.hh | |
| PointWaterPotential.cc | |
| PointWaterPotential.fwd.hh | |
| PointWaterPotential.hh | |
| PoissonBoltzmannPotential.cc | PoissonBoltzmann potential class implementation |
| PoissonBoltzmannPotential.fwd.hh | PoissonBoltzmann potential class forward delcaration |
| PoissonBoltzmannPotential.hh | Poisson Boltzmann potential class delcaration |
| PolymerBondedEnergyContainer.cc | A container interface long range energies for polymer-bonded residue interactions only |
| PolymerBondedEnergyContainer.fwd.hh | |
| PolymerBondedEnergyContainer.hh | A container interface long range energies for polymer-bonded residue interactions only |
| ProQPotential.cc | |
| ProQPotential.fwd.hh | Membrane Potential |
| ProQPotential.hh | |
| ProteinTorsion.hh | Ramachandran potential class delcaration |
| Ramachandran.cc | Ramachandran potential class implementation |
| Ramachandran.fwd.hh | Ramachandran potential class forward declaration |
| Ramachandran.hh | Ramachandran potential class delcaration |
| Ramachandran2B.cc | Neighbor-dependent Ramachandran potential class implementation |
| Ramachandran2B.fwd.hh | |
| Ramachandran2B.hh | Neighbor-dependent Ramachandran potential class delcaration |
| RamaPrePro.cc | |
| RamaPrePro.fwd.hh | |
| RamaPrePro.hh | RamaPrePro potential class delcaration |
| ResidualDipolarCoupling.cc | Uses NMR RDC for scoring |
| ResidualDipolarCoupling.fwd.hh | |
| ResidualDipolarCoupling.hh | Uses NMR RDC for scoring |
| ResidualDipolarCoupling_Rohl.cc | Uses NMR RDC for scoring |
| ResidualDipolarCoupling_Rohl.fwd.hh | |
| ResidualDipolarCoupling_Rohl.hh | |
| ResidueNeighborList.cc | |
| ResidueNeighborList.fwd.hh | Forward declaration of a container class for use by the Etable and FA_Elec classes for storing residue-pair level atom-neighbor information |
| ResidueNeighborList.hh | A container class for use by the Etable and FA_Elec classes for storing lists of atom neighbors |
| rms_enum.hh | |
| rms_util.cc | RMS stuff from rosetta++ |
| rms_util.hh | |
| rms_util.tmpl.hh | |
| sasa.cc | Routines which calculate solvent accessible surface area |
| sasa.hh | Routines which calculate solvent accessible surface area |
| SASAPotential.cc | |
| SASAPotential.fwd.hh | |
| SASAPotential.hh | |
| ScoreFunction.cc | Atom pair energy functions |
| ScoreFunction.fwd.hh | Core::scoring::ScoreFunction forward declarations |
| ScoreFunction.hh | Score function class |
| ScoreFunctionFactory.cc | |
| ScoreFunctionFactory.hh | |
| ScoreFunctionInfo.cc | Score function class descriptor |
| ScoreFunctionInfo.fwd.hh | |
| ScoreFunctionInfo.hh | |
| ScoreType.cc | |
| ScoreType.hh | Score type enumeration |
| ScoreTypeManager.cc | Method definitions for ScoreTypeManager |
| ScoreTypeManager.hh | Score type enumeration |
| ScoringManager.cc | Scoring manager class |
| ScoringManager.fwd.hh | |
| ScoringManager.hh | Scoring manager class header |
| SecondaryStructurePotential.cc | Scoring manager class header |
| SecondaryStructurePotential.fwd.hh | |
| SecondaryStructurePotential.hh | |
| SecondaryStructureWeights.cc | |
| SecondaryStructureWeights.hh | |
| SmoothEnvPairPotential.cc | |
| SmoothEnvPairPotential.fwd.hh | |
| SmoothEnvPairPotential.hh | |
| SplitUnfoldedTwoBodyPotential.cc | Reads in and stores the two body energies for each residue type for the split unfolded energy |
| SplitUnfoldedTwoBodyPotential.fwd.hh | |
| SplitUnfoldedTwoBodyPotential.hh | Reads in and stores the two body energies for each residue type for the split unfolded energy |
| SS_Info.cc | |
| SS_Info.fwd.hh | Data cache forward declarations for the secondary-structure based scores |
| SS_Info.hh | |
| SS_Killhairpins_Info.cc | |
| SS_Killhairpins_Info.fwd.hh | |
| SS_Killhairpins_Info.hh | Scoring manager class header |
| TenANeighborGraph.cc | Neighbor graph to represent for each residue the number of other residues within 10 Angstroms |
| TenANeighborGraph.fwd.hh | Ten Angstrom Neighbor graph class forward declaration |
| TenANeighborGraph.hh | Ten Angstrom Neighbor Graph class declaration |
| TMscore.cc | |
| TMscore.hh | Reimplementation of TMscore sequence-based structure superposition |
| TwelveANeighborGraph.cc | Neighbor graph to represent for each residue the number of other residues within 12 Angstroms |
| TwelveANeighborGraph.fwd.hh | Twelve Angstrom Neighbor graph class forward declaration |
| TwelveANeighborGraph.hh | Twelve Angstrom Neighbor Graph class declaration |
| types.hh | Core::scoring package type declarations |
| UnfoldedStatePotential.cc | Unfolded state energies based on energies of residues in fragments, definition file |
| UnfoldedStatePotential.fwd.hh | Unfolded state energies based on energies of residues in fragments, forward declaration |
| UnfoldedStatePotential.hh | Unfolded state energies based on energies of residues in fragments, declaration (header) file |
| util.cc | Nonmember functions for evaluating some or all energy methods on residues or residue pairs |
| util.hh | Nonmember functions for evaluating some or all energy methods on residues or residue pairs |
| VdWTinkerPotential.cc | |
| VdWTinkerPotential.fwd.hh | |
| VdWTinkerPotential.hh | |
| WaterAdductHBondPotential.cc | |
| WaterAdductHBondPotential.fwd.hh | |
| WaterAdductHBondPotential.hh | |
| xml_util.cc | Score function utilities useful in RosettaScripts |
| xml_util.hh | Score function utilities useful in RosettaScripts |
| ► select | |
| ► jump_selector | |
| AndJumpSelector.cc | The AndJumpSelector combines logic from multiple JumpSelectors |
| AndJumpSelector.fwd.hh | Forward declaration of a class that combines JumpSelector logic |
| AndJumpSelector.hh | The AndJumpSelector combines logic from multiple JumpSelectors |
| AndJumpSelectorCreator.hh | Creator for Boolean "AND" jump selector |
| InterchainJumpSelector.cc | |
| InterchainJumpSelector.fwd.hh | Forward declaration of a class that combines JumpSelector logic |
| InterchainJumpSelector.hh | The InterchainJumpSelector selects jumps that land on different chains than they took off from |
| InterchainJumpSelectorCreator.hh | Creator for interchain jump selector |
| JumpIndexSelector.cc | |
| JumpIndexSelector.fwd.hh | Forward declaration of a class that combines JumpSelector logic |
| JumpIndexSelector.hh | The JumpIndexSelector selects a jump with a given index |
| JumpIndexSelectorCreator.hh | Creator for jump index selector |
| JumpSelector.cc | The JumpSelector class identifies a subset of jumps from a Pose |
| JumpSelector.fwd.hh | Forward declaration of a class that identifies a subset of residues from a Pose |
| JumpSelector.hh | The JumpSelector class identifies a subset of jumps from a Pose |
| JumpSelectorCreator.fwd.hh | Forward declaration of a class that instantiates a particular JumpSelector |
| JumpSelectorCreator.hh | Class for instantiating a particular JumpSelector |
| JumpSelectorFactory.cc | Implementation of the class for instantiating arbitrary JumpSelectors from a string –> JumpSelectorCreator map |
| JumpSelectorFactory.hh | Class for instantiating arbitrary JumpSelectors from a string –> JumpSelectorCreator map |
| JumpSelectorRegistrator.hh | Declaration of the template class for registrating JumpSelectorCreators with the JumpSelectorFactory |
| NotJumpSelector.cc | The NotJumpSelector negates the logic of its loaded JumpSelector |
| NotJumpSelector.fwd.hh | |
| NotJumpSelector.hh | The NotJumpSelector negates the logic of its loaded JumpSelector |
| NotJumpSelectorCreator.hh | Creator for boolean "Not" jump selector |
| OrJumpSelector.cc | The OrJumpSelector combines logic from multiple JumpSelectors |
| OrJumpSelector.fwd.hh | Forward declaration of a class that negates JumpSelector logic |
| OrJumpSelector.hh | The OrJumpSelector combines logic from multiple JumpSelectors |
| OrJumpSelectorCreator.hh | Creator for boolean "OR" jump selector |
| util.cc | Utility functions for the jump selector classes, primarily, in constructing XML-Schema type definitions |
| util.hh | Utility functions for the jump selector classes, primarily, in constructing XML-Schema type definitions |
| ► movemap | |
| MoveMapFactory.cc | The MoveMapFactory class builds a MoveMap given a Pose using instructions from ResidueSelectors, and JumpSelectors (and eventually, TorsionIDSelectors) |
| MoveMapFactory.fwd.hh | Forward declaration of MoveMapFactory class |
| MoveMapFactory.hh | The MoveMapFactory class builds a MoveMap given a Pose using instructions from ResidueSelectors, and JumpSelectors (and eventually, TorsionIDSelectors) |
| util.cc | Utility functions for the move map factory class |
| util.hh | Utility functions for the MoveMapFactory class |
| ► residue_selector | |
| AndResidueSelector.cc | The AndResidueSelector combines logic from multiple ResidueSelectors |
| AndResidueSelector.fwd.hh | Forward declaration of a class that combines ResidueSelector logic |
| AndResidueSelector.hh | The AndResidueSelector combines logic from multiple ResidueSelectors |
| AsymmetricUnitSelector.cc | |
| AsymmetricUnitSelector.fwd.hh | A residue selector for selecting the master subunit in a symmetrical pose. If not symmetrical, will select the whole pose |
| AsymmetricUnitSelector.hh | A residue selector for selecting the master subunit in a symmetrical pose. If not symmetrical, will select the whole pose |
| AsymmetricUnitSelectorCreator.hh | A residue selector for selecting the master subunit in a symmetrical pose. If not symmetrical, will select the whole pose |
| BinSelector.cc | |
| BinSelector.fwd.hh | A ResidueSelector that selects residues based on their torsion bin (e.g. ABEGO bin) |
| BinSelector.hh | A ResidueSelector that selects residues based on their torsion bin (e.g. ABEGO bin) |
| BondedResidueSelector.cc | Selects residues with chemical bonds to the passed input residues |
| BondedResidueSelector.fwd.hh | Forward declaration of a class that selects residues bonded to a given residue |
| BondedResidueSelector.hh | Selects residues with chemical bonds to the passed input residues |
| CachedResidueSubset.cc | CacheableData wrapper for ResidueSubset storage |
| CachedResidueSubset.fwd.hh | |
| CachedResidueSubset.hh | |
| ChainSelector.cc | The ChainSelector combines logic from multiple ResidueSelectors |
| ChainSelector.fwd.hh | The ChainSelector selects all the residues from a given chain, given either as a number or a character |
| ChainSelector.hh | The ChainSelector selects all the residues from a given chain, given either as a number or a character. Clears the passed ResidueSubset |
| CloseContactResidueSelector.cc | |
| CloseContactResidueSelector.fwd.hh | A class that finds the neighboring residues for a particular residue by looking at atom-atom distances |
| CloseContactResidueSelector.hh | A class that finds the neighboring residues for a particular residue by looking at atom-atom distances |
| CloseContactResidueSelectorCreator.hh | Class declaration for the CloseContactResidueSelectorCreator |
| DensityFitResidueSelector.cc | |
| DensityFitResidueSelector.fwd.hh | Select residues that have a good fit to provided electron denisty map |
| DensityFitResidueSelector.hh | Select residues that have a bad fit to provided electron denisty map |
| FalseResidueSelector.cc | The FalseResidueSelector creates an appropriate all-false vector |
| FalseResidueSelector.fwd.hh | |
| FalseResidueSelector.hh | The FalseResidueSelector creates an appropriate all-false vector |
| GlycanLayerSelector.cc | |
| GlycanLayerSelector.fwd.hh | A selector for choosing glycan residues based on their layer - as measured by the residue distance to the start of the glycan tree |
| GlycanLayerSelector.hh | A selector for choosing glycan residues based on their layer - as measured by the residue distance to the start of the glycan tree |
| GlycanLayerSelectorCreator.hh | A selector for choosing glycan residues based on their layer - as measured by the residue distance to the start of the glycan tree |
| GlycanPositionSelector.cc | |
| GlycanPositionSelector.fwd.hh | A Residue Selector for selecting specific parts of arbitrary glycans |
| GlycanPositionSelector.hh | A Residue Selector for selecting specific parts of arbitrary glycans |
| GlycanResidueSelector.cc | |
| GlycanResidueSelector.fwd.hh | A ResidueSelector for carbohydrates and individual carbohydrate trees |
| GlycanResidueSelector.hh | A ResidueSelector for carbohydrates and individual carbohydrate trees |
| GlycanSequonsSelector.cc | |
| GlycanSequonsSelector.fwd.hh | Find glycosylation sequons in pose |
| GlycanSequonsSelector.hh | Find glycosylation sequons in pose |
| InterGroupInterfaceByVectorSelector.cc | |
| InterGroupInterfaceByVectorSelector.fwd.hh | |
| InterGroupInterfaceByVectorSelector.hh | |
| JumpDownstreamSelector.cc | |
| JumpDownstreamSelector.fwd.hh | Forward declaration of a class that selects residues downstream of a specified jump |
| JumpDownstreamSelector.hh | The JumpDownstreamSelector selects residues downstream of a given jump in a FoldTree |
| JumpUpstreamSelector.cc | |
| JumpUpstreamSelector.fwd.hh | Forward declaration of a class that selects residues upstream of a specified jump |
| JumpUpstreamSelector.hh | The JumpUpstreamSelector selects residues downstream of a given jump in a FoldTree |
| LayerSelector.cc | A ResidueSelector for selecting residues based on layers defined by burial (core, boundary, surface, etc.) |
| LayerSelector.fwd.hh | Forward definitions for a ResidueSelector for selecting residues based on layers defined by burial (core, boundary, surface, etc.) |
| LayerSelector.hh | Header file for a ResidueSelector for selecting residues based on layers defined by burial (core, boundary, surface, etc.) |
| NeighborhoodResidueSelector.cc | |
| NeighborhoodResidueSelector.fwd.hh | Forward declaration of a class that selects residues from the neighborhood of a set of focus residues |
| NeighborhoodResidueSelector.hh | The NeighborhoodResidueSelector selects residues in a given proximity of set focus residues |
| NotResidueSelector.cc | The NotResidueSelector negates the logic of its loaded ResidueSelector |
| NotResidueSelector.fwd.hh | |
| NotResidueSelector.hh | The NotResidueSelector negates the logic of its loaded ResidueSelector |
| NumNeighborsSelector.cc | The NumNeighborsSelector identifies all residues that have at least X neighbors within a distance D |
| NumNeighborsSelector.fwd.hh | Forward declaration of a class that identifies residues with at least X neighbors within a cutoff distance D |
| NumNeighborsSelector.hh | The NumNeighborsSelector identifies residues that have at least X neighbors within a distance Y. Clears the given ResidueSubset |
| OrResidueSelector.cc | The OrResidueSelector combines logic from multiple ResidueSelectors |
| OrResidueSelector.fwd.hh | Forward declaration of a class that negates ResidueSelector logic |
| OrResidueSelector.hh | The OrResidueSelector combines logic from multiple ResidueSelectors |
| PhiSelector.cc | |
| PhiSelector.fwd.hh | A ResidueSelector that selects alpha-amino acids that are either in the positive phi or negative phi region of Ramachandran space (depending on user preferences) |
| PhiSelector.hh | A ResidueSelector that selects alpha-amino acids that are either in the positive phi or negative phi region of Ramachandran space (depending on user preferences) |
| PrimarySequenceNeighborhoodSelector.cc | |
| PrimarySequenceNeighborhoodSelector.fwd.hh | Forward declaration of a class that selects residues using their names |
| PrimarySequenceNeighborhoodSelector.hh | The PrimarySequenceNeighborhoodSelector selects residues using a string containing residue names |
| PrimarySequenceNeighborhoodSelectorCreator.hh | |
| RandomGlycanFoliageSelector.cc | |
| RandomGlycanFoliageSelector.fwd.hh | Selects a random carbohydrate residue from a subset or selector, then selects the rest of the glycan foliage. Used for sampling |
| RandomGlycanFoliageSelector.hh | Selects a random carbohydrate residue from a subset or selector, then selects the rest of the glycan foliage. Used for sampling |
| RandomResidueSelector.cc | |
| RandomResidueSelector.fwd.hh | Forward declaration of a class that selects residues at random |
| RandomResidueSelector.hh | The RandomResidueSelector selects residues using a string containing residue names |
| ResidueIndexSelector.cc | |
| ResidueIndexSelector.fwd.hh | Forward declaration of a class that selects residues using a string containing pose indices |
| ResidueIndexSelector.hh | The ResidueIndexSelector selects residues using a string containing pose indices |
| ResidueInMembraneSelector.cc | |
| ResidueInMembraneSelector.fwd.hh | Forward declaration of a class that selects residues either in or out of the membrane |
| ResidueInMembraneSelector.hh | The ResidueInMembraneSelector selects residues either in or out of the membrane |
| ResidueInSequenceMotifSelector.cc | |
| ResidueInSequenceMotifSelector.fwd.hh | Select residues by motif search |
| ResidueInSequenceMotifSelector.hh | Select residues by motif search |
| ResidueNameSelector.cc | |
| ResidueNameSelector.fwd.hh | Forward declaration of a class that selects residues using their names |
| ResidueNameSelector.hh | The ResidueNameSelector selects residues using a string containing residue names |
| ResiduePDBInfoHasLabelSelector.cc | The ResiduePDBInfoHasLabelSelector selects residues using a string containing residue names |
| ResiduePDBInfoHasLabelSelector.fwd.hh | Forward declaration of a class that selects residues using their names |
| ResiduePDBInfoHasLabelSelector.hh | The ResiduePDBInfoHasLabelSelector selects residues using a string containing residue names |
| ResiduePropertySelector.cc | |
| ResiduePropertySelector.fwd.hh | A residue selector that selects based on set residue properties |
| ResiduePropertySelector.hh | A residue selector that selects based on set residue properties |
| ResiduePropertySelectorCreator.hh | A residue selector that selects based on set residue properties |
| ResidueRanges.cc | The ResidueRanges class identifies contiguous segments of a pose from a subset |
| ResidueRanges.fwd.hh | Forward declaration of a class that identifies continguous segments from a subset of residues from a Pose |
| ResidueRanges.hh | The ResidueRanges class identifies a subset of residues from a Pose |
| ResidueSelector.cc | The ResidueSelector class identifies a subset of residues from a Pose |
| ResidueSelector.fwd.hh | Forward declaration of a class that identifies a subset of residues from a Pose |
| ResidueSelector.hh | The ResidueSelector class identifies a subset of residues from a Pose |
| ResidueSelectorCreator.fwd.hh | Forward declaration of a class that instantiates a particular ResidueSelector |
| ResidueSelectorCreator.hh | Class for instantiating a particular ResidueSelector |
| ResidueSelectorCreators.hh | Class declarations for the ResidueSelectorCreators for a set of simple ResidueSelectors |
| ResidueSelectorFactory.cc | Implementation of the class for instantiating arbitrary ResidueSelectors from a string –> ResidueSelectorCreator map |
| ResidueSelectorFactory.hh | Class for instantiating arbitrary ResidueSelectors from a string –> ResidueSelectorCreator map |
| ResidueSelectorRegistrator.hh | Declaration of the template class for registrating ResidueSelectorCreators with the ResidueSelectorFactory |
| ResidueSpanSelector.cc | |
| ResidueSpanSelector.fwd.hh | Forward declaration of a class that selects residues using span endpoints |
| ResidueSpanSelector.hh | The ResidueSpanSelector selects residues using start/end defintions |
| ResidueVector.cc | The ResidueVector class identifies contiguous segments of a pose from a subset |
| ResidueVector.fwd.hh | Forward declaration of a class that identifies continguous segments from a subset of residues from a Pose |
| ResidueVector.hh | The ResidueVector class identifies a subset of residues from a Pose |
| ReturnResidueSubsetSelector.cc | |
| ReturnResidueSubsetSelector.fwd.hh | |
| ReturnResidueSubsetSelector.hh | A simple selector that returns the set subset. This to enable simplification of code-based interfaces to residue selectors, so that one may accept only selectors, but using this selector, we can set subsets. This greatly reduces the interface complexity and code-complexity arising from accepting BOTH ResidueSubsets and ResidueSelectors (Which I'm terribly sick of doing at this point) |
| ScoreTermValueBasedSelector.cc | Selects residues based on per residue score of the given score_type. Residues with scores equal to or within the lower and upper thresholds are selected |
| ScoreTermValueBasedSelector.fwd.hh | |
| ScoreTermValueBasedSelector.hh | Selects residues based on per residue score of the given score_type. Residues with scores equal to or below the given threshold are selected |
| SecondaryStructureSelector.cc | The SecondaryStructureSelector selects residues based on secondary structure |
| SecondaryStructureSelector.fwd.hh | Forward declaration of a class to select residues based on their secondary structure |
| SecondaryStructureSelector.hh | The SecondaryStructureSelector selects residues based on their secondary structure |
| SelectorLogicParser.cc | |
| SelectorLogicParser.fwd.hh | Construct selectors as logical combinations of other residue selectors using AND, NOT, and OR |
| SelectorLogicParser.hh | Construct selectors as logical combinations of other residue selectors using AND, NOT, and OR |
| SliceResidueSelector.cc | The SliceResidueSelector allows slicing of the returned values of other residue selectors |
| SliceResidueSelector.fwd.hh | The SliceResidueSelector allows slicing of the returned values of other residue selectors |
| SliceResidueSelector.hh | The SliceResidueSelector allows slicing of the returned values of other residue selectors |
| SSElementSelector.cc | The SSElementSelector selects based on the secondary element using DSSP |
| SSElementSelector.fwd.hh | The SSElementSelector selects based on the secondary element using DSSP |
| SSElementSelector.hh | The SSElementSelector selects based on the secondary element using DSSP |
| SymmetricalResidueSelector.cc | The SymmetricalResidueSelector selects symmetrical counterparts of the input residues |
| SymmetricalResidueSelector.fwd.hh | Forward declaration of a class that selects symmetrical versions of residues |
| SymmetricalResidueSelector.hh | The SymmetricalResidueSelector selects symmetrically generated residues of a given ResidueSelector input |
| SymmetricalResidueSelectorCreator.hh | Creator for symmetrical residue selector |
| TrueResidueSelector.cc | The TrueResidueSelector creates an appropriate all-true vector |
| TrueResidueSelector.fwd.hh | Forward declaration of a class that combines ResidueSelector logic |
| TrueResidueSelector.hh | The TrueResidueSelector creates an appropriate all-true vector |
| util.cc | Utility functions for the residue selector classes, primarily, in constructing XML-Schema type definitions |
| util.hh | Utility functions for the residue selector classes, primarily, in constructing XML-Schema type definitions |
| ► util | |
| burial_utilities.cc | Utilities for determining whether a point is within a cone |
| burial_utilities.hh | Utilities for determining whether a point is within a cone |
| interface_vector_calculate.cc | |
| interface_vector_calculate.hh | Calculates an interface definition based on a short distance |
| SelectResiduesByLayer.cc | Select residues depending on layer: core, boundary, and surface The layer of residues are defined by accessible sufrace area of CB + mainchain, or by the number of sidechains within a cone along the CA-CB vector |
| SelectResiduesByLayer.fwd.hh | Forward declarations for a class permitting selection of residues by layer (burial) |
| SelectResiduesByLayer.hh | Select residues depending on layer: core, boundary, and surface and the layer are defined by accessible sufrace area of each residue |
| iterators.hh | Pose iterator utilities |
| util.cc | Utilities to help in selecting residues |
| util.hh | Utilities to help in selecting residues |
| ► sequence | |
| ABEGOManager.cc | Class for ABEGO |
| ABEGOManager.fwd.hh | |
| ABEGOManager.hh | Header file for class of ABEGO plus |
| Aligner.cc | Class definition for a class that aligns two Sequence objects using dynamic programming algorithms |
| Aligner.fwd.hh | Forward declaration for Aligner class |
| Aligner.hh | Class definition for a class that aligns two Sequence objects using an dynamic programming and an arbitrary scoring scheme |
| AlignerFactory.cc | |
| AlignerFactory.hh | |
| AnnotatedSequence.cc | |
| AnnotatedSequence.hh | |
| BasicSequenceCreators.cc | |
| BasicSequenceCreators.hh | |
| Blosum62Map.hh | Creates a std::unordered_map that maps a char pair of name1s to their BLOSUM62 score |
| ChemicalShiftScoringScheme.cc | Method implementations for ChemicalShiftScoringScheme class |
| ChemicalShiftScoringScheme.hh | |
| ChemicalShiftSequence.cc | |
| ChemicalShiftSequence.fwd.hh | Forward declaration for class ChemicalShiftSequence |
| ChemicalShiftSequence.hh | Class definition for a sequence profile that represents each position in a sequence as a probability distribution over the allowed amino acids at that position |
| CompassScoringScheme.cc | Method implementations for CompassScoringScheme class |
| CompassScoringScheme.hh | Class definition for a profile-profile scoring scheme for comparing two sequence profiles using the Compass method, published by Sadreyev and Grishin |
| CompositeScoringScheme.cc | Class definition for a given scoring scheme for an alignment |
| CompositeScoringScheme.fwd.hh | Forward declaration for CompositeScoringScheme.fwd.hh |
| CompositeScoringScheme.hh | Class definition for a given scoring scheme for an alignment |
| CompositeSequence.cc | |
| CompositeSequence.fwd.hh | Forward declaration for class CompositeSequence |
| CompositeSequence.hh | Class definition for a sequence profile that represents each position in a sequence as a probability distribution over the allowed amino acids at that position |
| DerivedSequenceMapping.cc | |
| DerivedSequenceMapping.fwd.hh | |
| DerivedSequenceMapping.hh | |
| DP_Matrix.cc | |
| DP_Matrix.hh | Class for holding information on a dynamic programming matrix |
| DPScoringScheme.cc | Method implementations for DPScoringScheme class |
| DPScoringScheme.hh | Class definition for a profile-profile scoring scheme for comparing two sequence profiles using the DP city-block distance |
| L1ScoringScheme.cc | Method implementations for L1ScoringScheme class |
| L1ScoringScheme.hh | Class definition for a profile-profile scoring scheme for comparing two sequence profiles using the L1 city-block distance |
| MatrixScoringScheme.cc | Class definition for a given scoring scheme for an alignment |
| MatrixScoringScheme.hh | Class definition for a given scoring scheme for an alignment |
| MCAligner.cc | Class definition for a class that aligns two Sequence objects using a stochastic version of the Needleman-Wunsch algorithm |
| MCAligner.hh | Class definition for a class that aligns two Sequence objects using a the Needleman-Wunsch alignment algorithm |
| NWAligner.cc | Class definition for a class that aligns two Sequence objects using the Needleman-Wunsch alignment algorithm |
| NWAligner.fwd.hh | Forward declaration for NWAligner class |
| NWAligner.hh | Class definition for a class that aligns two Sequence objects using a the Needleman-Wunsch alignment algorithm |
| PairScoringScheme.cc | |
| PairScoringScheme.fwd.hh | Forward declaration for PairScoringScheme.fwd.hh |
| PairScoringScheme.hh | Class definition for a given scoring scheme for an alignment |
| ProfSimScoringScheme.cc | |
| ProfSimScoringScheme.hh | Class definition for a given scoring scheme for an alignment |
| ScoringScheme.cc | Abstract base class for representing scoring schemes for alignments |
| ScoringScheme.fwd.hh | Forward declaration for ScoringScheme.fwd.hh |
| ScoringScheme.hh | Abstract base class for representing scoring schemes for alignments |
| ScoringSchemeFactory.cc | Factory for creating various types of ScoringSchemes for use in sequence alignment |
| ScoringSchemeFactory.hh | |
| Sequence.cc | Method definitions for Sequence class |
| Sequence.fwd.hh | Forward declaration for Sequence class |
| Sequence.hh | Class definition for a sequence |
| sequence_motif.cc | |
| sequence_motif.hh | |
| SequenceAlignment.cc | |
| SequenceAlignment.fwd.hh | Forward declaration for SequenceAlignment class |
| SequenceAlignment.hh | Class definition for a multiple sequence alignment |
| SequenceCoupling.cc | |
| SequenceCoupling.fwd.hh | |
| SequenceCoupling.hh | Class definition for a sequence coupling profile that |
| SequenceCreator.cc | |
| SequenceCreator.fwd.hh | |
| SequenceCreator.hh | Base class for SequenceCreators for the Sequence load-time factory registration scheme |
| SequenceFactory.cc | Factory for creating various types of sequences |
| SequenceFactory.fwd.hh | |
| SequenceFactory.hh | Factory for creating various types of sequence |
| SequenceProfile.cc | Class definition for a given scoring scheme for an alignment |
| SequenceProfile.fwd.hh | Forward declaration for class SequenceProfile |
| SequenceProfile.hh | Class definition for a sequence profile that represents each position in a sequence as a probability distribution over the allowed amino acids at that position |
| SimpleScoringScheme.cc | Class definition for a given scoring scheme for an alignment |
| SimpleScoringScheme.hh | Class definition for a given scoring scheme for an alignment |
| SSManager.cc | Class for converting SS to int. For use with the ss hashed fragment database |
| SSManager.fwd.hh | |
| SSManager.hh | |
| SWAligner.cc | |
| SWAligner.fwd.hh | Forward declaration for SWAligner class |
| SWAligner.hh | Class definition for a class that aligns two Sequence objects using a ScoringScheme object and the Smith-Waterman alignment algorithm |
| util.cc | Utilities for working with sequence motifs |
| util.hh | Small bundle of utilities for dealing with sequences |
| ► simple_metrics | |
| ► composite_metrics | |
| CompositeEnergyMetric.cc | |
| CompositeEnergyMetric.fwd.hh | |
| CompositeEnergyMetric.hh | |
| ElectrostaticComplementarityMetric.cc | Simple metric for ElectrostaticComplementarityCalculator |
| ElectrostaticComplementarityMetric.fwd.hh | |
| ElectrostaticComplementarityMetric.hh | Header file for ElectrostaticComplementarityMetric class |
| ProtocolSettingsMetric.cc | This Metric reports options that have been set in the command line and splits script_vars. Each option name is the type and the setting is the value in the map. This is primarily aimed at benchmarking and record-keeping for large-scale rosetta runs or experiments. It works with both the global and local OptionsCollection to enable its use in JD3. It is analogous to the ProtocolFeatures reporter, with more options for xml-based variables |
| ProtocolSettingsMetric.fwd.hh | This Metric reports options that have been set in the command line and splits script_vars. Each option name is the type and the setting is the value in the map. This is primarily aimed at benchmarking and record-keeping for large-scale rosetta runs or experiments. It works with both the global and local OptionsCollection to enable its use in JD3. It is analogous to the ProtocolFeatures reporter, with more options for xml-based variables |
| ProtocolSettingsMetric.hh | This Metric reports options that have been set in the command line and splits script_vars. Each option name is the type and the setting is the value in the map. This is primarily aimed at benchmarking and record-keeping for large-scale rosetta runs or experiments. It works with both the global and local OptionsCollection to enable its use in JD3. It is analogous to the ProtocolFeatures reporter, with more options for xml-based variables |
| ► metrics | |
| CalculatorMetric.cc | A metric which can combine other metrics in a (semi) abitrary calculation |
| CalculatorMetric.fwd.hh | A metric which can combine other metrics |
| CalculatorMetric.hh | A metric which can combine other metrics in a (semi) arbitrary calculation |
| CalculatorMetricCreator.hh | A metric which can combine other metrics |
| DihedralDistanceMetric.cc | A metric to calculate the dihedral distance between two poses or the input and the set cmd-line native. Can set a subset of residues to calculate via ResidueSelector |
| DihedralDistanceMetric.fwd.hh | A metric to calculate the dihedral distance between two poses or the input and the set cmd-line native. Can set a subset of residues to calculate via ResidueSelector |
| DihedralDistanceMetric.hh | A metric to calculate the dihedral distance between two poses or the input and the set cmd-line native. Can set a subset of residues to calculate via ResidueSelector |
| InteractionEnergyMetric.cc | Calculate the interaction energy between residues in two ResidueSelectors in a single pose, including long-range interactions |
| InteractionEnergyMetric.fwd.hh | Calculate the interaction energy between residues in two ResidueSelectors in a single pose, including long-range interactions |
| InteractionEnergyMetric.hh | Calculate the interaction energy between residues in two ResidueSelectors in a single pose, including long-range interactions |
| ResidueSummaryMetric.cc | A SimpleMetric that takes a PerResidueMetric and calculates different summaries of the overall data |
| ResidueSummaryMetric.fwd.hh | A SimpleMetric that takes a PerResidueMetric and calculates different summaries of the overall data |
| ResidueSummaryMetric.hh | A SimpleMetric that takes a PerResidueMetric and calculates different summaries of the overall data |
| RMSDMetric.cc | A metric to calculate the RMSD between two poses or the input and the set cmd-line native. Can set a subset of residues to calculate via ResidueSelector |
| RMSDMetric.fwd.hh | A metric to calculate the RMSD between two poses or the input and the set cmd-line native. Can set a subset of residues to calculate via ResidueSelector |
| RMSDMetric.hh | A metric to calculate the RMSD between two poses or the input. Can set a subset of residues to calculate via ResidueSelector |
| SasaMetric.cc | |
| SasaMetric.fwd.hh | |
| SasaMetric.hh | |
| SecondaryStructureMetric.cc | A SimpleMetric to output the secondary structure of the protein or residues selected by a residue selector |
| SecondaryStructureMetric.fwd.hh | A SimpleMetric to output the secondary structure of the protein or residues selected by a residue selector |
| SecondaryStructureMetric.hh | A SimpleMetric to output the secondary structure of the protein or residues selected by a residue selector |
| SelectedResidueCountMetric.cc | A SimpleMetric that counts the number of residues in a residue selection |
| SelectedResidueCountMetric.fwd.hh | A SimpleMetric that counts the number of residues in a residue selection |
| SelectedResidueCountMetric.hh | A SimpleMetric that counts the number of residues in a residue selection |
| SelectedResiduesMetric.cc | Output residue-selected residues to a score file as rosetta resnums or pdbnums |
| SelectedResiduesMetric.fwd.hh | Output residue-selected residues to a score file as rosetta resnums or pdbnums |
| SelectedResiduesMetric.hh | Output residue-selected residues to a score file as rosetta resnums or pdbnums |
| SelectedResiduesPyMOLMetric.cc | A utility metric to output a string of selected residues from a residue selector as a pymol selection |
| SelectedResiduesPyMOLMetric.fwd.hh | A utility metric to output a string of selected residues from a residue selector as a pymol selection |
| SelectedResiduesPyMOLMetric.hh | A utility metric to output a string of selected residues from a residue selector as a pymol selection |
| SequenceMetric.cc | A SimpleMetric to output the single-letter OR three-letter sequence of a protein or subset of positions/regions using a ResidueSelector |
| SequenceMetric.fwd.hh | A SimpleMetric to output the single-letter OR three-letter sequence of a protein or subset of positions/regions using a ResidueSelector |
| SequenceMetric.hh | A SimpleMetric to output the single-letter OR three-letter sequence of a protein or subset of positions/regions using a ResidueSelector |
| SequenceSimilarityMetric.cc | Compares the sequences of the native structure (using native flag) to the sequence of a given pose |
| SequenceSimilarityMetric.fwd.hh | Compares the sequences of the native structure (using native flag) to the sequence of a given pose |
| SequenceSimilarityMetric.hh | Compares the sequences of the native structure (using native flag) to the sequence of a given pose using BLOSUM62 |
| TimingProfileMetric.cc | Calculate the time difference between construction and apply/calculate. Useful to time protocols in RosettaScripts or through mover containers |
| TimingProfileMetric.fwd.hh | Calculate the time difference between construction and apply/calculate. Useful to time protocols in RosettaScripts or through mover containers |
| TimingProfileMetric.hh | Calculate the time difference between construction and apply/calculate. Useful to time protocols in RosettaScripts or through mover containers |
| TotalEnergyMetric.cc | A metric to report the total energy of the system or the delta total energy between another input pose or the set native |
| TotalEnergyMetric.fwd.hh | A metric to report the total energy of the system or the delta total energy between another input pose or the set native |
| TotalEnergyMetric.hh | A metric to report the total energy of the system or the delta total energy between another input pose |
| ► per_residue_metrics | |
| HbondMetric.cc | A metric to report the total h-bonds of a residue, or from a set of residues to another set of residues. Use the SummaryMetric to get total hbonds of a selection or between selections. See the WaterMediatedBridgedHBondMetric for water-mediated h-bonds |
| HbondMetric.fwd.hh | A metric to report the total h-bonds of a residue, or from a set of residues to another set of residues. Use the SummaryMetric to get total hbonds of a selection or between selections. See the WaterMediatedBridgedHBondMetric for water-mediated h-bonds |
| HbondMetric.hh | A metric to report the total h-bonds of a residue, or from a set of residues to another set of residues. Use the SummaryMetric to get total hbonds of a selection or between selections. See the WaterMediatedBridgedHBondMetric for water-mediated h-bonds |
| PerResidueClashMetric.cc | A SimpleMetric that calculates the number of atomic clashes per residue using the LJ radius (at 0). Can use a soft radius, which reduces it by 33% |
| PerResidueClashMetric.fwd.hh | A SimpleMetric that calculates the number of atomic clashes per residue using the LJ radius (at 0). Can use a soft radius, which reduces it by 33% |
| PerResidueClashMetric.hh | A SimpleMetric that calculates the number of atomic clashes per residue using the LJ radius (at 0) |
| PerResidueDensityFitMetric.cc | A per-residue metric that will calculate the density fit for each residue using either a correlation or a zscore |
| PerResidueDensityFitMetric.fwd.hh | A per-residue metric that will calculate the density fit for each residue using either a correlation or a zscore |
| PerResidueDensityFitMetric.hh | A per-residue metric that will calculate the density fit for each residue using either a correlation or a zscore |
| PerResidueEnergyMetric.cc | A per-residue metric that will calculate/output per residue total energies or a specific score component. Correctly decomposes energies to per-residue |
| PerResidueEnergyMetric.fwd.hh | A per-residue metric that will calculate/output per residue total energies or a specific score component. Correctly decomposes energies to per-residue |
| PerResidueEnergyMetric.hh | A per-residue metric that will calculate/output per residue total energies or a specific score component. Correctly decomposes energies to per-residue |
| PerResidueGlycanLayerMetric.cc | A metric that outputs the layer of the glycan tree as measured by the residue distance to the root |
| PerResidueGlycanLayerMetric.fwd.hh | A metric that outputs the layer of the glycan tree as measured by the residue distance to the root |
| PerResidueGlycanLayerMetric.hh | A metric that outputs the layer of the glycan tree as measured by the residue distance to the root |
| PerResidueRMSDMetric.cc | A per-residue metric thtat will calculate the RMSD for each residue given in a residue selector to a reference pose |
| PerResidueRMSDMetric.fwd.hh | A per-residue metric thtat will calculate the RMSD for each residue given in a residue selector to a reference pose |
| PerResidueRMSDMetric.hh | A per-residue metric thtat will calculate the RMSD for each residue given in a residue selector to a reference pose |
| PerResidueSasaMetric.cc | A per-residue metric that will calculate SASA for each residue given in a selector |
| PerResidueSasaMetric.fwd.hh | A per-residue metric that will calculate SASA for each residue given in a selector |
| PerResidueSasaMetric.hh | A per-residue metric that will calculate SASA for each residue given in a selector |
| WaterMediatedHbondMetric.cc | A metric to measure hydrogen bonds between a set of residues that are water-mediated. Depth of 1 is default where one water mediates the interface between these residues. Depth can be set. Make sure to use the -include_waters flag to have Rosetta not ignore HOH |
| WaterMediatedHbondMetric.fwd.hh | A metric to measure hydrogen bonds between a set of residues that are water-mediated. Depth of 1 is default where one water mediates the interface between these residues. Depth can be set. Make sure to use the -include_waters flag to have Rosetta not ignore HOH |
| WaterMediatedHbondMetric.hh | A metric to measure hydrogen bonds between a set of residues that are water-mediated. Depth of 1 is default where one water mediates the interface between these residues. Depth can be set. Make sure to use the -include_waters flag to have Rosetta not ignore HOH |
| CompositeRealMetric.cc | Main class for simple metrics |
| CompositeRealMetric.fwd.hh | |
| CompositeRealMetric.hh | Base class for core::Real CompositeRealMetrics |
| CompositeRealMetricCreator.fwd.hh | Forward declaration of a class that instantiates a particular CompositeRealMetric |
| CompositeStringMetric.cc | Main class for simple metrics |
| CompositeStringMetric.fwd.hh | |
| CompositeStringMetric.hh | Base class for core::Real CompositeStringMetrics |
| CompositeStringMetricCreator.fwd.hh | Forward declaration of a class that instantiates a particular CompositeStringMetric |
| PerResidueRealMetric.cc | Main class for simple metrics |
| PerResidueRealMetric.fwd.hh | |
| PerResidueRealMetric.hh | Base class for core::Real PerResidueRealMetrics |
| PerResidueRealMetricCreator.fwd.hh | Forward declaration of a class that instantiates a particular PerResidueRealMetric |
| PerResidueStringMetric.cc | Main class for simple metrics |
| PerResidueStringMetric.fwd.hh | |
| PerResidueStringMetric.hh | Base class for core::Real PerResidueStringMetrics |
| PerResidueStringMetricCreator.fwd.hh | Forward declaration of a class that instantiates a particular PerResidueStringMetric |
| RealMetric.cc | Main class for simple metrics |
| RealMetric.fwd.hh | |
| RealMetric.hh | Base class for core::Real RealMetrics |
| RealMetricCreator.fwd.hh | Forward declaration of a class that instantiates a particular RealMetric |
| simple_metric_creators.hh | Creators for Core simple metrics |
| SimpleMetric.cc | The base class for Metrics in the Metric/Filter/Reporter system |
| SimpleMetric.fwd.hh | |
| SimpleMetric.hh | The base class for Metrics in the Metric/Filter/Reporter system |
| SimpleMetricCreator.fwd.hh | |
| SimpleMetricCreator.hh | Class for instantiating a particular SimpleMetric |
| SimpleMetricData.cc | A container class for all Simple Metrics stored in the pose |
| SimpleMetricData.fwd.hh | |
| SimpleMetricData.hh | A container class for all SMs stored in the pose |
| SimpleMetricFactory.cc | |
| SimpleMetricFactory.hh | Class for instantiating arbitrary SimpleMetrics from a string –> SimpleMetricCreator map |
| SimpleMetricRegistrator.hh | |
| SimpleMetricStruct.hh | |
| StringMetric.cc | Main class for simple metrics |
| StringMetric.fwd.hh | |
| StringMetric.hh | Base class for core::Real StringMetrics |
| StringMetricCreator.fwd.hh | Forward declaration of a class that instantiates a particular StringMetric |
| test_classes.cc | |
| test_classes.fwd.hh | |
| test_classes.hh | |
| test_classes_creators.hh | |
| util.cc | Util files for SimpleMetrics |
| util.hh | Test files for any testing of overall SimpleMetric Framework |
| ► util | |
| ChainbreakUtil.cc | |
| ChainbreakUtil.hh | |
| cryst_util.cc | |
| cryst_util.hh | |
| disulfide_util.cc | A collection of procedures for manipulating disulfide bonds |
| disulfide_util.hh | A collection of procedures for manipulating disulfide bonds |
| kinematics_util.cc | |
| kinematics_util.hh | |
| metalloproteins_util.cc | |
| metalloproteins_util.hh | Utilities for working with metalloproteins |
| SwitchResidueTypeSet.cc | Functions for switching the residue type set of a pose |
| SwitchResidueTypeSet.hh | Functions for switching the residue type set of a pose |
| dummy.cc | |
| types.hh | Rosetta project type declarations |
| ► protocols | |
| ► aa_composition | |
| AddCompositionConstraintMover.cc | Assigns an AACompositionConstraint to a pose, initializing it from a file |
| AddCompositionConstraintMover.fwd.hh | Forward declarations for the AddCompositionConstraintMover |
| AddCompositionConstraintMover.hh | Headers for the AddCompositionConstraintMover |
| AddCompositionConstraintMoverCreator.hh | |
| AddHelixSequenceConstraintsMover.cc | This mover adds sequence constraints to the ends of each helix, requiring at least one positively-charged residue in the three C-terminal residues, and at least one negatively-charged resiude in the three N-terminal residues |
| AddHelixSequenceConstraintsMover.fwd.hh | This mover adds sequence constraints to the ends of each helix, requiring at least one positively-charged residue in the three C-terminal residues, and at least one negatively-charged resiude in the three N-terminal residues |
| AddHelixSequenceConstraintsMover.hh | This mover adds sequence constraints to the ends of each helix, requiring at least one positively-charged residue in the three C-terminal residues, and at least one negatively-charged resiude in the three N-terminal residues |
| AddHelixSequenceConstraintsMoverCreator.hh | This mover adds sequence constraints to the ends of each helix, requiring at least one positively-charged residue in the three C-terminal residues, and at least one negatively-charged resiude in the three N-terminal residues |
| AddMHCEpitopeConstraintMover.cc | Assigns an MHCEpitopeConstraint to a pose, initializing it from a file |
| AddMHCEpitopeConstraintMover.fwd.hh | Forward declarations for the AddMHCEpitopeConstraintMover |
| AddMHCEpitopeConstraintMover.hh | Headers for the AddMHCEpitopeConstraintMover |
| AddMHCEpitopeConstraintMoverCreator.hh | This class will create instances of the AddMHCEpitopeConstraintMover for the protocols::moves::MoverFactory |
| AddNetChargeConstraintMover.cc | Assigns an NetChargeConstraint to a pose, initializing it from a file |
| AddNetChargeConstraintMover.fwd.hh | Forward declarations for the AddNetChargeConstraintMover |
| AddNetChargeConstraintMover.hh | Headers for the AddNetChargeConstraintMover |
| AddNetChargeConstraintMoverCreator.hh | This class will create instances of the AddNetChargeConstraintMover for the protocols::moves::MoverFactory |
| ClearCompositionConstraintsMover.cc | Clears all AACompositionConstraints from a pose |
| ClearCompositionConstraintsMover.fwd.hh | Forward declarations for the ClearCompositionConstraintsMover |
| ClearCompositionConstraintsMover.hh | Headers for the ClearCompositionConstraintsMover |
| ClearCompositionConstraintsMoverCreator.hh | |
| util.cc | Utility functions for aa_composition-related protocols |
| util.hh | Utility functions for aa_composition-related protocols |
| ► abinitio | |
| ► abscript | |
| AbscriptLoopCloserCM.cc | |
| AbscriptLoopCloserCM.fwd.hh | Definition of the AbscriptLoopCloserCM class |
| AbscriptLoopCloserCM.hh | |
| AbscriptLoopCloserCMCreator.hh | |
| AbscriptMover.cc | |
| AbscriptMover.fwd.hh | Definition of the AbscriptMover class |
| AbscriptMover.hh | |
| AbscriptMoverCreator.hh | This class will create instances of Mover AbscriptMover for the MoverFactory |
| AbscriptStageMover.cc | |
| AbscriptStageMover.fwd.hh | Definition of the AbscriptStageMover class |
| AbscriptStageMover.hh | |
| ConstraintPreparer.cc | |
| ConstraintPreparer.fwd.hh | Definition of the ConstraintPreparer class |
| ConstraintPreparer.hh | |
| ConstraintPreparerCreator.hh | This class will create instances of Mover ConstraintPreparer for the MoverFactory |
| FragmentCM.cc | |
| FragmentCM.fwd.hh | Definition of the FragmentCM class |
| FragmentCM.hh | |
| FragmentCMCreator.hh | This class will create instances of Mover AbscriptMover for the MoverFactory |
| FragmentJumpCM.cc | |
| FragmentJumpCM.fwd.hh | Definition of the FragmentJumpCM class |
| FragmentJumpCM.hh | |
| FragmentJumpCMCreator.hh | This class will create instances of Mover AbscriptMover for the MoverFactory |
| JumpSampleData.cc | |
| JumpSampleData.fwd.hh | Definition of the JumpSampleData class |
| JumpSampleData.hh | |
| JumpSampleDataCreator.hh | This class will create instances of Mover AbscriptMover for the MoverFactory |
| RigidChunkCM.cc | |
| RigidChunkCM.fwd.hh | |
| RigidChunkCM.hh | |
| RigidChunkCMCreator.hh | This class will create instances of Mover RigidChunk for the MoverFactory |
| StageID.hh | |
| StagePreparer.cc | |
| StagePreparer.fwd.hh | Definition of the StagePreparer class |
| StagePreparer.hh | |
| StructPerturberCM.cc | |
| StructPerturberCM.fwd.hh | |
| StructPerturberCM.hh | |
| StructPerturberCMCreator.hh | This class will create instances of Mover StructPerturber for the MoverFactory |
| AbrelaxApplication.cc | |
| AbrelaxApplication.hh | |
| AbrelaxMover.cc | This class will be handled to a SampleProtocol as a control instance |
| AbrelaxMover.fwd.hh | |
| AbrelaxMover.hh | |
| AllResiduesChanged.hh | |
| BrokerMain.cc | |
| BrokerMain.hh | |
| ClassicAbinitio.cc | Ab-initio fragment assembly protocol for proteins |
| ClassicAbinitio.fwd.hh | |
| ClassicAbinitio.hh | Header file for ClassicAbinitio protocol |
| ConstraintFragmentSampler.cc | Ab-initio fragment assembly protocol for proteins |
| ConstraintFragmentSampler.hh | Header file for ConstraintFragmentSampler protocol |
| DomainAssembly.cc | |
| DomainAssembly.hh | |
| DomainAssemblyCreator.hh | Declaration of the MoverCreator class for the DomainAssembly |
| DoubleLayerKinematicAbinitio.cc | |
| DoubleLayerKinematicAbinitio.fwd.hh | |
| DoubleLayerKinematicAbinitio.hh | |
| FoldConstraints.cc | Ab-initio fragment assembly protocol for proteins under the influence of contraints (e.g., NOE) |
| FoldConstraints.fwd.hh | |
| FoldConstraints.hh | |
| FragmentSampler.cc | Ab-initio fragment assembly protocol for proteins |
| FragmentSampler.fwd.hh | |
| FragmentSampler.hh | Header file for FragmentSampler protocol |
| HedgeArchive.cc | |
| HedgeArchive.fwd.hh | |
| HedgeArchive.hh | |
| IterativeAbrelax.cc | |
| IterativeAbrelax.hh | |
| IterativeBase.cc | |
| IterativeBase.hh | |
| IterativeCentroid.cc | |
| IterativeCentroid.hh | |
| IterativeFullatom.cc | |
| IterativeFullatom.hh | |
| KinematicAbinitio.cc | |
| KinematicAbinitio.fwd.hh | |
| KinematicAbinitio.hh | Abinitio - Type sampling controlled by KinematicControl object |
| KinematicControl.cc | |
| KinematicControl.fwd.hh | |
| KinematicControl.hh | |
| KinematicTaskControl.cc | |
| KinematicTaskControl.fwd.hh | |
| KinematicTaskControl.hh | |
| LoopJumpFoldCst.cc | |
| LoopJumpFoldCst.fwd.hh | |
| LoopJumpFoldCst.hh | |
| MembraneAbinitio.cc | Ab-initio fragment assembly protocol for membrane proteins |
| MembraneAbinitio.fwd.hh | |
| MembraneAbinitio.hh | Header file for MembraneAbinitio protocol |
| PairingStatistics.cc | |
| PairingStatistics.fwd.hh | |
| PairingStatistics.hh | |
| Protocol.cc | |
| Protocol.fwd.hh | |
| Protocol.hh | |
| ResolutionSwitcher.cc | |
| ResolutionSwitcher.fwd.hh | |
| ResolutionSwitcher.hh | |
| StrandConstraints.cc | |
| StrandConstraints.hh | |
| Template.cc | |
| Template.fwd.hh | |
| Template.hh | |
| TemplateJumpSetup.cc | |
| TemplateJumpSetup.fwd.hh | |
| TemplateJumpSetup.hh | |
| Templates.cc | |
| Templates.fwd.hh | |
| Templates.hh | |
| util.cc | |
| util.hh | |
| vs_test.cc | |
| vs_test.hh | |
| ► analysis | |
| ► burial_metrics | |
| PolarGroupBurialPyMolStringMetric.cc | A string metric that generates a string of PyMol commands to colour a structure's polar groups based on burial |
| PolarGroupBurialPyMolStringMetric.fwd.hh | Forward declarations for a string metric that generates a string of PyMol commands to colour a structure's polar groups based on burial |
| PolarGroupBurialPyMolStringMetric.hh | Headers for a string metric that generates a string of PyMol commands to colour a structure's polar groups based on burial |
| PolarGroupBurialPyMolStringMetricCreator.hh | Creator for a string metric that generates a string of PyMol commands to colour a structure's polar groups based on burial |
| ► simple_metrics | |
| RunSimpleMetricsMover.cc | Run a set of SimpleMetrics (used primarily for RosettaScripts) |
| RunSimpleMetricsMover.fwd.hh | Runs SimpleMetrics defined in block |
| RunSimpleMetricsMover.hh | Run the set of SimpleMetrics. Add the data to the pose, which will be output int the score file |
| RunSimpleMetricsMoverCreator.hh | |
| SequenceRecoveryMetric.cc | Calculate sequence recovery statistics on a protein, relative to a reference |
| SequenceRecoveryMetric.fwd.hh | Calculate sequence recovery statistics on a protein, relative to a reference |
| SequenceRecoveryMetric.hh | Calculate sequence recovery statistics on a protein, relative to a reference |
| SequenceRecoveryMetricCreator.hh | Calculate sequence recovery statistics on a protein, relative to a reference |
| GlycanInfoMover.cc | Simple class for outputting glycan information. Currently, it simply prints the information |
| GlycanInfoMover.fwd.hh | Simple class for outputting glycan information. Currently, it simply prints the information |
| GlycanInfoMover.hh | Simple class for outputting glycan information. Currently, it simply prints the information |
| GlycanInfoMoverCreator.hh | Simple class for outputting glycan information. Currently, it simply prints the information |
| InterfaceAnalyzerMover.cc | InterfaceAnalyzerMover implementation - class for in-depth interface quality analysis |
| InterfaceAnalyzerMover.fwd.hh | Fwd declaration for InterfaceAnalyzer: intense analysis of interface quality |
| InterfaceAnalyzerMover.hh | |
| InterfaceAnalyzerMoverCreator.hh | This class will create instances of Mover InterfaceAnalyzerMover for the MoverFactory |
| LoopAnalyzerFilter.cc | LoopAnalyzerFilter examines loop structures and packages extra scores into a Job object; you can filter on its "LAM score". This was originally LoopAnalyzerMover (which treated its Pose as const anyway), but has been converted to a filter |
| LoopAnalyzerFilter.fwd.hh | Intense analysis of loop quality |
| LoopAnalyzerFilter.hh | LoopAnalyzerFilter examines loop structures and packages extra scores into a Job object; you can filter on its "LAM score". This was originally LoopAnalyzerMover (which treated its Pose as const anyway), but has been converted to a filter |
| LoopAnalyzerFilterCreator.hh | Intense analysis of loop quality (creator) |
| LoopAnalyzerMover.cc | LoopAnalyzerMover implementation - class for in-depth loop structure quality analysis |
| LoopAnalyzerMover.fwd.hh | Fwd declaration for LoopAnalyzer: intense analysis of loop quality |
| LoopAnalyzerMover.hh | LoopAnalyzerMover examines loop structures and packages extra scores into a Job object |
| LoopAnalyzerMoverCreator.hh | |
| PackStatMover.cc | |
| PackStatMover.fwd.hh | Created on: Jan 25, 2012 |
| PackStatMover.hh | |
| ► anchored_design | |
| Anchor.cc | |
| Anchor.fwd.hh | |
| Anchor.hh | |
| AnchorMovers.cc | Anchored design movers (protocol-level, perturb, refine) |
| AnchorMovers.fwd.hh | Anchor Movers forward declarations header |
| AnchorMovers.hh | Protocol-level outermost movers for anchored design; wraps a set of other moves |
| AnchorMoversData.cc | |
| AnchorMoversData.fwd.hh | |
| AnchorMoversData.hh | |
| ► antibody | |
| ► clusters | |
| CDRCluster.cc | Simple class to hold and access CDRCluster information of a region in a pose |
| CDRCluster.fwd.hh | |
| CDRCluster.hh | Simple class to hold and access CDRcluster info at a region in the pose. Construct in CDRClusterSet |
| CDRClusterEnum.hh | Enumerators for antibody clusters |
| CDRClusterEnumManager.cc | |
| CDRClusterEnumManager.fwd.hh | |
| CDRClusterEnumManager.hh | Functions for CDRClusterEnums |
| CDRClusterFeatures.cc | |
| CDRClusterFeatures.fwd.hh | |
| CDRClusterFeatures.hh | |
| CDRClusterFeaturesCreator.cc | |
| CDRClusterFeaturesCreator.hh | |
| CDRClusterMatcher.cc | Simple class for identifying CDR cluster in an antibody |
| CDRClusterMatcher.fwd.hh | |
| CDRClusterMatcher.hh | Simple class for identifying CDR clusters of an antibody |
| CDRClusterSet.cc | |
| CDRClusterSet.fwd.hh | |
| CDRClusterSet.hh | |
| util.cc | |
| util.hh | |
| ► constraints | |
| CDRDihedralConstraintMover.cc | |
| CDRDihedralConstraintMover.fwd.hh | |
| CDRDihedralConstraintMover.hh | Add CDR cluster-based Dihedral CircularHarmonic constraints or general CircHarmonic csts to a CDR |
| CDRDihedralConstraintMoverCreator.hh | |
| ParatopeEpitopeSiteConstraintMover.cc | |
| ParatopeEpitopeSiteConstraintMover.fwd.hh | |
| ParatopeEpitopeSiteConstraintMover.hh | Add SiteConstraints from the Epitope to the Paratope and from the Paratope to the Epitope |
| ParatopeEpitopeSiteConstraintMoverCreator.hh | |
| ParatopeSiteConstraintMover.cc | |
| ParatopeSiteConstraintMover.fwd.hh | |
| ParatopeSiteConstraintMover.hh | Adds and removes ambiguos site constraints for the Antibody Paratope to antigen, defined for simplicity as the CDRs |
| ParatopeSiteConstraintMoverCreator.hh | |
| util.cc | |
| util.hh | |
| ► database | |
| AntibodyDatabaseManager.cc | |
| AntibodyDatabaseManager.fwd.hh | |
| AntibodyDatabaseManager.hh | |
| CDRSetOptions.cc | |
| CDRSetOptions.fwd.hh | |
| CDRSetOptions.hh | |
| CDRSetOptionsParser.cc | |
| CDRSetOptionsParser.fwd.hh | |
| CDRSetOptionsParser.hh | |
| ► design | |
| AntibodyDesignEnum.hh | Antibody Design enumerators |
| AntibodyDesignEnumManager.cc | |
| AntibodyDesignEnumManager.fwd.hh | |
| AntibodyDesignEnumManager.hh | |
| AntibodyDesignMover.cc | Class that initially designs antibodies through grafting using an AntibodyDatabase + North_AHO numbering scheme |
| AntibodyDesignMover.fwd.hh | |
| AntibodyDesignMover.hh | Class that initially designs antibodies through grafting using an AntibodyDatabase + North_AHO numbering scheme |
| AntibodyDesignMoverCreator.hh | |
| AntibodySeqDesignTFCreator.cc | Class for generating TaskFactories and TaskOperations for antibody design from a set of options |
| AntibodySeqDesignTFCreator.fwd.hh | |
| AntibodySeqDesignTFCreator.hh | Class for creating a TaskFactory from SeqDesignOptions for use in various protocols |
| CDRGraftDesignOptions.cc | |
| CDRGraftDesignOptions.fwd.hh | |
| CDRGraftDesignOptions.hh | GraftDesign options class and parser |
| CDRSeqDesignOptions.cc | |
| CDRSeqDesignOptions.fwd.hh | |
| CDRSeqDesignOptions.hh | Option control for Sequence Design of a single CDR |
| GeneralAntibodyModeler.cc | |
| GeneralAntibodyModeler.fwd.hh | |
| GeneralAntibodyModeler.hh | |
| MutateFrameworkForCluster.cc | |
| MutateFrameworkForCluster.fwd.hh | |
| MutateFrameworkForCluster.hh | Mutates Framework regions after insertion of a particular cluster |
| MutateFrameworkForClusterCreator.hh | |
| NativeAntibodySeq.cc | |
| NativeAntibodySeq.fwd.hh | |
| NativeAntibodySeq.hh | |
| ResnumFromStringsWithRangesSelector.cc | |
| ResnumFromStringsWithRangesSelector.hh | |
| util.cc | |
| util.hh | Utility functions for antibody design namespace |
| ► grafting | |
| antibody_sequence.cc | |
| antibody_sequence.hh | |
| cdr_detection.cc | |
| cdr_detection.hh | Base class detection of CDRS's |
| chothia_numberer.cc | Chothia numberer |
| chothia_numberer.hh | Chothia numberer |
| exception.hh | Exceptions classes for antibody grafting code |
| grafter.cc | Grafter implementation: take SCS results and create antibody Pose with CDR loops from results |
| grafter.hh | Grafter implementation: take SCS results and create antibody Pose with CDR loops from results |
| json_based_cdr_detection.cc | |
| json_based_cdr_detection.hh | Json based detection of CRS's |
| regex_based_cdr_detection.cc | |
| regex_based_cdr_detection.hh | RegEx based detection of CRS's |
| regex_manager.cc | |
| regex_manager.fwd.hh | |
| regex_manager.hh | |
| scs_blast.cc | Structural Component Selector (SCS) implementation with NCBI-BLAST+ |
| scs_blast.fwd.hh | Structural Component Selector (SCS) implementation with NCBI-BLAST+ |
| scs_blast.hh | Structural Component Selector (SCS) implementation with NCBI-BLAST+ |
| scs_functor.cc | Structural Component Selector (SCS): implemetation of predicates for filtering and sorting |
| scs_functor.fwd.hh | Structural Predicates for Structural Component Selector (SCS) layer |
| scs_functor.hh | Structural Component Selector (SCS): implemetation of predicates for filtering and sorting |
| scs_helper.cc | Singleton to store and load data for Structural Component Selector (SCS) filters |
| scs_helper.fwd.hh | Singleton to store and load data for Structural Component Selector (SCS) filters |
| scs_helper.hh | Singleton to store and load data for Structural Component Selector (SCS) filters |
| scs_multi_template.cc | |
| scs_multi_template.hh | Structural Component Selector (SCS) implementation of Multi-template selection |
| scs_subst_mat.cc | |
| scs_subst_mat.fwd.hh | Structural Component Selector (SCS) implementation using substition matrices |
| scs_subst_mat.hh | Structural Component Selector (SCS) implementation using substition matrices |
| util.cc | Helpers for antibody grafting code |
| util.hh | Helpers for antibody grafting code |
| ► residue_selector | |
| AntibodyRegionSelector.cc | |
| AntibodyRegionSelector.fwd.hh | A simple selector to select residues of particular antibody regions |
| AntibodyRegionSelector.hh | A simple selector to select residues of particular antibody regions |
| AntibodyRegionSelectorCreator.hh | |
| CDRResidueSelector.cc | |
| CDRResidueSelector.fwd.hh | Select CDR residues |
| CDRResidueSelector.hh | Select CDR residues |
| CDRResidueSelectorCreator.hh | |
| ► snugdock | |
| SnugDock.cc | |
| SnugDock.fwd.hh | Forward declaration |
| SnugDock.hh | |
| SnugDockCreator.hh | Declaration of the MoverCreator class for SnugDock |
| SnugDockProtocol.cc | |
| SnugDockProtocol.fwd.hh | Forward declaration |
| SnugDockProtocol.hh | |
| ► task_operations | |
| AddCDRProfileSetsOperation.cc | |
| AddCDRProfileSetsOperation.fwd.hh | |
| AddCDRProfileSetsOperation.hh | |
| AddCDRProfileSetsOperationCreator.hh | |
| AddCDRProfilesOperation.cc | |
| AddCDRProfilesOperation.fwd.hh | |
| AddCDRProfilesOperation.hh | Add CDR Cluster-based profile ResidueProbDesignOperation to sample within a CDR cluster profile |
| AddCDRProfilesOperationCreator.hh | |
| DisableAntibodyRegionOperation.cc | Task Operation to disable a region of an antibody |
| DisableAntibodyRegionOperation.fwd.hh | Task operation to disable regions of an antibody |
| DisableAntibodyRegionOperation.hh | Task Operation to Disable a Region of Antibody |
| DisableAntibodyRegionOperationCreator.hh | |
| DisableCDRsOperation.cc | Task Operation to disable specific CDRs |
| DisableCDRsOperation.fwd.hh | |
| DisableCDRsOperation.hh | |
| DisableCDRsOperationCreator.hh | |
| RestrictToCDRsAndNeighbors.cc | |
| RestrictToCDRsAndNeighbors.fwd.hh | |
| RestrictToCDRsAndNeighbors.hh | TaskOperation to restrict to Specific CDRs and neighbors |
| RestrictToCDRsAndNeighborsCreator.hh | |
| Ab_TemplateInfo.cc | |
| Ab_TemplateInfo.fwd.hh | |
| Ab_TemplateInfo.hh | |
| AntibodyCDRGrafter.cc | Class to graft CDR loops from an antibody to a new antibody or from a CDR pose into a different antibody |
| AntibodyCDRGrafter.fwd.hh | Class to graft CDR loops from an antibody to a new antibody or from a CDR pose into a different antibody |
| AntibodyCDRGrafter.hh | Class to graft CDR loops from an antibody to a new antibody or from a CDR pose into a different antibody |
| AntibodyCDRGrafterCreator.hh | Class to graft CDR loops from an antibody to a new antibody or from a CDR pose into a different antibody |
| AntibodyEnum.hh | Enumerators + TypeDefs for Antibody namespace |
| AntibodyEnumManager.cc | Functions for AntibodyEnumerators |
| AntibodyEnumManager.fwd.hh | |
| AntibodyEnumManager.hh | Functions for AntibodyEnumerators |
| AntibodyFeatures.cc | |
| AntibodyFeatures.fwd.hh | |
| AntibodyFeatures.hh | |
| AntibodyFeaturesCreator.cc | |
| AntibodyFeaturesCreator.hh | |
| AntibodyInfo.cc | Class for getting antibody-specific objects and information |
| AntibodyInfo.fwd.hh | AntibodyInfo class forward declarations header |
| AntibodyInfo.hh | Class for getting antibody-specific objects and information |
| AntibodyModelerProtocol.cc | Build a homology model of an antibody |
| AntibodyModelerProtocol.fwd.hh | Forward declaration |
| AntibodyModelerProtocol.hh | Build a homology model of an antibody |
| AntibodyNumberingConverterMover.cc | Converts numbering schemes of an antibody |
| AntibodyNumberingConverterMover.fwd.hh | Converts numbering schemes of an antibody |
| AntibodyNumberingConverterMover.hh | Converts numbering schemes of an antibody |
| AntibodyNumberingConverterMoverCreator.hh | Converts numbering schemes of an antibody |
| AntibodyNumberingParser.cc | |
| AntibodyNumberingParser.fwd.hh | |
| AntibodyNumberingParser.hh | Read Antibody Numbering schemes and transform info from the database |
| CDRsMinPackMin.cc | Build a homology model of an antibody |
| CDRsMinPackMin.fwd.hh | Forward declaration |
| CDRsMinPackMin.hh | Main CDR minimization method in protocols/antibody |
| CloseOneCDRLoop.cc | Grafts a cdr onto the template of an antibody framework |
| CloseOneCDRLoop.fwd.hh | |
| CloseOneCDRLoop.hh | |
| GraftCDRLoopsProtocol.cc | Build a homology model of an antibody |
| GraftCDRLoopsProtocol.fwd.hh | Forward declaration |
| GraftCDRLoopsProtocol.hh | Build a homology model of an antibody |
| GraftedStemOptimizer.cc | Optimize the CDR Grafted stem |
| GraftedStemOptimizer.fwd.hh | |
| GraftedStemOptimizer.hh | Optimize the CDR Grafted stem |
| GraftOneCDRLoop.cc | Grafts a cdr onto the template of an antibody framework |
| GraftOneCDRLoop.fwd.hh | |
| GraftOneCDRLoop.hh | Grafts a cdr onto the template of an antibody framework |
| H3CterInsert.cc | Build a homology model of an antibody |
| H3CterInsert.fwd.hh | Build a homology model of an antibody |
| H3CterInsert.hh | Build a homology model of an antibody |
| H3PerturbCCD.cc | Build a homology model of an antibody |
| H3PerturbCCD.fwd.hh | |
| H3PerturbCCD.hh | Build a homology model of an antibody |
| H3RefineCCD.cc | Build a homology model of an antibody |
| H3RefineCCD.fwd.hh | |
| H3RefineCCD.hh | Build a homology model of an antibody |
| LHRepulsiveRamp.cc | Build a homology model of an antibody |
| LHRepulsiveRamp.fwd.hh | |
| LHRepulsiveRamp.hh | Build a homology model of an antibody |
| metrics.cc | Routines to measure antibodies |
| metrics.hh | |
| RefineBetaBarrel.cc | Build a homology model of an antibody |
| RefineBetaBarrel.fwd.hh | Forward declaration |
| RefineBetaBarrel.hh | Build a homology model of an antibody |
| util.cc | |
| util.hh | Utility functions for the Antibody namespace |
| ► antibody_legacy | |
| AntibodyClass.cc | |
| AntibodyClass.fwd.hh | Antibody class forward declarations header |
| AntibodyClass.hh | |
| AntibodyModeler.cc | |
| AntibodyModeler.fwd.hh | Forward declaration |
| AntibodyModeler.hh | |
| CDRH3Modeler.cc | Models CDR H3 loop using loop modeling |
| CDRH3Modeler.hh | |
| GraftMover.cc | |
| GraftMover.hh | |
| LHRepulsiveRampLegacy.cc | |
| LHRepulsiveRampLegacy.fwd.hh | |
| LHRepulsiveRampLegacy.hh | |
| LHSnugFitLegacy.cc | |
| LHSnugFitLegacy.fwd.hh | |
| LHSnugFitLegacy.hh | |
| Ubiquitin_E2C_Modeler.cc | |
| Ubiquitin_E2C_Modeler.fwd.hh | Forward declaration |
| Ubiquitin_E2C_Modeler.hh | Build model for di-ubiquitin and e2c enzyme complex |
| ► backbone_moves | |
| ► local_backbone_mover | |
| ► free_peptide_movers | |
| CircularPermuteFreePeptideMover.cc | Circularly permute the torsions on the free peptide |
| CircularPermuteFreePeptideMover.fwd.hh | Circularly permute the torsions on the free peptide |
| CircularPermuteFreePeptideMover.hh | Circularly permute the torsions on the free peptide |
| FreePeptideMover.cc | Base class for free peptide movers |
| FreePeptideMover.fwd.hh | Base class for free peptide movers |
| FreePeptideMover.hh | Base class for free peptide movers |
| LongAxisRotationFreePeptideMover.cc | Rotate the free peptide along the axis formed by its first and last CA atom |
| LongAxisRotationFreePeptideMover.fwd.hh | Rotate the free peptide along the axis formed by its first and last CA atom |
| LongAxisRotationFreePeptideMover.hh | Rotate the free peptide along the axis formed by its first and last CA atom |
| ShearFreePeptideMover.cc | Change the psi torsion of a residue and phi torsion of its subsequent residue by a opposite value |
| ShearFreePeptideMover.fwd.hh | Change the psi torsion of a residue and phi torsion of its subsequent residue by a opposite value |
| ShearFreePeptideMover.hh | Change the psi torsion of a residue and phi torsion of its subsequent residue by a opposite value |
| TranslationFreePeptideMover.cc | Translate the free peptide by a cartesian vector |
| TranslationFreePeptideMover.fwd.hh | Translate the free peptide by a cartesian vector |
| TranslationFreePeptideMover.hh | Translate the free peptide by a cartesian vector |
| ► gap_solution_pickers | |
| GapSolutionPicker.cc | Base class for picking solution for a gap |
| GapSolutionPicker.fwd.hh | Base class for picking solution for a gap |
| GapSolutionPicker.hh | Base class for picking solution for a gap |
| RandomGapSolutionPicker.cc | Pick a solution randomly |
| RandomGapSolutionPicker.fwd.hh | Pick a solution randomly |
| RandomGapSolutionPicker.hh | Pick a solution randomly |
| FreePeptide.cc | FreePeptide represents a free peptide |
| FreePeptide.fwd.hh | FreePeptide represents a free peptide |
| FreePeptide.hh | FreePeptide represents a free peptide |
| GapCloser.cc | GapCloser closes the gaps after moving the free peptide |
| GapCloser.fwd.hh | GapCloser closes the gaps after moving the free peptide |
| GapCloser.hh | GapCloser closes the gaps after moving the free peptide |
| LocalBackboneMover.cc | LocalBackboneMover moves a stretch of backbone locally |
| LocalBackboneMover.fwd.hh | LocalBackboneMover moves a stretch of backbone locally |
| LocalBackboneMover.hh | LocalBackboneMover moves a stretch of backbone locally |
| LocalBackboneMoverCreator.hh | LocalBackboneMover moves a stretch of backbone locally |
| types.hh | |
| util.cc | Utility functions for the local_backbone_mover |
| util.hh | Utility functions for the local_backbone_mover |
| RandomizeBBByRamaPrePro.cc | A simple mover to randomize a backbone, or a portion of a backbone, biased by the rama_prepro score of each residue |
| RandomizeBBByRamaPrePro.fwd.hh | A simple mover to randomize a backbone, or a portion of a backbone, biased by the rama_prepro score of each residue |
| RandomizeBBByRamaPrePro.hh | A simple mover to randomize a backbone, or a portion of a backbone, biased by the rama_prepro score of each residue |
| RandomizeBBByRamaPreProCreator.hh | A simple mover to randomize a backbone, or a portion of a backbone, biased by the rama_prepro score of each residue |
| ► backrub | |
| BackrubMover.cc | Implementation of BackrubMover class and functions |
| BackrubMover.fwd.hh | |
| BackrubMover.hh | Definition of BackrubMover class and functions |
| BackrubMoverCreator.hh | This class will create instances of Mover BackrubMover for the MoverFactory |
| BackrubProtocol.cc | |
| BackrubProtocol.fwd.hh | |
| BackrubProtocol.hh | |
| BackrubProtocolCreator.hh | |
| BackrubSegment.cc | Implmentation of BackrubSegment class |
| BackrubSegment.hh | Definition/implmentation of BackrubSegment class |
| BackrubSidechainMover.cc | BackrubSidechainMover methods implemented |
| BackrubSidechainMover.fwd.hh | BackrubSidechainMover forward declarations header |
| BackrubSidechainMover.hh | |
| BackrubSidechainMoverCreator.hh | This class will create instances of Mover BackrubSidechainMover for the MoverFactory |
| util.cc | |
| util.hh | |
| ► boinc | |
| boinc.cc | Wrappers to make BOINC work |
| boinc.hh | Wrappers to make BOINC work |
| boinc_shmem.hh | |
| BoincPoseObserver.cc | BoincPoseObserver class |
| BoincPoseObserver.fwd.hh | |
| BoincPoseObserver.hh | BoincPoseObserver class |
| util.cc | |
| util.hh | |
| watchdog.cc | |
| watchdog.hh | |
| ► branch_angle | |
| BranchAngleOptimizer.cc | |
| BranchAngleOptimizer.fwd.hh | BranchAngleOptimizer class forward declaration |
| BranchAngleOptimizer.hh | |
| BranchCoef1.fwd.hh | BranchCoef1 class forward declaration |
| BranchCoef1.hh | Definition/implementation of BranchCoef1 class and methods |
| BranchCoef2.fwd.hh | BranchCoef2 class forward declaration |
| BranchCoef2.hh | Definition/implementation of BranchCoef2 class and methods |
| BranchParam1.fwd.hh | BranchParam1 class forward declaration |
| BranchParam1.hh | Definition/implementation of BranchParam1 class and methods |
| BranchParam2.fwd.hh | BranchParam2 class forward declaration |
| BranchParam2.hh | Definition/implementation of BranchParam2 class and methods |
| ► calc_taskop_filters | |
| ConservedPosMutationFilter.cc | |
| ConservedPosMutationFilter.fwd.hh | |
| ConservedPosMutationFilter.hh | Header file for ConservedPosMutationFitler class |
| ConservedPosMutationFilterCreator.hh | FilterCreator for the ConservedPosMutationFilter |
| MultipleSigmoidsFilter.cc | |
| MultipleSigmoidsFilter.fwd.hh | |
| MultipleSigmoidsFilter.hh | |
| MultipleSigmoidsFilterCreator.hh | FilterCreators for the MultipleSigmoidsFilter |
| OperatorFilter.cc | |
| OperatorFilter.fwd.hh | |
| OperatorFilter.hh | |
| OperatorFilterCreator.hh | FilterCreators for the OperatorFilter |
| RelativePoseFilter.cc | |
| RelativePoseFilter.fwd.hh | |
| RelativePoseFilter.hh | Computes a filter's value on a pose that is modified from one that is read from disk. Useful for computing values for the same sequence across many structures |
| RelativePoseFilterCreator.hh | |
| RotamerBoltzmannWeight.cc | |
| RotamerBoltzmannWeight.fwd.hh | |
| RotamerBoltzmannWeight.hh | Reports to Tracer which residues are designable in a taskfactory |
| RotamerBoltzmannWeight2.cc | Next-generation RotamerBoltzmannWeight filter |
| RotamerBoltzmannWeight2.fwd.hh | Next-generation RotamerBoltzmannWeight filter |
| RotamerBoltzmannWeight2.hh | Next-generation RotamerBoltzmannWeight filter |
| RotamerBoltzmannWeight2Creator.hh | Next-generation RotamerBoltzmannWeight filter |
| RotamerBoltzmannWeightFilterCreator.hh | FilterCreators for the RotamerBoltzmannWeightFilter |
| SigmoidFilter.cc | |
| SigmoidFilter.fwd.hh | |
| SigmoidFilter.hh | |
| SigmoidFilterCreator.hh | FilterCreators for the SigmoidFilter |
| ► calc_taskop_movers | |
| ConsensusDesignMover.cc | Cc file for ConsensusDesignMover |
| ConsensusDesignMover.fwd.hh | Fwd.hh file for ConsensusDesignMover |
| ConsensusDesignMover.hh | Header file for ConsensusDesignMover |
| ConsensusDesignMoverCreator.hh | |
| CreateSequenceMotifMover.cc | Create a sequence motif in a region of protein using the SequenceMotifTaskOperation. Uses psueo-regular expressions to define the motif |
| CreateSequenceMotifMover.fwd.hh | Create a sequence motif in a region of protein using the SequenceMotifTaskOperation. Uses psueo-regular expressions to define the motif |
| CreateSequenceMotifMover.hh | Create a sequence motif in a region of protein using the SequenceMotifTaskOperation. Uses psueo-regular expressions to define the motif |
| CreateSequenceMotifMoverCreator.hh | Create a sequence motif in a region of protein using the SequenceMotifTaskOperation. Uses psueo-regular expressions to define the motif |
| DesignRepackMover.cc | |
| DesignRepackMover.fwd.hh | Forward declations for DesignRepackMover |
| DesignRepackMover.hh | |
| ForceDisulfidesMover.cc | |
| ForceDisulfidesMover.fwd.hh | ForceDisulfidesMover forward declarations header |
| ForceDisulfidesMover.hh | |
| ForceDisulfidesMoverCreator.hh | |
| ► canonical_sampling | |
| ► mc_convergence_checks | |
| Heat_ConvergenceCheck.hh | |
| HierarchicalLevel.cc | |
| HierarchicalLevel.fwd.hh | |
| HierarchicalLevel.hh | |
| HPool.cc | Hierarchical pool |
| HPool.fwd.hh | Hierarchical pool |
| HPool.hh | Hierarchical pool |
| MPIBPool_ConvergenceCheck.cc | |
| MPIBPool_ConvergenceCheck.fwd.hh | |
| MPIBPool_ConvergenceCheck.hh | |
| MPIHPool_ConvergenceCheck.cc | |
| MPIHPool_ConvergenceCheck.fwd.hh | |
| MPIHPool_ConvergenceCheck.hh | |
| MPIPool_ConvergenceCheck.cc | |
| MPIPool_ConvergenceCheck.fwd.hh | |
| MPIPool_ConvergenceCheck.hh | |
| Pool_ConvergenceCheck.cc | |
| Pool_ConvergenceCheck.hh | |
| pool_util.cc | |
| pool_util.hh | |
| util.cc | |
| util.hh | |
| AsyncMPITemperingBase.cc | |
| AsyncMPITemperingBase.hh | |
| BiasedMonteCarlo.cc | |
| BiasedMonteCarlo.fwd.hh | |
| BiasedMonteCarlo.hh | |
| BiasEnergy.cc | |
| BiasEnergy.fwd.hh | |
| BiasEnergy.hh | |
| BiasEnergy.tmpl.hh | |
| CanonicalSamplingApplication.cc | |
| CanonicalSamplingApplication.hh | |
| CanonicalSamplingMover.cc | |
| CanonicalSamplingMover.fwd.hh | |
| CanonicalSamplingMover.hh | |
| DbTrajectoryRecorder.cc | |
| DbTrajectoryRecorder.fwd.hh | |
| DbTrajectoryRecorder.hh | |
| DbTrajectoryRecorderCreator.hh | This class will create instances of Mover DbTrajectoryRecorder for the MoverFactory |
| HamiltonianExchange.cc | |
| HamiltonianExchange.fwd.hh | |
| HamiltonianExchange.hh | |
| HamiltonianExchangeCreator.hh | This class will create instances of Mover HamiltonianExchange for the MoverFactory |
| MetricRecorder.cc | |
| MetricRecorder.fwd.hh | Forward declarations for class MetricRecorder |
| MetricRecorder.hh | |
| MetricRecorderCreator.hh | This class will create instances of Mover MetricRecorder for the MoverFactory |
| MetropolisHastingsMover.cc | MetropolisHastingsMover methods implemented |
| MetropolisHastingsMover.fwd.hh | MetropolisHastingsMover forward declarations header |
| MetropolisHastingsMover.hh | Implement replica exchange in the MetropolisHastingsMover Framework |
| MetropolisHastingsMoverCreator.hh | This class will create instances of Mover MetropolisHastingsMover for the MoverFactory |
| MultiTemperatureTrialCounter.cc | |
| MultiTemperatureTrialCounter.hh | |
| ParallelTempering.cc | |
| ParallelTempering.fwd.hh | |
| ParallelTempering.hh | |
| ParallelTemperingCreator.hh | This class will create instances of Mover ParallelTempering for the MoverFactory |
| PDBTrajectoryRecorder.cc | |
| PDBTrajectoryRecorder.fwd.hh | |
| PDBTrajectoryRecorder.hh | |
| PDBTrajectoryRecorderCreator.hh | This class will create instances of Mover PDBTrajectoryRecorder for the MoverFactory |
| ProgressBarObserver.cc | |
| ProgressBarObserver.fwd.hh | |
| ProgressBarObserver.hh | |
| ProgressBarObserverCreator.hh | |
| readme.hh | |
| SidechainMetropolisHastingsMover.cc | SidechainMetropolisHastingsMover methods implemented |
| SidechainMetropolisHastingsMover.fwd.hh | |
| SidechainMetropolisHastingsMover.hh | |
| SidechainMetropolisHastingsMoverCreator.hh | This class will create instances of Mover SidechainMetropolisHastingsMover for the MoverFactory |
| SilentTrajectoryRecorder.cc | |
| SilentTrajectoryRecorder.fwd.hh | Forward declarations for class SilentTrajectoryRecorder |
| SilentTrajectoryRecorder.hh | |
| SilentTrajectoryRecorderCreator.hh | This class will create instances of Mover SilentTrajectoryRecorder for the MoverFactory |
| SimulatedTempering.cc | |
| SimulatedTempering.fwd.hh | |
| SimulatedTempering.hh | |
| SimulatedTemperingCreator.hh | This class will create instances of Mover SimulatedTempering for the MoverFactory |
| TemperatureController.cc | |
| TemperatureController.fwd.hh | |
| TemperatureController.hh | |
| TemperingBase.cc | |
| TemperingBase.fwd.hh | |
| TemperingBase.hh | |
| ThermodynamicMover.cc | ThermodynamicMover methods implemented |
| ThermodynamicMover.fwd.hh | ThermodynamicMover forward declarations header |
| ThermodynamicMover.hh | |
| ThermodynamicObserver.cc | ThermodynamicObserver methods implemented |
| ThermodynamicObserver.fwd.hh | ThermodynamicObserver forward declarations header |
| ThermodynamicObserver.hh | |
| TrajectoryRecorder.cc | |
| TrajectoryRecorder.fwd.hh | Forward declarations for class TrajectoryRecorder |
| TrajectoryRecorder.hh | |
| TrialCounterObserver.cc | Protocols::canonical_sampling::TrialCounterObserver methods implemented |
| TrialCounterObserver.hh | |
| TrialCounterObserverCreator.hh | This class will create instances of Mover TrialCounterObserver for the MoverFactory |
| WTEBiasEnergy.cc | |
| WTEBiasEnergy.hh | |
| ► carbohydrates | |
| CreateGlycanSequonMover.cc | Mutates residues to create a potential glycosylation site using known sequence motifs of N- or C- linked glycans. Includes options for Enhanced Sequons for N-linked glycans that have been shown to have higher rates of glycosylation as well as other positions that have been shown to influence the glycosylation chemistry |
| CreateGlycanSequonMover.fwd.hh | Mutates residues to create a potential glycosylation site using known sequence motifs of N- or C- linked glycans. Includes options for Enhanced Sequons for N-linked glycans that have been shown to have higher rates of glycosylation as well as other positions that have been shown to influence the glycosylation chemistry |
| CreateGlycanSequonMover.hh | Mutates residues to create a potential glycosylation site using known sequence motifs of N- or C- linked glycans. Includes options for Enhanced Sequons for N-linked glycans that have been shown to have higher rates of glycosylation as well as other positions that have been shown to influence the glycosylation chemistry |
| CreateGlycanSequonMoverCreator.hh | Mutates residues to create a potential glycosylation site using known sequence motifs of N- or C- linked glycans. Includes options for Enhanced Sequons for N-linked glycans that have been shown to have higher rates of glycosylation as well as other positions that have been shown to influence the glycosylation chemistry |
| GlycanSampler.cc | Main mover for Glycan Relax, which optimizes glycans in a pose |
| GlycanSampler.fwd.hh | Main mover for Glycan Relax, which optimizes glycans in a pose |
| GlycanSampler.hh | Main mover for Glycan Relax, which optimizes glycans in a pose |
| GlycanSamplerCreator.hh | Main mover for Glycan Relax, which optimizes glycans in a pose |
| GlycanTreeMinMover.cc | A class that selects the downstream branch from residues in a movemap/selector, and minimizes those residues if on in the primary glycan movemap. Multiple Applies randomly select a different residue in the movemap/selector |
| GlycanTreeMinMover.fwd.hh | A class that selects the downstream branch from residues in a movemap/selector, and minimizes those residues if on in the primary glycan movemap. Multiple Applies randomly select a different residue in the movemap/selector |
| GlycanTreeMinMover.hh | A class that selects the downstream branch from residues in a movemap/selector, and minimizes those residues if on in the primary glycan movemap. Multiple Applies randomly select a different residue in the movemap/selector |
| GlycanTreeMinMoverCreator.hh | A class that selects the downstream branch from residues in a movemap/selector, and minimizes those residues if on in the primary glycan movemap. Multiple Applies randomly select a different residue in the movemap/selector |
| GlycanTreeModeler.cc | A protocol for optimizing glycan trees using the GlycanSampler from the base of the tree out to the leaves |
| GlycanTreeModeler.fwd.hh | A protocol for optimizing glycan trees using the GlycanSampler from the base of the tree out to the leaves |
| GlycanTreeModeler.hh | A protocol for optimizing glycan trees using the GlycanSampler from the base of the tree out to the leaves |
| GlycanTreeModelerCreator.hh | A protocol for optimizing glycan trees using the GlycanSampler from the base of the tree out to the leaves |
| IdealizeAnomericHydrogens.cc | Mover to idealize carbohydrate anomeric hydrogens |
| IdealizeAnomericHydrogens.fwd.hh | |
| IdealizeAnomericHydrogens.hh | Mover to idealize carbohydrate anomeric hydrogens |
| IdealizeAnomericHydrogensCreator.hh | This code changes all of the dihedrals of a particular glycosidic linkage based on database info, esentially sampling carbohydrate dihedral conformers of two residues |
| LinkageConformerMover.cc | This code changes all of the dihedrals of a particular glycosidic linkage based on database info, essentially sampling carbohydrate dihedral conformers of two residues |
| LinkageConformerMover.fwd.hh | This code changes all of the dihedrals of a particular glycosidic linkage based on database info, essentially sampling carbohydrate dihedral conformers of two residues |
| LinkageConformerMover.hh | This code changes all of the dihedrals of a particular glycosidic linkage based on database info, esentially sampling carbohydrate dihedral conformers of two residues |
| LinkageConformerMoverCreator.hh | This code changes all of the dihedrals of a particular glycosidic linkage based on database info, esentially sampling carbohydrate dihedral conformers of two residues |
| RingPlaneFlipMover.cc | Method definitions for RingPlaneFlipMover |
| RingPlaneFlipMover.fwd.hh | Forward declarations for RingPlaneFlipMover |
| RingPlaneFlipMover.hh | Declarations and simple accessor/mutator definitions for RingPlaneFlipMover |
| RingPlaneFlipMoverCreator.hh | Method declarations for RingPlaneFlipMoverCreator |
| SimpleGlycosylateMover.cc | A mover for glycosylation of common biological glycosylations |
| SimpleGlycosylateMover.fwd.hh | A mover for glycosylation of common biological glycosylations |
| SimpleGlycosylateMover.hh | A mover for glycosylation of common biological glycosylations |
| SimpleGlycosylateMoverCreator.hh | A mover for glycosylation of common biological glycosylations |
| TautomerizeAnomerMover.cc | Method definitions for TautomerizeAnomerMover |
| TautomerizeAnomerMover.fwd.hh | Forward declarations for TautomerizeAnomerMover |
| TautomerizeAnomerMover.hh | Declarations and simple accessor/mutator definitions for TautomerizeAnomerMover |
| TautomerizeAnomerMoverCreator.hh | Method declarations for TautomerizeAnomerMoverCreator |
| util.cc | Util functions for Carbohydrates |
| util.hh | Util functions for Carbohydrates |
| ► cartesian | |
| md.cc | |
| md.hh | |
| ► checkpoint | |
| Checkpoint.cc | |
| Checkpoint.fwd.hh | |
| Checkpoint.hh | |
| CheckPointer.cc | |
| CheckPointer.fwd.hh | |
| CheckPointer.hh | |
| ► chemically_conjugated_docking | |
| Gp_extra_bodies.cc | |
| Gp_extra_bodies.hh | Helper quantification metrics for the original publication of the UBQ_Gp code |
| Gp_quantification_metrics.cc | |
| Gp_quantification_metrics.hh | Helper quantification metrics for the original publication of the UBQ_Gp code |
| UBQ_GTPaseMover.cc | A mover typically used for binding ubiquitin to a substrate protein |
| UBQ_GTPaseMover.fwd.hh | A mover typically used for binding ubiquitin to a substrate protein |
| UBQ_GTPaseMover.hh | A mover typically used for binding ubiquitin to a substrate protein |
| UBQ_GTPaseMoverCreator.hh | A mover typically used for binding ubiquitin to a substrate protein |
| ► cluster | |
| ► calibur | |
| AdjacentList.cc | |
| AdjacentList.hh | |
| Clustering.cc | |
| Clustering.hh | |
| cubic.cc | |
| cubic.hh | |
| InitCluster.cc | |
| InitCluster.hh | |
| jacobi.cc | |
| jacobi.hh | |
| pdb_util.cc | |
| pdb_util.hh | |
| PreloadedPDB.cc | |
| PreloadedPDB.fwd.hh | |
| PreloadedPDB.hh | |
| rmsd.cc | |
| rmsd.hh | |
| SimPDB.cc | |
| SimPDB.fwd.hh | |
| SimPDB.hh | |
| APCluster.cc | |
| APCluster.fwd.hh | |
| APCluster.hh | |
| cluster.cc | |
| cluster.hh | |
| ► comparative_modeling | |
| ► features | |
| ResidueFeature.cc | |
| ResidueFeature.fwd.hh | Forward declaration for ResidueFeature class |
| ResidueFeature.hh | Abstract base class for per-residue features used in comparative modeling |
| ResidueFeatureFactory.cc | Factory for creating various types of ResidueFeatures |
| ResidueFeatureFactory.hh | |
| SSFeature.cc | |
| SSFeature.fwd.hh | Forward declaration for SSFeature class |
| SSFeature.hh | |
| TorsionFeature.cc | |
| TorsionFeature.fwd.hh | Forward declaration for TorsionFeature class |
| TorsionFeature.hh | |
| Align_RmsdEvaluator.cc | |
| Align_RmsdEvaluator.fwd.hh | Forward declaration for Align_RmsdEvaluator class |
| Align_RmsdEvaluator.hh | |
| Align_RotamerEvaluator.cc | |
| Align_RotamerEvaluator.fwd.hh | Forward declaration for Align_RotamerEvaluator class |
| Align_RotamerEvaluator.hh | |
| AlignmentClustering.cc | |
| AlignmentClustering.fwd.hh | |
| AlignmentClustering.hh | Divide input alns into clusters based on gdtmm comparison of partial models. Uses the top e-value or hh-value sample as the cluster center |
| AlignmentSet.cc | |
| AlignmentSet.fwd.hh | Forward declaration for AlignmentSet class |
| AlignmentSet.hh | |
| AlignRmsdTargetEvaluatorCreator.cc | |
| AlignRmsdTargetEvaluatorCreator.hh | Header for AlignRmsdTargetEvaluatorCreator |
| cm_main.cc | |
| cm_main.hh | |
| coord_util.cc | |
| coord_util.hh | |
| ExtraThreadingMover.cc | Method declarations for ExtraThreadingMover |
| ExtraThreadingMover.hh | Class for copying extra stuff (ligands,dna,peptides,etc) from a template Pose |
| GenericJobInputter.cc | |
| GenericJobInputter.fwd.hh | Header file for ThreadingJobInputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| GenericJobInputter.hh | |
| GenericJobInputterCreator.hh | |
| IgnoreSubsetConstraintSet.cc | |
| IgnoreSubsetConstraintSet.fwd.hh | Forward declaration for IgnoreSubsetConstraintSet class |
| IgnoreSubsetConstraintSet.hh | |
| LoopRelaxMover.cc | |
| LoopRelaxMover.fwd.hh | Forward declaration for LoopRelaxMover class |
| LoopRelaxMover.hh | |
| LoopRelaxMoverCreator.hh | |
| LoopRelaxThreadingMover.cc | |
| LoopRelaxThreadingMover.fwd.hh | Forward declaration for LoopRelaxThreadingMover class |
| LoopRelaxThreadingMover.hh | |
| MultiThreadingMover.cc | |
| MultiThreadingMover.hh | |
| PartialThreadingMover.cc | |
| PartialThreadingMover.hh | |
| RecoverSideChainsMover.cc | |
| RecoverSideChainsMover.fwd.hh | Forward declaration for RecoverSideChainsMover class |
| RecoverSideChainsMover.hh | |
| StealLigandMover.cc | |
| StealLigandMover.fwd.hh | Forward declaration for StealLigandMover class |
| StealLigandMover.hh | |
| StealSideChainsMover.cc | |
| StealSideChainsMover.fwd.hh | Forward declaration for StealSideChainsMover class |
| StealSideChainsMover.hh | |
| ThreadingJob.cc | |
| ThreadingJob.fwd.hh | Header file for ThreadingJob classes |
| ThreadingJob.hh | Header file for ThreadingJob classes |
| ThreadingJobInputter.cc | |
| ThreadingJobInputter.fwd.hh | |
| ThreadingJobInputter.hh | |
| ThreadingJobInputterCreator.hh | |
| ThreadingMover.cc | Method declarations for ThreadingMover |
| ThreadingMover.hh | |
| util.cc | Set of utilities used in comparative modeling of protein structures |
| util.hh | Small bundle of utilities for comparative modeling |
| ► constel | |
| AromaticFilter.cc | Definition of a filter to extract constellations containing aromatic rings |
| AromaticFilter.hh | Declaration of a filter to extract constellations containing aromatic rings |
| ChainTerm.cc | Implementation of class ChainTerm |
| ChainTerm.fwd.hh | Forward declaration of class ChainTerm |
| ChainTerm.hh | Class identifying the N- and C-terminal residues of a chain |
| cnl_info.cc | Definition of generic functions returning information on a constellation |
| cnl_info.hh | Declaration generic functions returning info on a constellation |
| ExcludedFilter.cc | Definition of class ExcludedFilter |
| ExcludedFilter.hh | Declaration of a filter to exclude a given set of residues |
| FilterByProxTerm.cc | Implementation of class FilterByProxTerm |
| FilterByProxTerm.hh | Class to filter out constellations based on proximity constraints on the N- and C-termini of their chains |
| FilterBySASA.cc | Definition of class FilterBySASA |
| FilterBySASA.hh | A class to filter out constellations based on SASA (Solvent Accessible Surface Area) |
| InterfaceFilter.cc | Definition of a filter to extract constellations shared by multiple chains |
| InterfaceFilter.hh | Declaration of a filter to extract constellations shared by multiple chains |
| MasterFilter.cc | Definition of class MasterFilter |
| MasterFilter.hh | Class to manage the application of filters to constellations |
| NeighTeller.cc | A class to determine neighboring relationships between or among residues |
| NeighTeller.hh | A class to determine neighboring relationships between or among residues |
| PairConstelFilters.cc | Definition of filters for constellations formed by a pair of residues |
| PairConstelFilters.hh | Filters for constellations formed by a pair of residues |
| Primitives.cc | Definition of primitive functions and classes used by the constel program |
| Primitives.hh | Declarations of primitive functions and classes used by the constel program |
| ResidueMask.cc | Definition of class ResidueMask |
| ResidueMask.hh | Class implementing a boolean mask over the residues of a pose |
| SearchOptions.cc | Definition of the search functions declared in SearchOption.hh |
| SearchOptions.hh | Declaration of the different ways in which a pose is searched for constellations |
| SingResCnlCrea.cc | Definition of the class to create single-residue constellations |
| SingResCnlCrea.hh | Definition of a class to create single-residue constellations |
| ► constraint_filters | |
| ConstraintScoreCutoffFilter.cc | |
| ConstraintScoreCutoffFilter.fwd.hh | |
| ConstraintScoreCutoffFilter.hh | Header file for ConstraintScoreCutoffFitler class |
| ConstraintScoreCutoffFilterCreator.hh | FilterCreator for the ConstraintScoreCutoffFilter |
| ConstraintScoreFilter.cc | Filter that computes scores of constraints generated by ConstraintGenerators |
| ConstraintScoreFilter.fwd.hh | Filter that computes scores of constraints generated by ConstraintGenerators |
| ConstraintScoreFilter.hh | Filter that computes scores of constraints generated by ConstraintGenerators |
| ConstraintScoreFilterCreator.hh | Filter that computes scores of constraints generated by ConstraintGenerators |
| SavePoseConstraintToFileFilter.cc | |
| SavePoseConstraintToFileFilter.hh | Filter for outputing information about the pose |
| SavePoseConstraintToFileFilterCreator.hh | FilterCreator for the SavePoseConstraintToFileFilter |
| ShowConstraintsFilter.cc | Iterate over all constraints on the pose and invoke their show methods |
| ShowConstraintsFilter.fwd.hh | Iterate over all constraints on the pose and invoke their show methods |
| ShowConstraintsFilter.hh | Iterate over all constraints on the pose and invoke their show methods |
| ShowConstraintsFilterCreator.hh | FilterCreators for the ShowConstraintsFilterCreator |
| ► constraint_generator | |
| AddConstraints.cc | Adds constraints generated by ConstraintGenerators to a pose |
| AddConstraints.fwd.hh | Adds constraints generated by ConstraintGenerators to a pose |
| AddConstraints.hh | Adds constraints generated by ConstraintGenerators to a pose |
| AddConstraintsCreator.hh | Adds constraints generated by ConstraintGenerators to a pose |
| AtomPairConstraintGenerator.cc | Generates atom pair constraints for a set of residues from the current or reference pose |
| AtomPairConstraintGenerator.fwd.hh | Generates atom pair constraints for a set of residues from the current or reference pose |
| AtomPairConstraintGenerator.hh | Generates atom pair constraints for a set of residues from the current or reference pose |
| AtomPairConstraintGeneratorCreator.hh | Generates atom pair constraints for a set of residues from the current or reference pose |
| ConstraintGenerator.cc | Abstract class for generating constraints |
| ConstraintGenerator.fwd.hh | |
| ConstraintGenerator.hh | Abstract base class that generates constraints |
| ConstraintGeneratorCreator.fwd.hh | Forward declaration of a class that instantiates a particular ConstraintGenerator |
| ConstraintGeneratorCreator.hh | Class for instantiating a particular ConstraintGenerator |
| ConstraintGeneratorFactory.cc | Implementation of the class for instantiating arbitrary ConstraintGenerators from a string –> ConstraintGeneratorCreator map |
| ConstraintGeneratorFactory.hh | |
| ConstraintGeneratorRegistrator.hh | Declaration of the template class for registrating ConstraintGeneratorCreators with the ConstriantGeneratorFactory |
| ConstraintsManager.cc | Manages lists of constraints generated by ConstraintGenerators |
| ConstraintsManager.fwd.hh | Manages lists of constraints generated by ConstraintGenerators |
| ConstraintsManager.hh | Manages lists of constraints generated by ConstraintGenerators |
| ConstraintsMap.cc | Cacheable data map to cache constraint pointers in the pose |
| ConstraintsMap.fwd.hh | Cacheable data map to cache constraint pointers in the pose |
| ConstraintsMap.hh | Cacheable data map to cache constraint pointers in the pose |
| CoordinateConstraintGenerator.cc | Generates coodinate constraints |
| CoordinateConstraintGenerator.fwd.hh | Generates coodinate constraints |
| CoordinateConstraintGenerator.hh | Generates coodinate constraints |
| CoordinateConstraintGeneratorCreator.hh | Generates coodinate constraints |
| DihedralConstraintGenerator.cc | A cst generator that creates Dihedral constraints for specified residues using a residue selector |
| DihedralConstraintGenerator.fwd.hh | A cst generator that creates Dihedral constraints for specified residues using a residue selector |
| DihedralConstraintGenerator.hh | A cst generator that creates Dihedral constraints for specified residues using a residue selector |
| DihedralConstraintGeneratorCreator.hh | A cst generator that creates Dihedral constraints for specified residues using a residue selector |
| DistanceConstraintGenerator.cc | Generates AtomPair constraints to enforce a given distance between two residue subsets |
| DistanceConstraintGenerator.fwd.hh | Generates AtomPair constraints to enforce a given distance between two residue subsets |
| DistanceConstraintGenerator.hh | Generates AtomPair constraints to enforce a given distance between two residue subsets |
| DistanceConstraintGeneratorCreator.hh | Generates AtomPair constraints to enforce a given distance between two residue subsets |
| HydrogenBondConstraintGenerator.cc | |
| HydrogenBondConstraintGenerator.fwd.hh | |
| HydrogenBondConstraintGenerator.hh | |
| HydrogenBondConstraintGeneratorCreator.hh | Base class for ConstraintCreators for the Constraint |
| MembraneSpanConstraintGenerator.cc | Generates constraints for membrane spans to stay in the membrane |
| MembraneSpanConstraintGenerator.fwd.hh | Generates constraints for membrane spans to stay in the membrane |
| MembraneSpanConstraintGenerator.hh | Generates constraints for membrane spans to stay in the membrane |
| MembraneSpanConstraintGeneratorCreator.hh | Generates constraints for membrane spans to stay in the membrane |
| MetalContactsConstraintGenerator.cc | This constraint generator takes residue selectors for a residue/residues containing metal ion(s) and for residue(s) for which to set up contacts. It allows users to specify which base atoms will be used to define angles/dihedrals to constrain; ideal values for angles/dihedrals/distances; and an option to constrain to native values |
| MetalContactsConstraintGenerator.fwd.hh | This constraint generator takes residue selectors for a residue/residues containing metal ion(s) and for residue(s) for which to set up contacts. It allows users to specify which base atoms will be used to define angles/dihedrals to constrain; ideal values for angles/dihedrals/distances; and an option to constrain to native values |
| MetalContactsConstraintGenerator.hh | This constraint generator takes residue selectors for a residue containing metal ion(s) and for residue(s) for which to set up contacts. It allows users to specify which base atoms will be used to define angles/dihedrals to constrain; ideal values for angles/dihedrals/distances; and an option to constrain to native values |
| MetalContactsConstraintGeneratorCreator.hh | This constraint generator takes residue selectors for a residue/residues containing metal ion(s) and for residue(s) for which to set up contacts. It allows users to specify which base atoms will be used to define angles/dihedrals to constrain; ideal values for angles/dihedrals/distances; and an option to constrain to native values |
| RemoveConstraints.cc | Removes constraints generated by a ConstraintGenerator |
| RemoveConstraints.fwd.hh | Removes constraints generated by a ConstraintGenerator |
| RemoveConstraints.hh | Removes constraints generated by a ConstraintGenerator |
| RemoveConstraintsCreator.hh | Removes constraints generated by a ConstraintGenerator |
| ResidueTypeConstraintGenerator.cc | Generates residue type constraints for a set of residues from the current or reference pose |
| ResidueTypeConstraintGenerator.fwd.hh | Generates residue type constraints for a set of residues from the current or reference pose |
| ResidueTypeConstraintGenerator.hh | Generates residue type constraints for a set of residues from the current or reference pose |
| ResidueTypeConstraintGeneratorCreator.hh | Generates residue type constraints for a set of residues from the current pose |
| TerminiConstraintGenerator.cc | Generates distance constraints between the upper and lower termini |
| TerminiConstraintGenerator.fwd.hh | Generates distance constraints between the upper and lower termini |
| TerminiConstraintGenerator.hh | Generates distance constraints between the upper and lower termini |
| TerminiConstraintGeneratorCreator.hh | Generates distance constraints between the upper and lower termini |
| util.cc | Utility functions for constraint generators |
| util.hh | Utility functions for constraint generators |
| ► constraint_movers | |
| AddConstraintsToCurrentConformationMover.cc | Add constraints to the current pose conformation |
| AddConstraintsToCurrentConformationMover.hh | Add constraints to the current pose conformation |
| AddConstraintsToCurrentConformationMoverCreator.hh | |
| ClearConstraintsMover.cc | Remove constraints from the current pose conformation |
| ClearConstraintsMover.hh | Add constraints to the current pose conformation |
| ClearConstraintsMoverCreator.hh | |
| ConstraintSetMover.cc | Assigns a ConstraintSet to a pose. Reads and creats ConstraintSet from file via command line option -constraints::cst_file, unless a ConstraintSet is supplied via the constructor or the constraint_set() method |
| ConstraintSetMover.fwd.hh | |
| ConstraintSetMover.hh | Assigns a ConstraintSet to a pose. Reads and creats ConstraintSet from file via command line option -constraints::cst_file, unless a ConstraintSet is supplied via the constructor or the constraint_set() method |
| ConstraintSetMoverCreator.hh | |
| CstInfoMover.cc | A Mover to output information about constraints |
| CstInfoMover.fwd.hh | A Mover to output information about constraints |
| CstInfoMover.hh | A Mover to output information about constraints |
| CstInfoMoverCreator.hh | A Mover to output information about constraints |
| ResidueTypeConstraintMover.cc | Assigns a ResidueTypeConstraint to a pose |
| ResidueTypeConstraintMover.fwd.hh | |
| ResidueTypeConstraintMover.hh | Assigns a ResidueTypeConstraint to a pose |
| ResidueTypeConstraintMoverCreator.hh | This class will create instances of protocols::moves::Mover ResidueTypeConstraintMover for the protocols::moves::MoverFactory |
| ► constraints_additional | |
| AdditionalConstraintCreators.cc | |
| AdditionalConstraintCreators.hh | |
| AmbiguousMultiConstraint.cc | Declarations for a type of constraint that holds a number of constraints |
| AmbiguousMultiConstraint.fwd.hh | |
| AmbiguousMultiConstraint.hh | Declarations for a type of constraint that holds multiple other |
| BindingSiteConstraint.cc | This constrains some set of three or more atoms to maintain the same geometry as the starting pose. Constrainted binding sites are read in using the ConstraintIO class (maybe only with the defunct section-based constraints?) Binding-site constraints use the same weight as atom-pair constraints, and (should) work with any protocol where atom-pair constraints are respected. Constraints on sidechain atoms are automatically converted to constraints on centroids when performing centroid-level manipulation |
| BindingSiteConstraint.hh | |
| CombinedConstraintEvaluator.cc | |
| CombinedConstraintEvaluator.hh | |
| CombinedConstraintEvaluatorCreator.cc | |
| CombinedConstraintEvaluatorCreator.hh | |
| COMCoordinateConstraint.cc | |
| COMCoordinateConstraint.hh | |
| ConstraintEvaluator.cc | |
| ConstraintEvaluator.fwd.hh | |
| ConstraintEvaluator.hh | |
| ConstraintEvaluatorCreator.cc | |
| ConstraintEvaluatorCreator.hh | |
| MaxSeqSepConstraintSet.cc | |
| MaxSeqSepConstraintSet.fwd.hh | |
| MaxSeqSepConstraintSet.hh | Helper class for FoldConstraints Protocol, filters constraints by sequence separation |
| SequenceCoupling1BDConstraint.cc | |
| SequenceCoupling1BDConstraint.fwd.hh | This is a constraint that refers to a core::sequence::SequenceCoupling? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design) |
| SequenceCoupling1BDConstraint.hh | This is a constraint that refers to a core::sequence::SequenceCoupling1BD? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design) |
| SequenceCouplingConstraint.cc | |
| SequenceCouplingConstraint.fwd.hh | This is a constraint that refers to a core::sequence::SequenceCoupling? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design) |
| SequenceCouplingConstraint.hh | This is a constraint that refers to a core::sequence::SequenceCoupling? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design) |
| ► contact_map | |
| ContactMap.cc | Method code and full headers for ContactMapCreator, ContactMap, ContactPartner and contact |
| ContactMap.fwd.hh | |
| ContactMap.hh | Mover to create a ContactMap |
| ContactMapCreator.hh | |
| ► coupled_moves | |
| CoupledMovesProtocol.cc | Mover that implements the CoupledMovesProtocol |
| CoupledMovesProtocol.fwd.hh | CoupledMovesProtocol forward declarations header |
| CoupledMovesProtocol.hh | Mover that implements the CoupledMovesProtocol |
| CoupledMovesProtocolCreator.hh | |
| ► cryst | |
| CheshireCell.hh | A struct used by spacegroup.cc and its helper functions |
| cryst_movers.cc | Protocols for folding into density |
| cryst_movers.hh | |
| cryst_movers_creator.hh | |
| cryst_rms.cc | |
| cryst_rms.hh | |
| refinable_lattice.cc | Protocols for folding into density |
| refinable_lattice.hh | |
| refinable_lattice_creator.hh | |
| spacegroup.cc | |
| spacegroup.hh | |
| spacegroup_symmops1.cc | Contains helper functions for the symmetry operations. Split from spacegroups.cc to prevent the 32-bit compilation from running out of memory during compilation |
| spacegroup_symmops1.hh | Contains helper functions for the symmetry operations. Split from spacegroups.cc to prevent the 32-bit compilation from running out of memory during compilation |
| spacegroup_symmops2.cc | Contains helper functions for the symmetry operations. Split from spacegroups.cc to prevent the 32-bit compilation from running out of memory during compilation |
| spacegroup_symmops2.hh | Contains helper functions for the symmetry operations. Split from spacegroups.cc to prevent the 32-bit compilation from running out of memory during compilation |
| spacegroup_symmops3.cc | Contains helper functions for the symmetry operations. Split from spacegroups.cc to prevent the 32-bit compilation from running out of memory during compilation |
| spacegroup_symmops3.hh | Contains helper functions for the symmetry operations. Split from spacegroups.cc to prevent the 32-bit compilation from running out of memory during compilation |
| spacegroup_symmops4.cc | Contains helper functions for the symmetry operations. Split from spacegroups.cc to prevent the 32-bit compilation from running out of memory during compilation |
| spacegroup_symmops4.hh | Contains helper functions for the symmetry operations. Split from spacegroups.cc to prevent the 32-bit compilation from running out of memory during compilation |
| TwoDLattice.cc | Protocols for folding into density |
| TwoDLattice.hh | |
| util.hh | |
| wallpaper.cc | |
| wallpaper.hh | |
| ► cutoutdomain | |
| CutOutDomain.cc | |
| CutOutDomain.fwd.hh | |
| CutOutDomain.hh | |
| CutOutDomainCreator.hh | |
| ► cyclic_peptide | |
| ► crosslinker | |
| CrosslinkerMoverHelper.cc | A base class for helper objects that the CrosslinkerMover uses to set up specific types of linkers |
| CrosslinkerMoverHelper.fwd.hh | A base class for helper objects that the CrosslinkerMover uses to set up specific types of threefold linkers |
| CrosslinkerMoverHelper.hh | A base class for helper objects that the CrosslinkerMover uses to set up specific types of linkers |
| Metal_HelperBase.cc | A base class for setting up metals. This is a pure virtual class that must be subclassed for specific metal geometries |
| Metal_HelperBase.fwd.hh | Forward declarations for a base class for setting up metals. This is a pure virtual class that must be subclassed for specific metal geometries |
| Metal_HelperBase.hh | Headers for a base class for setting up metals. This is a pure virtual class that must be subclassed for specific metal geometries |
| OctahedralMetal_Helper.cc | A helper class for setting up octahedrally-coordinated metals |
| OctahedralMetal_Helper.fwd.hh | |
| OctahedralMetal_Helper.hh | A helper class for setting up octahedrally-coordinated metals |
| SquarePlanarMetal_Helper.cc | A helper class for setting up square planarly-coordinated metals like Ni |
| SquarePlanarMetal_Helper.fwd.hh | |
| SquarePlanarMetal_Helper.hh | A helper class for setting up square planarly-coordinated metals like Ni |
| SquarePyramidalMetal_Helper.cc | A helper class for setting up square pyramidally-coordinated metals like Ni |
| SquarePyramidalMetal_Helper.fwd.hh | A helper class for setting up square pyramidally-coordinated metals like Ni |
| SquarePyramidalMetal_Helper.hh | A helper class for setting up square pyramidally-coordinated metals like Ni |
| TBMB_Helper.cc | A derived class of the CrosslinkerMoverHelper base class, used to set up the 1,3,5-tris(bromomethyl)benzene (TBMB) cross-linker |
| TBMB_Helper.fwd.hh | A derived class of the CrosslinkerMoverHelper base class, used to set up the 1,3,5-tris(bromomethyl)benzene (TBMB) cross-linker |
| TBMB_Helper.hh | A derived class of the CrosslinkerMoverHelper base class, used to set up the 1,3,5-tris(bromomethyl)benzene (TBMB) cross-linker |
| TetrahedralMetal_Helper.cc | A helper class for setting up tetrahedrally-coordinated metals like Zn or Cu |
| TetrahedralMetal_Helper.fwd.hh | |
| TetrahedralMetal_Helper.hh | A helper class for setting up tetrahedrally-coordinated metals like Zn or Cu |
| TMA_Helper.cc | A derived class of the CrosslinkerMoverHelper base class, used to set up the trimesic acid (TMA) cross-linker |
| TMA_Helper.fwd.hh | A derived class of the CrosslinkerMoverHelper base class, used to set up the trimesic acid (TMA) cross-linker |
| TMA_Helper.hh | A derived class of the CrosslinkerMoverHelper base class, used to set up the trimesic acid (TMA) cross-linker |
| TrigonalPlanarMetal_Helper.cc | A helper class for setting up trigonal planarly-coordinated metals like Zn or Cu |
| TrigonalPlanarMetal_Helper.fwd.hh | |
| TrigonalPlanarMetal_Helper.hh | A helper class for setting up trigonal planarly-coordinated metals like Zn or Cu |
| TrigonalPyramidalMetal_Helper.cc | A helper class for setting up trigonal pyramidally-coordinated metals like Zn or Cu |
| TrigonalPyramidalMetal_Helper.fwd.hh | A helper class for setting up trigonal pyramidally-coordinated metals like Zn or Cu |
| TrigonalPyramidalMetal_Helper.hh | A helper class for setting up trigonal pyramidally-coordinated metals like Zn or Cu |
| CreateAngleConstraint.cc | Add angle constraints to the current pose conformation |
| CreateAngleConstraint.fwd.hh | Defines owning pointers for CreateAngleConstraint mover class |
| CreateAngleConstraint.hh | Add angle constraints to the current pose conformation |
| CreateAngleConstraintCreator.hh | |
| CreateDistanceConstraint.cc | Add distance constraints to the current pose conformation |
| CreateDistanceConstraint.fwd.hh | Defines owning pointers for CreateDistanceConstraint mover class |
| CreateDistanceConstraint.hh | Add distance constraints to the current pose conformation |
| CreateDistanceConstraintCreator.hh | |
| CreateTorsionConstraint.cc | Add torsion constraints to the current pose conformation |
| CreateTorsionConstraint.fwd.hh | Defines owning pointers for CreateTorsionConstraint mover class |
| CreateTorsionConstraint.hh | Add torsion constraints to the current pose conformation |
| CreateTorsionConstraintCreator.hh | |
| CrosslinkerMover.cc | This mover links two or more residues with a (possibly symmetric) cross-linker. It adds the crosslinker, sets up constraints, optionally packs and energy-mimizes it into place (packing/minimizing only the crosslinker and the side-chains to which it connects), and then optionally relaxes the whole structure |
| CrosslinkerMover.fwd.hh | This mover links three cysteine residues with a three-way cross-linker. It adds the crosslinker, sets up constraints, optionally packs and energy-mimizes it into place (packing/minimizing only the crosslinker and the side-chains to which it connects), andthen optionally relaxes the whole structure |
| CrosslinkerMover.hh | This mover links two or more residues with a (possibly symmetric) cross-linker. It adds the crosslinker, sets up constraints, optionally packs and energy-mimizes it into place (packing/minimizing only the crosslinker and the side-chains to which it connects), and then optionally relaxes the whole structure |
| CrosslinkerMoverCreator.hh | This mover links three cysteine residues with a three-way cross-linker. It adds the crosslinker, sets up constraints, optionally packs and energy-mimizes it into place (packing/minimizing only the crosslinker and the side-chains to which it connects), andthen optionally relaxes the whole structure |
| CycpepSymmetryFilter.cc | A filter that examines a cyclic peptide's structure and returns TRUE if and only if it has a desired backbone symmetry |
| CycpepSymmetryFilter.fwd.hh | A filter that examines a cyclic peptide's structure and returns TRUE if and only if it has a desired backbone symmetry |
| CycpepSymmetryFilter.hh | A filter that examines a cyclic peptide's structure and returns TRUE if and only if it has a desired backbone symmetry |
| CycpepSymmetryFilterCreator.hh | A filter that examines a cyclic peptide's structure and returns TRUE if and only if it has a desired backbone symmetry |
| DeclareBond.cc | Add constraints to the current pose conformation |
| DeclareBond.fwd.hh | Defines owning pointers for DeclareBond mover class |
| DeclareBond.hh | Add constraints to the current pose conformation |
| DeclareBondCreator.hh | |
| FlipChiralityMover.cc | Add constraints to the current pose conformation |
| FlipChiralityMover.fwd.hh | Defines owning pointers for FlipChiralityMover mover class |
| FlipChiralityMover.hh | Mirrors a pose |
| FlipChiralityMoverCreator.hh | |
| OversaturatedHbondAcceptorFilter.cc | This filter flags poses containing more than two hydrogen bonds to an oxygen atom, a common pathology that results from Rosetta's pairwise-decomposible scorefunction, which can't penalize excessive hydrogen bonds |
| OversaturatedHbondAcceptorFilter.fwd.hh | Forward declarations and owning pointers for the OversaturatedHbondAcceptorFilter |
| OversaturatedHbondAcceptorFilter.hh | Headers for the OversaturatedHbondAcceptorFilter. This filter flags poses containing more than two hydrogen bonds to an oxygen atom, a common pathology that results from Rosetta's pairwise-decomposible scorefunction, which can't penalize excessive hydrogen bonds |
| OversaturatedHbondAcceptorFilterCreator.hh | Creators for the OversaturatedHbondAcceptorFilter. This filter flags poses containing more than two hydrogen bonds to an oxygen atom, a common pathology that results from Rosetta's pairwise-decomposible scorefunction, which can't penalize excessive hydrogen bonds |
| PeptideCyclizeMover.cc | Adds all the required constraints and bonds to cyclize a pose |
| PeptideCyclizeMover.fwd.hh | Defines owning pointers for PeptideCyclizeMover mover class |
| PeptideCyclizeMover.hh | PeptideCyclizeMover a pose, by default with a peptide bond to N and C terminal and constraints |
| PeptideCyclizeMoverCreator.hh | |
| PeptideInternalHbondsFilter.cc | A filter that thinly wraps the PeptideInternalHbondsMetric |
| PeptideInternalHbondsFilter.fwd.hh | A filter that thinly wraps the PeptideInternalHbondsMetric |
| PeptideInternalHbondsFilter.hh | A filter that thinly wraps the PeptideInternalHbondsMetric |
| PeptideInternalHbondsFilterCreator.hh | A filter that thinly wraps the PeptideInternalHbondsMetric |
| PeptideInternalHbondsMetric.cc | A simple metric for measuring the hydrogen bonds within a peptide backbone, ignoring hydrogen bonds to other parts of a pose. Note that this metric does not count intra-residue hydrogen bonds |
| PeptideInternalHbondsMetric.fwd.hh | A simple metric for measuring the backbone hydrogen bonds within a peptide backbone, ignoring hydrogen bonds to other parts of a pose |
| PeptideInternalHbondsMetric.hh | A simple metric for measuring the hydrogen bonds within a peptide backbone, ignoring hydrogen bonds to other parts of a pose. Note that this metric does not count intra-residue hydrogen bonds |
| PeptideInternalHbondsMetricCreator.hh | A simple metric for measuring the hydrogen bonds within a peptide backbone, ignoring hydrogen bonds to other parts of a pose |
| PeptideInternalHbondsMetricTests.fwd.hh | |
| PeptideStubMover.cc | The PeptideStubMover prepends, appends, or inserts residues into an existing pose, or builds a new polymeric chain |
| PeptideStubMover.fwd.hh | Defines owning pointers for PeptideStubMover mover class |
| PeptideStubMover.hh | The PeptideStubMover prepends, appends, or inserts residues into an existing pose, or builds a new polymeric chain |
| PeptideStubMoverCreator.hh | |
| RamaMutationSelector.cc | |
| RamaMutationSelector.fwd.hh | Selects positions that would have a rama_prepro score below a given threshold IF mutated to a given residue type |
| RamaMutationSelector.hh | Selects positions that would have a rama_prepro score below a given threshold IF mutated to a given residue type |
| RamaMutationSelectorCreator.hh | Selects positions that would have a rama_prepro score below a given threshold IF mutated to a given residue type |
| SymmetricCycpepAlign.cc | Given a quasi-symmetric cyclic peptide, this mover aligns the peptide so that the cyclic symmetry axis lies along the Z-axis and the centre of mass is at the origin. It then optionally removes all but one symmetry repeat, so that true symmetry may be set up with the SetupForSymmetry mover |
| SymmetricCycpepAlign.fwd.hh | Given a quasi-symmetric cyclic peptide, this mover aligns the peptide so that the cyclic symmetry axis lies along the Z-axis and the centre of mass is at the origin. It then optionally removes all but one symmetry repeat, so that true symmetry may be set up with the SetupForSymmetry mover |
| SymmetricCycpepAlign.hh | Given a quasi-symmetric cyclic peptide, this mover aligns the peptide so that the cyclic symmetry axis lies along the Z-axis and the centre of mass is at the origin. It then optionally removes all but one symmetry repeat, so that true symmetry may be set up with the SetupForSymmetry mover |
| SymmetricCycpepAlignCreator.hh | Given a quasi-symmetric cyclic peptide, this mover aligns the peptide so that the cyclic symmetry axis lies along the Z-axis and the centre of mass is at the origin. It then optionally removes all but one symmetry repeat, so that true symmetry may be set up with the SetupForSymmetry mover |
| TryDisulfPermutations.cc | Tries all permutations of disulfide bonds between disulfide-forming residues in a pose |
| TryDisulfPermutations.fwd.hh | Defines owning pointers for TryDisulfPermutations mover class |
| TryDisulfPermutations.hh | Headers for TryDisulfPermutations.cc. Tries all permutations of disulfide bonds between disulfide-forming residues in a pose |
| TryDisulfPermutationsCreator.hh | This class will create instances of Mover TryDisulfPermutations for the MoverFactory |
| ► cyclic_peptide_predict | |
| HierarchicalHybridJD_JobResultsSummary.cc | A small helper class used by the SimpleCycpepPredict_MPI class |
| HierarchicalHybridJD_JobResultsSummary.fwd.hh | Defines owning pointers for a small helper class used by the SimpleCycpepPredict_MPI class |
| HierarchicalHybridJD_JobResultsSummary.hh | A small helper class used by the SimpleCycpepPredict_MPI class – headers |
| HierarchicalHybridJD_PNearToArbitraryStateSummary.cc | A class for storing the PNear, Keq, and DeltaG_folding values to an arbitrary state that has been sampled |
| HierarchicalHybridJD_PNearToArbitraryStateSummary.fwd.hh | A class for storing the PNear, Keq, and DeltaG_folding values to an arbitrary state that has been sampled |
| HierarchicalHybridJD_PNearToArbitraryStateSummary.hh | A class for storing the PNear, Keq, and DeltaG_folding values to an arbitrary state that has been sampled |
| HierarchicalHybridJD_ResultsSummaryBase.cc | A pure virtual base class for the helper classes used by the HierarchicalHybridJDApplication class for transmitting information up the MPI hierarchy |
| HierarchicalHybridJD_ResultsSummaryBase.fwd.hh | A pure virtual base class for the helper classes used by the HierarchicalHybridJDApplication class for transmitting information up the MPI hierarchy |
| HierarchicalHybridJD_ResultsSummaryBase.hh | A pure virtual base class for the helper classes used by the HierarchicalHybridJDApplication class for transmitting information up the MPI hierarchy |
| HierarchicalHybridJD_RMSDToBestSummary.cc | A small helper class used by the HierarchicalHybridJDApplication class for transmitting RMSD information up the MPI hierarchy |
| HierarchicalHybridJD_RMSDToBestSummary.fwd.hh | A small helper class used by the HierarchicalHybridJDApplication class for transmitting RMSD information up the MPI hierarchy |
| HierarchicalHybridJD_RMSDToBestSummary.hh | A small helper class used by the HierarchicalHybridJDApplication class for transmitting RMSD information up the MPI hierarchy |
| HierarchicalHybridJD_SASASummary.cc | A class for storing information about solvent-exposed surface area and for transmitting it up the MPI hierarchy |
| HierarchicalHybridJD_SASASummary.fwd.hh | A class for storing information about solvent-exposed surface area and for transmitting it up the MPI hierarchy |
| HierarchicalHybridJD_SASASummary.hh | A class for storing information about solvent-exposed surface area and for transmitting it up the MPI hierarchy |
| HierarchicalHybridJDApplication.cc | Application-level code for the simple_cycpep_predict app, MPI version |
| HierarchicalHybridJDApplication.fwd.hh | Defines owning pointers for the MPI version of the HierarchicalHybridJDApplication base class |
| HierarchicalHybridJDApplication.hh | Application-level code for the simple_cycpep_predict app, MPI version |
| PNearCalculator.cc | A class to compute P_Near and DG_folding |
| PNearCalculator.fwd.hh | A class to compute P_Near and DG_folding |
| PNearCalculator.hh | A class to compute P_Near and DG_folding |
| SimpleCycpepPredictApplication.cc | Application-level code for the simple_cycpep_predict app |
| SimpleCycpepPredictApplication.fwd.hh | Defines owning pointers for SimpleCycpepPredictApplication class |
| SimpleCycpepPredictApplication.hh | Application-level code for the simple_cycpep_predict app |
| SimpleCycpepPredictApplication_MPI.cc | Wrapper for SimpleCycpepPredictApplication that allows the app to use hierarchical MPI/pthreads based job distribution |
| SimpleCycpepPredictApplication_MPI.fwd.hh | Wrapper for SimpleCycpepPredictApplication that allows the app to use hierarchical MPI/pthreads based job distribution |
| SimpleCycpepPredictApplication_MPI.hh | Wrapper for SimpleCycpepPredictApplication that allows the app to use hierarchical MPI/pthreads based job distribution |
| util.cc | Utility code for the simple_cycpep_predict app and its MPI version |
| util.hh | Utility code for the simple_cycpep_predict app and its MPI version |
| ► ddg | |
| CartesianddG.cc | |
| CartesianddG.hh | |
| ddG_main.cc | |
| ddG_main.hh | |
| ddGData.cc | |
| ddGData.fwd.hh | |
| ddGData.hh | |
| ddGMover.cc | |
| ddGMover.fwd.hh | |
| ddGMover.hh | |
| ► denovo_design | |
| ► architects | |
| BetaSheetArchitect.cc | Architect that creates a beta sheet |
| BetaSheetArchitect.fwd.hh | Architect that creates a beta sheet |
| BetaSheetArchitect.hh | Architect that creates a beta sheet |
| BetaSheetArchitectCreator.hh | Class for instantiating a particular DeNovoArchitect |
| BlueprintArchitect.cc | Designs a structure using a Blueprint file |
| BlueprintArchitect.fwd.hh | Designs a structure using a Blueprint file |
| BlueprintArchitect.hh | Designs a structure using a Blueprint file |
| BlueprintArchitectCreator.hh | Class for instantiating a particular DeNovoArchitect |
| CompoundArchitect.cc | Architect that creates a StructureData using multiple architects |
| CompoundArchitect.fwd.hh | Architect that creates a StructureData using multiple architects |
| CompoundArchitect.hh | Architect that creates a StructureData using multiple architects |
| CompoundArchitectCreator.hh | Class for instantiating a particular DeNovoArchitect |
| DeNovoArchitect.cc | Designs topologies |
| DeNovoArchitect.fwd.hh | Designs topologies |
| DeNovoArchitect.hh | |
| DeNovoArchitectCreator.fwd.hh | Forward declaration of a class that instantiates a particular DeNovoArchitect |
| DeNovoArchitectCreator.hh | Class for instantiating a particular DeNovoArchitect |
| DeNovoArchitectFactory.cc | Creates DeNovo architects |
| DeNovoArchitectFactory.fwd.hh | Creates DeNovo architects |
| DeNovoArchitectFactory.hh | Creates DeNovo architects |
| HelixArchitect.cc | Architect for helices |
| HelixArchitect.fwd.hh | Architect for helices |
| HelixArchitect.hh | Architect for helices |
| HelixArchitectCreator.hh | Class for instantiating a particular DeNovoArchitect |
| PoseArchitect.cc | Design segments based on a pose |
| PoseArchitect.fwd.hh | Design segments based on a pose |
| PoseArchitect.hh | Design segments based on a pose |
| PoseArchitectCreator.hh | Class for instantiating a particular DeNovoArchitect |
| StrandArchitect.cc | Architect that creates a beta strand |
| StrandArchitect.fwd.hh | Architect that creates a beta strand |
| StrandArchitect.hh | Architect that creates a beta strand |
| StrandArchitectCreator.hh | Class for instantiating a particular DeNovoArchitect |
| StructureArchitect.cc | Designs topologies |
| StructureArchitect.fwd.hh | Designs topologies |
| StructureArchitect.hh | Designs topologies |
| util.cc | Utility functions for architects |
| util.hh | Utility functions for architects |
| ► calculators | |
| CavityCalculator.cc | Calculate centrality for all (or a subset of) residues |
| CavityCalculator.hh | Header file for CavityCalculator class. Roughly, fragment quality is number of fragments which are close to a pose in rmsd |
| ► components | |
| DivideAndConqueror.cc | Splits a denovo structure into pieces, and devises a strategy for folding the structure piece-by-piece |
| DivideAndConqueror.fwd.hh | Splits a denovo structure into pieces, and devises a strategy for folding the structure piece-by-piece |
| DivideAndConqueror.hh | Splits a denovo structure into pieces, and devises a strategy for folding the structure piece-by-piece |
| ExtendedPoseBuilder.cc | Builds a pose using a blueprint from a structure architect |
| ExtendedPoseBuilder.fwd.hh | Builds a pose using a blueprint from a structure architect |
| ExtendedPoseBuilder.hh | Builds a pose using a blueprint from a structure architect |
| FoldGraph.cc | FoldGraph - a fold-tree which takes two-way dependencies into account |
| FoldGraph.fwd.hh | |
| FoldGraph.hh | FoldGraph - a fold-tree which takes two-way dependencies into account |
| IdealAbegoGenerator.cc | Logic for selection of abego values |
| IdealAbegoGenerator.fwd.hh | Logic for selection of abego values |
| IdealAbegoGenerator.hh | Logic for selection of abego values |
| NullPoseFolder.cc | Pose folder that does nothing |
| NullPoseFolder.fwd.hh | Pose folder that does nothing |
| NullPoseFolder.hh | Pose folder that does nothing |
| Picker.cc | Auto-caching fragment picker |
| Picker.fwd.hh | Picker forward header |
| Picker.hh | Auto-caching fragment picker |
| PoseFolder.cc | Given a pose with all residues, assign a 3D conformation to that pose |
| PoseFolder.fwd.hh | Given a pose with all residues, assign a 3D conformation to that pose |
| PoseFolder.hh | Given a pose with all residues, assign a 3D conformation to that pose |
| RandomTorsionPoseFolder.cc | Folds a pose using random phi/psi torsions |
| RandomTorsionPoseFolder.fwd.hh | Folds a pose using random phi/psi torsions |
| RandomTorsionPoseFolder.hh | Folds a pose using random phi/psi torsions |
| RemodelLoopMoverPoseFolder.cc | Folds residues in a pose using RemodelLoopMover |
| RemodelLoopMoverPoseFolder.fwd.hh | Folds residues in a pose using RemodelLoopMover |
| RemodelLoopMoverPoseFolder.hh | Folds residues in a pose using RemodelLoopMover |
| Segment.cc | Named segment of residues |
| Segment.fwd.hh | |
| Segment.hh | Segment functions for building structures from components |
| SegmentPairing.cc | Handles user-specified pairing between/among segments |
| SegmentPairing.fwd.hh | Handles user-specified pairing between/among segments |
| SegmentPairing.hh | Handles user-specified pairing between/among segments |
| SheetDB.cc | |
| SheetDB.fwd.hh | |
| SheetDB.hh | |
| StructureData.cc | |
| StructureData.fwd.hh | StructureData forward header |
| StructureData.hh | StructureData functions for building structures from components |
| StructureDataCreator.hh | Creator for StructureData WriteableCacheableData |
| StructureDataFactory.cc | Singleton for creating StructureData objects |
| StructureDataFactory.fwd.hh | Singleton for creating StructureData objects |
| StructureDataFactory.hh | Singleton for creating StructureData objects |
| StructureDataObserver.cc | Observes a pose and updates StructureData accordingly |
| StructureDataObserver.fwd.hh | StructureDataObserver forward header |
| StructureDataObserver.hh | Observes a pose and updates StructureData accordingly |
| StructureDataPerturber.cc | Classes for altering StructureData objects on the fly |
| StructureDataPerturber.fwd.hh | Classes for altering StructureData objects on the fly |
| StructureDataPerturber.hh | Classes for altering StructureData objects on the fly |
| StructureDataWithPose.cc | StructureData with pose attached |
| VectorSelector.fwd.hh | Selects items from a vector using different methods |
| VectorSelector.hh | Selects items from a vector using different methods |
| ► connection | |
| ConnectionArchitect.cc | Architect for covalently joining two segments of a pose |
| ConnectionArchitect.fwd.hh | Architect for covalently joining two segments of a pose |
| ConnectionArchitect.hh | Architect for covalently joining two segments of a pose |
| util.cc | Utility functions for connection architects |
| util.hh | Utility functions for connection architects |
| ► constraints | |
| FileConstraintGenerator.cc | |
| FileConstraintGenerator.fwd.hh | |
| FileConstraintGenerator.hh | |
| FileConstraintGeneratorCreator.hh | This class will create instances of the ConstraintFileRCG mover |
| ► filters | |
| CavityVolumeFilter.cc | Tom's Denovo design protocol |
| CavityVolumeFilter.fwd.hh | Fwd declarations for Tom's denovo design protocol |
| CavityVolumeFilter.hh | Tom's Denovo Protocol. This is freely mutable and used for playing around with stuff |
| CavityVolumeFilterCreator.hh | |
| ExposedHydrophobicsFilter.cc | Tom's Denovo design protocol |
| ExposedHydrophobicsFilter.fwd.hh | Fwd declarations for Tom's denovo design protocol |
| ExposedHydrophobicsFilter.hh | Tom's Denovo Protocol. This is freely mutable and used for playing around with stuff |
| ExposedHydrophobicsFilterCreator.hh | |
| PreProlineFilter.cc | Tom's Denovo design protocol |
| PreProlineFilter.fwd.hh | Fwd declarations for Tom's denovo design protocol |
| PreProlineFilter.hh | Tom's Denovo Protocol. This is freely mutable and used for playing around with stuff |
| PreProlineFilterCreator.hh | |
| SSPredictionFilter.cc | Filter to determine agreement with SSPrediction for secondary structure prediction |
| SSPredictionFilter.fwd.hh | Header file for filter to determine agreement with psipred for secondary structure prediction |
| SSPredictionFilter.hh | Header file for filter to determine agreement with psipred for secondary structure prediction |
| SSPredictionFilterCreator.hh | Header file for filter creator to determine agreement with psipred for secondary structure prediction |
| SSShapeComplementarityFilter.cc | Tom's Denovo design protocol |
| SSShapeComplementarityFilter.fwd.hh | Fwd declarations for Tom's denovo design protocol |
| SSShapeComplementarityFilter.hh | Tom's Denovo Protocol. This is freely mutable and used for playing around with stuff |
| SSShapeComplementarityFilterCreator.hh | |
| ► movers | |
| AddSegmentDataMover.cc | Adds a segment to the structuredata |
| AddSegmentDataMover.fwd.hh | Adds a segment to the structuredata |
| AddSegmentDataMover.hh | Adds a segment to the structuredata |
| AddSegmentDataMoverCreator.hh | Adds a segment to the structuredata |
| AlignResiduesMover.cc | Aligns one residue onto another |
| AlignResiduesMover.fwd.hh | Aligns one residue onto another |
| AlignResiduesMover.hh | Aligns one residue onto another |
| AlignResiduesMoverCreator.hh | Aligns one residue onto another |
| BridgeChainsMover.cc | Creates a bridge connection between two chains using remodel |
| BridgeChainsMover.fwd.hh | Creates a bridge connection between two chains using remodel |
| BridgeChainsMover.hh | Creates a bridge connection between two chains using remodel |
| BridgeChainsMoverCreator.hh | Creates a bridge connection between two chains using remodel |
| BuildDeNovoBackboneMover.cc | Mover that builds and folds a structure via fragment insertion |
| BuildDeNovoBackboneMover.fwd.hh | Mover that builds and folds a structure via fragment insertion |
| BuildDeNovoBackboneMover.hh | Mover that builds and folds a structure via fragment insertion |
| BuildDeNovoBackboneMoverCreator.hh | Mover that builds and folds a structure via fragment insertion |
| DeclareStructureDataCovalentBondMover.cc | Declares covalent bond |
| DeclareStructureDataCovalentBondMover.fwd.hh | Declares covalent bond |
| DeclareStructureDataCovalentBondMover.hh | Declares covalent bond |
| DeclareStructureDataCovalentBondMoverCreator.hh | Declares covalent bond |
| DisulfidizeMover.cc | The DisulfidizeMover |
| DisulfidizeMover.fwd.hh | |
| DisulfidizeMover.hh | The DisulfidizeMover Protocol |
| DisulfidizeMoverCreator.hh | |
| ExtendChainMover.cc | Extends a chain by a structural motif |
| ExtendChainMover.fwd.hh | ExtendChainMover forward header |
| ExtendChainMover.hh | The ExtendChainMover Protocol |
| ExtendChainMoverCreator.hh | |
| FastDesign.cc | Similar to FastRelax, but with design and a few additional options |
| FastDesign.fwd.hh | FastDesign forward header |
| FastDesign.hh | The FastDesign Protocol |
| FastDesignCreator.hh | The FastDesign Protocol, adapted from src/protocols/relax/FastRelax |
| FoldTreeFromFoldGraphMover.cc | Creates and sets a new fold tree for the pose by traversing a FoldGraph |
| FoldTreeFromFoldGraphMover.fwd.hh | Creates and sets a new fold tree for the pose by traversing a FoldGraph |
| FoldTreeFromFoldGraphMover.hh | Creates and sets a new fold tree for the pose by traversing a FoldGraph |
| FoldTreeFromFoldGraphMoverCreator.hh | Creates and sets a new fold tree for the pose by traversing a FoldGraph |
| MakeAsymmetricStructureDataMover.cc | Converts a StructureData for a symmetric pose into an asymmetric representation |
| MakeAsymmetricStructureDataMover.fwd.hh | Converts a StructureData for a symmetric pose into an asymmetric representation |
| MakeAsymmetricStructureDataMover.hh | Converts a StructureData for a symmetric pose into an asymmetric representation |
| MakeAsymmetricStructureDataMoverCreator.hh | Converts a StructureData for a symmetric pose into an asymmetric representation |
| RotateSegmentMover.cc | Rotates a segment in the pose |
| RotateSegmentMover.fwd.hh | Rotates a segment in the pose |
| RotateSegmentMover.hh | Rotates a segment in the pose |
| RotateSegmentMoverCreator.hh | Rotates a segment in the pose |
| SealFoldTreeMover.cc | Creates a sealed foldtree, and removes all cutpoints from the pose |
| SealFoldTreeMover.fwd.hh | Creates a sealed foldtree, and removes all cutpoints from the pose |
| SealFoldTreeMover.hh | Creates a sealed foldtree, and removes all cutpoints from the pose |
| SealFoldTreeMoverCreator.hh | Creates a sealed foldtree, and removes all cutpoints from the pose |
| SetResidueAliasMover.cc | Sets a residue alias in the StructureData |
| SetResidueAliasMover.fwd.hh | Sets a residue alias in the StructureData |
| SetResidueAliasMover.hh | Sets a residue alias in the StructureData |
| SetResidueAliasMoverCreator.hh | Sets a residue alias in the StructureData |
| ► residue_selectors | |
| NamedSegmentSelector.cc | |
| NamedSegmentSelector.fwd.hh | Selects residues from a named segment generated by StructureArchitects |
| NamedSegmentSelector.hh | Selects residues from a named segment generated by StructureArchitects |
| NamedSegmentSelectorCreator.hh | |
| PairedSheetResidueSelector.cc | |
| PairedSheetResidueSelector.fwd.hh | Selects residues that are involved in strand-strand pairings |
| PairedSheetResidueSelector.hh | Selects residues that are involved in strand-strand pairings |
| PairedSheetResidueSelectorCreator.hh | |
| ► task_operations | |
| ConsensusLoopDesignOperation.cc | Restrict loop residue identities to those commonly found in nature |
| ConsensusLoopDesignOperation.fwd.hh | Restrict loop residue identities to those commonly found in nature |
| ConsensusLoopDesignOperation.hh | Restrict loop residue identities to those commonly found in nature |
| ConsensusLoopDesignOperationCreator.hh | |
| types.hh | |
| util.cc | Util functions for denovo design of structures |
| util.hh | |
| ► design_opt | |
| GreedyOptMutationMover.cc | |
| GreedyOptMutationMover.fwd.hh | |
| GreedyOptMutationMover.hh | |
| GreedyOptMutationMoverCreator.hh | |
| ParetoOptMutationMover.fwd.hh | |
| PointMutationCalculator.cc | |
| PointMutationCalculator.fwd.hh | |
| PointMutationCalculator.hh | |
| ► dna | |
| DesignProteinBackboneAroundDNA.cc | Performs a round flexible backbone sampling/design. (Interim(?) encapsulation of some loose code in a mover class.) |
| DesignProteinBackboneAroundDNA.fwd.hh | |
| DesignProteinBackboneAroundDNA.hh | Performs a round flexible backbone sampling/design. (Interim(?) encapsulation of some loose code in a mover class.) |
| DesignProteinBackboneAroundDNACreator.hh | |
| DnaChains.cc | |
| DnaChains.fwd.hh | |
| DnaChains.hh | Descriptive but lightweight class to keep track of (usually basepaired) dna chains |
| DnaDesignDef.cc | |
| DnaDesignDef.fwd.hh | |
| DnaDesignDef.hh | |
| DnaInterfaceFinder.cc | |
| DnaInterfaceFinder.fwd.hh | |
| DnaInterfaceFinder.hh | |
| DnaInterfaceMinMover.cc | |
| DnaInterfaceMinMover.fwd.hh | |
| DnaInterfaceMinMover.hh | A mover that minimizes protein residues near DNA |
| DnaInterfaceMinMoverCreator.hh | |
| DnaInterfaceMultiStateDesign.cc | |
| DnaInterfaceMultiStateDesign.fwd.hh | |
| DnaInterfaceMultiStateDesign.hh | |
| DnaInterfaceMultiStateDesignCreator.hh | |
| DnaInterfacePacker.cc | |
| DnaInterfacePacker.fwd.hh | |
| DnaInterfacePacker.hh | Intended to perform anything one would want to do in a DNA interface that uses a single incarnation of the RotamerSets/InteractionGraph combo |
| DnaInterfacePackerCreator.hh | |
| DNAParameters.cc | A class to query for base-paired partners as well as base pair and base step parameters |
| DNAParameters.fwd.hh | |
| DNAParameters.hh | A class to query for base-paired partners as well as base pair and base step parameters |
| PDBOutput.cc | |
| PDBOutput.fwd.hh | |
| PDBOutput.hh | |
| RestrictDesignToProteinDNAInterface.cc | |
| RestrictDesignToProteinDNAInterface.fwd.hh | |
| RestrictDesignToProteinDNAInterface.hh | When operated on a PackerTask, pack/design is limited to the protein-DNA interface |
| RestrictDesignToProteinDNAInterfaceCreator.hh | |
| RotamerDNAHBondFilter.cc | Filters rotamers for contact to DNA in an -ex dependent manner |
| RotamerDNAHBondFilter.fwd.hh | |
| RotamerDNAHBondFilter.hh | Filters rotamers for contact to DNA in an -ex dependent manner |
| SeparateDnaFromNonDna.cc | |
| SeparateDnaFromNonDna.fwd.hh | |
| SeparateDnaFromNonDna.hh | |
| SeparateDnaFromNonDnaCreator.hh | |
| typedefs.hh | |
| util.cc | |
| util.hh | |
| WatsonCrickRotamerCouplings.cc | |
| WatsonCrickRotamerCouplings.fwd.hh | |
| WatsonCrickRotamerCouplings.hh | When operated on a PackerTask, adds RotamerCouplings to it that will trigger the use of a FixbbCoupledRotamerAnnealer by pack_rotamers, which will make base-paired DNA rotamer substitutions |
| WatsonCrickRotamerCouplingsCreator.hh | |
| ► dna_dock | |
| DNAClashCheckFilter.cc | Checks for fa_rep clashes between docked pose and DNA backbone |
| DNAClashCheckFilter.fwd.hh | |
| DNAClashCheckFilter.hh | Header file for DNAClashCheckFilter class |
| DNAClashCheckFilterCreator.hh | FilterCreator for DNAClashCheckFilter |
| PropagateClashCheckFilter.cc | Checks for fa_rep clashes between docked pose and DNA backbone |
| PropagateClashCheckFilter.fwd.hh | |
| PropagateClashCheckFilter.hh | Header file for PropagateClashCheckFilter class |
| PropagateClashCheckFilterCreator.hh | FilterCreator for PropagateClashCheckFilter |
| ► docking | |
| ► membrane | |
| MPDockingMover.cc | |
| MPDockingMover.fwd.hh | |
| MPDockingMover.hh | |
| MPDockingMoverCreator.hh | |
| MPDockingSetupMover.cc | |
| MPDockingSetupMover.fwd.hh | |
| MPDockingSetupMover.hh | |
| MPDockingSetupMoverCreator.hh | |
| MPFindInterfaceMover.cc | |
| MPFindInterfaceMover.fwd.hh | |
| MPFindInterfaceMover.hh | |
| MPFindInterfaceMoverCreator.hh | Sample protein-protein interface in the membrane |
| QuickRelaxPartnersSeparately.cc | |
| QuickRelaxPartnersSeparately.fwd.hh | |
| QuickRelaxPartnersSeparately.hh | |
| QuickRelaxPartnersSeparatelyCreator.hh | |
| ► stateless | |
| SaneDockingProtocol.cc | |
| SaneDockingProtocol.fwd.hh | |
| SaneDockingProtocol.hh | DockingProtocol class that doesn't use the more esoteric features of the Mover base class (e.g get_input_pose()) |
| ConformerSwitchMover.cc | Code for the conformer switch mover in ensemble docking |
| ConformerSwitchMover.fwd.hh | ConformerSwitchMover forward declarations header |
| ConformerSwitchMover.hh | |
| ConformerSwitchMoverCreator.hh | |
| DockFilters.cc | |
| DockFilters.fwd.hh | |
| DockFilters.hh | |
| DockingEnsemble.cc | Container class for ensemble docking information to be used with ConformerSwitchMover |
| DockingEnsemble.fwd.hh | |
| DockingEnsemble.hh | |
| DockingEnsemblePrepackProtocol.cc | Prepacking of the bound structure before docking with ensembles |
| DockingEnsemblePrepackProtocol.fwd.hh | |
| DockingEnsemblePrepackProtocol.hh | |
| DockingHighRes.cc | |
| DockingHighRes.fwd.hh | |
| DockingHighRes.hh | |
| DockingHighResFactory.cc | Factory for creating DockingHighRes objects |
| DockingHighResFactory.fwd.hh | Factory for creating DockingHighRes objects |
| DockingHighResFactory.hh | Factory for creating DockingHighRes objects |
| DockingHighResLegacy.cc | |
| DockingHighResLegacy.fwd.hh | Forward declarations for DockingHighResLegacy (high resolution docking protocol as it existed in mini before the GrayLab refactor) |
| DockingHighResLegacy.hh | |
| DockingHighResLegacyCreator.hh | Declaration of the MoverCreator class for DockingHighResLegacy |
| DockingInitialPerturbation.cc | Initial position functions |
| DockingInitialPerturbation.fwd.hh | |
| DockingInitialPerturbation.hh | |
| DockingInitialPerturbationCreator.hh | |
| DockingLowRes.cc | |
| DockingLowRes.fwd.hh | |
| DockingLowRes.hh | |
| DockingLowResEnsemble.cc | |
| DockingLowResEnsemble.fwd.hh | |
| DockingLowResEnsemble.hh | |
| DockingPrepackProtocol.cc | Prepacking of the bound sturcture before docking |
| DockingPrepackProtocol.fwd.hh | |
| DockingPrepackProtocol.hh | |
| DockingPrepackProtocolCreator.hh | Declaration of the MoverCreator class for the DockingPrepackProtocol |
| DockingProtocol.cc | |
| DockingProtocol.fwd.hh | |
| DockingProtocol.hh | |
| DockingProtocolCreator.hh | |
| DockingSlideIntoContactCreator.hh | |
| DockMCMCycle.cc | |
| DockMCMCycle.fwd.hh | Forward declarations for DockMCMCycle (high resolution min) docking |
| DockMCMCycle.hh | |
| DockMCMProtocol.cc | |
| DockMCMProtocol.fwd.hh | Forward declarations for DockMCMProtocol (high resolution min) docking |
| DockMCMProtocol.hh | Declaration of the MoverCreator class for the DockMCMProtocol |
| DockMCMProtocolCreator.hh | |
| DockMinMover.cc | |
| DockMinMover.fwd.hh | Forward declarations for DockMinMover (high resolution min) docking |
| DockMinMover.hh | |
| DockMinMoverCreator.hh | Declaration of the MoverCreator class for the DockMinMover |
| DockSetupMover.cc | |
| DockSetupMover.fwd.hh | |
| DockSetupMover.hh | Allows low-resolution docking using simulated or parallel tempering |
| DockSetupMoverCreator.hh | |
| DockTaskFactory.cc | |
| DockTaskFactory.fwd.hh | Forward declarations for DockTaskFactory |
| DockTaskFactory.hh | |
| EllipsoidalRandomizationMover.cc | |
| EllipsoidalRandomizationMover.fwd.hh | Forward declarations for EllipsoidalRandomizationMover (docking initial placement mover) |
| EllipsoidalRandomizationMover.hh | |
| metrics.cc | |
| metrics.hh | |
| RigidBodyInfo.cc | |
| RigidBodyInfo.fwd.hh | |
| RigidBodyInfo.hh | |
| SidechainMinMover.cc | |
| SidechainMinMover.fwd.hh | |
| SidechainMinMover.hh | |
| TemperedDocking.cc | |
| TemperedDocking.fwd.hh | |
| TemperedDocking.hh | Allows low-resolution docking using simulated or parallel tempering |
| TemperedDockingCreator.hh | |
| types.hh | Additionl types for Docking protocol |
| util.cc | |
| util.hh | |
| ► domain_assembly | |
| AddAssemblyConstraints.cc | |
| AddAssemblyConstraints.fwd.hh | Adds constraints for the assembling process |
| AddAssemblyConstraints.hh | |
| AssembleLinkerMover.cc | A mover for assembling domains |
| AssembleLinkerMover.fwd.hh | A mover for assembling domains |
| AssembleLinkerMover.hh | |
| CombineChainsMover.cc | Takes a multichain pose and returns a single-chain one |
| CombineChainsMover.fwd.hh | A mover for assembling chains |
| CombineChainsMover.hh | |
| PostDockAssemblyScorer.cc | Computes crmsd of the assembly to the staring point |
| PostDockAssemblyScorer.fwd.hh | Computes crmsd of the assembly to the staring point |
| PostDockAssemblyScorer.hh | |
| ► electron_density | |
| BfactorFittingMover.cc | Set up morphing with electron density map |
| BfactorFittingMover.hh | |
| BfactorFittingMoverCreator.hh | |
| DensitySymmInfo.cc | |
| DensitySymmInfo.hh | |
| DockIntoDensityMover.cc | Protocols for folding into density |
| DockIntoDensityMover.hh | Protocols for folding into density |
| ReportFSC.cc | |
| ReportFSC.hh | |
| ReportFSCCreator.hh | |
| ScaleMapIntensities.cc | |
| ScaleMapIntensities.hh | |
| ScaleMapIntensitiesCreator.hh | |
| SetupForDensityScoringMover.cc | Protocols for folding into density |
| SetupForDensityScoringMover.hh | Protocols for folding into density |
| SetupForDensityScoringMoverCreator.hh | |
| util.cc | Protocols for folding into density |
| util.hh | Protocols for folding into density |
| VoxelSpacingRefinementMover.cc | Set up morphing with electron density map |
| VoxelSpacingRefinementMover.hh | |
| VoxelSpacingRefinementMoverCreator.hh | |
| ► energy_based_clustering | |
| EnergyBasedClusteringOptions.cc | A container for the options used by the EnergyBasedClusteringProtocol |
| EnergyBasedClusteringOptions.fwd.hh | |
| EnergyBasedClusteringOptions.hh | A container for the options used by the EnergyBasedClusteringProtocol |
| EnergyBasedClusteringProtocol.cc | Performs the work done by the energy_based_clustering app. Uses an energy-biased cookie-cutter approach to cluster a large number of structures without generating an all-by-all RMSD matrix |
| EnergyBasedClusteringProtocol.fwd.hh | |
| EnergyBasedClusteringProtocol.hh | Performs the work done by the energy_based_clustering app. Uses an energy-biased cookie-cutter approach to cluster a large number of structures without generating an all-by-all RMSD matrix |
| EnergyBasedClusteringTests.fwd.hh | |
| ► environment | |
| ► claims | |
| BrokerElements.cc | Some implementation details of the BrokerElements (such as they are) |
| BrokerElements.hh | |
| ClaimStrength.cc | ClaimStrength tracks the prioirty of a particular claim with respect to its initialization |
| ClaimStrength.fwd.hh | |
| ClaimStrength.hh | Header file for ClaimStrength, which tracks the prioirty of a particular claim with respect to its initialization |
| CutBiasClaim.cc | |
| CutBiasClaim.fwd.hh | |
| CutBiasClaim.hh | |
| EnvClaim.cc | Abstract class for implementing an EnvClaim (e.g. TorsionClaim) |
| EnvClaim.fwd.hh | |
| EnvClaim.hh | |
| EnvLabelSelector.cc | The EnvLabelSelector holds a selection that another object can set inside of it |
| EnvLabelSelector.fwd.hh | The EnvLabelSelector holds a selection that another object can set inside of it |
| EnvLabelSelector.hh | The EnvLabelSelector holds a set of local positions that are converted to seqids at apply |
| JumpClaim.cc | |
| JumpClaim.fwd.hh | |
| JumpClaim.hh | |
| TorsionClaim.cc | Implementation file for TorsionClaim |
| TorsionClaim.fwd.hh | |
| TorsionClaim.hh | An EnvClaim object for claiming arbitrary regions and types of torsional angles within a pose |
| VirtResClaim.cc | |
| VirtResClaim.fwd.hh | |
| VirtResClaim.hh | A claim for expressing the desire for new sequence to be inserted at a particular point |
| XYZClaim.cc | |
| XYZClaim.fwd.hh | |
| XYZClaim.hh | |
| AutoCutData.cc | |
| AutoCutData.fwd.hh | Definition of the AutoCutData class |
| AutoCutData.hh | |
| AutoCutDataCreator.hh | |
| ClientMover.cc | |
| ClientMover.fwd.hh | Definition of the ClientMover class |
| ClientMover.hh | An environment that automatically distributes rights to shared degrees of freedom (e.g. fold tree) |
| CoMTrackerCM.cc | |
| CoMTrackerCM.fwd.hh | Definition of the CoMTrackerCM class |
| CoMTrackerCM.hh | Header file for CoMTracker |
| CoMTrackerCMCreator.hh | |
| DofUnlock.cc | |
| DofUnlock.fwd.hh | Definition of the DofUnlock class |
| DofUnlock.hh | A class that is used to express a mover-specific DoF-unlock on a ProtectedPose. Its destruction expresses a re-locking |
| EnvClaimBroker.cc | |
| EnvClaimBroker.fwd.hh | Definition of the EnvClaimBroker class |
| EnvClaimBroker.hh | A class responsible for managing claims from ClientMovers, and retaining important information about the result of the brokering process |
| EnvExcn.cc | |
| EnvExcn.hh | Subclasses of EXCN_Env_Exception that require inclusion of the stuff in protocols |
| Environment.cc | |
| Environment.fwd.hh | Definition of the BrokeredEnvironment class |
| Environment.hh | |
| EnvMover.cc | |
| EnvMover.fwd.hh | Definition of the EnvMover class |
| EnvMover.hh | |
| EnvMoverCreator.hh | This class will create instances of the EnvMover for the MoverFactory |
| ProtectedConformation.cc | |
| ProtectedConformation.fwd.hh | Definition of the ProtectedConformation class |
| ProtectedConformation.hh | A conformation built by the environment to be protected |
| ScriptCM.cc | |
| ScriptCM.fwd.hh | Definition of the ScriptCM class |
| ScriptCM.hh | Header file for CoMTracker |
| ScriptCMCreator.hh | |
| ► enzdes | |
| AddLigandMotifRotamersOperationCreator.hh | |
| AddorRemoveCsts.cc | |
| AddorRemoveCsts.hh | |
| AddOrRemoveMatchCstsCreator.hh | |
| AddRigidBodyLigandConfsCreator.hh | |
| BackboneSampler.cc | |
| BackboneSampler.hh | Adapted from backrub mover in protein interface design |
| BackboneSamplerCreator.hh | |
| DesignVsNativeComparison.cc | |
| DesignVsNativeComparison.hh | |
| DetectProteinLigandInterfaceOperationCreator.hh | |
| enzdes_util.cc | Bunch of utility functions used in enzdes |
| enzdes_util.hh | Bunch of utility functions used in enzdes |
| EnzdesBaseProtocol.cc | |
| EnzdesBaseProtocol.fwd.hh | |
| EnzdesBaseProtocol.hh | |
| EnzdesFixBBProtocol.cc | |
| EnzdesFixBBProtocol.hh | |
| EnzdesFlexBBProtocol.cc | |
| EnzdesFlexBBProtocol.hh | |
| EnzdesJobInputter.cc | Job inputter that adds some stuff for enzdes to the pose |
| EnzdesJobInputter.fwd.hh | |
| EnzdesJobInputter.hh | |
| EnzdesJobInputterCreator.hh | |
| EnzdesJobOutputter.cc | Implementation for EnzdesJobOutputter |
| EnzdesJobOutputter.fwd.hh | Forward declaration for EnzdesJobOutputters |
| EnzdesJobOutputter.hh | |
| EnzdesJobOutputterCreator.hh | |
| EnzdesMovers.cc | |
| EnzdesMovers.fwd.hh | |
| EnzdesMovers.hh | Collection of movers that are used at different stages in enzyme design |
| EnzdesMoversCreator.hh | |
| EnzdesTaskOperations.cc | |
| EnzdesTaskOperations.fwd.hh | |
| EnzdesTaskOperations.hh | |
| EnzFilterCreators.hh | FilterCreators for the enzyme design filters |
| EnzFilters.cc | |
| EnzFilters.fwd.hh | |
| EnzFilters.hh | Definition of filter classes for enzdes in rosetta_scripts framework |
| EnzRepackMinimize.cc | Repack/minimize class for rosetta_scripts-compatible enzdes |
| EnzRepackMinimize.fwd.hh | |
| EnzRepackMinimize.hh | |
| EnzRepackMinimizeCreator.hh | |
| ModifyStoredLigandRBConfsMovers.cc | |
| ModifyStoredLigandRBConfsMovers.fwd.hh | |
| ModifyStoredLigandRBConfsMovers.hh | |
| PackRotamersMoverPartGreedy.cc | Partly greedy pack rotamers mover. given a set of target residues, choose their neighbors greedily and then |
| PackRotamersMoverPartGreedy.hh | |
| PackRotamersMoverPartGreedyCreator.hh | |
| ProteinLigandInterfaceUpweighterOperationCreator.hh | |
| RemoveLigandFilter.cc | |
| RemoveLigandFilter.fwd.hh | |
| RemoveLigandFilter.hh | |
| RemoveLigandFilterCreator.hh | |
| SecondaryMatchProtocol.cc | |
| SecondaryMatchProtocol.hh | |
| SetCatalyticResPackBehaviorCreator.hh | |
| ► enzymatic_movers | |
| DNAMethyltransferaseMover.cc | Method definitions for DNAMethyltransferaseMover |
| DNAMethyltransferaseMover.fwd.hh | Forward declarations for DNAMethyltransferaseMover |
| DNAMethyltransferaseMover.hh | Declarations and simple accessor/mutator definitions for DNAMethyltransferaseMover |
| DNAMethyltransferaseMoverCreator.hh | Method declarations for DNAMethyltransferaseMoverCreator |
| EnzymaticMover.cc | |
| EnzymaticMover.fwd.hh | Method definitions for the base class EnzymaticMover |
| EnzymaticMover.hh | |
| GlycosyltransferaseMover.cc | Method definitions for GlycosyltransferaseMover |
| GlycosyltransferaseMover.fwd.hh | Forward declarations for GlycosyltransferaseMover |
| GlycosyltransferaseMover.hh | Declarations and simple accessor/mutator definitions for GlycosyltransferaseMover |
| GlycosyltransferaseMoverCreator.hh | Method declarations for GlycosyltransferaseMoverCreator |
| KinaseMover.cc | Method definitions for KinaseMover |
| KinaseMover.fwd.hh | Forward declarations for KinaseMover |
| KinaseMover.hh | Declarations and simple accessor/mutator definitions for KinaseMover |
| KinaseMoverCreator.hh | Method declarations for KinaseMoverCreator |
| NTerminalAcetyltransferaseMover.cc | Method definitions for NTerminalAcetyltransferaseMover |
| NTerminalAcetyltransferaseMover.fwd.hh | Forward declarations for NTerminalAcetyltransferaseMover |
| NTerminalAcetyltransferaseMover.hh | Declarations and simple accessor/mutator definitions for NTerminalAcetyltransferaseMover |
| NTerminalAcetyltransferaseMoverCreator.hh | Method declarations for NTerminalAcetyltransferaseMoverCreator |
| ► evaluation | |
| AlignEvaluator.cc | |
| AlignEvaluator.fwd.hh | Forward declaration for AlignEvaluator class |
| AlignEvaluator.hh | |
| EvaluatorCreator.fwd.hh | Forward Header for base class for EvaluatorCreators for the Evaluator load-time factory registration scheme |
| EvaluatorCreator.hh | |
| EvaluatorFactory.cc | Factory for creating Evaluators objects |
| EvaluatorFactory.fwd.hh | Report data to database |
| EvaluatorFactory.hh | Factory for creating Evaluator objects |
| PCA.cc | |
| PCA.fwd.hh | |
| PCA.hh | |
| PoseEvaluator.cc | |
| PoseEvaluator.fwd.hh | |
| PoseEvaluator.hh | |
| TimeEvaluator.cc | |
| TimeEvaluator.fwd.hh | |
| TimeEvaluator.hh | |
| util.cc | |
| util.hh | |
| ► evolution | |
| AASynthesisFitnessCostFilter.cc | |
| AASynthesisFitnessCostFilter.fwd.hh | |
| AASynthesisFitnessCostFilter.hh | |
| AASynthesisFitnessCostFilterCreator.hh | FilterCreators for the AASynthesisFitnessCostFilter |
| AlignmentAAFinderFilter.cc | |
| AlignmentAAFinderFilter.fwd.hh | |
| AlignmentAAFinderFilter.hh | |
| AlignmentAAFinderFilterCreator.hh | FilterCreators for the AlignmentAAFinderFilter |
| AlignmentCleanerTools.cc | |
| AlignmentCleanerTools.hh | |
| AlignmentGapInserterFilter.cc | |
| AlignmentGapInserterFilter.fwd.hh | |
| AlignmentGapInserterFilter.hh | |
| AlignmentGapInserterFilterCreator.hh | FilterCreators for the AlignmentGapInserterFilter |
| EvolutionaryDynamicsMover.cc | Overwrites the boltzmann function in GenericMonteCarloMover to sample according to evolutionary dynamics instead |
| EvolutionaryDynamicsMover.fwd.hh | |
| EvolutionaryDynamicsMover.hh | Perform a given mover and sample structures by MonteCarlo |
| EvolutionaryDynamicsMoverCreator.hh | |
| NucleotideMutation.cc | Substitutes amino acids in pose based on mutations in nucleotide space |
| NucleotideMutation.fwd.hh | NucleotideMutation forward declarations header |
| NucleotideMutation.hh | |
| NucleotideMutationCreator.hh | |
| ► farnesyl | |
| InstallFarnesylMover.cc | Modifies a free cysteine residue with a branch of 3 DMA residues (the terpene monomer) to create farnesyl-cysteine |
| InstallFarnesylMover.fwd.hh | Modifies a free cysteine residue with a branch of 3 DMA residues (the terpene monomer) to create farnesyl-cysteine |
| InstallFarnesylMover.hh | Modifies a free cysteine residue with a branch of 3 DMA residues (the terpene monomer) to create farnesyl-cysteine |
| InstallFarnesylMoverCreator.hh | Modifies a free cysteine residue with a branch of 3 DMA residues (the terpene monomer) to create farnesyl-cysteine |
| SampleFarnesylMover.cc | Modifies a free cysteine residue with a branch of 3 DMA residues (the terpene monomer) to create farnesyl-cysteine |
| SampleFarnesylMover.fwd.hh | Modifies a free cysteine residue with a branch of 3 DMA residues (the terpene monomer) to create farnesyl-cysteine |
| SampleFarnesylMover.hh | Modifies a free cysteine residue with a branch of 3 DMA residues (the terpene monomer) to create farnesyl-cysteine |
| SampleFarnesylMoverCreator.hh | Modifies a free cysteine residue with a branch of 3 DMA residues (the terpene monomer) to create farnesyl-cysteine |
| ► features | |
| ► helixAssembly | |
| ConcurrencyTest.cc | |
| ConcurrencyTest.fwd.hh | |
| ConcurrencyTest.hh | |
| ConcurrencyTestCreator.cc | |
| ConcurrencyTestCreator.hh | |
| HelicalFragment.cc | |
| HelicalFragment.fwd.hh | |
| HelicalFragment.hh | Small helper class that stores the start and end of a helix secondary structure |
| HelixBundleFeatures.cc | Search through a pose for sets of 3 helices and generate RMSD calculations between all pairs of them |
| HelixBundleFeatures.fwd.hh | |
| HelixBundleFeatures.hh | |
| HelixBundleFeaturesCreator.cc | |
| HelixBundleFeaturesCreator.hh | |
| ► strand_assembly | |
| CheckForSandwichFeatures.cc | Check various properties for SandwichFeatures |
| CheckForSandwichFeatures.hh | Check various properties for SandwichFeatures |
| SandwichFeatures.cc | Extract and analyze beta-sandwich features |
| SandwichFeatures.fwd.hh | Report sandwich data to database |
| SandwichFeatures.hh | Extract and analyze beta-sandwich features |
| SandwichFeaturesCreator.cc | |
| SandwichFeaturesCreator.hh | |
| SandwichFragment.cc | Small helper class that stores the start and end of a strand secondary structure |
| SandwichFragment.hh | Small helper class that stores the start and end of a strand secondary structure |
| StrandAssemblyCommon.hh | Has most common/shared inclusions and namespace usings |
| StrandBundleFeatures.cc | Extract beta strand, strand pairs, sandwiches in pdb file, see wiki.rosettacommons.org/index.php/MultiBodyFeaturesReporters#StrandBundleFeatures for detail |
| StrandBundleFeatures.fwd.hh | |
| StrandBundleFeatures.hh | |
| StrandBundleFeaturesCreator.cc | |
| StrandBundleFeaturesCreator.hh | |
| StrandFragment.cc | |
| StrandFragment.hh | |
| WriteToDBFromSandwichFeatures.cc | Write to a DB after SandwichFeatures |
| WriteToDBFromSandwichFeatures.hh | Write to a DB after SandwichFeatures |
| WriteToFileFromSandwichFeatures.cc | Write to a file after SandwichFeatures |
| WriteToFileFromSandwichFeatures.hh | Write to a file after SandwichFeatures |
| AtomAtomPairFeatures.cc | Report atom-atom pair geometry and scores to features statistics scientific benchmark |
| AtomAtomPairFeatures.fwd.hh | Report atom-atom pair geometry and scores to features Statistics Scientific Benchmark |
| AtomAtomPairFeatures.hh | Report atom-atom pair geometry and scores to features Statistics Scientific Benchmark |
| AtomAtomPairFeaturesCreator.cc | |
| AtomAtomPairFeaturesCreator.hh | Header for AtomAtomPairFeaturesCreator for the AtomAtomPairFeatures load-time factory registration scheme |
| AtomInResidueAtomInResiduePairFeatures.cc | Report atom-atom pair geometry and scores to features statistics scientific benchmark |
| AtomInResidueAtomInResiduePairFeatures.fwd.hh | Report atom-atom pair geometry and scores to features Statistics Scientific Benchmark |
| AtomInResidueAtomInResiduePairFeatures.hh | Report atom-atom pair geometry and scores to features Statistics Scientific Benchmark |
| AtomInResidueAtomInResiduePairFeaturesCreator.cc | |
| AtomInResidueAtomInResiduePairFeaturesCreator.hh | Header for AtomInResidueAtomInResiduePairFeaturesCreator for the AtomInResidueAtomInResiduePairFeatures load-time factory registration scheme |
| AtomTypesFeatures.cc | Report AtomType properties to features Statistics Scientific Benchmark |
| AtomTypesFeatures.fwd.hh | Report AtomTypes geometry and scores to features Statistics Scientific Benchmark |
| AtomTypesFeatures.hh | Report AtomType features Statistics Scientific Benchmark |
| AtomTypesFeaturesCreator.cc | |
| AtomTypesFeaturesCreator.hh | Header for AtomTypesFeaturesCreator for the AtomTypesFeatures load-time factory registration scheme |
| BatchFeatures.cc | |
| BatchFeatures.fwd.hh | |
| BatchFeatures.hh | |
| BetaTurnDetection.cc | Determine the presence and type of beta turn at a specific postion in a pose |
| BetaTurnDetection.fwd.hh | Determine if there is a beta turn at particular postion |
| BetaTurnDetection.hh | Determine the presence and type of beta turn at a specific postion in a pose |
| BetaTurnDetectionFeatures.cc | Report beta turns to a DB |
| BetaTurnDetectionFeatures.fwd.hh | Report residue level geometry and scores to features Statistics Scientific Benchmark |
| BetaTurnDetectionFeatures.hh | |
| BetaTurnDetectionFeaturesCreator.cc | |
| BetaTurnDetectionFeaturesCreator.hh | Header for BetaTurnDetectionFeaturesCreator for the BetaTurnDetectionFeatures load-time factory registration scheme |
| ChargeChargeFeatures.cc | Report geometric solvation energy for each polar site to a features database |
| ChargeChargeFeatures.fwd.hh | Report geometric solvation for each polar site to features Statistics Scientific Benchmark |
| ChargeChargeFeatures.hh | Report comments stored with each pose |
| ChargeChargeFeaturesCreator.cc | |
| ChargeChargeFeaturesCreator.hh | Header for ChargeChargeFeaturesCreator for the ChargeChargeFeatures load-time factory registration scheme |
| DatabaseFilters.cc | |
| DatabaseFilters.fwd.hh | Report data to database |
| DatabaseFilters.hh | Report atom-atom pair geometry and scores to features Statistics Scientific Benchmark |
| DatabaseJobInputter.cc | |
| DatabaseJobInputter.fwd.hh | |
| DatabaseJobInputter.hh | Header file for DatabaseJobInputter class |
| DatabaseJobInputterCreator.hh | |
| DatabaseJobOutputter.cc | Job Outputter to a database |
| DatabaseJobOutputter.fwd.hh | Header file for DatabaseJobOutputter class |
| DatabaseJobOutputter.hh | Header file for DatabaseJobOutputter class |
| DatabaseJobOutputterCreator.hh | |
| DatabaseStatements.cc | |
| DatabaseStatements.hh | |
| DdGFeatures.cc | Report the per-residue ddG score to the features database |
| DdGFeatures.fwd.hh | Report the per-residue ddG score to the features database |
| DdGFeatures.hh | Report the per-residue ddG score to the features database |
| DdGFeaturesCreator.cc | |
| DdGFeaturesCreator.hh | Header for DdGFeaturesCreator for the DdGFeatures load-time factory registration scheme |
| feature_schemas.cc | |
| feature_schemas.hh | |
| FeaturesReporter.cc | Base class to report geometry and scores to features Statistics Scientific Benchmark |
| FeaturesReporter.fwd.hh | Report data to database |
| FeaturesReporter.hh | Base class to report geometry and scores to features Statistics Scientific Benchmark |
| FeaturesReporterCreator.fwd.hh | |
| FeaturesReporterCreator.hh | |
| FeaturesReporterFactory.cc | Factory for creating FeaturesReporters objects |
| FeaturesReporterFactory.fwd.hh | Report data to database |
| FeaturesReporterFactory.hh | Factory for creating FeaturesReporter objects |
| GeometricSolvationFeatures.cc | Report geometric solvation energy for each polar site to a features database |
| GeometricSolvationFeatures.fwd.hh | Report geometric solvation for each polar site to features Statistics Scientific Benchmark |
| GeometricSolvationFeatures.hh | Report hydrogen bonding based solvation model to a features database |
| GeometricSolvationFeaturesCreator.cc | |
| GeometricSolvationFeaturesCreator.hh | Header for GeometricSolvationFeaturesCreator for the GeometricSolvationFeatures load-time factory registration scheme |
| HBondFeatures.cc | Report HBond geometry and scores to features Statistics Scientific Benchmark |
| HBondFeatures.fwd.hh | Report HBond geometry and scores to features Statistics Scientific Benchmark |
| HBondFeatures.hh | Report HBond geometry and scores to features Statistics Scientific Benchmark |
| HBondFeaturesCreator.cc | |
| HBondFeaturesCreator.hh | Header for HBondFeaturesCreator for the HBondFeatures load-time factory registration scheme |
| HBondParameterFeatures.cc | Report HBond Parameters to features Statistics Scientific Benchmark |
| HBondParameterFeatures.fwd.hh | Report HBondParameter geometry and scores to features Statistics Scientific Benchmark |
| HBondParameterFeatures.hh | Report HBond Parameter features Statistics Scientific Benchmark |
| HBondParameterFeaturesCreator.cc | |
| HBondParameterFeaturesCreator.hh | Header for HBondParameterFeaturesCreator for the HBondParameterFeatures load-time factory registration scheme |
| HelixCapFeatures.cc | |
| HelixCapFeatures.fwd.hh | |
| HelixCapFeatures.hh | |
| HelixCapFeaturesCreator.cc | |
| HelixCapFeaturesCreator.hh | |
| InterfaceDdGMover.cc | Calculates ddG of binding |
| InterfaceDdGMover.fwd.hh | Calculates ddG of binding |
| InterfaceDdGMover.hh | Calculates ddG of binding |
| InterfaceDdGMoverCreator.cc | Calculates ddG of binding |
| InterfaceDdGMoverCreator.hh | Calculates ddG of binding |
| InterfaceFeatures.cc | |
| InterfaceFeatures.fwd.hh | |
| InterfaceFeatures.hh | Analyzes interfaces and interface residues of a pose mainly using InterfaceAnalayzerMover |
| InterfaceFeaturesCreator.cc | |
| InterfaceFeaturesCreator.hh | |
| JobDataFeatures.cc | |
| JobDataFeatures.fwd.hh | |
| JobDataFeatures.hh | |
| JobDataFeaturesCreator.cc | |
| JobDataFeaturesCreator.hh | Header for JobDataFeaturesCreator for the JobDataFeatures load-time factory registration scheme |
| LoopAnchorFeatures.cc | Report loop anchor features to a features database |
| LoopAnchorFeatures.fwd.hh | Report residue level geometry and scores to features Statistics Scientific Benchmark |
| LoopAnchorFeatures.hh | Report beta turns to a DB |
| LoopAnchorFeaturesCreator.cc | |
| LoopAnchorFeaturesCreator.hh | Header for LoopAnchorFeaturesCreator for the LoopAnchorFeatures load-time factory registration scheme |
| ModelFeatures.cc | |
| ModelFeatures.fwd.hh | |
| ModelFeatures.hh | |
| ModelFeaturesCreator.cc | |
| ModelFeaturesCreator.hh | |
| OrbitalsFeatures.cc | Report orbital geometry and scores to features statistics scientific benchmark |
| OrbitalsFeatures.fwd.hh | Report Orbital geometry and scores to features Statistics Scientific Benchmark |
| OrbitalsFeatures.hh | Report Orbital geometry and scores to features Statistics Scientific Benchmark |
| OrbitalsFeaturesCreator.cc | |
| OrbitalsFeaturesCreator.hh | Header for OrbitalsFeaturesCreator for the OrbitalsFeatures load-time factory registration scheme |
| PairFeatures.cc | Report orbital geometry and scores to features statistics scientific benchmark |
| PairFeatures.fwd.hh | Report atom-atom pair geometry and scores to features Statistics Scientific Benchmark |
| PairFeatures.hh | Report residue and atom pair geometry and scores to features Statistics Scientific Benchmark |
| PairFeaturesCreator.cc | |
| PairFeaturesCreator.hh | Header for PairFeaturesCreator for the PairFeatures load-time factory registration scheme |
| PdbDataFeatures.cc | |
| PdbDataFeatures.fwd.hh | |
| PdbDataFeatures.hh | |
| PdbDataFeaturesCreator.cc | |
| PdbDataFeaturesCreator.hh | Header for PdbDataFeaturesCreator for the PdbDataFeatures load-time factory registration scheme |
| PoseCommentsFeatures.cc | Report comments stored with each pose |
| PoseCommentsFeatures.fwd.hh | Report residue level geometry and scores to features Statistics Scientific Benchmark |
| PoseCommentsFeatures.hh | Report comments stored with each pose |
| PoseCommentsFeaturesCreator.cc | |
| PoseCommentsFeaturesCreator.hh | Header for PoseCommentsFeaturesCreator for the PoseCommentsFeatures load-time factory registration scheme |
| PoseConformationFeatures.cc | Report comments stored with each pose |
| PoseConformationFeatures.fwd.hh | Report pose fold tree related features |
| PoseConformationFeatures.hh | Report comments stored with each pose |
| PoseConformationFeaturesCreator.cc | |
| PoseConformationFeaturesCreator.hh | Header for PoseConformationFeaturesCreator for the PoseConformationFeatures load-time factory registration scheme |
| ProteinBackboneAtomAtomPairFeatures.cc | Report atom-atom pair distances between atoms in protein backbones to features Statistics Scientific Benchmark |
| ProteinBackboneAtomAtomPairFeatures.fwd.hh | Report atom-atom pair distances between atoms in protein backbones to features Statistics Scientific Benchmark |
| ProteinBackboneAtomAtomPairFeatures.hh | Report atom-atom pair distances between atoms in protein backbones to features Statistics Scientific Benchmark |
| ProteinBackboneAtomAtomPairFeaturesCreator.cc | |
| ProteinBackboneAtomAtomPairFeaturesCreator.hh | Header for ProteinBackboneAtomAtomPairFeaturesCreator for the ProteinBackboneAtomAtomPairFeatures load-time factory registration scheme |
| ProteinBackboneTorsionAngleFeatures.cc | Report Backbone Torsional Angle features |
| ProteinBackboneTorsionAngleFeatures.fwd.hh | Report protein backbone torsion angle features |
| ProteinBackboneTorsionAngleFeatures.hh | Report protein backbone torsion angle features |
| ProteinBackboneTorsionAngleFeaturesCreator.cc | |
| ProteinBackboneTorsionAngleFeaturesCreator.hh | Header for ProteinBackboneTorsionAngleFeaturesCreator for the ProteinBackboneTorsionAngleFeatures load-time factory registration scheme |
| ProteinBondGeometryFeatures.cc | Report Backbone Torsional Angle features |
| ProteinBondGeometryFeatures.fwd.hh | Report protein bond geometry features |
| ProteinBondGeometryFeatures.hh | Report protein backbone torsion angle features |
| ProteinBondGeometryFeaturesCreator.cc | |
| ProteinBondGeometryFeaturesCreator.hh | Header for ProteinBondGeometryFeaturesCreator for the ProteinBondGeometryFeatures load-time factory registration scheme |
| ProteinResidueConformationFeatures.cc | Report idealized torsional DOFs Statistics Scientific Benchmark |
| ProteinResidueConformationFeatures.fwd.hh | Report residue level geometry and scores to features Statistics Scientific Benchmark |
| ProteinResidueConformationFeatures.hh | Report idealized torsional DOFs Statistics Scientific Benchmark |
| ProteinResidueConformationFeaturesCreator.cc | |
| ProteinResidueConformationFeaturesCreator.hh | Header for ProteinResidueConformationFeaturesCreator for the ProteinResidueConformationFeatures load-time factory registration scheme |
| ProteinRMSDFeatures.cc | Report the root mean squared deviation between two poses |
| ProteinRMSDFeatures.fwd.hh | Report RMSD similarity of a protein structure against supplied reference structure |
| ProteinRMSDFeatures.hh | Report ProteinRMSD similarity of structure against supplied reference structure |
| ProteinRMSDFeaturesCreator.cc | |
| ProteinRMSDFeaturesCreator.hh | Header for ProteinRMSDFeaturesCreator for the ProteinRMSDFeatures load-time factory registration scheme |
| ProteinRMSDNoSuperpositionFeatures.cc | Report the root mean squared deviation (without superposition) between two poses |
| ProteinRMSDNoSuperpositionFeatures.fwd.hh | Report (no superposition) RMSD similarity of a protein structure against supplied reference structure |
| ProteinRMSDNoSuperpositionFeatures.hh | Report ProteinRMSD similarity of structure against supplied reference structure without superposition |
| ProteinRMSDNoSuperpositionFeaturesCreator.cc | |
| ProteinRMSDNoSuperpositionFeaturesCreator.hh | Header for ProteinRMSDNoSuperpositionFeaturesCreator for the ProteinRMSDNoSuperpositionFeatures load-time factory registration scheme |
| ProteinSilentReport.cc | |
| ProteinSilentReport.fwd.hh | Report pose fold tree related features |
| ProteinSilentReport.hh | Report feature data to database |
| ProtocolFeatures.cc | Report protocol level features to features statistics scientific benchmark |
| ProtocolFeatures.fwd.hh | Report Orbital geometry and scores to features Statistics Scientific Benchmark |
| ProtocolFeatures.hh | Report Orbital geometry and scores to features Statistics Scientific Benchmark |
| RadiusOfGyrationFeatures.cc | Report the radius of gyration to features Statistics Scientific Benchmark |
| RadiusOfGyrationFeatures.fwd.hh | Report the radius of gyration to features Statistics Scientific Benchmark |
| RadiusOfGyrationFeatures.hh | Report the radius of gyration to features Statistics Scientific Benchmark |
| RadiusOfGyrationFeaturesCreator.cc | |
| RadiusOfGyrationFeaturesCreator.hh | Header for RadiusOfGyrationFeaturesCreator for the RadiusOfGyrationFeatures load-time factory registration scheme |
| Report.cc | |
| Report.fwd.hh | Report pose fold tree related features |
| Report.hh | Report feature data to database |
| ReportToDB.cc | Report all data to a database |
| ReportToDB.fwd.hh | Report data to sqlite database |
| ReportToDB.hh | Report feature data to sqlite database |
| ReportToDBCreator.hh | This class will create instances of Mover ReportToDB for the MoverFactory |
| ResidueBurialFeatures.cc | Report residue burial to features statistics scientific benchmark |
| ResidueBurialFeatures.fwd.hh | Report residue level geometry and scores to features Statistics Scientific Benchmark |
| ResidueBurialFeatures.hh | Report residue to features Statistics Scientific Benchmark |
| ResidueBurialFeaturesCreator.cc | |
| ResidueBurialFeaturesCreator.hh | Header for ResidueBurialFeaturesCreator for the ResidueBurialFeatures load-time factory registration scheme |
| ResidueConformationFeatures.cc | Report idealized torsional DOFs Statistics Scientific Benchmark |
| ResidueConformationFeatures.fwd.hh | Report residue level geometry and scores to features Statistics Scientific Benchmark |
| ResidueConformationFeatures.hh | |
| ResidueConformationFeaturesCreator.cc | |
| ResidueConformationFeaturesCreator.hh | Header for ResidueConformationFeaturesCreator for the ResidueConformationFeatures load-time factory registration scheme |
| ResidueFeatures.cc | Report residue features to features Statistics Scientific Benchmark |
| ResidueFeatures.fwd.hh | Report residue features to features Statistics Scientific Benchmark |
| ResidueFeatures.hh | Report residue to features Statistics Scientific Benchmark |
| ResidueFeaturesCreator.cc | |
| ResidueFeaturesCreator.hh | Header for ResidueFeaturesCreator for the ResidueFeatures load-time factory registration scheme |
| ResidueGridScoresFeatures.cc | Detailed per atom scores of Scoring Grids |
| ResidueGridScoresFeatures.fwd.hh | |
| ResidueGridScoresFeatures.hh | |
| ResidueGridScoresFeaturesCreator.hh | |
| ResidueScoresFeatures.cc | Report residue scores to features Statistics Scientific Benchmark |
| ResidueScoresFeatures.fwd.hh | Report residue scores to features Statistics Scientific Benchmark |
| ResidueScoresFeatures.hh | Report residue scores to features Statistics Scientific Benchmark |
| ResidueScoresFeaturesCreator.cc | |
| ResidueScoresFeaturesCreator.hh | Header for ResidueScoresFeaturesCreator for the ResidueScoresFeatures load-time factory registration scheme |
| ResidueSecondaryStructureFeatures.cc | Report ResidueSecondaryStructure geometry and scores to features Statistics Scientific Benchmark |
| ResidueSecondaryStructureFeatures.fwd.hh | Report ResidueSecondaryStructure geometry and scores to features Statistics Scientific Benchmark |
| ResidueSecondaryStructureFeatures.hh | Report ResidueSecondaryStructure geometry and scores to features Statistics Scientific Benchmark |
| ResidueSecondaryStructureFeaturesCreator.cc | |
| ResidueSecondaryStructureFeaturesCreator.hh | Header for ResidueSecondaryStructureFeaturesCreator for the ResidueSecondaryStructureFeatures load-time factory registration scheme |
| ResidueTotalScoresFeatures.cc | Report the total per residue score to a features database |
| ResidueTotalScoresFeatures.fwd.hh | Report the total per residue score to a features database |
| ResidueTotalScoresFeatures.hh | Report the total per residue score to a features database |
| ResidueTotalScoresFeaturesCreator.cc | |
| ResidueTotalScoresFeaturesCreator.hh | Header for ResidueTotalScoresFeaturesCreator for the ResidueTotalScoresFeatures load-time factory registration scheme |
| ResidueTypesFeatures.cc | Report ResidueTypes to features Statistics Scientific Benchmark |
| ResidueTypesFeatures.fwd.hh | Report ResidueTypes geometry and scores to features Statistics Scientific Benchmark |
| ResidueTypesFeatures.hh | Report ResidueTypes features Statistics Scientific Benchmark |
| ResidueTypesFeaturesCreator.cc | |
| ResidueTypesFeaturesCreator.hh | Header for ResidueTypesFeaturesCreator for the ResidueTypesFeatures load-time factory registration scheme |
| RotamerBoltzmannWeightFeatures.cc | Report residue burial to features statistics scientific benchmark |
| RotamerBoltzmannWeightFeatures.fwd.hh | Report rotamer boltzmann weights to features Statistics Scientific Benchmark |
| RotamerBoltzmannWeightFeatures.hh | Report rotamer boltzmann weights to features Statistics Scientific Benchmark |
| RotamerBoltzmannWeightFeaturesCreator.cc | |
| RotamerBoltzmannWeightFeaturesCreator.hh | Header for RotamerBoltzmannWeightFeaturesCreator for the RotamerBoltzmannWeightFeatures load-time factory registration scheme |
| RotamerFeatures.cc | Report rotamer library features to the database |
| RotamerFeatures.fwd.hh | Report residue level geometry and scores to features Statistics Scientific Benchmark |
| RotamerFeatures.hh | Report idealized torsional DOFs Statistics Scientific Benchmark |
| RotamerFeaturesCreator.cc | |
| RotamerFeaturesCreator.hh | Header for RotamerFeaturesCreator for the RotamerFeatures load-time factory registration scheme |
| RotamerRecoveryFeatures.cc | Report rotamer recover features and scores to features Statistics Scientific Benchmark |
| RotamerRecoveryFeatures.fwd.hh | Report Rotamer Recovery features to features Statistics Scientific Benchmark |
| RotamerRecoveryFeatures.hh | Report Rotamer Recovery Statistics Scientific Benchmark |
| RotamerRecoveryFeaturesCreator.cc | |
| RotamerRecoveryFeaturesCreator.hh | Header for RotamerRecoveryFeaturesCreator for the RotamerRecoveryFeatures load-time factory registration scheme |
| RuntimeFeatures.cc | |
| RuntimeFeatures.fwd.hh | |
| RuntimeFeatures.hh | |
| RuntimeFeaturesCreator.hh | |
| SaltBridgeFeatures.cc | Report geometric solvation energy for each polar site to a features database |
| SaltBridgeFeatures.fwd.hh | Report geometric solvation for each polar site to features Statistics Scientific Benchmark |
| SaltBridgeFeatures.hh | Report comments stored with each pose |
| SaltBridgeFeaturesCreator.cc | |
| SaltBridgeFeaturesCreator.hh | Header for SaltBridgeFeaturesCreator for the SaltBridgeFeatures load-time factory registration scheme |
| ScoreFunctionFeatures.cc | Report the score parameters to a features database |
| ScoreFunctionFeatures.fwd.hh | Structure scores to features Statistics Scientific Benchmark |
| ScoreFunctionFeatures.hh | Add score function parameters to a features database |
| ScoreFunctionFeaturesCreator.cc | |
| ScoreFunctionFeaturesCreator.hh | Header for ScoreFunctionFeaturesCreator for the ScoreFunctionFeatures load-time factory registration scheme |
| ScoreTypeFeatures.cc | Report protocol level features to features statistics scientific benchmark |
| ScoreTypeFeatures.fwd.hh | Structure scores to features Statistics Scientific Benchmark |
| ScoreTypeFeatures.hh | Structure scores to features Statistics Scientific Benchmark |
| ScoreTypeFeaturesCreator.cc | |
| ScoreTypeFeaturesCreator.hh | Header for ScoreTypeFeaturesCreator for the ScoreTypeFeatures load-time factory registration scheme |
| ScreeningFeatures.cc | Report JSON object with information needed for vHTS postprocessing |
| ScreeningFeatures.fwd.hh | Forward headers for ScreeningFeatuers |
| ScreeningFeatures.hh | Report JSON object with information needed for vHTS postprocessing |
| ScreeningFeaturesCreator.cc | |
| ScreeningFeaturesCreator.hh | |
| SecondaryStructureSegmentFeatures.cc | |
| SecondaryStructureSegmentFeatures.fwd.hh | |
| SecondaryStructureSegmentFeatures.hh | |
| SecondaryStructureSegmentFeaturesCreator.cc | |
| SecondaryStructureSegmentFeaturesCreator.hh | |
| SimpleMetricFeatures.cc | Report a set of simple metrics into a features database |
| SimpleMetricFeatures.fwd.hh | Report a set of simple metrics into a features database |
| SimpleMetricFeatures.hh | Report a set of simple metrics into a features database |
| SimpleMetricFeaturesCreator.cc | |
| SimpleMetricFeaturesCreator.hh | Report a set of simple metrics into a features database |
| SmotifFeatures.cc | Calculate 4 geometric values used to classify smotifs. Reference (http://www.ncbi.nlm.nih.gov/pubmed/20421995) |
| SmotifFeatures.fwd.hh | |
| SmotifFeatures.hh | |
| SmotifFeaturesCreator.cc | |
| SmotifFeaturesCreator.hh | |
| StructureFeatures.cc | |
| StructureFeatures.fwd.hh | Report structure features to features Statistics Scientific Benchmark |
| StructureFeatures.hh | Report structure identifiers to a features database |
| StructureFeaturesCreator.cc | |
| StructureFeaturesCreator.hh | Header for StructureFeaturesCreator for the StructureFeatures load-time factory registration scheme |
| StructureScoresFeatures.cc | Report structure score features to a features database |
| StructureScoresFeatures.fwd.hh | Structure scores to features Statistics Scientific Benchmark |
| StructureScoresFeatures.hh | Structure scores to features Statistics Scientific Benchmark |
| StructureScoresFeaturesCreator.cc | |
| StructureScoresFeaturesCreator.hh | Header for StructureScoresFeaturesCreator for the StructureScoresFeatures load-time factory registration scheme |
| TaskOperationFeatures.cc | Report |
| TaskOperationFeatures.fwd.hh | Report |
| TaskOperationFeatures.hh | Report |
| TaskOperationFeaturesCreator.cc | |
| TaskOperationFeaturesCreator.hh | Header |
| TotalScoreFeatures.cc | |
| TotalScoreFeatures.fwd.hh | |
| TotalScoreFeatures.hh | |
| TotalScoreFeaturesCreator.hh | |
| TrajectoryMapFeatures.cc | Map trajectory structure_ids to cycle number |
| TrajectoryMapFeatures.fwd.hh | Map trajectory structure_ids to cycle number |
| TrajectoryMapFeatures.hh | Map trajectory structure_ids to cycle number |
| TrajectoryMapFeaturesCreator.cc | |
| TrajectoryMapFeaturesCreator.hh | Header for TrajectoryMapFeaturesCreator for the TrajectoryMapFeatures load-time factory registration scheme |
| TrajectoryReportToDB.cc | Report features data to database multiple times per structure, creating a trajectory |
| TrajectoryReportToDB.fwd.hh | Report features data to database multiple times per structure, creating a trajectory |
| TrajectoryReportToDB.hh | Report features data to database multiple times per structure, creating a trajectory |
| TrajectoryReportToDBCreator.hh | This class will create instances of Mover TrajectoryReportToDB for the MoverFactory |
| UnrecognizedAtomFeatures.cc | Report unrecognized atoms features to features Statistics Scientific Benchmark |
| UnrecognizedAtomFeatures.fwd.hh | Report residue features to features Statistics Scientific Benchmark |
| UnrecognizedAtomFeatures.hh | Report residue to features Statistics Scientific Benchmark |
| UnrecognizedAtomFeaturesCreator.cc | |
| UnrecognizedAtomFeaturesCreator.hh | Header for UnrecognizedAtomFeaturesCreator for the UnrecognizedAtomFeatures load-time factory registration scheme |
| util.cc | |
| util.hh | |
| WaterFeatures.cc | |
| WaterFeatures.fwd.hh | |
| WaterFeatures.hh | Report geometry between water and hbond sites |
| WaterFeaturesCreator.cc | |
| WaterFeaturesCreator.hh | Header for WaterFeaturesCreator for the WaterFeatures load-time factory registration scheme |
| ► fibril | |
| fibril_util.cc | |
| fibril_util.hh | Utility functions for handling of fibril symmetry modeling |
| SetupForFibrilMover.cc | |
| SetupForFibrilMover.fwd.hh | |
| SetupForFibrilMover.hh | |
| ► filters | |
| BasicFilterCreators.hh | FilterCreators for the most basic of filters |
| BasicFilters.cc | |
| BasicFilters.fwd.hh | |
| BasicFilters.hh | Header file for very simple Filter classes |
| CalculatorFilter.cc | Combine several filters in a (semi) arbitrary calculation |
| CalculatorFilter.fwd.hh | |
| CalculatorFilter.hh | Combine several filters in a (semi) arbitrary calculation |
| CalculatorFilterCreator.hh | FilterCreator for the CalculatorFilter |
| ContingentFilter.cc | |
| ContingentFilter.fwd.hh | |
| ContingentFilter.hh | A filter that is contingent on some other mover to set its pass/fail value |
| ContingentFilterCreator.hh | FilterCreator for the ContingentFilter |
| Filter.cc | |
| Filter.fwd.hh | |
| Filter.hh | Header file for Filter base class |
| filter_schemas.cc | |
| filter_schemas.hh | |
| FilterCreator.cc | |
| FilterCreator.hh | Base class for FilterCreators for the Filter load-time factory registration scheme |
| FilterFactory.cc | |
| FilterFactory.fwd.hh | Forward declaration of Factory class for Filters |
| FilterFactory.hh | |
| FilterValueMetric.cc | Convert the result of a Filter's report_sm() to a SimpleMetric |
| FilterValueMetric.fwd.hh | Convert the result of a Filter's report_sm() to a SimpleMetric |
| FilterValueMetric.hh | Convert the result of a Filter's report_sm() to a SimpleMetric |
| FilterValueMetricCreator.hh | Convert the result of a Filter's report_sm() to a SimpleMetric |
| ReplicateFilter.cc | Repeat a subfilter multiple times, and pass a value based on the aggregate results |
| ReplicateFilter.fwd.hh | |
| ReplicateFilter.hh | Repeat a subfilter multiple times, and pass a value based on the aggregate results |
| ReplicateFilterCreator.hh | FilterCreator for the ReplicateFilter |
| TimeFilter.cc | |
| TimeFilter.hh | |
| TimeFilterCreator.hh | FilterCreator for the TimeFilter |
| VectorPoseFilter.cc | Designates a filter that can be passed multiple poses by the VectorPoseJobDistributor Any filters deriving from this subclass can then act on all of the input poses simultaneously Only accessible through recon application |
| VectorPoseFilter.fwd.hh | Used for filters that require multiple poses to act upon Only accessible through recon application |
| VectorPoseFilter.hh | Designates a filter that can be passed multiple poses by the VectorPoseJobDistributor Any filters deriving from this subclass can then act on all of the input poses simultaneously Only accessible through recon application |
| ► fldsgn | |
| ► filters | |
| CoreDunbrackFilter.cc | |
| CoreDunbrackFilter.fwd.hh | |
| CoreDunbrackFilter.hh | Header file for CoreDunbrackFilter class |
| CoreDunbrackFilterCreator.hh | FilterCreators for the CoreDunbrackFilter |
| FragQualFilter.cc | |
| FragQualFilter.fwd.hh | |
| FragQualFilter.hh | Header file for FragQualFilter class |
| FragQualFilterCreator.hh | FilterCreators for the FragQualFilter |
| HelixBendFilter.cc | Filter used in 'Principles for designing proteins with cavities formed by curved b-sheets' to control helix geometry |
| HelixBendFilter.fwd.hh | Filter used in 'Principles for designing proteins with cavities formed by curved b-sheets' to control helix geometry |
| HelixBendFilter.hh | Filter used in 'Principles for designing proteins with cavities formed by curved b-sheets' to control helix geometry |
| HelixBendFilterCreator.hh | Filter used in 'Principles for designing proteins with cavities formed by curved b-sheets' to control helix geometry |
| HelixKinkFilter.cc | |
| HelixKinkFilter.fwd.hh | |
| HelixKinkFilter.hh | Header file for HelixKinkFilter class |
| HelixKinkFilterCreator.hh | FilterCreators for the HelixKinkFilter |
| HelixPairingFilter.cc | |
| HelixPairingFilter.fwd.hh | |
| HelixPairingFilter.hh | Header file for HelixPairingFilter class |
| HelixPairingFilterCreator.hh | FilterCreators for the HelixPairingFilter |
| HSSTripletFilter.cc | |
| HSSTripletFilter.fwd.hh | |
| HSSTripletFilter.hh | Header file for HSSTripletFilter class |
| HSSTripletFilterCreator.hh | FilterCreators for the HSSTripletFilter |
| InterlockingAromaFilter.cc | |
| InterlockingAromaFilter.fwd.hh | |
| InterlockingAromaFilter.hh | Header file for InterlockingAromaFilter class |
| InterlockingAromaFilterCreator.hh | FilterCreators for the InterlockingAromaFilter |
| NcontactsFilter.cc | |
| NcontactsFilter.fwd.hh | |
| NcontactsFilter.hh | Header file for NcontactsFilter class |
| NcontactsFilterCreator.hh | FilterCreators for the NcontactsFilter |
| ParallelBetaPairingPreferenceFilter.cc | |
| ParallelBetaPairingPreferenceFilter.fwd.hh | |
| ParallelBetaPairingPreferenceFilter.hh | Header file for ParallelBetaPairingPreferenceFilter class |
| ParallelBetaPairingPreferenceFilterCreator.hh | FilterCreators for the ParallelBetaPairingPreferenceFilter |
| SecondaryStructureCountFilter.cc | |
| SecondaryStructureCountFilter.fwd.hh | |
| SecondaryStructureCountFilter.hh | Header file for SecondaryStructureCountFilter class |
| SecondaryStructureCountFilterCreator.hh | FilterCreators for the SecondaryStructureCountFilter |
| SecondaryStructureFilter.cc | |
| SecondaryStructureFilter.fwd.hh | |
| SecondaryStructureFilter.hh | Header file for SecondaryStructureFilter class |
| SecondaryStructureFilterCreator.hh | FilterCreators for the SecondaryStructureFilter |
| SecondaryStructureHasResidueFilter.cc | |
| SecondaryStructureHasResidueFilter.fwd.hh | |
| SecondaryStructureHasResidueFilter.hh | Header file for SecondaryStructureHasResidueFilter class |
| SecondaryStructureHasResidueFilterCreator.hh | FilterCreators for the SecondaryStructureHasResidueFilter |
| SheetTopologyFilter.cc | |
| SheetTopologyFilter.fwd.hh | |
| SheetTopologyFilter.hh | Header file for SheetTopologyFilter class |
| SheetTopologyFilterCreator.hh | FilterCreators for the SheetTopologyFilter |
| StrandCurvatureByLevels.cc | Newer version of filter used in Marcos & Basanta et al. 2017 |
| StrandCurvatureByLevels.fwd.hh | Newer version of filter used in Marcos & Basanta et al. 2017 |
| StrandCurvatureByLevels.hh | Newer version of filter used in Marcos & Basanta et al. 2017 |
| StrandCurvatureByLevelsCreator.hh | Newer version of filter used in Marcos & Basanta et al. 2017 |
| StrandHelixGeometryFilter.cc | Another filter used in Marcos & Basanta et al. 2017 that needs to be updated |
| StrandHelixGeometryFilter.fwd.hh | Another filter used in Marcos & Basanta et al. 2017 that needs to be updated |
| StrandHelixGeometryFilter.hh | Another filter used in Marcos & Basanta et al. 2017 that needs to be updated |
| StrandHelixGeometryFilterCreator.hh | Another filter used in Marcos & Basanta et al. 2017 that needs to be updated |
| ► potentials | |
| ► sspot | |
| HSPairPotential.cc | |
| HSPairPotential.fwd.hh | |
| HSPairPotential.hh | |
| NatbiasHelicesSheetPotential.cc | Native-biased centroid score for helices on sheets |
| NatbiasHelicesSheetPotential.fwd.hh | |
| NatbiasHelicesSheetPotential.hh | Centroid score for helices on sheet |
| NatbiasHelixPairPotential.cc | Calss for helix-pairing potential |
| NatbiasHelixPairPotential.fwd.hh | |
| NatbiasHelixPairPotential.hh | |
| NatbiasSecondaryStructureEnergy.cc | Native biased centroid score for secondary structures |
| NatbiasSecondaryStructureEnergy.fwd.hh | |
| NatbiasSecondaryStructureEnergy.hh | Native biased centroid score for secondary structure |
| NatbiasSecondaryStructureEnergyCreator.hh | Declaration for the class that connects NatbiasSecondaryStructureEnergy with the ScoringManager |
| NatbiasStrandPairPotential.cc | |
| NatbiasStrandPairPotential.fwd.hh | |
| NatbiasStrandPairPotential.hh | Native biased centroid score for strand pairings |
| SSPairPotential.cc | |
| SSPairPotential.fwd.hh | |
| SSPairPotential.hh | |
| util.cc | |
| util.hh | Helper functions for SSPairPotential and HSPairPotential |
| AACompositionEnergy.cc | |
| AACompositionEnergy.fwd.hh | |
| AACompositionEnergy.hh | Amino acid composition energy |
| AACompositionEnergyCreator.hh | |
| SetAACompositionPotential.cc | |
| SetAACompositionPotential.fwd.hh | |
| SetAACompositionPotential.hh | |
| SetAACompositionPotentialCreator.hh | |
| SetSecStructEnergies.cc | |
| SetSecStructEnergies.fwd.hh | |
| SetSecStructEnergies.hh | Mover for setting centroid score of secondary structure through parser |
| SetSecStructEnergiesCreator.hh | |
| ► topology | |
| BB_Pos.cc | |
| BB_Pos.fwd.hh | |
| BB_Pos.hh | Bb_pos class header |
| BetaAlphaBetaMotif.cc | |
| BetaAlphaBetaMotif.fwd.hh | |
| BetaAlphaBetaMotif.hh | |
| DimerPairing.cc | |
| DimerPairing.fwd.hh | |
| DimerPairing.hh | |
| HelixPairing.cc | Class for helix pairings |
| HelixPairing.fwd.hh | |
| HelixPairing.hh | Header file of HelixPairing.cc |
| HSSTriplet.cc | |
| HSSTriplet.fwd.hh | |
| HSSTriplet.hh | |
| Sheet.cc | |
| Sheet.fwd.hh | |
| Sheet.hh | |
| SheetFoldTypeManager.cc | |
| SheetFoldTypeManager.fwd.hh | |
| SheetFoldTypeManager.hh | |
| SS_Info2.cc | |
| SS_Info2.fwd.hh | |
| SS_Info2.hh | |
| StrandPairing.cc | |
| StrandPairing.fwd.hh | |
| StrandPairing.hh | |
| util.cc | Utilities for fldsgn/topology |
| util.hh | |
| BluePrintBDR.cc | |
| BluePrintBDR.fwd.hh | Forward declaration for BluePrintBDR |
| BluePrintBDR.hh | |
| BluePrintBDRCreator.hh | This class will create instances of Mover BluePrintBDR for the MoverFactory |
| CircularPermutation.cc | Perform circularpermutation give a pose ( under development ) |
| CircularPermutation.fwd.hh | Forward declaration for CircularPermutation |
| CircularPermutation.hh | |
| CircularPermutationCreator.hh | |
| MatchResidues.cc | |
| MatchResidues.hh | Header file for MatchResidues class |
| MatchResiduesMover.cc | |
| MatchResiduesMover.fwd.hh | |
| MatchResiduesMover.hh | Header file for MatchResiduesMover class |
| MatchResiduesMoverCreator.hh | MoverCreator for the MatchResiduesMover |
| NcontactsCalculator.cc | |
| NcontactsCalculator.hh | Header file for NcontactsCalculator class |
| SheetConstraintGenerator.cc | |
| SheetConstraintGenerator.fwd.hh | |
| SheetConstraintGenerator.hh | |
| SheetConstraintGeneratorCreator.hh | This class will create instances of the SheetConstraintGenerator |
| SheetRemodelConstraintGenerator.cc | Remodel constraint generator for adding sheet constraints |
| SheetRemodelConstraintGenerator.fwd.hh | Remodel constraint generator for adding sheet constraints |
| SheetRemodelConstraintGenerator.hh | Remodel constraint generator for adding sheet constraints |
| SheetRemodelConstraintGeneratorCreator.hh | MoverCreator for the SheetRemodelConstraintGenerator |
| ► flexpack | |
| ► annealer | |
| FlexbbSimAnnealer.cc | Annealer for optimizing both backbone and sidechain conformations implementation |
| FlexbbSimAnnealer.fwd.hh | Forward declarations and typedefs for the FlexbbSimAnnealer class |
| FlexbbSimAnnealer.hh | |
| ► interaction_graph | |
| FlexbbIGFactory.cc | |
| FlexbbIGFactory.fwd.hh | |
| FlexbbIGFactory.hh | |
| FlexbbInteractionGraph.cc | |
| FlexbbInteractionGraph.fwd.hh | Forward declaration of base-class FlexbbIG and associated typedefs |
| FlexbbInteractionGraph.hh | |
| FlexbbSparseMatrixIndex.hh | Declaration of class for maintaining sparse matrix indices for flexbb states |
| MinimalistFlexbbInteractionGraph.cc | Class implementation for minimimalist on-the-fly RPE calculating FlexbbInteractionGraph |
| MinimalistFlexbbInteractionGraph.fwd.hh | Class forward declaration for minimimalist on-the-fly RPE calculating FlexbbInteractionGraph |
| MinimalistFlexbbInteractionGraph.hh | Class declaration for minimimalist on-the-fly RPE calculating FlexbbInteractionGraph |
| OTFFlexbbInteractionGraph.cc | Class implementation for OTF flexbb IG |
| OTFFlexbbInteractionGraph.fwd.hh | |
| OTFFlexbbInteractionGraph.hh | |
| PrecomputedFlexbbInteractionGraph.cc | |
| PrecomputedFlexbbInteractionGraph.fwd.hh | |
| PrecomputedFlexbbInteractionGraph.hh | |
| ► rotamer_set | |
| FlexbbRotamerSet.cc | |
| FlexbbRotamerSet.fwd.hh | |
| FlexbbRotamerSet.hh | Declaration for a class to hold rotamers for a single backbone conformation in a flexible packing run |
| FlexbbRotamerSets.cc | |
| FlexbbRotamerSets.fwd.hh | |
| FlexbbRotamerSets.hh | Declaration for a class to hold a set of rotamers for a flexible packing run |
| FlexPacker.cc | |
| FlexPacker.fwd.hh | |
| FlexPacker.hh | |
| OtherContextScoreFunction.cc | |
| OtherContextScoreFunction.hh | |
| ► flexpep_docking | |
| FlexPepDockingAbInitio.cc | |
| FlexPepDockingAbInitio.fwd.hh | |
| FlexPepDockingAbInitio.hh | Low-resolution part of docking protocol |
| FlexPepDockingFlags.cc | Flags structure for FlexPepDocking protocols |
| FlexPepDockingFlags.fwd.hh | Flags structure for FlexPepDocking protocols - forward declarations |
| FlexPepDockingFlags.hh | Flags structure for FlexPepDocking protocols |
| FlexPepDockingLowRes.cc | |
| FlexPepDockingLowRes.fwd.hh | |
| FlexPepDockingLowRes.hh | Low-resolution part of docking protocol |
| FlexPepDockingPoseMetrics.cc | Metrics calculations specific for FlexPepDock (at least for now) |
| FlexPepDockingPoseMetrics.fwd.hh | |
| FlexPepDockingPoseMetrics.hh | Metrics calculations specific for FlexPepDock (at least for now) |
| FlexPepDockingProtocol.cc | Protocol for docking flexible peptides onto globular proteins |
| FlexPepDockingProtocol.hh | Protocol for docking flexible peptides onto globular proteins |
| FlexPepDockingProtocolCreator.hh | |
| ► floppy_tail | |
| FloppyTail_publication.cc | FloppyTail extra functions from original publication - this calculates some statistics used for the first published use of the code (Kleiger G, Saha A, Lewis S, Kuhlman B, Deshaies RJ. Rapid E2-E3 assembly and disassembly enable processive ubiquitylation of cullin-RING ubiquitin ligase substrates. Cell. 2009 Nov 25;139(5):957-68. PubMed PMID: 19945379.) |
| FloppyTail_publication.hh | FloppyTail extra functions from original publication - this calculates some statistics used for the first published use of the code (Kleiger G, Saha A, Lewis S, Kuhlman B, Deshaies RJ. Rapid E2-E3 assembly and disassembly enable processive ubiquitylation of cullin-RING ubiquitin ligase substrates. Cell. 2009 Nov 25;139(5):957-68. PubMed PMID: 19945379.) |
| FloppyTailMover.cc | This app was initially intended for modeling the binding of a long unstructured C-terminal tail to some other part of a protein. It now works for N-terminal, C-terminal, and internal flexible regions. It works best as a method for sampling space to see what is possible, preferably in conjunction with extensive experimental constraints. It is not meant to produce ab-initio style models of folded complexes. It has now been expanded to work on symmetric proteins (tested on a homohexamer). Symmetry has not been tested with some flags. To run symmetry one needs a symm file and movemap. Symmetry has not been tested with fragments or constraints |
| FloppyTailMover.fwd.hh | FloppyTail forward declaration |
| FloppyTailMover.hh | FloppyTail headers |
| ► flxbb | |
| DesignTask.cc | |
| DesignTask.fwd.hh | |
| DesignTask.hh | |
| FilterStructs.cc | |
| FilterStructs.fwd.hh | |
| FilterStructs.hh | Filter structures |
| FlxbbDesign.cc | Perform cycles of design and relax with filter |
| FlxbbDesign.fwd.hh | Perform cycles of design and relax with filter |
| FlxbbDesign.hh | Perform cycles of design and relax with filter |
| FlxbbDesign_main.cc | |
| FlxbbDesign_main.hh | |
| FlxbbDesignCreator.hh | |
| InterlockAroma.cc | Place interlocking aromatic residues |
| InterlockAroma.fwd.hh | |
| InterlockAroma.hh | Perform cycles of design and relax with filter |
| InterlockAromaCreator.hh | This class will create instances of Mover InterlockAroma for the MoverFactory |
| LayerDesignOperation.cc | Design residues with selected amino acids depending on the enviroment: layer. The layer of each residue is assigned as core, boundary, or surface, which are defined by accessible surface of mainchain + CB |
| LayerDesignOperation.fwd.hh | |
| LayerDesignOperation.hh | Design residues with selected amino acids depending on the enviroment: layer. The layer of each residue is assigned as core, boundary, or surface, which are defined by accessible surface of mainchain + CB. If resfile is read before calling this operation, this operation is not applied for the residues defined by PIKAA |
| LayerDesignOperationCreator.hh | |
| utility.cc | |
| utility.hh | |
| ► fold_from_loops | |
| ► constraint_generator | |
| AutomaticSheetConstraintGenerator.cc | |
| AutomaticSheetConstraintGenerator.fwd.hh | |
| AutomaticSheetConstraintGenerator.hh | |
| AutomaticSheetConstraintGeneratorCreator.hh | |
| SegmentedAtomPairConstraintGenerator.cc | |
| SegmentedAtomPairConstraintGenerator.fwd.hh | |
| SegmentedAtomPairConstraintGenerator.hh | |
| SegmentedAtomPairConstraintGeneratorCreator.hh | |
| ► filters | |
| ConstraintFulfilmentFilter.cc | |
| ConstraintFulfilmentFilter.fwd.hh | Checks if the Pose fulfils the constraints that is carrying (AtomPair,Angle,Dihedral) |
| ConstraintFulfilmentFilter.hh | |
| ConstraintFulfilmentFilterCreator.hh | |
| RmsdFromResidueSelectorFilter.cc | |
| RmsdFromResidueSelectorFilter.fwd.hh | Evaluate RMSD between two poses allowing to select the regions to compare in each pose through ResidueSelector |
| RmsdFromResidueSelectorFilter.hh | |
| RmsdFromResidueSelectorFilterCreator.hh | |
| ScorePoseSegmentFromResidueSelectorFilter.cc | |
| ScorePoseSegmentFromResidueSelectorFilter.fwd.hh | Applies the scoring function only on the selected segment of the pose |
| ScorePoseSegmentFromResidueSelectorFilter.hh | |
| ScorePoseSegmentFromResidueSelectorFilterCreator.hh | |
| ► movers | |
| AlignByResidueSelectorMover.cc | |
| AlignByResidueSelectorMover.fwd.hh | |
| AlignByResidueSelectorMover.hh | |
| AlignByResidueSelectorMoverCreator.hh | |
| DisplayPoseLabelsMover.cc | |
| DisplayPoseLabelsMover.fwd.hh | |
| DisplayPoseLabelsMover.hh | |
| DisplayPoseLabelsMoverCreator.hh | |
| LabelPoseFromResidueSelectorMover.cc | |
| LabelPoseFromResidueSelectorMover.fwd.hh | |
| LabelPoseFromResidueSelectorMover.hh | |
| LabelPoseFromResidueSelectorMoverCreator.hh | |
| MoveMapFactoryToNamedMoveMapMover.cc | |
| MoveMapFactoryToNamedMoveMapMover.fwd.hh | |
| MoveMapFactoryToNamedMoveMapMover.hh | |
| MoveMapFactoryToNamedMoveMapMoverCreator.hh | |
| NubInitioLoopClosureMover.cc | |
| NubInitioLoopClosureMover.fwd.hh | |
| NubInitioLoopClosureMover.hh | |
| NubInitioLoopClosureMoverCreator.hh | |
| ReleaseConstraintFromResidueMover.cc | |
| ReleaseConstraintFromResidueMover.fwd.hh | |
| ReleaseConstraintFromResidueMover.hh | |
| ReleaseConstraintFromResidueMoverCreator.hh | |
| ResidueLabelsToPymolSelectionMover.cc | |
| ResidueLabelsToPymolSelectionMover.fwd.hh | |
| ResidueLabelsToPymolSelectionMover.hh | |
| ResidueLabelsToPymolSelectionMoverCreator.hh | |
| SavePDBInfoMover.cc | |
| SavePDBInfoMover.fwd.hh | |
| SavePDBInfoMover.hh | |
| SavePDBInfoMoverCreator.hh | |
| SplitAndMixPoseMover.cc | Splits a Pose according to a ResidueSelector |
| SplitAndMixPoseMover.fwd.hh | |
| SplitAndMixPoseMover.hh | Splits a Pose according to a ResidueSelector |
| SplitAndMixPoseMoverCreator.hh | |
| ► selectors | |
| ConstraintResidueSelector.cc | |
| ConstraintResidueSelector.fwd.hh | |
| ConstraintResidueSelector.hh | |
| ConstraintResidueSelectorCreator.hh | |
| CutpointResidueSelector.cc | |
| CutpointResidueSelector.fwd.hh | |
| CutpointResidueSelector.hh | |
| CutpointResidueSelectorCreator.hh | |
| ProteinResidueSelector.cc | |
| ProteinResidueSelector.fwd.hh | |
| ProteinResidueSelector.hh | |
| ProteinResidueSelectorCreator.hh | |
| ► utils | |
| Nub.cc | |
| Nub.fwd.hh | Ab Initio with a pre-folded segment (nub - pun intended) |
| Nub.hh | |
| utils.cc | Helper functions for nub initio |
| utils.hh | Helper functions for nub initio |
| NubInitioMover.cc | |
| NubInitioMover.fwd.hh | Ab Initio with a pre-folded segment (nub - pun intended) |
| NubInitioMover.hh | Ab Initio with a pre-folded segment (nub - pun intended) |
| NubInitioMoverCreator.hh | |
| ► forge | |
| ► build | |
| ► SegmentInsertConnectionScheme | |
| SegmentInsertConnectionScheme_Enum.hh | |
| Bridge.cc | Connect two contiguous but disjoint sections of a Pose into one continuous section |
| Bridge.fwd.hh | Forward declaration for Bridge |
| Bridge.hh | Connect two contiguous but disjoint sections of a Pose into one continuous section |
| BuildInstruction.cc | |
| BuildInstruction.fwd.hh | Forward declaration for BuildInstruction |
| BuildInstruction.hh | Tracks modifications to be made and is capable of residue length changes on a Pose |
| BuildManager.cc | |
| BuildManager.fwd.hh | Forward declaration for BuildManager |
| BuildManager.hh | Container for managing BuildInstructions |
| ConnectRight.cc | Instruction to connect one Pose onto the right side of another |
| ConnectRight.fwd.hh | Forward declaration for ConnectRight |
| ConnectRight.hh | Instruction to connect one Pose onto the right side of another |
| GrowLeft.cc | Instruction to create an n-side extension |
| GrowLeft.fwd.hh | Forward declaration for GrowLeft |
| GrowLeft.hh | Instruction to create an n-side extension |
| GrowRight.cc | Instruction to create a c-side extension |
| GrowRight.fwd.hh | Forward declaration for GrowRight |
| GrowRight.hh | Instruction to create a c-side extension |
| Interval.fwd.hh | Forward declaration for Interval |
| Interval.hh | |
| RelativeConnectRight.cc | Version of ConnectRight instruction that depends upon results from another BuildInstruction |
| RelativeConnectRight.fwd.hh | Forward declaration for RelativeConnectRight |
| RelativeConnectRight.hh | Version of ConnectRight instruction that depends upon results from another BuildInstruction |
| RelativeSequencePosition.fwd.hh | Forward declaration for RelativeSequencePosition |
| RelativeSequencePosition.hh | Function objects to compute relative positions for RelativeConnectRight |
| SegmentInsert.cc | Insert an external segment flanked by new regions |
| SegmentInsert.fwd.hh | Forward declaration for SegmentInsert |
| SegmentInsert.hh | Insert an external segment flanked by new regions |
| SegmentRebuild.cc | Instruction to rebuild a segment |
| SegmentRebuild.fwd.hh | Forward declaration for SegmentRebuild |
| SegmentRebuild.hh | Instruction to rebuild a segment |
| SegmentSwap.cc | Instruction to swap a segment with an external segment |
| SegmentSwap.fwd.hh | Forward declaration for SegmentSwap |
| SegmentSwap.hh | Instruction to swap a segment with an external segment |
| ► components | |
| BDR.cc | |
| BDR.fwd.hh | Forward declaration for BDR |
| BDR.hh | |
| VarLengthBuild.cc | Component that performs a simplified version of a protocol for variable length remodeling of protein backbone segments |
| VarLengthBuild.fwd.hh | Forward declaration for protocols::forge::components::VarLengthBuild |
| VarLengthBuild.hh | |
| ► constraints | |
| InverseRotamersCstGeneratorCreator.hh | This class will create instances of the InverseRotamersRCG mover |
| InverseRotamersRCG.cc | |
| InverseRotamersRCG.fwd.hh | |
| InverseRotamersRCG.hh | |
| InvrotTreeCstGeneratorCreator.hh | This class will create instances of the InvrotTreeRCG mover |
| InvrotTreeRCG.cc | |
| InvrotTreeRCG.fwd.hh | |
| InvrotTreeRCG.hh | |
| NtoCConstraintGenerator.cc | |
| NtoCConstraintGenerator.fwd.hh | |
| NtoCConstraintGenerator.hh | |
| NtoCConstraintGeneratorCreator.hh | This class will create instances of the NtoCConstraintGenerator mover |
| RemoveRemodelCsts.cc | |
| RemoveRemodelCsts.hh | |
| RemoveRemodelCstsCreator.hh | This class will create instances of the RemoveRemodelCsts mover |
| ► methods | |
| chainbreak_eval.cc | Methods for chainbreak evaluation |
| chainbreak_eval.hh | Methods for chainbreak evaluation |
| fold_tree_functions.cc | Methods for manipulating FoldTrees |
| fold_tree_functions.hh | Methods for manipulating FoldTrees |
| fragment_functions.cc | Methods for manipulating fragments |
| fragment_functions.hh | Methods for manipulating fragments |
| pose_mod.cc | Methods for Pose modifications |
| pose_mod.hh | Methods for Pose modifications |
| util.cc | Miscellaneous utility functions for forge |
| util.hh | Miscellaneous utility functions for forge |
| ► remodel | |
| RemodelAccumulator.cc | |
| RemodelAccumulator.hh | |
| RemodelConstraintGenerator.cc | |
| RemodelConstraintGenerator.fwd.hh | |
| RemodelConstraintGenerator.hh | Abstract base class that generates constraints during forge loop remodelling |
| RemodelData.cc | |
| RemodelData.hh | |
| RemodelDesignMover.cc | |
| RemodelDesignMover.hh | |
| RemodelEnzdesCstModule.cc | |
| RemodelEnzdesCstModule.fwd.hh | |
| RemodelEnzdesCstModule.hh | This file handles merging constraint defined by enzdes type cstfile |
| RemodelGlobalFrame.cc | |
| RemodelGlobalFrame.fwd.hh | |
| RemodelGlobalFrame.hh | |
| RemodelLigandHandler.cc | |
| RemodelLigandHandler.fwd.hh | |
| RemodelLigandHandler.hh | |
| RemodelLoopMover.cc | Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++ |
| RemodelLoopMover.fwd.hh | Forward declaration for RemodelLoopMover |
| RemodelLoopMover.hh | Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++ |
| RemodelMover.cc | |
| RemodelMover.fwd.hh | |
| RemodelMover.hh | |
| RemodelMoverCreator.hh | |
| RemodelRotamerLinks.cc | |
| RemodelRotamerLinks.fwd.hh | |
| RemodelRotamerLinks.hh | When operated on a PackerTask, adds RotamerLinks to it that will |
| RemodelRotamerLinksCreator.hh | |
| RemodelWorkingSet.cc | |
| RemodelWorkingSet.hh | |
| ResidueVicinityCstGeneratorCreator.hh | This class will create instances of the ResidueVicinityRCG mover |
| ResidueVicinityRCG.cc | |
| ResidueVicinityRCG.hh | |
| ► frag_picker | |
| ► nonlocal | |
| NonlocalFrags.cc | |
| NonlocalFrags.fwd.hh | |
| NonlocalFrags.hh | |
| NonlocalFragsMain.cc | |
| NonlocalFragsMain.hh | |
| NonlocalPair.fwd.hh | Forward declaration for NonlocalPair |
| NonlocalPair.hh | Nonlocal fragment pair |
| ► quota | |
| ABEGO_SS_Config.cc | |
| ABEGO_SS_Config.hh | Reads a config file for quota selector |
| ABEGO_SS_Map.cc | Map ABEGO vs. SS combinations |
| ABEGO_SS_Map.fwd.hh | |
| ABEGO_SS_Map.hh | Class for a quota pool based on secondary structure prediction and ABEGO torsion bin classification |
| ABEGO_SS_Pool.cc | |
| ABEGO_SS_Pool.fwd.hh | Class for a quota pool based on secondary structure prediction and ABEGO torsion bin classification |
| ABEGO_SS_Pool.hh | Quota selector based on difefrent secondary structure predicitons |
| QuotaCollector.cc | |
| QuotaCollector.fwd.hh | Forward declaration for QuotaCollector |
| QuotaCollector.hh | Pure virtual base class for a container holding fragment candidates |
| QuotaConfig.cc | |
| QuotaConfig.hh | Reads a config file for quota selector |
| QuotaPool.fwd.hh | Base class for a quota pool |
| QuotaPool.hh | Single pool used by quota |
| QuotaSelector.cc | |
| QuotaSelector.fwd.hh | |
| QuotaSelector.hh | Selector that picks best fragments based on their total score |
| SecondaryStructurePool.cc | |
| SecondaryStructurePool.fwd.hh | Class for a quota pool based on secondary structure prediction |
| SecondaryStructurePool.hh | Quota selector based on difefrent secondary structure predicitons |
| ► scores | |
| ABEGO_SS_Score.cc | Scores a fragment by secondary structure similarity |
| ABEGO_SS_Score.hh | Scores a fragment by secondary structure similarity |
| AdaptiveScoreHistogram.cc | |
| AdaptiveScoreHistogram.fwd.hh | AdaptiveScoreHistogram forward declaration |
| AdaptiveScoreHistogram.hh | A very basic histogram to keep statistics of scores |
| AmbigCSScore.cc | Object that scores a fragment by target-observed/vall-predicted chemical shift distances |
| AmbigCSScore.hh | Object that scores a fragment by its crmsd to the native |
| AtomBasedConstraintsScore.cc | |
| AtomBasedConstraintsScore.fwd.hh | AtomBasedConstraintsScore forward declaration |
| AtomBasedConstraintsScore.hh | |
| AtomPairConstraintsScore.cc | |
| AtomPairConstraintsScore.fwd.hh | |
| AtomPairConstraintsScore.hh | |
| BFactor.cc | Base class for fragment scoring |
| BFactor.hh | Base class for fragment scoring |
| CachingScoringMethod.hh | Adds cashing functionality to a FragmentScoringMethod object |
| ConstScore.hh | Score that adds a constant (so basically it does nothing!) |
| CSScore.cc | Object that scores a fragment by target-observed/vall-predicted chemical shift distances |
| CSScore.hh | Object that scores a fragment by its crmsd to the native |
| DihedralConstraintsScore.cc | Calculates a score based on how close are dihdral angles in a Vall chunk to their target values |
| DihedralConstraintsScore.fwd.hh | DihedralConstraintsScore forward declaration |
| DihedralConstraintsScore.hh | |
| DisulfideDistance.cc | |
| DisulfideDistance.hh | |
| DisulfideIdentity.cc | Base class for fragment scoring |
| DisulfideIdentity.hh | Base class for fragment scoring |
| FourAtomsConstraintData.cc | |
| FourAtomsConstraintData.fwd.hh | |
| FourAtomsConstraintData.hh | Holder for data necessary to create a single constraint based on four atoms |
| fragment_scoring_utilities.cc | |
| fragment_scoring_utilities.hh | Functions and data types common for fragment scoring |
| FragmentAllAtomCrmsd.cc | Object that scores a fragment by its crmsd to the native |
| FragmentAllAtomCrmsd.hh | Object that scores a fragment by its crmsd to the native |
| FragmentChunkCrms.cc | |
| FragmentChunkCrms.hh | Object that scores a fragment by its tmscore to the native |
| FragmentCrmsd.cc | Scores fragments by disulfide-linke Calpha distances |
| FragmentCrmsd.hh | Object that scores a fragment by its crmsd to the native |
| FragmentCrmsdResDepth.cc | Object that scores a fragment by its crmsd to the native |
| FragmentCrmsdResDepth.hh | Object that scores a fragment by its crmsd and residue depth to the native |
| FragmentDME.cc | Object that scores a fragment by its Distance Matrix Error (DME) to the native |
| FragmentDME.hh | Object that scores a fragment by its Distance Matrix Error (DME) to the native |
| FragmentScoreManager.cc | |
| FragmentScoreManager.fwd.hh | FragmentScoreManager forward declaration |
| FragmentScoreManager.hh | FragmentScoreManager forward declaration |
| FragmentScoreMap.fwd.hh | FragmentScoreMap forward declaration |
| FragmentScoreMap.hh | |
| FragmentScoringMethod.fwd.hh | |
| FragmentScoringMethod.hh | FragmentScoringMethod forward declaration |
| GunnCost.cc | |
| GunnCost.hh | |
| GunnCostScore.cc | Object that scores a fragment by its crmsd to the native |
| GunnCostScore.hh | Object that scores a fragment by Gunn cost function (how it fits to the local structure) |
| HydrophobicityProfileSimilarity.cc | Base class for fragment scoring |
| HydrophobicityProfileSimilarity.hh | Object that scores a fragment by hydrophobicity |
| HydrophobicitySimilarity.cc | Base class for fragment scoring |
| HydrophobicitySimilarity.hh | Object that scores a fragment by hydrophobicity |
| InterbondAngleScore.cc | |
| InterbondAngleScore.fwd.hh | |
| InterbondAngleScore.hh | |
| JCoupling.cc | |
| JCoupling.hh | |
| LAMBEGO_Similarity.cc | |
| LAMBEGO_Similarity.hh | |
| MidPhiOut.cc | |
| MidPhiOut.hh | Scores fragments by disulfide-linke Calpha distances |
| MidPsiOut.cc | |
| MidPsiOut.hh | Object that scores a fragment by its crmsd to the native |
| PartialSecondarySimilarity.cc | Scores a fragment by secondary structure similarity but throws out the worst 20% of the residue matches |
| PartialSecondarySimilarity.hh | |
| PCS_FragDistance.cc | |
| PCS_FragDistance.hh | |
| Phi.cc | Base class for fragment scoring |
| Phi.hh | Object that scores a fragment by predicted Phi torsions |
| PhiPsiRmsd.cc | |
| PhiPsiRmsd.hh | Object that scores a fragment by its crmsd to the native |
| PhiPsiSquareWell.cc | |
| PhiPsiSquareWell.hh | |
| ProfileScore.cc | Scores a fragment by an amino acid sequence identity |
| ProfileScore.fwd.hh | |
| ProfileScore.hh | FragmentScoringMethod forward declaration |
| ProfileScoreBlosum62.cc | |
| ProfileScoreBlosum62.hh | |
| ProfileScoreDistWeight.cc | |
| ProfileScoreDistWeight.hh | |
| ProfileScoreL1.cc | |
| ProfileScoreL1.hh | |
| ProfileScoreStructL1.cc | Scores a fragment using structure based profiles |
| ProfileScoreStructL1.hh | Scores a fragment by L1 structure based profile score |
| ProfileScoreSubMatrix.cc | Scores a fragment by substitution matrix (e.g. Blosum62) profile score |
| ProfileScoreSubMatrix.hh | Scores a fragment by substitution matrix (e.g. Blosum62) profile score |
| ProlinePhiScore.cc | |
| ProlinePhiScore.hh | Base class for fragment scoring |
| Psi.cc | Base class for fragment scoring |
| Psi.hh | Object that scores a fragment by predicted Psi torsions |
| PValuedFragmentScoreManager.cc | |
| PValuedFragmentScoreManager.hh | Score manager that stores statistics of all scores. This allows estimate p-value for a score |
| RamaScore.cc | |
| RamaScore.hh | Base class for fragment scoring |
| RDCScore.cc | Object that scores a fragment by its RDC |
| RDCScore.hh | Object that scores a fragment by its crmsd to the native |
| ScoreEValuator.cc | Scores a fragment by an amino acid sequence identity |
| ScoreEValuator.hh | Object that scores a fragment by its crmsd to the native |
| SecondaryIdentity.cc | Scores a fragment by an amino acid sequence identity |
| SecondaryIdentity.hh | Scores a fragment by an amino acid sequence identity |
| SecondarySimilarity.cc | Scores a fragment by secondary structure similarity |
| SecondarySimilarity.hh | Scores a fragment by secondary structure similarity |
| SequenceIdentity.cc | Base class for fragment scoring |
| SequenceIdentity.hh | Base class for fragment scoring |
| SolventAccessibility.cc | Base class for fragment scoring |
| SolventAccessibility.hh | Object that scores a fragment by predicted solvent accessibility |
| TalosSSSimilarity.cc | Scores a fragment by secondary structure similarity |
| TalosSSSimilarity.hh | Scores a fragment by secondary structure similarity |
| TorsionBinSimilarity.cc | |
| TorsionBinSimilarity.hh | |
| BestTotalScoreSelector.cc | |
| BestTotalScoreSelector.fwd.hh | |
| BestTotalScoreSelector.hh | Selector that picks best fragments based on their total score |
| BoundedCollector.fwd.hh | |
| BoundedCollector.hh | |
| CandidatesCollector.fwd.hh | Forward declaration for CandidatesCollector |
| CandidatesCollector.hh | Pure virtual base class for a container holding fragment candidates |
| CommonFragmentComparators.fwd.hh | Few ways to compare fragment candidates (forward definitions) |
| CommonFragmentComparators.hh | Few ways to compare fragment candidates |
| CompositeFragmentSelector.cc | Selector that picks best fragments based on their total score |
| CompositeFragmentSelector.hh | Selector that picks best fragments based on their total score |
| Contact.fwd.hh | |
| Contact.hh | A contact |
| ContactCounts.fwd.hh | |
| ContactCounts.hh | Contact counts |
| ContactTypes.cc | Fragment picker contact types |
| ContactTypes.hh | Fragment picker type declarations |
| CS2ndShift.cc | |
| CS2ndShift.hh | |
| CSTalosIO.cc | |
| CSTalosIO.hh | Class that converts Talos object into secondary shifts list |
| CustomScoreSelector.cc | |
| CustomScoreSelector.fwd.hh | |
| CustomScoreSelector.hh | Selector that picks best fragments based on their total score |
| DiversifyCrmsdByClustering.cc | |
| DiversifyCrmsdByClustering.hh | Selector that picks fragments diversified by crmsd (by means of hierarchical clustering) |
| DiversifyCrmsdSelector.cc | |
| DiversifyCrmsdSelector.hh | Selector that picks best fragments based on their total score |
| DiversifyDihedralsSelector.cc | |
| DiversifyDihedralsSelector.hh | Selector that picks best fragments based on their total score |
| Faraggi_SA.cc | Faraggi maximum SA values from Faraggi et al. Proteins 2008 |
| Faraggi_SA.hh | Faraggi maximum SA values from Faraggi et al. Proteins 2008 |
| FragmentCandidate.cc | |
| FragmentCandidate.fwd.hh | |
| FragmentCandidate.hh | Something that might become a fragment if its scores will be good enough |
| FragmentComparatorBase.fwd.hh | |
| FragmentComparatorBase.hh | Defines a base class for all fragment comparators |
| FragmentPicker.cc | Fragment picker - the core part of picking machinery |
| FragmentPicker.fwd.hh | Fragment picker - forward declaration |
| FragmentPicker.hh | Fragment picker - the core part of picking machinery |
| FragmentScoreFilter.cc | This filter analyzes fragment quality. How it does so is highly customizeable, but it is reccommended that you average the RMSD of all 200 fragments picked at every position. This is also the default behavior. It requires paths to external programs like SPARKS-X and blast-pgp, depending on your method of fragment picking |
| FragmentScoreFilter.fwd.hh | |
| FragmentScoreFilter.hh | |
| FragmentScoreFilterCreator.hh | FilterCreators for the FragmentScoreFilterCreator |
| FragmentSelectingRule.fwd.hh | |
| FragmentSelectingRule.hh | Selector that picks best fragments based on their total score |
| GrabAllCollector.hh | |
| JCouplingIO.cc | |
| JCouplingIO.hh | |
| LAMBEGO_IO.cc | |
| LAMBEGO_IO.hh | Reader for a probability distribution over A,B,E,G,O torsion bins |
| LazySortedVector1.hh | |
| PdbIdChunkFilter.cc | |
| PdbIdChunkFilter.fwd.hh | |
| PdbIdChunkFilter.hh | |
| PhiPsiTalosIO.cc | |
| PhiPsiTalosIO.hh | Class that reads and writes Phi-Psi in TALOS format |
| SidechainContactDistCutoff.cc | Defines sidechain contact distance cutoffs |
| SidechainContactDistCutoff.fwd.hh | |
| SidechainContactDistCutoff.hh | Defines sidechain contact distance cutoffs |
| TorsionBinIO.cc | |
| TorsionBinIO.hh | Reader for a probability distribution over A,B,E,G,O torsion bins |
| VallChunk.cc | Contiguous chunk of residues taken from a vall |
| VallChunk.fwd.hh | Forward declaration for VallChunk |
| VallChunk.hh | Contiguous chunk of residues taken from a vall |
| VallChunkFilter.fwd.hh | Forward declaration for VallChunkFilter |
| VallChunkFilter.hh | Defines two basic chunk filters based on pdb id |
| VallProvider.cc | Reads a vall library and serves the data in chunks |
| VallProvider.fwd.hh | Forward declaration for VallProvider |
| VallProvider.hh | Reads a vall library and serves the data in chunks |
| VallResidue.cc | Class for managing a line of the Vall fragment library |
| VallResidue.fwd.hh | Forward declaration for core::fragment::picking::vall:VallResidue |
| VallResidue.hh | Class for managing a line of the Vall fragment library |
| ► frags | |
| heap.cc | |
| heap.hh | |
| RMSVallData.hh | |
| TorsionFragment.cc | |
| TorsionFragment.fwd.hh | |
| TorsionFragment.hh | |
| VallData.cc | |
| VallData.fwd.hh | |
| VallData.hh | |
| ► generalized_kinematic_closure | |
| ► filter | |
| GeneralizedKICfilter.cc | Helper class defining success filters for generalized closure of arbitrary segments that could go through side-chains (e.g. disulfides) |
| GeneralizedKICfilter.fwd.hh | Defines owning pointers for GeneralizedKICfilter class |
| GeneralizedKICfilter.hh | Headers for GeneralizedKICfilter class (helper class for the GeneralizedKIC mover that defines filters to accept/reject closure solutions). Filters must be pass/fail (i.e. there are no shades of grey, here.) |
| ► perturber | |
| GeneralizedKICperturber.cc | Helper class for generalized closure of arbitrary segments that could go through side-chains (e.g. disulfides) |
| GeneralizedKICperturber.fwd.hh | Defines owning pointers for GeneralizedKICperturber class |
| GeneralizedKICperturber.hh | Headers for GeneralizedKICperturber class (helper class for the GeneralizedKIC mover) |
| ► selector | |
| GeneralizedKICselector.cc | Helper class for GeneralizedKIC defining how solutions are chosen that pass filters |
| GeneralizedKICselector.fwd.hh | Defines owning pointers for GeneralizedKICselector class |
| GeneralizedKICselector.hh | Headers for GeneralizedKICselector class (helper class for the GeneralizedKIC mover that defines how closure solutions that pass filters are chosen) |
| GeneralizedKIC.cc | Kinematic closure of arbitrary segments that could go through side-chains (e.g. disulfides) |
| GeneralizedKIC.fwd.hh | Defines owning pointers for GeneralizedKIC mover class |
| GeneralizedKIC.hh | Headers for GeneralizedKIC mover class |
| GeneralizedKICCreator.hh | This class will create instances of Mover GeneralizedKIC for the MoverFactory |
| util.cc | Utility functions for generalized kinematic closure |
| util.hh | |
| ► genetic_algorithm | |
| Entity.cc | |
| Entity.fwd.hh | |
| Entity.hh | Unit employed/optimized by GeneticAlgorithm |
| EntityRandomizer.cc | |
| EntityRandomizer.fwd.hh | Fowrad declaration of the class that controls the alteration of the traits that define an Entity |
| EntityRandomizer.hh | Controls the alteration of the traits that define Entity |
| FitnessFunction.hh | Determines the fitness of Entity for GeneticAlgorithm |
| GeneticAlgorithm.cc | |
| GeneticAlgorithm.fwd.hh | |
| GeneticAlgorithm.hh | Template class for genetic algorithm protocols |
| Mutate1Randomizer.cc | Class to mutate only a single position at a time in any given entity |
| Mutate1Randomizer.fwd.hh | Fowrad declaration of the class that controls the alteration of the traits that define an Entity |
| Mutate1Randomizer.hh | Class to mutate only a single position at a time in any given entity |
| ► grafting | |
| ► simple_movers | |
| DeleteRegionMover.cc | |
| DeleteRegionMover.fwd.hh | |
| DeleteRegionMover.hh | |
| DeleteRegionMoverCreator.hh | |
| InsertPoseIntoPoseMover.cc | |
| InsertPoseIntoPoseMover.fwd.hh | |
| InsertPoseIntoPoseMover.hh | |
| InsertPoseIntoPoseMoverCreator.hh | |
| KeepRegionMover.cc | |
| KeepRegionMover.fwd.hh | |
| KeepRegionMover.hh | Keep a region of a pose, delete the rest |
| KeepRegionMoverCreator.hh | |
| ReplaceRegionMover.cc | |
| ReplaceRegionMover.fwd.hh | |
| ReplaceRegionMover.hh | |
| ReplaceRegionMoverCreator.hh | |
| AnchoredGraftMover.cc | Method definitions for AnchoredGraftMover |
| AnchoredGraftMover.fwd.hh | |
| AnchoredGraftMover.hh | Class to graft a piece into a pose. Jared Adolf-Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com) |
| AnchoredGraftMoverCreator.hh | |
| CCDEndsGraftMover.cc | Method definitions for CCDEndsGraftMover |
| CCDEndsGraftMover.fwd.hh | |
| CCDEndsGraftMover.hh | Class to graft a piece into a pose. Jared Adolf-Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com) |
| CCDEndsGraftMoverCreator.hh | |
| GraftMoverBase.cc | Base class for GraftMovers |
| GraftMoverBase.fwd.hh | Forward declarations for GraftMoverBase class |
| GraftMoverBase.hh | Base class for graftmovers |
| util.cc | Utility functions for grafting |
| util.hh | Header for grafting utility functions |
| ► hbnet | |
| ConstrainHBondNetworkCreator.hh | |
| HBNet.cc | Base class HBNet; to explicitly detect and design h-bond networks |
| HBNet.fwd.hh | |
| HBNet.hh | Base class HBNet; to detect and design h-bond networks |
| HBNet_util.cc | |
| HBNet_util.hh | |
| HBNetCreator.hh | This class will create instances of Mover HBNet for the MoverFactory |
| HBNetScore.cc | |
| HBNetScore.fwd.hh | |
| HBNetScore.hh | Header file for HBNet filter |
| HBNetScoreFilterCreator.hh | FilterCreator for HBNetScore |
| HBNetStapleInterface.cc | Inherits from HBNet; protocol for designing h-bond networks to "staple" Prot/Prot interfaces; |
| HBNetStapleInterface.fwd.hh | |
| HBNetStapleInterface.hh | Inherits from HBNet; protocol for designing h-bond networks at Prot/Prot interfaces; |
| HBNetStapleInterfaceCreator.hh | This class will create instances of Mover HBNetStapleInterface for the MoverFactory |
| HBNetTaskOperations.cc | Task operations for HBNet |
| HBNetTaskOperations.fwd.hh | |
| HBNetTaskOperations.hh | |
| NetworkState.cc | |
| NetworkState.hh | Specialized structs for MC HBNet to store hbond network info |
| UnsatSelector.cc | |
| UnsatSelector.fwd.hh | |
| UnsatSelector.hh | |
| UnsatSelectorCreator.hh | |
| ► helical_bundle | |
| ► parameters | |
| BundleParameters.cc | A class for holding parameters for parametric helical bundle generation |
| BundleParameters.fwd.hh | Owning pointers and whatnot for the class for holding parameters for parametric helical bundle generation |
| BundleParameters.hh | Prototypes and method declarations for the BundleParameters class, a class for holding parameters for helical bundle backbone generation |
| BundleParametersSet.cc | A class for holding sets of parameters for parametric backbone generation |
| BundleParametersSet.fwd.hh | Owning pointers and whatnot for the class for holding sets of parameters for helical bundle backbone generation |
| BundleParametersSet.hh | Prototypes and method declarations for the BundleParametersSet class, a class for holding sets of parameters for parametric helical bundle generation |
| OmegaBundleParameter.cc | A class for the omega paremeter, derived from the generic RealValuedParameter class. Omega has a few additional options that can be configured, for pitch-copying vs. value-copying |
| OmegaBundleParameter.fwd.hh | Forward declarations for a class for the omega paremeter, derived from the generic RealValuedParameter class |
| OmegaBundleParameter.hh | Headers for a class for the omega paremeter, derived from the generic RealValuedParameter class |
| BackboneGridSampler.cc | This mover samples conformations of a repeating chain of a residue type by grid-sampling mainchain torsion values and setting all residues in a range to have the same mainchain torsion values |
| BackboneGridSampler.fwd.hh | Defines owning pointers for BackboneGridSampler mover class |
| BackboneGridSampler.hh | Headers for BackboneGridSampler.cc. Samples conformations of a repeating chain of a residue type by grid-sampling mainchain torsion values and setting all residues in a range to have the same mainchain torsion values |
| BackboneGridSamplerCreator.hh | This class will create instances of Mover BackboneGridSampler for the MoverFactory |
| BackboneGridSamplerHelper.cc | A class that stores the various mainchain torsion values that will be sampled by the BackboneGridSampler mover |
| BackboneGridSamplerHelper.fwd.hh | Owning pointers and whatnot for BackboneGridSamplerHelper class |
| BackboneGridSamplerHelper.hh | A class that stores the various mainchain torsion values that will be sampled by the BackboneGridSampler mover |
| BundleGridSampler.cc | This mover samples conformations of a helical bundle by performing a grid search in Crick parameter space |
| BundleGridSampler.fwd.hh | Defines owning pointers for BundleGridSampler mover class |
| BundleGridSampler.hh | Headers for BundleGridSampler.cc. Samples conformations of a helical bundle by performing a grid search in Crick parameter space |
| BundleGridSamplerCreator.hh | This class will create instances of Mover BundleGridSampler for the MoverFactory |
| BundleGridSamplerHelper.cc | A class that stores the various parameter perturbations that will be sampled by the BundleGridSampler mover |
| BundleGridSamplerHelper.fwd.hh | Owning pointers and whatnot for BundleGridSamplerHelper class |
| BundleGridSamplerHelper.hh | Prototypes and method declarations for the BundleGridSamplerHelper class |
| BundleParametrizationCalculator.cc | |
| BundleParametrizationCalculator.fwd.hh | Forward declarations for the BundleParametrizationCalculator class |
| BundleParametrizationCalculator.hh | Prototypes and method declarations for the BundleParametrizationCalculator class |
| BundleReporterFilter.cc | A filter that is mainly intended for reporting helical bundle parameters and an associated energy |
| BundleReporterFilter.fwd.hh | |
| BundleReporterFilter.hh | Header files for a filter that is mainly intended for reporting helical bundle parameters and an associated energy |
| BundleReporterFilterCreator.hh | Creators for the BundleReporterFilterCreator |
| FitSimpleHelix.cc | Determines the Crick parameters describing a straight helix, given an input pose |
| FitSimpleHelix.fwd.hh | Defines owning pointers for FitSimpleHelix mover class |
| FitSimpleHelix.hh | Headers for FitSimpleHelix mover class |
| FitSimpleHelixCreator.hh | This class will create instances of Mover FitSimpleHelix for the MoverFactory |
| FitSimpleHelixMultiFunc.cc | Multifunction class implementation for fitting a simple (straight) helix to the Crick parameters |
| FitSimpleHelixMultiFunc.hh | Multifunction class implementation for fitting a simple (straight) helix to the Crick parameters |
| MakeBundle.cc | Builds a helical bundle using the Crick parameters |
| MakeBundle.fwd.hh | Defines owning pointers for MakeBundle mover class |
| MakeBundle.hh | Headers for MakeBundle.cc. Builds a helical bundle using the Crick parameters |
| MakeBundleCreator.hh | This class will create instances of Mover MakeBundle for the MoverFactory |
| MakeBundleHelix.cc | Builds a single helix as part of a helical bundle |
| MakeBundleHelix.fwd.hh | Defines owning pointers for MakeBundleHelix mover class |
| MakeBundleHelix.hh | Headers for MakeBundleHelix.cc. Builds a single helix as part of a helical bundle |
| MakeBundleHelixCreator.hh | This class will create instances of Mover MakeBundleHelix for the MoverFactory |
| PerturbBundle.cc | Perturbs a helical bundle by altering the Crick parameters |
| PerturbBundle.fwd.hh | Defines owning pointers for PerturbBundle mover class |
| PerturbBundle.hh | Headers for PerturbBundle.cc. Perturbs a helical bundle by altering the Crick parameters |
| PerturbBundleCreator.hh | This class will create instances of Mover PerturbBundle for the MoverFactory |
| PerturbBundleHelix.cc | Reads the Crick parameters for a piece of a pose from the input pose and sets the mainchain torsions accordingly. The parameters are presumed to have been perturbed by another mover. This mover is intended to be called by the PerturbBundle mover, which handles the perturbation of the Crick parameters |
| PerturbBundleHelix.fwd.hh | Defines owning pointers for PerturbBundleHelix mover class |
| PerturbBundleHelix.hh | Headers for PerturbBundleHelix.cc. Reads the Crick parameters for a piece of a pose from the input pose and sets the mainchain torsions accordingly. The parameters are presumed to have been perturbed by another mover. This mover is intended to be called by the PerturbBundle mover, which handles the perturbation of the Crick parameters |
| PerturbBundleHelixCreator.hh | This class will create instances of Mover PerturbBundleHelix for the MoverFactory |
| util.cc | Utility functions for helical bundle construction |
| util.hh | |
| ► helical_bundle_predict | |
| HBP_FinalFullatomRefinementMoveGenerator.cc | A class to generate ParsedProtocols for the final full-atom refinement step |
| HBP_FinalFullatomRefinementMoveGenerator.fwd.hh | A class to generate ParsedProtocols for the final full-atom refinement step |
| HBP_FinalFullatomRefinementMoveGenerator.hh | A class to generate ParsedProtocols for the final full-atom refinement step |
| HBP_HelixCoilMoveGenerator.cc | A class for a module to generate ParsedProtocols for the next move in a Monte Carlo trajectory, based on the current state of the pose. This version uses helix-coil transition theory to nucleate and extend helices |
| HBP_HelixCoilMoveGenerator.fwd.hh | A class for a module to generate ParsedProtocols for the next move in a Monte Carlo trajectory, based on the current state of the pose. This version uses helix-coil transition theory to nucleate and extend helices |
| HBP_HelixCoilMoveGenerator.hh | A class for a module to generate ParsedProtocols for the next move in a Monte Carlo trajectory, based on the current state of the pose. This version uses helix-coil transition theory to nucleate and extend helices |
| HBP_MoveGenerator.cc | A base class for a module to generate ParsedProtocols for the next move in a Monte Carlo trajectory, based on the current state of the pose |
| HBP_MoveGenerator.fwd.hh | A base class for a module to generate ParsedProtocols for the next move in a Monte Carlo trajectory, based on the current state of the pose |
| HBP_MoveGenerator.hh | A base class for a module to generate ParsedProtocols for the next move in a Monte Carlo trajectory, based on the current state of the pose |
| HBP_SigmoidalTemperatureScheduleGenerator.cc | A class to generate a temperature ramping scheme for a simulated annealing trajectory. This version ramps sigmoidally |
| HBP_SigmoidalTemperatureScheduleGenerator.fwd.hh | A class to generate a temperature ramping scheme for a simulated annealing trajectory. This version ramps sigmoidally |
| HBP_SigmoidalTemperatureScheduleGenerator.hh | A class to generate a temperature ramping scheme for a simulated annealing trajectory. This version ramps sigmoidally |
| HBP_TemperatureScheduleGenerator.cc | A base class to generate a temperature ramping scheme for a simulated annealing trajectory |
| HBP_TemperatureScheduleGenerator.fwd.hh | A base class to generate a temperature ramping scheme for a simulated annealing trajectory |
| HBP_TemperatureScheduleGenerator.hh | A base class to generate a temperature ramping scheme for a simulated annealing trajectory |
| HBPHelixAssignments.cc | A class for storing the helix assignments for a pose. This can represent those proposed from an input file, or those at the current state of a trajectory |
| HBPHelixAssignments.fwd.hh | A class for storing the helix assignments for a pose. This can represent those proposed from an input file, or those at the current state of a trajectory |
| HBPHelixAssignments.hh | A class for storing the helix assignments for a pose. This can represent those proposed from an input file, or those at the current state of a trajectory |
| HelicalBundlePredictApplication.cc | The meat-and-potatoes for the helical_bundle_predict application, used to predict structures of helical bundles made from canonical or noncanonical building-blocks |
| HelicalBundlePredictApplication.fwd.hh | The meat-and-potatoes for the helical_bundle_predict application, used to predict structures of helical bundles made from canonical or noncanonical building-blocks |
| HelicalBundlePredictApplication.hh | The meat-and-potatoes for the helical_bundle_predict application, used to predict structures of helical bundles made from canonical or noncanonical building-blocks |
| HelicalBundlePredictApplication_MPI.cc | MPI implementation of HelicalBundlePredictApplication |
| HelicalBundlePredictApplication_MPI.fwd.hh | MPI implementation of HelicalBundlePredictApplication |
| HelicalBundlePredictApplication_MPI.hh | MPI implementation of HelicalBundlePredictApplication |
| ► helix_capper | |
| HelixNCapperMover.cc | Mover to find and fix poorly N-capped helices |
| HelixNCapperMover.hh | |
| ► hotspot_hashing | |
| ► movers | |
| PlaceProbeMover.cc | |
| PlaceProbeMover.fwd.hh | |
| PlaceProbeMover.hh | |
| PlaceSurfaceProbe.cc | |
| PlaceSurfaceProbe.fwd.hh | |
| PlaceSurfaceProbe.hh | |
| PlaceSurfaceProbeCreator.hh | |
| HotspotStub.cc | |
| HotspotStub.fwd.hh | |
| HotspotStub.hh | |
| HotspotStubSet.cc | |
| HotspotStubSet.fwd.hh | |
| HotspotStubSet.hh | |
| SearchPattern.cc | |
| SearchPattern.fwd.hh | |
| SearchPattern.hh | |
| SearchPatternRotSetOp.cc | Creates rigid body variants from search pattern during repacking |
| SearchPatternRotSetOp.fwd.hh | |
| SearchPatternRotSetOp.hh | Creates rigid body variants from search pattern during repacking |
| SICSearchPattern.cc | |
| SICSearchPattern.hh | |
| StubGenerator.cc | |
| StubGenerator.fwd.hh | |
| StubGenerator.hh | |
| SurfaceSearchPattern.cc | |
| SurfaceSearchPattern.hh | |
| ► hybridization | |
| AllResiduesChanged.hh | |
| BackboneTorsionPerturbation.cc | |
| BackboneTorsionPerturbation.hh | Declaration of the MoverCreator class for the BackboneTorsionPerturbation |
| BackboneTorsionPerturbationCreator.hh | |
| BackboneTorsionSampler.cc | |
| BackboneTorsionSampler.hh | Declaration of the MoverCreator class for the BackboneTorsionSampler |
| BackboneTorsionSamplerCreator.hh | |
| CartesianHybridize.cc | |
| CartesianHybridize.fwd.hh | |
| CartesianHybridize.hh | |
| CartesianSampler.cc | |
| CartesianSampler.fwd.hh | |
| CartesianSampler.hh | |
| ChunkTrialMover.cc | Wrapper for InsertChunkMover. It can take a random template and steal coordinates of all chunks or a random one |
| ChunkTrialMover.fwd.hh | |
| ChunkTrialMover.hh | Wrapper for InsertChunkMover. It can take a random template and steal coordinates of all chunks or a random one |
| DDomainParse.cc | A reimplementation of DDomain domain parsing algorithm, Protein Sci.16,947–955 (2007) |
| DDomainParse.hh | A reimplementation of DDomain domain parsing algorithm, Protein Sci.16,947–955 (2007) |
| DomainAssembly.cc | Domain Assembly |
| DomainAssembly.fwd.hh | |
| DomainAssembly.hh | |
| FoldTreeHybridize.cc | Align a random jump to template |
| FoldTreeHybridize.fwd.hh | |
| FoldTreeHybridize.hh | Align a random jump to template |
| FragmentBiasAssigner.cc | Take out the "compute_frag_bias()" from CartesianSampler |
| FragmentBiasAssigner.hh | Take out the "compute_frag_bias()" from CartesianSampler |
| HybridizeFoldtreeDynamic.cc | A mover to dynamically manipulate fold tree during the template hybridization sampling |
| HybridizeFoldtreeDynamic.fwd.hh | |
| HybridizeFoldtreeDynamic.hh | |
| HybridizeProtocol.cc | |
| HybridizeProtocol.fwd.hh | |
| HybridizeProtocol.hh | Add constraints to the current pose conformation |
| HybridizeProtocolCreator.hh | |
| InsertChunkMover.cc | Align a random jump to template |
| InsertChunkMover.hh | Align a random jump to template |
| MRMover.cc | |
| MRMover.hh | |
| TemplateHistory.cc | |
| TemplateHistory.fwd.hh | |
| TemplateHistory.hh | |
| TMalign.cc | A reimplementation of TM-align algorithm |
| TMalign.hh | A reimplementation of TM-align algorithm |
| util.cc | Align a random jump to template |
| util.hh | Align a random jump to template |
| WeightedFragmentSmoothTrialMover.cc | Fragment insertion and trial, each residue has a customized weight for the frequency of insertion |
| WeightedFragmentSmoothTrialMover.fwd.hh | |
| WeightedFragmentSmoothTrialMover.hh | Fragment insertion and trial, each residue has a customized weight for the frequency of insertion |
| WeightedFragmentTrialMover.cc | Fragment insertion and trial, each residue has a customized weight for the frequency of insertion |
| WeightedFragmentTrialMover.fwd.hh | |
| WeightedFragmentTrialMover.hh | Fragment insertion and trial, each residue has a customized weight for the frequency of insertion |
| ► hydrate | |
| Hydrate.cc | A protocol to add explicit water molecules as part of Hydrate/SPaDES |
| Hydrate.fwd.hh | |
| Hydrate.hh | |
| hydrate_functions.cc | |
| hydrate_functions.hh | |
| ► idealize | |
| idealize.cc | |
| idealize.hh | Protocols for idealizing a Pose |
| IdealizeMover.cc | |
| IdealizeMover.fwd.hh | Protocols for idealizing a Pose |
| IdealizeMover.hh | Protocols for idealizing a Pose |
| IdealizeMoverCreator.hh | |
| ► indel | |
| IndelOptimizationMover.cc | |
| IndelOptimizationMover.fwd.hh | |
| IndelOptimizationMover.hh | |
| ► indexed_structure_store | |
| ► filters | |
| FragmentLookupFilter.cc | FragmentLookupFilter class implementation |
| FragmentLookupFilter.fwd.hh | |
| FragmentLookupFilter.hh | Header for FragmentLookupFilter class |
| FragmentLookupFilterCreator.hh | FilterCreators for the FragmentLookupFilter |
| ► movers | |
| DirectSegmentLookupMover.cc | |
| DirectSegmentLookupMover.fwd.hh | |
| DirectSegmentLookupMover.hh | |
| DirectSegmentLookupMoverCreator.hh | |
| SegmentSequenceProfileMover.cc | |
| SegmentSequenceProfileMover.fwd.hh | |
| SegmentSequenceProfileMover.hh | |
| SegmentSequenceProfileMoverCreator.hh | |
| ► search | |
| QueryDatabase.cc | Database for generic alignment-based queries over structure stores |
| QueryDatabase.fwd.hh | Database for generic alignment-based queries over structure stores |
| QueryDatabase.hh | Database for generic alignment-based queries over structure stores |
| QueryDatabase.json.hh | |
| QueryDatabase.py.hh | Database for generic alignment-based queries over structure stores |
| BinaryFragmentStoreBackend.cc | |
| BinaryFragmentStoreBackend.fwd.hh | |
| BinaryFragmentStoreBackend.hh | |
| Datatypes.fwd.hh | Indexed_structure_store primitive datatypes |
| Datatypes.hh | Indexed_structure_store primitive datatypes |
| Datatypes.json.hh | Json-support functions for indexed_structure_store primitive datatypes |
| Datatypes.py.hh | Pybind11 converter support for indexed_structure_store datatypes |
| DirectSegmentLookup.cc | |
| DirectSegmentLookup.hh | Support class for direct rmsd-based segment lookup |
| DirectSegmentLookup.json.hh | |
| DirStructureStoreBackend.cc | Directory-backed protein structure store |
| DirStructureStoreBackend.fwd.hh | Directory-backed protein structure store |
| DirStructureStoreBackend.hh | Directory-backed protein structure store |
| FragmentLookup.cc | |
| FragmentLookup.fwd.hh | |
| FragmentLookup.hh | |
| FragmentStore.cc | |
| FragmentStore.fwd.hh | |
| FragmentStore.hh | |
| FragmentStoreManager.cc | |
| FragmentStoreManager.fwd.hh | |
| FragmentStoreManager.hh | |
| FragmentStoreProvider.fwd.hh | Abstract fragment store backing interface |
| FragmentStoreProvider.hh | Abstract fragment store backing interface |
| H5FragmentStoreBackend.cc | |
| H5FragmentStoreBackend.fwd.hh | |
| H5FragmentStoreBackend.hh | |
| H5StructureStoreBackend.cc | |
| H5StructureStoreBackend.fwd.hh | |
| H5StructureStoreBackend.hh | |
| JSONStructureStoreBackend.cc | |
| JSONStructureStoreBackend.hh | |
| nonpod_dtype_support.h | |
| orient_array.hh | |
| pose_utility.cc | |
| pose_utility.hh | |
| pose_utility.py.hh | |
| SegmentSequenceProfile.cc | Generate lookup-based sequence profiles for contiguous structureal elements |
| SegmentSequenceProfile.hh | Generate lookup-based sequence profiles for contiguous structureal elements |
| SegmentSequenceProfile.json.hh | Json-support for segment sequence profile configuration |
| SilentStructureStoreBackend.cc | SilentFile-backed protein structure store |
| SilentStructureStoreBackend.fwd.hh | SilentFile-backed protein structure store |
| SilentStructureStoreBackend.hh | SilentFile-backed protein structure store |
| SSHashedFragmentStore.cc | |
| SSHashedFragmentStore.fwd.hh | A wrapper to allow me to load the hashed fragment store on the datacache |
| SSHashedFragmentStore.hh | Parses the VALL by secondary structure after it is read in hdf5 format |
| StructureStore.cc | A POD-based database of residue-level protein structures |
| StructureStore.fwd.hh | A POD-based database of residue-level protein structures |
| StructureStore.hh | A POD-based database of residue-level protein structures |
| StructureStore.py.hh | Python bindings for a POD-based database of residue-level protein structures |
| StructureStoreManager.cc | Manages access to structure store via name-specific backends |
| StructureStoreManager.fwd.hh | |
| StructureStoreManager.hh | Manages access to structure store via name-specific backends |
| StructureStoreProvider.fwd.hh | Abstract structure store backing interface |
| StructureStoreProvider.hh | Abstract structure store backing interface |
| utility.cc | |
| utility.hh | |
| vector_tools.hh | Support templates for working with vectors |
| ► init | |
| init.cc | Declare WidgetRegistrators as static (global) variables in this .cc file so that at load time, they will be initialized, and the Creator classes they register will be handed to the appropriate WidgetFactory |
| init.hh | Initialization function to ensure all load-time factory registration occurs for classes that live in the protocols library. protocols::init::init() calls core::init::init(), and devel::init() call protocols::init::init() |
| register1.cc | Declare WidgetRegistrators as static (global) variables in this .cc file so that at load time, they will be initialized, and the Creator classes they register will be handed to the appropriate WidgetFactory |
| register1.hh | Initialization function to ensure all load-time factory registration occurs for classes that live in the protocols library. protocols::init::init() calls core::init::init(), and devel::init() call protocols::init::init(). We split this off such that the compiler isn't attempting to compile all of the registration classes at once |
| register2.cc | Declare WidgetRegistrators as static (global) variables in this .cc file so that at load time, they will be initialized, and the Creator classes they register will be handed to the appropriate WidgetFactory |
| register2.hh | Initialization function to ensure all load-time factory registration occurs for classes that live in the protocols library. protocols::init::init() calls core::init::init(), and devel::init() call protocols::init::init(). We split this off such that the compiler isn't attempting to compile all of the registration classes at once |
| register3.cc | Declare WidgetRegistrators as static (global) variables in this .cc file so that at load time, they will be initialized, and the Creator classes they register will be handed to the appropriate WidgetFactory |
| register3.hh | Initialization function to ensure all load-time factory registration occurs for classes that live in the protocols library. protocols::init::init() calls core::init::init(), and devel::init() call protocols::init::init(). We split this off such that the compiler isn't attempting to compile all of the registration classes at once |
| register4.cc | Declare WidgetRegistrators as static (global) variables in this .cc file so that at load time, they will be initialized, and the Creator classes they register will be handed to the appropriate WidgetFactory |
| register4.hh | Initialization function to ensure all load-time factory registration occurs for classes that live in the protocols library. protocols::init::init() calls core::init::init(), and devel::init() call protocols::init::init(). We split this off such that the compiler isn't attempting to compile all of the registration classes at once |
| ► interface | |
| util.cc | |
| util.hh | Collection of useful interface functions - both by chain and by groups. In one place. The namespace is for interface classes and functions that are general-use and protocol level. Many more specific classes and functions for interfaces can be found in their appropriate namespaces such as TaskOperations in protocols/task_operations |
| ► jd2 | |
| ► archive | |
| ArchiveBase.cc | |
| ArchiveBase.fwd.hh | |
| ArchiveBase.hh | |
| ArchiveManager.cc | |
| ArchiveManager.fwd.hh | |
| ArchiveManager.hh | |
| EvaluatedArchive.cc | |
| EvaluatedArchive.hh | |
| MPIArchiveJobDistributor.cc | |
| MPIArchiveJobDistributor.fwd.hh | |
| MPIArchiveJobDistributor.hh | |
| NormalizedEvaluatedArchive.cc | |
| NormalizedEvaluatedArchive.hh | |
| VarianceStatisticsArchive.cc | |
| VarianceStatisticsArchive.fwd.hh | |
| VarianceStatisticsArchive.hh | |
| AtomTreeDiffJobInputter.cc | |
| AtomTreeDiffJobInputter.fwd.hh | |
| AtomTreeDiffJobInputter.hh | Header file for AtomTreeDiffJobInputter class |
| AtomTreeDiffJobInputterCreator.hh | |
| AtomTreeDiffJobOutputter.cc | AtomTreeDiffJobOutputter |
| AtomTreeDiffJobOutputter.fwd.hh | Header file for AtomTreeDiffJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| AtomTreeDiffJobOutputter.hh | Header file for AtomTreeDiffJobOutputter class |
| AtomTreeDiffJobOutputterCreator.hh | |
| BatchJobInputter.cc | |
| BatchJobInputter.fwd.hh | |
| BatchJobInputter.hh | Header file for BatchJobInputter class |
| BOINCJobDistributor.cc | Implementation of BOINCJobDistributor |
| BOINCJobDistributor.hh | Implementation of BOINCJobDistributor |
| EmptyPoseJobInputter.cc | Base class EmptyPoseJobInputter |
| EmptyPoseJobInputter.fwd.hh | Header file for EmptyPoseJobInputter class |
| EmptyPoseJobInputter.hh | Header file for EmptyPoseJobInputter class |
| EmptyPoseJobInputterCreator.hh | Creator for EmptyPoseJobInputter |
| EnsembleJobInputter.cc | A Job Inputter for distributing a job based on a set of input structures that make up an ensemble |
| EnsembleJobInputter.fwd.hh | A Job Inputter for distributing a job based on a set of input structures that make up an ensemble |
| EnsembleJobInputter.hh | A Job Inputter for distributing a job based on a set of input structures that make up an ensemble |
| EnsembleJobInputterCreator.hh | |
| FileJobOutputter.cc | August 2008 job distributor as planned at RosettaCon08 - FileJobOutputter |
| FileJobOutputter.fwd.hh | Header file for FileJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| FileJobOutputter.hh | Header file for FileJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| FileSystemJobDistributor.cc | August 2008 job distributor as planned at RosettaCon08 - Simplest class FileSystemJobDistributor |
| FileSystemJobDistributor.fwd.hh | August 2008 job distributor as planned at RosettaCon08 - Simplest class FileSystemJobDistributor |
| FileSystemJobDistributor.hh | August 2008 job distributor as planned at RosettaCon08 - Simplest class FileSystemJobDistributor |
| InnerJob.cc | |
| InnerJob.fwd.hh | Header file for InnerJob class, part of August 2008 job distributor as planned at RosettaCon08 |
| InnerJob.hh | Header file for Job classes, part of August 2008 job distributor as planned at RosettaCon08. This file is responsible for three ideas: "inner" jobs, "outer" jobs (with which the job distributor works) and job container (currently just typdefed in the .fwd.hh) |
| InnerMultiThreadingJob.cc | |
| InnerMultiThreadingJob.fwd.hh | Header file for Job classes, part of August 2008 job distributor as planned at RosettaCon08 |
| InnerMultiThreadingJob.hh | |
| internal_util.cc | Utilities for JD2, intended to be used within the JD2 system itself |
| internal_util.hh | Utilities for JD2, intended to be used within the JD2 system itself |
| JD2ResourceManager.cc | |
| JD2ResourceManagerJobInputter.cc | |
| Job.cc | August 2008 job distributor as planned at RosettaCon08 - Job classes |
| Job.fwd.hh | Header file for Job classes, part of August 2008 job distributor as planned at RosettaCon08 |
| Job.hh | Header file for ThreadingJob classes, part of August 2008 job distributor as planned at RosettaCon08. This file is responsible for three ideas: "inner" jobs, "outer" jobs (with which the job distributor works) and job container (currently just typdefed in the .fwd.hh) |
| JobDistributor.cc | August 2008 job distributor as planned at RosettaCon08 - Base class |
| JobDistributor.fwd.hh | August 2008 job distributor as planned at RosettaCon08 - Base class |
| JobDistributor.hh | |
| JobDistributorFactory.cc | |
| JobDistributorFactory.fwd.hh | |
| JobDistributorFactory.hh | |
| JobInputter.cc | August 2008 job distributor as planned at RosettaCon08 - Interface base class JobInputter |
| JobInputter.fwd.hh | Header file for JobInputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| JobInputter.hh | Header file for JobInputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| JobInputterCreator.cc | |
| JobInputterCreator.hh | Base class for JobInputterCreators for the JobInputter load-time factory registration scheme |
| JobInputterFactory.cc | JobInputterCreator base |
| JobInputterFactory.fwd.hh | JobInputterFactory forward header |
| JobInputterFactory.hh | JobInputterFactory |
| JobOutputter.cc | August 2008 job distributor as planned at RosettaCon08 - Base class JobOutputter |
| JobOutputter.fwd.hh | Header file for JobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| JobOutputter.hh | Header file for JobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| JobOutputterCreator.cc | |
| JobOutputterCreator.hh | Base class for JobOutputterCreators for the JobOutputter load-time factory registration scheme |
| JobOutputterFactory.cc | JobOutputterCreator base |
| JobOutputterFactory.fwd.hh | JobOutputterFactory forward header |
| JobOutputterFactory.hh | JobOutputterFactory |
| JobOutputterObserver.hh | Classes that want to add score_value pairs to poses before they are output should derive from this Observer class |
| JobsContainer.cc | A container for an array of JobOPs |
| JobsContainer.fwd.hh | Header file for JobsContainer classes |
| JobsContainer.hh | Header file for Job classes, part of August 2008 job distributor as planned at RosettaCon08. This file is responsible for three ideas: "inner" jobs, "outer" jobs (with which the job distributor works) and job container (currently just typdefed in the .fwd.hh) |
| LargeNstructJobInputter.cc | A JobInputter for cases where the number of jobs is large enough to fill up memory |
| LargeNstructJobInputter.fwd.hh | Owning pointers and so forth for a JobInputter for cases where the number of jobs is large enough to fill up memory |
| LargeNstructJobInputter.hh | Header file for a JobInputter for cases where the number of jobs is large enough to fill up memory |
| LargeNstructJobInputterCreator.hh | Creator for a JobInputter for cases where the number of jobs is large enough to fill up memory |
| LazySilentFileJobInputter.cc | |
| LazySilentFileJobInputter.fwd.hh | |
| LazySilentFileJobInputter.hh | |
| LazySilentFileJobInputterCreator.hh | |
| mmCIFJobOutputter.cc | MmCIFJobOutputter writes mmCIF formatted outputs from finished Jobs in JD2 |
| mmCIFJobOutputter.fwd.hh | Header file for mmCIFJobOutputter class, written post chemXRW 2016 |
| mmCIFJobOutputter.hh | Header file for mmCIFJobOutputter class, part of JD2, implemented post 2016-chemXRW |
| mmCIFJobOutputterCreator.hh | |
| mmtfJobOutputter.cc | MmtfJobOutputter writes mmtf formatted outputs from finished Jobs in JD2 |
| mmtfJobOutputter.fwd.hh | Header file for mmtfJobOutputter class |
| mmtfJobOutputter.hh | Header file for mmtfJobOutputter class, part of JD2, implemented post 2016-chemXRW |
| mmtfJobOutputterCreator.hh | |
| MpiFileBuffer.cc | |
| MpiFileBuffer.fwd.hh | |
| MpiFileBuffer.hh | Header file for MPISilentFileJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| MPIFileBufJobDistributor.cc | Implementation of MPIFileBufJobDistributor |
| MPIFileBufJobDistributor.fwd.hh | |
| MPIFileBufJobDistributor.hh | |
| MPIMultiCommJobDistributor.cc | Implementation of MPIMultiCommJobDistributor |
| MPIMultiCommJobDistributor.fwd.hh | |
| MPIMultiCommJobDistributor.hh | |
| MPIWorkPartitionJobDistributor.cc | Implementation of MPIWorkPartitionJobDistributor - intended for MPI jobs on small numbers of nodes where the load can be balanced equally by the user |
| MPIWorkPartitionJobDistributor.fwd.hh | Forward header for MPIWorkPartitonJobDistributor |
| MPIWorkPartitionJobDistributor.hh | Header for MPIWorkPartitionJobDistributor - intended for MPI jobs on small numbers of nodes where the load can be balanced equally by the user |
| MPIWorkPoolJobDistributor.cc | Implementation of MPIWorkPoolJobDistributor |
| MPIWorkPoolJobDistributor.fwd.hh | Forward header for MPIWorkPoolJobDistributor |
| MPIWorkPoolJobDistributor.hh | Header for MPIWorkPoolJobDistributor - intended for continuous resamplig jobs that spawn new jobs based on a pool/archive of structures |
| MultiThreadingJob.cc | |
| MultiThreadingJob.fwd.hh | Header file for Job classes, part of August 2008 job distributor as planned at RosettaCon08 |
| MultiThreadingJob.hh | |
| NoOutputJobOutputter.hh | Header file for NoOutputJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| NoOutputJobOutputterCreator.cc | NoOutputJobOutputCreator class, part of November 2011 XRW2 |
| NoOutputJobOutputterCreator.hh | |
| PDBJobInputter.cc | August 2008 job distributor as planned at RosettaCon08 - Base class PDBJobInputter |
| PDBJobInputter.fwd.hh | Header file for PDBJobInputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| PDBJobInputter.hh | Header file for PDBJobInputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| PDBJobInputterCreator.hh | |
| PDBJobOutputter.cc | August 2008 job distributor as planned at RosettaCon08 - PDBJobOutputter |
| PDBJobOutputter.fwd.hh | Header file for PDBJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| PDBJobOutputter.hh | Header file for PDBJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| PDBJobOutputterCreator.hh | |
| PoseInputStreamJobInputter.cc | |
| PoseInputStreamJobInputter.fwd.hh | |
| PoseInputStreamJobInputter.hh | Header file for PoseInputStreamJobInputter class |
| PoseInputStreamJobInputterCreator.hh | |
| RNA_DeNovoJobOutputter.cc | |
| RNA_DeNovoJobOutputter.fwd.hh | Header file for RNA_DeNovoJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| RNA_DeNovoJobOutputter.hh | Header file for RNA_DeNovoJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| RNA_DeNovoJobOutputterCreator.hh | |
| ScoreOnlyJobOutputter.cc | |
| ScoreOnlyJobOutputter.fwd.hh | |
| ScoreOnlyJobOutputter.hh | |
| ScoreOnlyJobOutputterCreator.hh | |
| ScreeningJobInputter.cc | The ScreeningJobInputter The ScreeningJobInputter simplifies the process of inputting and handling input to a vHTS protocol. The ScreeningJobInputter takes in a JSON file using the -in:file:screening_job_file option This file is in the following format: { "jobs" : [ { "group_name" : "group_name_a", "proteins" : ["protein_a.pdb", "protein_b.pdb"], "ligands" : ["ligand_a.pdb", "ligand_b.pdb"] } ] "params : [ "aaa.param", "aab.param" |
| ScreeningJobInputter.fwd.hh | The ScreeningJobInputter forward headers |
| ScreeningJobInputter.hh | The ScreeningJobInputter forward headers |
| ScreeningJobInputterCreator.hh | Creator for ScreeningJobInputter |
| SerializedPoseJobInputter.cc | Parses inputs as serialized poses |
| SerializedPoseJobInputter.fwd.hh | Forward header file for SerializedPoseJobInputter class |
| SerializedPoseJobInputter.hh | Parses inputs as serialized poses |
| SerializedPoseJobInputterCreator.hh | Parses inputs as serialized poses |
| SerializedPoseJobOutputter.cc | Outputs serialized Poses that should only be read in by applications from the same git checkout on the same computer |
| SerializedPoseJobOutputter.fwd.hh | |
| SerializedPoseJobOutputter.hh | Outputs serialized Poses that should only be read in by applications from the same git checkout on the same computer |
| SerializedPoseJobOutputterCreator.hh | |
| ShuffleJobDistributor.cc | |
| ShuffleJobDistributor.hh | Implementation of ShuffleFileSystemJobDistributor |
| SilentFileJobInputter.cc | |
| SilentFileJobInputter.fwd.hh | |
| SilentFileJobInputter.hh | Header file for SilentFileJobInputter class |
| SilentFileJobInputterCreator.hh | |
| SilentFileJobOutputter.cc | |
| SilentFileJobOutputter.fwd.hh | Header file for SilentFileJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| SilentFileJobOutputter.hh | Header file for SilentFileJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| SilentFileJobOutputterCreator.hh | |
| SingleFileBuffer.cc | |
| SingleFileBuffer.fwd.hh | |
| SingleFileBuffer.hh | |
| util.cc | Utilities for JD2, which are somewhat safe to use outside of the JD2 system itself |
| util.hh | Utilities for JD2, which are somewhat safe to use outside of the JD2 system itself |
| VectorPoseJobDistributor.cc | Job distributor subclass for running RECON multistate design |
| VectorPoseJobDistributor.fwd.hh | Job distributor for running RECON MSD under MPI |
| VectorPoseJobDistributor.hh | Job distributor subclass for running RECON multistate design |
| wwPDBJobOutputter.cc | WwPDBJobOutputter class, interstitial between FileJobOutputter and PDBJobOutputter or mmCIFJobOutputter to share functionality |
| wwPDBJobOutputter.fwd.hh | Header file for wwPDBJobOutputter class, interstitial between FileJobOutputter and PDBJobOutputter or mmCIFJobOutputter to share functionality |
| wwPDBJobOutputter.hh | Header file for wwPDBJobOutputter class, interstitial between FileJobOutputter and PDBJobOutputter or mmCIFJobOutputter to share functionality |
| ► jd3 | |
| ► chunk_library | |
| ChunkLibraryInnerLarvalJob.cc | Method definitions for the InnerLarvalJob class |
| ChunkLibraryInnerLarvalJob.fwd.hh | Class declaration for the ChunkLibraryInnerLarvalJob |
| ChunkLibraryInnerLarvalJob.hh | Class definition for the ChunkLibraryInnerLarvalJob, which includes the index of the preliminary-job node that this ILJ originated from, or "0" if none |
| ChunkLibraryJobQueen.cc | ChunkLibraryJobQueen class's method definitions |
| ChunkLibraryJobQueen.fwd.hh | Class declaration for ChunkLibraryJobQueen |
| ChunkLibraryJobQueen.hh | Class declaration for ChunkLibraryJobQueen |
| MoverAndChunkLibraryJob.cc | The class method definitions for MoverAndChunkLibraryJob and ChunkLibraryJobResult |
| MoverAndChunkLibraryJob.fwd.hh | |
| MoverAndChunkLibraryJob.hh | |
| ► chunk_library_inputters | |
| chunk_library_inputter_schemas.cc | |
| chunk_library_inputter_schemas.hh | |
| ChunkLibraryInputSource.cc | |
| ChunkLibraryInputSource.fwd.hh | |
| ChunkLibraryInputSource.hh | |
| ChunkLibraryInputter.cc | Implementation of the ChunkLibraryInputter class |
| ChunkLibraryInputter.fwd.hh | Forward declaration of the ChunkLibraryInputter class |
| ChunkLibraryInputter.hh | Declaration of the ChunkLibraryInputter class |
| ChunkLibraryInputterCreator.fwd.hh | Forward declaration of the ChunkLibraryInputterCreator class |
| ChunkLibraryInputterCreator.hh | Declaration of the ChunkLibraryInputterCreator class |
| ChunkLibraryInputterFactory.cc | ChunkLibraryInputterFactory class that holds the list of classes able to create Poses from inputs |
| ChunkLibraryInputterFactory.fwd.hh | ChunkLibraryInputterFactory class that holds the list of classes able to create Poses from inputs |
| ChunkLibraryInputterFactory.hh | ChunkLibraryInputterFactory class that holds the list of classes able to create Poses from inputs |
| PDBChunkLibraryInputter.cc | PDBChunkLibraryInputter class definition |
| PDBChunkLibraryInputter.fwd.hh | Forward declaration of the PDBChunkLibraryInputter class for initializing Poses from .pdb or .pdb.gz files |
| PDBChunkLibraryInputter.hh | Declaration of the PDBChunkLibraryInputter class for initializing Poses from .pdb or .pdb.gz files |
| PDBChunkLibraryInputterCreator.hh | Declaration of the PDBChunkLibraryInputterCreator class |
| ► dag_node_managers | |
| EvenlyPartitionedNodeManager.cc | Auto-generated serialization template functions |
| EvenlyPartitionedNodeManager.fwd.hh | |
| EvenlyPartitionedNodeManager.hh | Node Manager that separates job results into different pools of equal size. Assignment of job results into pools is determined by you, the user, in the form of the "partition" argument in register_result(). If you are implementing a result threshold, this will also be evenly divided among all of the partitions |
| NodeManager.cc | Base class for the family of JD3 Node Managers. This class is intended to offload some of the result-sorting logic from a Job Queen for a single job-dag node |
| NodeManager.fwd.hh | |
| NodeManager.hh | Base class for the family of JD3 Node Managers. This class is intended to offload some of the result-sorting logic from a Job Queen for a single job-dag node |
| NodeManagerStorageMatrix.cc | |
| NodeManagerStorageMatrix.fwd.hh | |
| NodeManagerStorageMatrix.hh | |
| SimpleNodeManager.cc | Auto-generated serialization template functions |
| SimpleNodeManager.fwd.hh | |
| SimpleNodeManager.hh | Node Manager that does not discriminate between job results. All results are added to the same pool |
| ► deallocation | |
| DeallocationMessage.cc | The implementation for class protocols::jd3::deallocation::DeallocationMessage's methods |
| DeallocationMessage.fwd.hh | The forward declaration for class protocols::jd3::deallocation::DeallocationMessage |
| DeallocationMessage.hh | The definition for class protocols::jd3::DeallocationMessage |
| InputPoseDeallocationMessage.cc | The implementation for class protocols::jd3::deallocation::InputPoseDeallocationMessage's methods |
| InputPoseDeallocationMessage.fwd.hh | The forward declaration for class protocols::jd3::deallocation::InputPoseDeallocationMessage |
| InputPoseDeallocationMessage.hh | The definition for class protocols::jd3::InputPoseDeallocationMessage |
| ResourceDeallocationMessage.cc | The implementation for class protocols::jd3::deallocation::ResourceDeallocationMessage's methods |
| ResourceDeallocationMessage.fwd.hh | The forward declaration for class protocols::jd3::deallocation::ResourceDeallocationMessage |
| ResourceDeallocationMessage.hh | The definition for class protocols::jd3::ResourceDeallocationMessage |
| ► full_model | |
| FullModelInnerLarvalJob.cc | Method definitions for the InnerLarvalJob class |
| FullModelInnerLarvalJob.fwd.hh | Class declaration for the FullModelInnerLarvalJob |
| FullModelInnerLarvalJob.hh | Class definition for the FullModelInnerLarvalJob, which includes the index of the preliminary-job node that this ILJ originated from, or "0" if none |
| FullModelJobQueen.cc | FullModelJobQueen class's method definitions |
| FullModelJobQueen.fwd.hh | Class declaration for FullModelJobQueen |
| FullModelJobQueen.hh | Class declaration for FullModelJobQueen |
| ► full_model_inputters | |
| full_model_inputter_schemas.cc | |
| full_model_inputter_schemas.hh | |
| FullModelInputSource.cc | |
| FullModelInputSource.fwd.hh | |
| FullModelInputSource.hh | |
| FullModelInputter.cc | Implementation of the FullModelInputter class |
| FullModelInputter.fwd.hh | Forward declaration of the FullModelInputter class |
| FullModelInputter.hh | Declaration of the FullModelInputter class |
| FullModelInputterCreator.fwd.hh | Forward declaration of the FullModelInputterCreator class |
| FullModelInputterCreator.hh | Declaration of the FullModelInputterCreator class |
| FullModelInputterFactory.cc | FullModelInputterFactory class that holds the list of classes able to create Poses from inputs |
| FullModelInputterFactory.fwd.hh | FullModelInputterFactory class that holds the list of classes able to create Poses from inputs |
| FullModelInputterFactory.hh | FullModelInputterFactory class that holds the list of classes able to create Poses from inputs |
| PDBFullModelInputter.cc | PDBFullModelInputter class definition |
| PDBFullModelInputter.fwd.hh | Forward declaration of the PDBFullModelInputter class for initializing Poses from .pdb or .pdb.gz files |
| PDBFullModelInputter.hh | Declaration of the PDBFullModelInputter class for initializing Poses from .pdb or .pdb.gz files |
| PDBFullModelInputterCreator.hh | Declaration of the PDBFullModelInputterCreator class |
| SilentFileFullModelInputter.cc | |
| SilentFileFullModelInputter.fwd.hh | |
| SilentFileFullModelInputter.hh | |
| SilentFileFullModelInputterCreator.hh | Creator class for the SilentFile Pose Inputter |
| ► job_distributors | |
| JobExtractor.cc | A class for managing the complexity of requesting jobs from the JobQueen and keeping track of what JobNodes in the JobDAG still have outstanding jobs and for updating the JobDAG |
| JobExtractor.fwd.hh | Forward header for JobExtractor |
| JobExtractor.hh | Class to handle the process of requesting jobs from the JobQueen, keeping track of which nodes have their work completed, and which nodes each jobs belong to |
| MPIWorkPoolJobDistributor.cc | Implementation of MPIWorkPoolJobDistributor |
| MPIWorkPoolJobDistributor.fwd.hh | Forward header for MPIWorkPoolJobDistributor |
| MPIWorkPoolJobDistributor.hh | Jd3 version of header for MPIWorkPoolJobDistributor - intended for MPI jobs on large numbers of nodes where the head node is dedicated to handing out new jobs to workers. This code cannot be compiled without C++11 and Serialization, but it can be compiled without MPI |
| MultiThreadedJobDistributor.cc | MultiThreadedJobDistributor class definition |
| MultiThreadedJobDistributor.fwd.hh | MultiThreadedJobDistributor class declaration |
| MultiThreadedJobDistributor.hh | |
| VanillaJobDistributor.cc | VanillaJobDistributor class method definitions |
| VanillaJobDistributor.fwd.hh | |
| VanillaJobDistributor.hh | |
| ► job_results | |
| PoseJobResult.cc | The class method definitions for PoseJobResult |
| PoseJobResult.fwd.hh | The declaration of class PoseJobResult |
| PoseJobResult.hh | A standard JobResult that takes and stores a pose. Derived classes may derive additional objects to store from the set pose |
| ► job_summaries | |
| EnergyJobSummary.cc | A JobSummary that simply stores the energy from a job |
| EnergyJobSummary.fwd.hh | A JobSummary that simply stores the energy from a job |
| EnergyJobSummary.hh | A JobSummary that simply stores the energy from a job |
| StandardPoseJobSummary.cc | A JobSummary for arbitrary SimpleMetrics |
| StandardPoseJobSummary.fwd.hh | A JobSummary for arbitrary SimpleMetrics |
| StandardPoseJobSummary.hh | A JobSummary for arbitrary Energies and SimpleMetrics |
| ► jobs | |
| MoverJob.cc | A base class for any job that takes and uses a mover |
| MoverJob.fwd.hh | A base class for any job that takes and uses a mover |
| MoverJob.hh | A base class for any job that takes and uses a mover |
| ► output | |
| MultipleOutputSpecification.cc | Method Definitions for the MultipleOutputSpecification class |
| MultipleOutputSpecification.fwd.hh | Declaration of the MultipleOutputSpecification class |
| MultipleOutputSpecification.hh | Definition of the MultipleOutputSpecification class |
| MultipleOutputter.cc | Definition of the MultipleOutputter class's methods |
| MultipleOutputter.fwd.hh | Declaration of the MultipleOutputter class |
| MultipleOutputter.hh | Definition of the MultipleOutputter class |
| OutputSpecification.cc | Method definitions of the OutputSpecification class |
| OutputSpecification.fwd.hh | Declaration of the OutputSpecification class |
| OutputSpecification.hh | Definition of the OutputSpecification class |
| ResultOutputter.cc | Method definitions for the ResultOutputter class |
| ResultOutputter.fwd.hh | Declaration of the ResultOutputter class |
| ResultOutputter.hh | Definition of the ResultOutputter class |
| ► pose_inputters | |
| PDBPoseInputter.cc | PDBPoseInputter class definition |
| PDBPoseInputter.fwd.hh | Forward declaration of the PDBPoseInputter class for initializing Poses from .pdb or .pdb.gz files |
| PDBPoseInputter.hh | Declaration of the PDBPoseInputter class for initializing Poses from .pdb or .pdb.gz files |
| PDBPoseInputterCreator.cc | Auto-generated serialization template functions |
| PDBPoseInputterCreator.hh | Declaration of the PDBPoseInputterCreator class |
| pose_inputter_schemas.cc | |
| pose_inputter_schemas.hh | |
| PoseInputSource.cc | Definition of the PoseInputSource class |
| PoseInputSource.fwd.hh | Forward declaration of the PoseInputSource class |
| PoseInputSource.hh | Declaration of the PoseInputSource class |
| PoseInputter.cc | Implementation of the PoseInputter class |
| PoseInputter.fwd.hh | Forward declaration of the PoseInputter class |
| PoseInputter.hh | Declaration of the PoseInputter class |
| PoseInputterCreator.cc | Auto-generated serialization template functions |
| PoseInputterCreator.fwd.hh | Forward declaration of the PoseInputterCreator class |
| PoseInputterCreator.hh | Declaration of the PoseInputterCreator class |
| PoseInputterFactory.cc | PoseInputterFactory class that holds the list of classes able to create Poses from inputs |
| PoseInputterFactory.fwd.hh | PoseInputterFactory class that holds the list of classes able to create Poses from inputs |
| PoseInputterFactory.hh | PoseInputterFactory class that holds the list of classes able to create Poses from inputs |
| SilentFilePoseInputter.cc | |
| SilentFilePoseInputter.fwd.hh | |
| SilentFilePoseInputter.hh | |
| SilentFilePoseInputterCreator.cc | Auto-generated serialization template functions |
| SilentFilePoseInputterCreator.hh | Creator class for the SilentFile Pose Inputter |
| ► pose_outputters | |
| DeNovoSilentFilePoseOutputter.cc | |
| DeNovoSilentFilePoseOutputter.fwd.hh | |
| DeNovoSilentFilePoseOutputter.hh | |
| DeNovoSilentFilePoseOutputterCreator.cc | Auto-generated serialization template functions |
| DeNovoSilentFilePoseOutputterCreator.hh | Declaration of the DeNovoSilentFilePoseOutputterCreator class |
| mmTFPoseOutputSpecification.cc | Method definitions of the mmTFPoseOutputSpecification class |
| mmTFPoseOutputSpecification.fwd.hh | Declaration of the mmTFPoseOutputSpecification class |
| mmTFPoseOutputSpecification.hh | Definition of the mmTFPoseOutputSpecification class |
| mmTFPoseOutputter.cc | |
| mmTFPoseOutputter.fwd.hh | |
| mmTFPoseOutputter.hh | |
| mmTFPoseOutputterCreator.cc | Auto-generated serialization template functions |
| mmTFPoseOutputterCreator.hh | Declaration of the mmTFPoseOutputterCreator class |
| PDBPoseOutputSpecification.cc | Method definitions of the PDBPoseOutputSpecification class |
| PDBPoseOutputSpecification.fwd.hh | Declaration of the PDBPoseOutputSpecification class |
| PDBPoseOutputSpecification.hh | Definition of the PDBPoseOutputSpecification class |
| PDBPoseOutputter.cc | |
| PDBPoseOutputter.fwd.hh | |
| PDBPoseOutputter.hh | |
| PDBPoseOutputterCreator.cc | Auto-generated serialization template functions |
| PDBPoseOutputterCreator.hh | Declaration of the PDBPoseOutputterCreator class |
| pose_outputter_schemas.cc | |
| pose_outputter_schemas.hh | |
| PoseOutputSpecification.cc | Method definitions of the PoseOutputSpecification class |
| PoseOutputSpecification.fwd.hh | Declaration of the PoseOutputSpecification class |
| PoseOutputSpecification.hh | Definition of the PoseOutputSpecification class |
| PoseOutputter.cc | Definition of the PoseOutputter class's methods |
| PoseOutputter.fwd.hh | Declaration of the PoseOutputter class |
| PoseOutputter.hh | Definition of the PoseOutputter class |
| PoseOutputterCreator.cc | Auto-generated serialization template functions |
| PoseOutputterCreator.fwd.hh | Forward declaration of the PoseOutputterCreator class |
| PoseOutputterCreator.hh | Declaration of the PoseOutputterCreator class |
| PoseOutputterFactory.cc | PoseOutputterFactory class that holds the list of classes able to create Poses from inputs |
| PoseOutputterFactory.fwd.hh | PoseOutputterFactory class that holds the list of classes able to create Poses from inputs |
| PoseOutputterFactory.hh | PoseOutputterFactory class that holds the list of classes able to create Poses from inputs |
| ScoreFileOutputSpecification.cc | Method definitions of the ScoreFileOutputSpecification class |
| ScoreFileOutputSpecification.fwd.hh | Declaration of the ScoreFileOutputSpecification class |
| ScoreFileOutputSpecification.hh | Definition of the ScoreFileOutputSpecification class |
| ScoreFileOutputter.cc | Definition of the ScoreFileOutputter class's methods |
| ScoreFileOutputter.fwd.hh | Declaration of the ScoreFileOutputter class |
| ScoreFileOutputter.hh | |
| ScoreFileOutputterCreator.hh | Declaration of the ScoreFileOutputterCreator class |
| SecondaryPoseOutputter.cc | Definition of the SecondaryPoseOutputter class's methods |
| SecondaryPoseOutputter.fwd.hh | Declaration of the SecondaryPoseOutputter class |
| SecondaryPoseOutputter.hh | Definition of the SecondaryPoseOutputter class |
| SecondaryPoseOutputterCreator.fwd.hh | Forward declaration of the SecondaryPoseOutputterCreator class |
| SecondaryPoseOutputterCreator.hh | Declaration of the SecondaryPoseOutputterCreator class |
| SilentFilePoseOutputSpecification.cc | Method definitions of the SilentFilePoseOutputSpecification class |
| SilentFilePoseOutputSpecification.fwd.hh | Declaration of the SilentFilePoseOutputSpecification class |
| SilentFilePoseOutputSpecification.hh | Definition of the SilentFilePoseOutputSpecification class |
| SilentFilePoseOutputter.cc | |
| SilentFilePoseOutputter.fwd.hh | |
| SilentFilePoseOutputter.hh | |
| SilentFilePoseOutputterCreator.cc | Auto-generated serialization template functions |
| SilentFilePoseOutputterCreator.hh | Declaration of the SilentFilePoseOutputterCreator class |
| ► standard | |
| PDBPoseOutputSpecification.hh | |
| PreliminaryLarvalJob.cc | A simple class for that stores input information for each job defintion/input nstruct as a PreliminaryLarvalJob |
| PreliminaryLarvalJob.fwd.hh | A simple class for that stores input information for each job defintion/input nstruct as a PreliminaryLarvalJob |
| PreliminaryLarvalJob.hh | A simple class for that stores input information for each job defintion/input nstruct as a PreliminaryLarvalJob |
| PreliminaryLarvalJobTracker.cc | A class that tracks PreliminaryLarvalJobs in the SJQ |
| PreliminaryLarvalJobTracker.fwd.hh | A class that tracks PreliminaryLarvalJobs in the SJQ |
| PreliminaryLarvalJobTracker.hh | A class that tracks PreliminaryLarvalJobs in the SJQ |
| StandardInnerLarvalJob.cc | Method definitions for the StandardInnerLarvalJob class |
| StandardInnerLarvalJob.fwd.hh | Class declaration for the StandardInnerLarvalJob |
| StandardInnerLarvalJob.hh | Class definition for the StandardInnerLarvalJob, which holds the index of the preliminary job node from which it was derived, in addition to the other data held by the InnerLarvalJob base class |
| StandardJobQueen.cc | StandardJobQueen class's method definitions |
| StandardJobQueen.fwd.hh | Class declaration for StandardJobQueen |
| StandardJobQueen.hh | Class declaration for StandardJobQueen |
| StandardResultOutputter.cc | |
| StandardResultOutputter.fwd.hh | |
| StandardResultOutputter.hh | Definition of the StandardResultOutputter class |
| CompletedJobOutput.fwd.hh | Forward declaration for the stuct return type of Job::run |
| CompletedJobOutput.hh | Typedef for the return type of Job::run |
| InnerLarvalJob.cc | Method definitions for the InnerLarvalJob class |
| InnerLarvalJob.fwd.hh | Class declaration for the InnerLarvalJob |
| InnerLarvalJob.hh | Class definition for the InnerLarvalJob, which describes the main details of a collection of Jobs that differ only in their random number seed |
| InputSource.cc | Definition of the InputSource class |
| InputSource.fwd.hh | Forward declaration of the InputSource class |
| InputSource.hh | Declaration of the InputSource class |
| Job.cc | The definitions of class protocols::jd3::Job's methods |
| Job.fwd.hh | |
| Job.hh | The declaration for class protocols::jd3::Job and the JobStatus enum |
| JobDigraph.cc | Graph base classes |
| JobDigraph.fwd.hh | Directed graph base class forward declarations |
| JobDigraph.hh | Directed graph for representing the relationship between batches of jobs |
| JobDistributor.cc | JobDistributor class method definitions |
| JobDistributor.fwd.hh | |
| JobDistributor.hh | |
| JobDistributorFactory.cc | JobDistributorFactory class; reads the command line to create a JobDistributor |
| JobDistributorFactory.fwd.hh | Declaration of the JobDistributorFactory class |
| JobDistributorFactory.hh | Definition of the JobDistributorFactory class |
| JobGenealogist.cc | Class method definitions for JobGenealogist |
| JobGenealogist.fwd.hh | |
| JobGenealogist.hh | Class declaration for JobGenealogist |
| JobOutputIndex.cc | Auto-generated serialization template functions |
| JobOutputIndex.fwd.hh | |
| JobOutputIndex.hh | Definition of the JobOutputIndex class |
| JobOutputWritter.hh | |
| JobQueen.cc | The (mostly empty) definition of the JobQueen class |
| JobQueen.fwd.hh | Forward declaration of the JobQueen class |
| JobQueen.hh | Class declaration for JobQueen |
| JobResult.cc | The implementation for class protocols::jd3::JobResult's methods |
| JobResult.fwd.hh | The declaration for class protocols::jd3::JobResult |
| JobResult.hh | The definition for class protocols::jd3::JobResult |
| JobSummary.cc | The implementation for class protocols::jd3::JobSummary's methods |
| JobSummary.fwd.hh | The forward declaration for class protocols::jd3::JobSummary |
| JobSummary.hh | The definition for class protocols::jd3::JobSummary |
| JobTracker.cc | A simple class for tracking job progress within JD3 |
| JobTracker.fwd.hh | A simple class for tracking job progress within JD3 |
| JobTracker.hh | A simple class for tracking job progress within JD3 |
| LarvalJob.cc | The definition for class protocols::jd3::LarvalJob's methods |
| LarvalJob.fwd.hh | The declaration for class protocols::jd3::LarvalJob |
| LarvalJob.hh | The definition for clas protocols::jd3::LarvalJob |
| strong_types.cc | |
| strong_types.hh | |
| util.cc | Utility functions for JD3 |
| util.hh | Utility functions for JD3 |
| ► jobdist | |
| JobDistributors.cc | |
| JobDistributors.fwd.hh | |
| JobDistributors.hh | |
| Jobs.cc | |
| Jobs.fwd.hh | Objects representing inputs for the JobDistributor |
| Jobs.hh | Objects representing inputs for the JobDistributor |
| not_universal_main.cc | Simple main method for applying a Mover to a set of input Poses |
| not_universal_main.hh | Simple main method for applying a Mover to a set of input Poses |
| standard_mains.cc | |
| standard_mains.hh | Main methods that implement the typical running patterns for executables |
| ► jumping | |
| DisulfPairingLibrary.cc | |
| DisulfPairingLibrary.hh | |
| DisulfPairingsList.cc | |
| DisulfPairingsList.fwd.hh | Fwd headers for ns jumping |
| DisulfPairingsList.hh | |
| JumpSample.cc | |
| JumpSample.hh | |
| JumpSetup.cc | |
| JumpSetup.fwd.hh | |
| JumpSetup.hh | |
| MembraneJump.cc | |
| MembraneJump.fwd.hh | |
| MembraneJump.hh | |
| PairingLibrary.cc | |
| PairingLibrary.fwd.hh | Fwd headers for ns jumping |
| PairingLibrary.hh | |
| RandomSheetBuilder.cc | Secondary structure will hold statistics about secondary structure predictions sources can be from |
| RandomSheetBuilder.hh | |
| ResiduePairJump.cc | Class to create jump transform from a pair of residues |
| ResiduePairJump.fwd.hh | |
| ResiduePairJump.hh | Class to create jump transform from a pair of residues |
| ResiduePairJumpSetup.cc | |
| ResiduePairJumpSetup.fwd.hh | |
| ResiduePairJumpSetup.hh | |
| SameStrand.cc | Secondary structure will hold statistics about secondary structure predictions sources can be from |
| SameStrand.fwd.hh | Fwd headers for ns jumping |
| SameStrand.hh | Secondary structure will hold statistics about secondary structure predictions sources can be from |
| SheetBuilder.cc | Secondary structure will hold statistics about secondary structure predictions sources can be from |
| SheetBuilder.hh | |
| util.cc | |
| util.hh | |
| ► kinematic_closure | |
| ► perturbers | |
| BondAnglePerturber.cc | |
| BondAnglePerturber.fwd.hh | |
| BondAnglePerturber.hh | |
| FragmentPerturber.cc | |
| FragmentPerturber.fwd.hh | |
| FragmentPerturber.hh | |
| IdealizeNonPhiPsi.cc | |
| IdealizeNonPhiPsi.fwd.hh | |
| IdealizeNonPhiPsi.hh | |
| LogFilePerturber.cc | |
| LogFilePerturber.fwd.hh | |
| LogFilePerturber.hh | |
| OmegaPerturber.cc | |
| OmegaPerturber.fwd.hh | |
| OmegaPerturber.hh | |
| Perturber.cc | |
| Perturber.fwd.hh | |
| Perturber.hh | |
| PerturberSet.cc | |
| PerturberSet.fwd.hh | |
| PerturberSet.hh | |
| Rama2bPerturber.cc | |
| Rama2bPerturber.fwd.hh | |
| Rama2bPerturber.hh | |
| RamaPerturber.cc | |
| RamaPerturber.fwd.hh | |
| RamaPerturber.hh | |
| readme.hh | |
| UniformPerturber.cc | |
| UniformPerturber.fwd.hh | |
| UniformPerturber.hh | |
| VicinityPerturber.cc | |
| VicinityPerturber.fwd.hh | |
| VicinityPerturber.hh | |
| WalkingBondAnglePerturber.cc | |
| WalkingBondAnglePerturber.fwd.hh | |
| WalkingBondAnglePerturber.hh | |
| WalkingPerturber.cc | |
| WalkingPerturber.fwd.hh | |
| WalkingPerturber.hh | |
| ► pivot_pickers | |
| EndToEndPivots.cc | |
| EndToEndPivots.fwd.hh | |
| EndToEndPivots.hh | |
| FixedOffsetPivots.cc | |
| FixedOffsetPivots.fwd.hh | |
| FixedOffsetPivots.hh | |
| FixedOffsetsPivots.cc | |
| FixedOffsetsPivots.fwd.hh | |
| FixedOffsetsPivots.hh | |
| FixedPivots.cc | |
| FixedPivots.fwd.hh | |
| FixedPivots.hh | |
| LoopPivots.cc | |
| LoopPivots.fwd.hh | |
| LoopPivots.hh | |
| PivotPicker.fwd.hh | |
| PivotPicker.hh | |
| readme.hh | |
| StandardPivots.cc | |
| StandardPivots.fwd.hh | |
| StandardPivots.hh | |
| ► solution_pickers | |
| FilteredSolutions.cc | |
| FilteredSolutions.fwd.hh | |
| FilteredSolutions.hh | |
| RandomSolutions.cc | |
| RandomSolutions.fwd.hh | |
| RandomSolutions.hh | |
| readme.hh | |
| SolutionPicker.fwd.hh | |
| SolutionPicker.hh | |
| BalancedKicMover.cc | |
| BalancedKicMover.fwd.hh | |
| BalancedKicMover.hh | |
| ClosureProblem.cc | Source file for ClosureProblem |
| ClosureProblem.fwd.hh | Forward header for ClosureProblem |
| ClosureProblem.hh | Header file for ClosureProblem |
| ClosureSolution.cc | Source file for ClosureSolution |
| ClosureSolution.fwd.hh | Forward header for ClosureSolution |
| ClosureSolution.hh | Header file for ClosureSolution |
| internal.cc | Source file for internal helpers |
| internal.hh | |
| KicMover.cc | |
| KicMover.fwd.hh | |
| KicMover.hh | |
| KicMoverCreator.hh | |
| readme.hh | |
| types.hh | Header file for shared types |
| ► kinmatch | |
| FunGroupTK.cc | |
| FunGroupTK.hh | ToolKit for rapid IK based functional group placement |
| ► legacy_sewing | |
| ► conformation | |
| Assembly.cc | |
| Assembly.fwd.hh | |
| Assembly.hh | A set of simple container classes used by the SewingProtocol. These classes are used during the Hashing of coordinates, as well as during assembly of low-resolution assemblies |
| AssemblyFactory.cc | A super-simple factory for generating Assembly classes |
| AssemblyFactory.hh | A super-simple factory for generating Assembly classes |
| ContinuousAssembly.cc | |
| ContinuousAssembly.hh | A set of simple container classes used by the SewingProtocol. These classes are used during the Hashing of coordinates, as well as during assembly of low-resolution assemblies |
| DisembodiedAssembly.cc | |
| DisembodiedAssembly.hh | A set of simple container classes used by the SewingProtocol. These classes are used during the Hashing of coordinates, as well as during assembly of low-resolution assemblies |
| Model.cc | |
| Model.fwd.hh | |
| Model.hh | |
| ► hashing | |
| Hasher.cc | |
| Hasher.fwd.hh | |
| Hasher.hh | A geometric hashing class used by the SEWING protocol. The hasher functions by hashing the coordinates of a given Model after transformation into a local coordinate from defined by the N,CA,C atoms of each residues. Once a hash table is generate, new models (or models that have already been inserted into the table) can be "scored" against the table by following the same transformation procedure. Any two residues from different models that hash many of their models to the same quarter angstrom voxels indicate a good alignment between two models |
| ► sampling | |
| ► requirements | |
| LegacyGlobalLengthRequirement.cc | |
| LegacyGlobalLengthRequirement.fwd.hh | |
| LegacyGlobalLengthRequirement.hh | Require that all segments of the specified secondary structure(s) are between the given min and max size |
| LegacyGlobalLengthRequirementCreator.hh | |
| LegacyGlobalRequirement.fwd.hh | |
| LegacyGlobalRequirement.hh | An interface for all LEGACY_SEWING requirements concerning an entire assembly |
| LegacyIntraSegmentRequirement.fwd.hh | |
| LegacyIntraSegmentRequirement.hh | An interface for all LEGACY_SEWING requirements concerning a single SewSegment |
| LegacyRequirementCreator.fwd.hh | |
| LegacyRequirementCreator.hh | Forward Header for base class for RequirementCreators for the Requirement load-time factory registration scheme |
| LegacyRequirementFactory.cc | Factory for creating Requirements objects |
| LegacyRequirementFactory.fwd.hh | |
| LegacyRequirementFactory.hh | |
| LegacyRequirementSet.cc | |
| LegacyRequirementSet.fwd.hh | |
| LegacyRequirementSet.hh | A container for all LEGACY_SEWING requirements |
| LegacyResidueRetentionRequirement.cc | |
| LegacyResidueRetentionRequirement.fwd.hh | |
| LegacyResidueRetentionRequirement.hh | A container for all LEGACY_SEWING requirements |
| LegacyResidueRetentionRequirementCreator.hh | |
| LegacySegmentDsspRequirement.cc | |
| LegacySegmentDsspRequirement.fwd.hh | |
| LegacySegmentDsspRequirement.hh | A requirement on the seconday structure of a given SewSegment |
| LegacySegmentDsspRequirementCreator.hh | |
| LegacySegmentLengthRequirement.cc | |
| LegacySegmentLengthRequirement.fwd.hh | |
| LegacySegmentLengthRequirement.hh | A requirement on the total number of residues for a given SewSegment |
| LegacySegmentLengthRequirementCreator.hh | |
| LegacyAddStartnodeFragments.cc | |
| LegacyAddStartnodeFragments.fwd.hh | |
| LegacyAddStartnodeFragments.hh | A Mover that uses loophash to find fragments that can bridge a gap with minimal modifications to the original pose |
| LegacyAddStartnodeFragmentsCreator.hh | |
| LegacyAppendAssemblyMover.cc | |
| LegacyAppendAssemblyMover.fwd.hh | |
| LegacyAppendAssemblyMover.hh | A Mover that uses loophash to find fragments that can bridge a gap with minimal modifications to the original pose |
| LegacyAppendAssemblyMoverCreator.hh | |
| LegacyAssemblyConstraintsMover.cc | |
| LegacyAssemblyConstraintsMover.fwd.hh | |
| LegacyAssemblyConstraintsMover.hh | A simple mover that reads a NativeRotamersFile generated by a an AssemblyMover run and generates the necessary ResidueType constraints to add to the pose |
| LegacyAssemblyConstraintsMoverCreator.hh | |
| LegacyAssemblyMover.cc | |
| LegacyAssemblyMover.fwd.hh | |
| LegacyAssemblyMover.hh | |
| LegacyAssemblyMoverCreator.hh | |
| LegacyEnumerateAssemblyMover.cc | Enumerate every possible assembly exhaustively |
| LegacyEnumerateAssemblyMover.fwd.hh | |
| LegacyEnumerateAssemblyMover.hh | |
| LegacyEnumerateAssemblyMoverCreator.hh | |
| LegacyGivenPathAssemblyMover.cc | |
| LegacyGivenPathAssemblyMover.fwd.hh | |
| LegacyGivenPathAssemblyMover.hh | This Mover generates assemblies by taking the best edge possible for each addition. This process is repeated cycles times and the best overall Assembly that was found is returned |
| LegacyGivenPathAssemblyMoverCreator.hh | |
| LegacyGreedyAssemblyMover.cc | |
| LegacyGreedyAssemblyMover.fwd.hh | |
| LegacyGreedyAssemblyMover.hh | This Mover generates assemblies by taking the best edge possible for each addition. This process is repeated cycles times and the best overall Assembly that was found is returned |
| LegacyGreedyAssemblyMoverCreator.hh | |
| LegacyLoophashAssemblyMover.cc | Derived from AssemblyMover, this mover generates an assembly and then uses Loophash segments to connect any broken segments resulting from the assembly process |
| LegacyLoophashAssemblyMover.fwd.hh | |
| LegacyLoophashAssemblyMover.hh | A Mover that uses loophash to find fragments that can bridge a gap with minimal modifications to the original pose |
| LegacyLoophashAssemblyMoverCreator.hh | |
| LegacyMonteCarloAssemblyMover.cc | Assembly substructures by MonteCarlo way |
| LegacyMonteCarloAssemblyMover.fwd.hh | |
| LegacyMonteCarloAssemblyMover.hh | Assembly substructures by LegacyMonteCarlo way |
| LegacyMonteCarloAssemblyMoverCreator.hh | |
| LegacyNodeConstraintAssemblyMover.cc | |
| LegacyNodeConstraintAssemblyMover.fwd.hh | |
| LegacyNodeConstraintAssemblyMover.hh | A Mover that combines Smotif models into a continuous protein design |
| LegacyNodeConstraintAssemblyMoverCreator.hh | |
| LegacyReadNativeRotamersFileCreator.hh | |
| LegacyReadRepeatNativeRotamersFileCreator.hh | |
| LegacyRehashAssemblyMover.cc | Derived from AssemblyMover, this mover generates an assembly and then uses Loophash segments to connect any broken segments resulting from the assembly process |
| LegacyRehashAssemblyMover.fwd.hh | |
| LegacyRehashAssemblyMover.hh | A Mover that uses more legacy_sewing to close gaps from discontinous assemblies |
| LegacyRehashAssemblyMoverCreator.hh | |
| LegacyRepeatAssemblyMover.cc | |
| LegacyRepeatAssemblyMover.fwd.hh | |
| LegacyRepeatAssemblyMover.hh | An AssemblyMover specific for repeating backbones. This Mover is currently pretty hacky and makes assumes that every node is exactly 3 segments long, and that the assembly is a continuous assembly |
| LegacyRepeatAssemblyMoverCreator.hh | |
| SewGraph.cc | |
| SewGraph.fwd.hh | |
| SewGraph.hh | |
| ► scoring | |
| LegacyAssemblyScorer.fwd.hh | |
| LegacyAssemblyScorer.hh | |
| LegacyBlosumScorer.cc | |
| LegacyBlosumScorer.fwd.hh | |
| LegacyBlosumScorer.hh | |
| LegacyCalciumMotifScorer.cc | |
| LegacyCalciumMotifScorer.fwd.hh | |
| LegacyCalciumMotifScorer.hh | Favors interactions between all segments of pdb substructure and all other substructures |
| LegacyClashScorer.cc | |
| LegacyClashScorer.fwd.hh | |
| LegacyClashScorer.hh | Identifies and scores backbone clashes in LEGACY_SEWING Assemblies |
| LegacyInterModelMotifScorer.cc | |
| LegacyInterModelMotifScorer.fwd.hh | |
| LegacyInterModelMotifScorer.hh | |
| LegacyMotifScorer.cc | |
| LegacyMotifScorer.fwd.hh | |
| LegacyMotifScorer.hh | |
| LegacyPartnerMotifScorer.cc | |
| LegacyPartnerMotifScorer.fwd.hh | |
| LegacyPartnerMotifScorer.hh | |
| ► util | |
| io.cc | |
| io.hh | |
| util.cc | |
| util.hh | |
| ► ligand_docking | |
| ► GALigandDock | |
| EntropyEstimator.cc | |
| EntropyEstimator.hh | |
| GALigandDock.cc | |
| GALigandDock.fwd.hh | |
| GALigandDock.hh | |
| GALigandDockCreator.hh | |
| GAOptimizer.cc | |
| GAOptimizer.hh | |
| GriddedAtomTreeMultifunc.cc | |
| GriddedAtomTreeMultifunc.hh | |
| GridHash3D.hh | |
| GridScorer.cc | |
| GridScorer.hh | Grid-based scoring for GA ligand docking |
| LigandAligner.cc | Align a ligand to a reference ligand or an inferred reference ligand |
| LigandAligner.hh | Align a ligand to a reference ligand or an inferred reference ligand |
| LigandConformer.cc | |
| LigandConformer.hh | |
| RotamerData.cc | |
| RotamerData.hh | |
| util.cc | |
| util.hh | |
| ► ligand_options | |
| Interface.cc | |
| Interface.fwd.hh | |
| Interface.hh | |
| interface_distance_functions.cc | |
| interface_distance_functions.hh | |
| ► rdf | |
| RDFBase.fwd.hh | Forward headers for RDFBase |
| RDFBase.hh | A base class that defines an RDF function. These functions computes one or more RDF values for a pair of atoms |
| RDFFunctionCreator.fwd.hh | Forward Header for base class for RDFFunctionCreator |
| RDFFunctionCreator.hh | |
| RDFFunctionFactory.cc | Factory for creating RDFBase objects |
| RDFFunctionFactory.fwd.hh | Forward headers for RDFFunctionFactory |
| RDFFunctionFactory.hh | Headers for RDFFunctionFactory |
| StandardRDFFunctions.cc | |
| StandardRDFFunctions.fwd.hh | Forward headers for standard RDF Functions used by RosettaHTS |
| StandardRDFFunctions.hh | Headers for standard RDF Functions used by RosettaHTS |
| AddHydrogen.cc | Lemmon |
| AddHydrogen.fwd.hh | |
| AddHydrogen.hh | |
| AddHydrogens.cc | Lemmon |
| AddHydrogens.fwd.hh | |
| AddHydrogens.hh | |
| AddHydrogensCreator.hh | This class will create instances of Mover AddHydrogens for the MoverFactory |
| AtomCountFilter.cc | Find packing defects at an interface using packstat score terms |
| AtomCountFilter.hh | Find packing defects at an interface using packstat score terms |
| AtomCountFilterCreator.hh | FilterCreator for the AtomCountFilter |
| ChainExistsFilter.cc | Find packing defects at an interface using packstat score terms |
| ChainExistsFilter.hh | Find packing defects at an interface using packstat score terms |
| ChainExistsFilterCreator.hh | FilterCreator for the ChainExistsFilter |
| CompleteConnectionsFilter.cc | |
| CompleteConnectionsFilter.hh | |
| CompleteConnectionsFilterCreator.hh | FilterCreator for the CompleteConnectionsFilter |
| CompoundTranslate.cc | |
| CompoundTranslate.hh | |
| CompoundTranslateCreator.hh | This class will create instances of Mover CompoundTranslateCreator for the MoverFactory |
| ComputeLigandRDF.cc | A mover for computing RDF functions |
| ComputeLigandRDF.fwd.hh | |
| ComputeLigandRDF.hh | Header file for ComputeLigandRDF mover |
| ComputeLigandRDFCreator.hh | |
| DistributionMap.cc | |
| DistributionMap.hh | |
| FinalMinimizer.cc | |
| FinalMinimizer.fwd.hh | |
| FinalMinimizer.hh | |
| FinalMinimizerCreator.hh | This class will create instances of Mover FinalMinimizerCreator for the MoverFactory |
| grid_functions.cc | |
| grid_functions.hh | |
| GrowLigand.cc | Lemmon |
| GrowLigand.fwd.hh | |
| GrowLigand.hh | |
| GrowLigandCreator.hh | This class will create instances of Mover GrowLigand for the MoverFactory |
| HBondAcceptorFilter.cc | Find packing defects at an interface using packstat score terms |
| HBondAcceptorFilter.hh | Find packing defects at an interface using packstat score terms |
| HBondAcceptorFilterCreator.hh | FilterCreator for the HBondAcceptorFilter |
| HBondDonorFilter.cc | Find packing defects at an interface using packstat score terms |
| HBondDonorFilter.hh | Find packing defects at an interface using packstat score terms |
| HBondDonorFilterCreator.hh | FilterCreator for the HBondDonorFilter |
| HeavyAtomFilter.cc | Find packing defects at an interface using packstat score terms |
| HeavyAtomFilter.hh | Find packing defects at an interface using packstat score terms |
| HeavyAtomFilterCreator.hh | FilterCreator for the HeavyAtomFilter |
| HighResDocker.cc | |
| HighResDocker.fwd.hh | |
| HighResDocker.hh | |
| HighResDockerCreator.hh | This class will create instances of Mover HighResDockerCreator for the MoverFactory |
| HighResEnsemble.cc | |
| HighResEnsemble.fwd.hh | |
| HighResEnsemble.hh | |
| HighResEnsembleCreator.hh | |
| InterfaceBuilder.cc | |
| InterfaceBuilder.fwd.hh | |
| InterfaceBuilder.hh | |
| InterfaceScoreCalculator.cc | |
| InterfaceScoreCalculator.fwd.hh | |
| InterfaceScoreCalculator.hh | |
| InterfaceScoreCalculatorCreator.hh | This class will create instances of Mover InterfaceScoreCalculator for the MoverFactory |
| ligand_dock_impl.cc | |
| ligand_dock_impl.hh | |
| ligand_functions.cc | |
| ligand_functions.hh | |
| ligand_scores.cc | |
| ligand_scores.hh | |
| LigandArea.cc | |
| LigandArea.fwd.hh | |
| LigandArea.hh | |
| LigandBaseProtocol.cc | |
| LigandBaseProtocol.hh | |
| LigandDesign.cc | Lemmon |
| LigandDesign.fwd.hh | |
| LigandDesign.hh | |
| LigandDesignCreator.hh | This class will create instances of Mover LigandDesign for the MoverFactory |
| LigandDockingLoaderCreators.hh | Creator classes for the ligand docking DataLoader classes: InterfaceBuilderLoader and MoveMapBuilderLoader |
| LigandDockingLoaders.cc | Implementation of the InterfaceBuilderLoader and MoveMapBuilderLoader classes |
| LigandDockingLoaders.hh | |
| LigandDockProtocol.cc | |
| LigandDockProtocol.fwd.hh | |
| LigandDockProtocol.hh | |
| MinimizeBackbone.cc | |
| MinimizeBackbone.fwd.hh | |
| MinimizeBackbone.hh | |
| MinimizeBackboneCreator.hh | This class will create instances of Mover MinimizeBackboneCreator for the MoverFactory |
| MinimizeLigand.cc | |
| MinimizeLigand.fwd.hh | |
| MinimizeLigand.hh | |
| MolarMassFilter.cc | Find packing defects at an interface using packstat score terms |
| MolarMassFilter.hh | Find packing defects at an interface using packstat score terms |
| MolarMassFilterCreator.hh | FilterCreator for the MolarMassFilter |
| MolecularMassFilter.cc | Find packing defects at an interface using packstat score terms |
| MolecularMassFilter.hh | Find packing defects at an interface using packstat score terms |
| MolecularMassFilterCreator.hh | FilterCreator for the MolecularMassFilter |
| MoveMapBuilder.cc | |
| MoveMapBuilder.fwd.hh | |
| MoveMapBuilder.hh | |
| ProtLigEnsemble.cc | Implementation of docking with protein and ligand ensembles |
| ProtLigEnsemble.fwd.hh | |
| ProtLigEnsemble.hh | |
| ProtLigEnsembleCreator.hh | This class will create instances of Mover ProtLigEnsembleCreator for the MoverFactory |
| RandomConformerMover.cc | |
| RandomConformerMover.fwd.hh | |
| RandomConformerMover.hh | |
| RandomConformers.cc | |
| RandomConformers.hh | |
| RandomConformersCreator.hh | This class will create instances of Mover RandomConformersCreator for the MoverFactory |
| ResidueTorsionRestraints.cc | |
| ResidueTorsionRestraints.fwd.hh | |
| ResidueTorsionRestraints.hh | |
| RigidSearchMover.cc | |
| RigidSearchMover.fwd.hh | |
| RigidSearchMover.hh | |
| Rotate.cc | |
| Rotate.fwd.hh | |
| Rotate.hh | |
| RotateCreator.hh | This class will create instances of Mover Rotate for the MoverFactory |
| Rotates.cc | |
| Rotates.fwd.hh | |
| Rotates.hh | |
| RotatesCreator.hh | This class will create instances of Mover Rotates for the MoverFactory |
| SlideTogether.cc | |
| SlideTogether.hh | |
| SlideTogetherCreator.hh | This class will create instances of Mover SlideTogether for the MoverFactory |
| StartFrom.cc | Mover to place a ligand at defined position(s) |
| StartFrom.fwd.hh | |
| StartFrom.hh | Mover to place a ligand at a defined position |
| StartFromCreator.hh | This class will create instances of Mover StartFrom for the MoverFactory |
| TetherLigand.cc | |
| TetherLigand.fwd.hh | |
| TetherLigand.hh | |
| Transform.cc | |
| Transform.fwd.hh | |
| Transform.hh | |
| TransformCreator.hh | This class will create instances of Mover Transform for the MoverFactory |
| TransformEnsemble.cc | |
| TransformEnsemble.fwd.hh | |
| TransformEnsemble.hh | |
| TransformEnsembleCreator.hh | This class will create instances of Mover TransformEnsemble for the MoverFactory |
| Translate.cc | |
| Translate.fwd.hh | |
| Translate.hh | |
| TranslateCreator.hh | This class will create instances of Mover Translate for the MoverFactory |
| UnconstrainedTorsionsMover.cc | |
| UnconstrainedTorsionsMover.fwd.hh | |
| UnconstrainedTorsionsMover.hh | |
| util.cc | |
| util.hh | Utilities for ligand docking |
| WriteLigandMolFile.cc | Ligand MolFile writer |
| WriteLigandMolFile.fwd.hh | Forward header class for Ligand MolFile writer |
| WriteLigandMolFile.hh | Header class for Ligand MolFile writer |
| WriteLigandMolFileCreator.hh | This class will create instances of Mover WriteLigandMolFile for the MoverFactory |
| ► loop_build | |
| LoopBuild.cc | |
| LoopBuild.hh | |
| LoopBuildMover.cc | |
| LoopBuildMover.fwd.hh | |
| LoopBuildMover.hh | |
| LoopmodelWrapper.cc | |
| LoopmodelWrapper.fwd.hh | |
| LoopmodelWrapper.hh | |
| LoopmodelWrapperCreator.hh | |
| LoopMover_SlidingWindow.cc | Kinematic loop closure main protocols |
| LoopMover_SlidingWindow.hh | |
| LoopMover_SlidingWindowCreator.cc | |
| LoopMover_SlidingWindowCreator.hh | Header for LoopMover_SlidingWindowCreator |
| ► loop_grower | |
| DensSkeleton.cc | |
| DensSkeleton.fwd.hh | |
| DensSkeleton.hh | |
| FragmentExtension.cc | |
| FragmentExtension.fwd.hh | |
| FragmentExtension.hh | |
| FragmentExtensionCreator.hh | |
| LoopGrower.cc | |
| LoopGrower.fwd.hh | |
| LoopGrower.hh | |
| SheetSampler.cc | |
| SheetSampler.fwd.hh | |
| SheetSampler.hh | |
| util.cc | Utility functions for the LoopGrowing protocol |
| util.hh | Utilities for Loop Growing Protocol |
| ► loop_modeler | |
| ► perturbers | |
| LoopHashPerturber.cc | |
| LoopHashPerturber.fwd.hh | |
| LoopHashPerturber.hh | |
| LoopModeler.cc | |
| LoopModeler.fwd.hh | |
| LoopModeler.hh | |
| LoopModelerCreator.hh | |
| ► loop_modeling | |
| ► refiners | |
| MinimizationRefiner.cc | |
| MinimizationRefiner.fwd.hh | |
| MinimizationRefiner.hh | |
| MinimizationRefinerCreator.hh | |
| packing_helper.hh | |
| readme.hh | |
| RepackingRefiner.cc | |
| RepackingRefiner.fwd.hh | |
| RepackingRefiner.hh | |
| RepackingRefinerCreator.hh | |
| RotamerTrialsRefiner.cc | |
| RotamerTrialsRefiner.fwd.hh | |
| RotamerTrialsRefiner.hh | |
| RotamerTrialsRefinerCreator.hh | |
| ► samplers | |
| LegacyKicSampler.cc | |
| LegacyKicSampler.fwd.hh | |
| LegacyKicSampler.hh | |
| LegacyKicSamplerCreator.hh | |
| readme.hh | |
| ► utilities | |
| AcceptanceCheck.cc | |
| AcceptanceCheck.fwd.hh | |
| AcceptanceCheck.hh | |
| LoopFilter.cc | |
| LoopFilter.fwd.hh | |
| LoopFilter.hh | |
| LoopMoverGroup.cc | |
| LoopMoverGroup.fwd.hh | |
| LoopMoverGroup.hh | |
| PrepareForCentroid.cc | |
| PrepareForCentroid.fwd.hh | |
| PrepareForCentroid.hh | |
| PrepareForCentroidCreator.hh | |
| PrepareForFullatom.cc | |
| PrepareForFullatom.fwd.hh | |
| PrepareForFullatom.hh | |
| PrepareForFullatomCreator.hh | |
| readme.hh | |
| rosetta_scripts.cc | |
| rosetta_scripts.hh | |
| TrajectoryLogger.cc | |
| TrajectoryLogger.fwd.hh | |
| TrajectoryLogger.hh | |
| LoopBuilder.cc | |
| LoopBuilder.fwd.hh | |
| LoopBuilder.hh | |
| LoopBuilderCreator.hh | |
| LoopModelerTests.fwd.hh | |
| LoopMover.cc | |
| LoopMover.fwd.hh | |
| LoopMover.hh | |
| LoopProtocol.cc | |
| LoopProtocol.fwd.hh | |
| LoopProtocol.hh | |
| LoopProtocolCreator.hh | |
| readme.hh | |
| types.hh | |
| ► loophash | |
| BackboneDB.cc | |
| BackboneDB.hh | I little in the spirit of fragments but way more memory and speed efficient. Backbones are stored as 16bit fixed comma integers. :) |
| Exceptions.hh | |
| FastGapMover.cc | |
| FastGapMover.fwd.hh | Closes gaps |
| FastGapMover.hh | Protocols for closing gaps |
| LocalInserter.cc | |
| LocalInserter.fwd.hh | LocalInserter class forward declarations header |
| LocalInserter.hh | |
| LoopHashDiversifier.cc | |
| LoopHashDiversifier.hh | |
| LoopHashDiversifierCreator.hh | Declaration of the MoverCreator class for the LoopHashDiversifierCreator |
| LoopHashLibrary.cc | |
| LoopHashLibrary.fwd.hh | LoopHashLibrary class forward declarations header |
| LoopHashLibrary.hh | |
| LoopHashLibraryLoader.cc | Load the Loop Hash library using the resource manager |
| LoopHashLibraryLoader.fwd.hh | Load the Loop Hash library using the resource manager |
| LoopHashLibraryLoader.hh | Load the Loop Hash library using the resource manager |
| LoopHashLibraryLoaderCreator.hh | Load the Loop Hash library using the resource manager |
| LoopHashLibraryOptions.cc | Load the Loop Hash library using the resource manager |
| LoopHashLibraryOptions.fwd.hh | Load the Loop Hash library using the resource manager |
| LoopHashMap.cc | |
| LoopHashMap.hh | |
| LoopHashMoverWrapper.cc | |
| LoopHashMoverWrapper.hh | |
| LoopHashMoverWrapperCreator.hh | Declaration of the MoverCreator class for the LoopHashMoverWrapper |
| LoopHashRelaxProtocol.cc | |
| LoopHashRelaxProtocol.hh | |
| LoopHashSampler.cc | |
| LoopHashSampler.fwd.hh | LoopHashSampler class forward declarations header |
| LoopHashSampler.hh | |
| Mover_LoopHashRefine.cc | |
| Mover_LoopHashRefine.hh | |
| MPI_LoopHashRefine.cc | |
| MPI_LoopHashRefine.hh | |
| MPI_LoopHashRefine_Emperor.cc | |
| MPI_LoopHashRefine_Emperor.hh | |
| MPI_LoopHashRefine_Master.cc | |
| MPI_LoopHashRefine_Master.hh | |
| WorkUnit_LoopHash.cc | |
| WorkUnit_LoopHash.hh | |
| ► loops | |
| ► loop_closure | |
| ► ccd | |
| ccd_closure.cc | |
| ccd_closure.hh | |
| CCDLoopClosureMover.cc | Method definitions for CCDLoopClosureMover |
| CCDLoopClosureMover.fwd.hh | Foward declarations for CCDLoopClosureMover |
| CCDLoopClosureMover.hh | Class definition and method declarations for CCDLoopClosureMover |
| CCDLoopClosureMoverCreator.hh | This class will create upcasted instances of CCDLoopClosureMover for the protocols::moves::MoverFactory |
| LoopClosure.cc | |
| LoopClosure.fwd.hh | Fwd headers for ns loops |
| LoopClosure.hh | |
| RamaCheck.cc | Implementation for RamaCheck classes (RamaCheckBase, RamaCheck1B, RamaCheck2B) |
| RamaCheck.fwd.hh | Forward declaration of RamaCheck classes (RamaCheckBase, RamaCheck1B, RamaCheck2B) |
| RamaCheck.hh | Header for RamaCheck classes (RamaCheckBase, RamaCheck1B, RamaCheck2B) |
| ShortLoopClosure.cc | |
| ShortLoopClosure.fwd.hh | |
| ShortLoopClosure.hh | |
| SlidingWindowLoopClosure.cc | |
| SlidingWindowLoopClosure.fwd.hh | Fwd headers for ns loops |
| SlidingWindowLoopClosure.hh | Header file for SlidingWindowLoopClosure protocol |
| WidthFirstSlidingWindowLoopClosure.cc | |
| WidthFirstSlidingWindowLoopClosure.fwd.hh | Fwd headers for ns loops |
| WidthFirstSlidingWindowLoopClosure.hh | |
| ► jacobi | |
| JacobiLoopClosureMover.cc | Loop closure mover that uses linearization of the kinematics to adjust all unlocked backbone torsion angles of a loop at the same time |
| JacobiLoopClosureMover.fwd.hh | Loop closure mover that uses linearization of the kinematics to adjust all unlocked backbone torsion angles of a loop at the same time |
| JacobiLoopClosureMover.hh | Class definition and method declarations for JacobiLoopClosureMover |
| JacobiLoopClosureMoverCreator.hh | Loop closure mover that uses linearization of the kinematics to adjust all unlocked backbone torsion angles of a loop at the same time |
| ► kinematic_closure | |
| KinematicMover.cc | |
| KinematicMover.fwd.hh | KinematicMover forward declarations header |
| KinematicMover.hh | |
| KinematicPerturber.cc | Implementations for KinematicPerturbers used by the kinematic mover |
| KinematicPerturber.fwd.hh | KinematicPerturber forward declarations header |
| KinematicPerturber.hh | Header file for KinematicPerturbers used by the kineamtic mover |
| KinematicWrapper.cc | KinematicWrapper methods implemented - this is a mover which simplifies use of KinematicMover loop modeling |
| KinematicWrapper.fwd.hh | KinematicWrapper forward declarations header |
| KinematicWrapper.hh | Wrapper for KinematicMover - useful when only apply() is available |
| ► loop_mover | |
| ► perturb | |
| LoopMover_CCD.cc | |
| LoopMover_CCD.fwd.hh | LoopMover_Perutrb_CCD forward declaration |
| LoopMover_CCD.hh | |
| LoopMover_CCDCreator.hh | Header for LoopMover_CCDCreator |
| LoopMover_KIC.cc | |
| LoopMover_KIC.fwd.hh | LoopMover_Perturb_KIC forward declaration |
| LoopMover_KIC.hh | |
| LoopMover_KICCreator.hh | |
| LoopMover_QuickCCD.cc | |
| LoopMover_QuickCCD.fwd.hh | LoopMover_QuickCCD forward declaration |
| LoopMover_QuickCCD.hh | |
| LoopMover_QuickCCD_Moves.cc | |
| LoopMover_QuickCCD_Moves.fwd.hh | LoopMover_QuickCCD_Moves forward declaration |
| LoopMover_QuickCCD_Moves.hh | |
| LoopMover_QuickCCD_MovesCreator.hh | |
| LoopMover_QuickCCDCreator.hh | Header for LoopMover_QuickCCDCreator |
| ► refine | |
| LoopMover_Backrub.cc | |
| LoopMover_Backrub.fwd.hh | LoopMover_Backrub forward declaration |
| LoopMover_Backrub.hh | |
| LoopMover_BackrubCreator.hh | Header for LoopMover_BackrubCreator |
| LoopMover_CCD.cc | |
| LoopMover_CCD.fwd.hh | |
| LoopMover_CCD.hh | |
| LoopMover_CCDCreator.hh | |
| LoopMover_KIC.cc | |
| LoopMover_KIC.fwd.hh | LoopMover_Backrub forward declaration |
| LoopMover_KIC.hh | |
| LoopMover_KICCreator.hh | |
| LoopRefineInnerCycle.cc | Abstract class to define interface for all types of "inner cycle" operations used for loop refinement |
| LoopRefineInnerCycle.fwd.hh | Forward declaration |
| LoopRefineInnerCycle.hh | Abstract class to define interface for all types of "inner cycle" operations used for loop refinement |
| LoopRefineInnerCycleContainer.cc | This class is a LoopRefineInnerCycle that contains one or more other LoopRefineInnerCycles to allow a developer to quickly string together existing LoopRefineInnerCycles in new ways to create new loop refinement protocols |
| LoopRefineInnerCycleContainer.fwd.hh | Forward declaration |
| LoopRefineInnerCycleContainer.hh | This class is a LoopRefineInnerCycle that contains one or more other LoopRefineInnerCycles to allow a developer to quickly string together existing LoopRefineInnerCycles in new ways to create new loop refinement protocols |
| LoopRefineInnerCycleContainerCreator.hh | |
| LoopRefineInnerCycleFactory.cc | Factory for creating LoopRefineInnerCycle objects |
| LoopRefineInnerCycleFactory.fwd.hh | |
| LoopRefineInnerCycleFactory.hh | Factory for creating LoopRefineInnerCycle objects |
| RepackTrial.cc | |
| RepackTrial.fwd.hh | Forward declaration |
| RepackTrial.hh | Abstract class to define interface for all types of "inner cycle" operations used for loop refinement |
| RepackTrialCreator.hh | |
| ShearMinCCDTrial.cc | Concrete class derived from LoopRefineInnerCycle to implement the CCD min trial flavor of inner cycle refinement |
| ShearMinCCDTrial.fwd.hh | Forward declaration |
| ShearMinCCDTrial.hh | Concrete class derived from LoopRefineInnerCycle to implement the CCD min trial flavor of inner cycle refinement |
| ShearMinCCDTrialCreator.hh | |
| SmallMinCCDTrial.cc | |
| SmallMinCCDTrial.fwd.hh | Forward declaration |
| SmallMinCCDTrial.hh | Perform a small move followed CCD closure, packing and minimization |
| SmallMinCCDTrialCreator.hh | |
| IndependentLoopMover.cc | Loop mover base class |
| IndependentLoopMover.fwd.hh | |
| IndependentLoopMover.hh | |
| LoopCM.cc | Loop mover base class |
| LoopCM.fwd.hh | LoopCM forward declarations |
| LoopCM.hh | |
| LoopCMCreator.hh | This class will create instances of Mover LoopCM for the MoverFactory |
| LoopMover.cc | Loop mover base class |
| LoopMover.fwd.hh | LoopMover base classes |
| LoopMover.hh | |
| ► loops_definers | |
| LoopsDatabaseDefiner.cc | A loops definer is creates a serialized loops list |
| LoopsDatabaseDefiner.fwd.hh | LoopsDatabaseDefiner class forward declarations header |
| LoopsDatabaseDefiner.hh | A loops definer is creates a serialized loops list |
| LoopsDatabaseDefinerCreator.cc | LoopsDatabaseDefinerCreator for the LoosDatabaseDefiner load-time factory registration scheme |
| LoopsDatabaseDefinerCreator.fwd.hh | Forward Header for base class for LoopsDatabaseDefinerCreator |
| LoopsDatabaseDefinerCreator.hh | Header for LoopsDatabaseDefinerCreator for the LoosDatabaseDefiner load-time factory registration scheme |
| LoopsDefiner.fwd.hh | LoopsDefiner class forward declarations header |
| LoopsDefiner.hh | A loops definer is creates a serialized loops list |
| LoopsDefinerCreator.fwd.hh | LoopsDefinerCreator class forward declarations header |
| LoopsDefinerCreator.hh | Base class LoopsDefinerCreator for the load-time factory registration scheme |
| LoopsDefinerFactory.cc | Factory for creating LoopsDefiner objects |
| LoopsDefinerFactory.fwd.hh | |
| LoopsDefinerFactory.hh | Factory for creating LoopsDefiner objects |
| LoopsDefinerLoader.cc | Implementation the LoopsDefinerLoader class which implements the DataLoader interface |
| LoopsDefinerLoader.hh | Declartion of the XML loops_definers's LoopsDefinerLoader class |
| LoopsDefinerLoaderCreator.hh | Creator classe for the LoopsDefinerLoader classe |
| LoopsExplicitDefiner.cc | A loops definer is creates a serialized loops list |
| LoopsExplicitDefiner.fwd.hh | LoopsExplicitDefiner class forward declarations header |
| LoopsExplicitDefiner.hh | A loops definer is creates a serialized loops list |
| LoopsExplicitDefinerCreator.cc | LoopsExplicitDefinerCreator for the LoosExplicitDefiner load-time factory registration scheme |
| LoopsExplicitDefinerCreator.fwd.hh | Forward Header for base class for LoopsExplicitDefinerCreator |
| LoopsExplicitDefinerCreator.hh | Header for LoopsExplicitDefinerCreator for the LoosExplicitDefiner load-time factory registration scheme |
| LoopsFileDefiner.cc | A loops definer is creates a serialized loops list |
| LoopsFileDefiner.fwd.hh | LoopsFileDefiner class forward declarations header |
| LoopsFileDefiner.hh | A loops definer is creates a serialized loops list |
| LoopsFileDefinerCreator.cc | LoopsFileDefinerCreator for the LoosFileDefiner load-time factory registration scheme |
| LoopsFileDefinerCreator.fwd.hh | Forward Header for base class for LoopsFileDefinerCreator |
| LoopsFileDefinerCreator.hh | Header for LoopsFileDefinerCreator for the LoosFileDefiner load-time factory registration scheme |
| LoopsStringDefiner.cc | A loops definer is creates a serialized loops list |
| LoopsStringDefiner.fwd.hh | LoopsStringDefiner class forward declarations header |
| LoopsStringDefiner.hh | Creates a serialized loops list based on a string specification |
| LoopsStringDefinerCreator.hh | Header for LoopsStringDefinerCreator for the LoosFileDefiner load-time factory registration scheme |
| util.cc | Utility functions useful in LoopDefiner classes |
| util.hh | Utility functions useful in LoopDefiner classes |
| Exceptions.hh | |
| FoldTreeFromLoopsWrapper.cc | |
| FoldTreeFromLoopsWrapper.fwd.hh | |
| FoldTreeFromLoopsWrapper.hh | |
| FoldTreeFromLoopsWrapperCreator.hh | |
| Loop.cc | |
| Loop.fwd.hh | Loop class forward declarations header |
| Loop.hh | |
| loopfinder.cc | |
| loopfinder.hh | |
| LoopMoverFactory.cc | |
| LoopMoverFactory.fwd.hh | Report data to database |
| LoopMoverFactory.hh | Factory for creating LoopMover objects |
| looprelax_protocols.cc | |
| looprelax_protocols.hh | |
| Loops.cc | |
| Loops.fwd.hh | Loops and Loop class forward declarations header |
| Loops.hh | |
| Loops.tmpl.hh | |
| loops_main.cc | Loop building tools |
| loops_main.hh | |
| LoopsFileFallbackConfiguration.cc | |
| LoopsFileIO.cc | |
| LoopsFileIO.fwd.hh | LoopsFileIO forward declarations header |
| LoopsFileIO.hh | This class exists to handle the reading and writing of loops files |
| LoopsFileLoader.cc | |
| LoopsFileLoader.fwd.hh | |
| LoopsFileLoader.hh | |
| LoopsFileLoaderCreator.hh | |
| make_loops.cc | |
| make_loops.hh | |
| util.cc | |
| util.hh | |
| ► magnesium | |
| MgHydrater.cc | |
| MgHydrater.fwd.hh | |
| MgHydrater.hh | |
| MgMinimizer.cc | |
| MgMinimizer.fwd.hh | |
| MgMinimizer.hh | |
| MgMonteCarlo.cc | |
| MgMonteCarlo.fwd.hh | |
| MgMonteCarlo.hh | |
| MgOrbitalFrameFinder.cc | |
| MgOrbitalFrameFinder.fwd.hh | |
| MgOrbitalFrameFinder.hh | |
| MgScanner.cc | |
| MgScanner.fwd.hh | |
| MgScanner.hh | |
| MgWaterHydrogenPacker.cc | |
| MgWaterHydrogenPacker.fwd.hh | |
| MgWaterHydrogenPacker.hh | |
| minimize_util.cc | |
| minimize_util.hh | |
| params.hh | |
| SampleGrid.cc | |
| SampleGrid.fwd.hh | |
| SampleGrid.hh | |
| util.cc | |
| util.hh | |
| ► mainchain_potential | |
| GenerateMainchainPotential.cc | A generator for mainchain potentials. Inputs are a noncanonical residue type with an already-generated sidechain potential; outputs are a potential file suitable for use by the RamaPrePro scoreterm |
| GenerateMainchainPotential.fwd.hh | Forward declarations for a generator for mainchain potentials. Inputs are a noncanonical residue type with an already-generated sidechain potential; outputs are a potential file suitable for use by the RamaPrePro scoreterm |
| GenerateMainchainPotential.hh | Headers for a generator for mainchain potentials. Inputs are a noncanonical residue type with an already-generated sidechain potential; outputs are a potential file suitable for use by the RamaPrePro scoreterm |
| GenerateMainchainPotentialOptions.cc | Options container for the generator for mainchain potentials |
| GenerateMainchainPotentialOptions.fwd.hh | Options container for the generator for mainchain potentials |
| GenerateMainchainPotentialOptions.hh | Options container for the generator for mainchain potentials |
| GenerateMainchainPotentialTests.fwd.hh | |
| ► make_rot_lib | |
| MakeRotLibJob.cc | |
| MakeRotLibJob.fwd.hh | Implimentation file for MakeRotLibJob class |
| MakeRotLibJob.hh | |
| MakeRotLibJobInputter.cc | Implementation file for MakeRotLibJobInputter class |
| MakeRotLibJobInputter.fwd.hh | Header file for MakeRotLibJobInputter class |
| MakeRotLibJobInputter.hh | Header file for MakeRotLibJobInputter class |
| MakeRotLibJobInputterCreator.hh | MakeRotLibJobInputterCreator function declarations |
| MakeRotLibMover.cc | |
| MakeRotLibMover.fwd.hh | |
| MakeRotLibMover.hh | Implementation file for MakeRotLibMover |
| MakeRotLibOptionsData.cc | |
| MakeRotLibOptionsData.fwd.hh | Forward header file for MakeRotLibOptionsData class |
| MakeRotLibOptionsData.hh | |
| RotData.cc | |
| RotData.fwd.hh | |
| RotData.hh | |
| ► match | |
| ► downstream | |
| ActiveSiteGrid.cc | |
| ActiveSiteGrid.fwd.hh | |
| ActiveSiteGrid.hh | |
| ClassicMatchAlgorithm.cc | |
| ClassicMatchAlgorithm.fwd.hh | |
| ClassicMatchAlgorithm.hh | |
| DownstreamAlgorithm.cc | |
| DownstreamAlgorithm.fwd.hh | |
| DownstreamAlgorithm.hh | Declaration for the base-class algorithm that creates hits from an upstream builder, while managing the logic of their creation. Furthermore, the downstream algorithm manages update of hits from previous rounds should they loose their potential to result in matches |
| DownstreamBuilder.cc | |
| DownstreamBuilder.fwd.hh | |
| DownstreamBuilder.hh | |
| GeometrySecMatchRPE.cc | |
| GeometrySecMatchRPE.fwd.hh | |
| GeometrySecMatchRPE.hh | |
| LigandConformerBuilder.cc | |
| LigandConformerBuilder.fwd.hh | |
| LigandConformerBuilder.hh | |
| RigidLigandBuilder.cc | |
| RigidLigandBuilder.fwd.hh | |
| RigidLigandBuilder.hh | |
| ScoringSecMatchRPE.cc | |
| ScoringSecMatchRPE.fwd.hh | |
| ScoringSecMatchRPE.hh | |
| SecMatchEvaluatorFactory.cc | |
| SecMatchEvaluatorFactory.hh | |
| SecMatchResiduePairEvaluator.cc | |
| SecMatchResiduePairEvaluator.fwd.hh | |
| SecMatchResiduePairEvaluator.hh | |
| SecondaryMatcherToDownstreamResidue.cc | Class implementation for secondary matcher that generates upstream-only hits matching the geometry of one upstream residue with another upstream residue generated in a previous round |
| SecondaryMatcherToDownstreamResidue.fwd.hh | |
| SecondaryMatcherToDownstreamResidue.hh | Class declaration for secondary matcher that generates upstream-only hits matching the geometry of one upstream residue with another upstream residue generated in a previous round |
| SecondaryMatcherToUpstreamResidue.cc | Class implementation for secondary matcher that generates upstream-only hits matching the geometry of one upstream residue with another upstream residue generated in a previous round |
| SecondaryMatcherToUpstreamResidue.fwd.hh | |
| SecondaryMatcherToUpstreamResidue.hh | Class declaration for secondary matcher that generates upstream-only hits matching the geometry of one upstream residue with another upstream residue generated in a previous round |
| ► output | |
| DownstreamRMSEvaluator.cc | |
| DownstreamRMSEvaluator.fwd.hh | |
| DownstreamRMSEvaluator.hh | |
| LimitHitsPerRotamerFilter.cc | |
| LimitHitsPerRotamerFilter.fwd.hh | |
| LimitHitsPerRotamerFilter.hh | |
| MatchConsolidator.cc | |
| MatchConsolidator.fwd.hh | |
| MatchConsolidator.hh | |
| MatchEvaluator.cc | |
| MatchEvaluator.fwd.hh | Forward declaration for abstract class to filter matches |
| MatchEvaluator.hh | |
| MatchFilter.cc | Implementation for abstract filter class |
| MatchFilter.fwd.hh | Forward declaration for abstract class to filter matches |
| MatchFilter.hh | Declaration for abstract class to filter matches |
| MatchGrouper.cc | |
| MatchGrouper.fwd.hh | |
| MatchGrouper.hh | |
| MatchOutputter.cc | Implementation of class to write output matches that pass filters This class does not "look ahead" to future matches to decide whether the current match to process should be output, however, filters are able to keep a history of what they've output so far |
| MatchOutputter.fwd.hh | Forward declaration for no-lookahead match processor |
| MatchOutputter.hh | |
| MatchProcessor.cc | |
| MatchProcessor.fwd.hh | |
| MatchProcessor.hh | |
| MatchScoreWriter.cc | |
| MatchScoreWriter.fwd.hh | |
| MatchScoreWriter.hh | |
| OutputWriter.cc | Implementation for the class to write output matches that have (presumably) passed the output filters |
| OutputWriter.fwd.hh | Forward declaration of class to write output matches that have (presumably) passed the output filters |
| OutputWriter.hh | |
| PDBWriter.cc | Forward declaration of class to write output matches that have (presumably) passed the output filters |
| PDBWriter.fwd.hh | |
| PDBWriter.hh | |
| PoseInserter.cc | |
| PoseInserter.fwd.hh | |
| PoseInserter.hh | |
| ProcessorFactory.cc | |
| ProcessorFactory.fwd.hh | |
| ProcessorFactory.hh | Implementation for a factory class responsible for instantiating MatchProcessor classes |
| SameChiBinComboGrouper.cc | |
| SameChiBinComboGrouper.fwd.hh | |
| SameChiBinComboGrouper.hh | |
| SameRotamerComboGrouper.cc | |
| SameRotamerComboGrouper.fwd.hh | |
| SameRotamerComboGrouper.hh | |
| SameSequenceGrouper.cc | |
| SameSequenceGrouper.fwd.hh | |
| SameSequenceGrouper.hh | |
| UpstreamCollisionFilter.cc | |
| UpstreamCollisionFilter.fwd.hh | Forward declaration for abstract class to filter matches |
| UpstreamCollisionFilter.hh | Implementation for class to filter matches where the upstream residues collide |
| UpstreamDownstreamCollisionFilter.cc | |
| UpstreamDownstreamCollisionFilter.fwd.hh | Forward declaration for abstract class to filter matches |
| UpstreamDownstreamCollisionFilter.hh | Implementation for class to filter matches where the upstream residues collide |
| UpstreamHitCacher.cc | |
| UpstreamHitCacher.fwd.hh | Forward declaration for class to cache and recall the conformations of upstream hits |
| UpstreamHitCacher.hh | Declaration for class to cache and recall the conformations of upstream hits |
| WriteKinemageOutputter.cc | Forward declaration of class to write output matches that have (presumably) passed the output filters |
| WriteKinemageOutputter.fwd.hh | |
| WriteKinemageOutputter.hh | |
| WriteUpstreamCoordinateKineamge.cc | |
| WriteUpstreamCoordinateKineamge.fwd.hh | |
| WriteUpstreamCoordinateKineamge.hh | |
| ► upstream | |
| OriginalScaffoldBuildPoint.cc | |
| OriginalScaffoldBuildPoint.fwd.hh | |
| OriginalScaffoldBuildPoint.hh | |
| ProteinSCSampler.cc | Class declarations for base class and simple derived class for SC sampling |
| ProteinSCSampler.fwd.hh | Forward declaration for base class and simple derived class for SC sampling in matcher |
| ProteinSCSampler.hh | Class declarations for base class and simple derived class for SC sampling |
| ProteinUpstreamBuilder.cc | |
| ProteinUpstreamBuilder.fwd.hh | |
| ProteinUpstreamBuilder.hh | |
| ScaffoldBuildPoint.cc | |
| ScaffoldBuildPoint.fwd.hh | |
| ScaffoldBuildPoint.hh | |
| UpstreamBuilder.cc | |
| UpstreamBuilder.fwd.hh | |
| UpstreamBuilder.hh | |
| UpstreamResTypeGeometry.cc | |
| UpstreamResTypeGeometry.fwd.hh | Forward declaration for class to measure the geometry of a given ResidueType |
| UpstreamResTypeGeometry.hh | |
| BumpGrid.cc | |
| BumpGrid.fwd.hh | |
| BumpGrid.hh | |
| Hit.cc | Constructors for match_dspos1 |
| Hit.fwd.hh | Hit class forward declaration |
| Hit.hh | Hit typedef |
| Matcher.cc | |
| Matcher.fwd.hh | |
| Matcher.hh | |
| MatcherMover.cc | Implementation of mover wrapper for matcher |
| MatcherMover.fwd.hh | |
| MatcherMover.hh | |
| MatcherMoverCreator.hh | This class will create instances of Mover FlxbbDesign for the MoverFactory |
| MatcherTask.cc | |
| MatcherTask.fwd.hh | |
| MatcherTask.hh | |
| MatchPositionModifiers.cc | Implementations for MatchPositionModifiers |
| MatchPositionModifiers.fwd.hh | Forward declaration for MatchPositionModifiers |
| MatchPositionModifiers.hh | Header file for MatchPositionModifiers |
| MatchSet.cc | |
| MatchSet.fwd.hh | |
| MatchSet.hh | |
| OccupiedSpaceHash.cc | Declaration for classes in 6D hasher |
| OccupiedSpaceHash.fwd.hh | |
| OccupiedSpaceHash.hh | Declaration for classes in 6D hasher |
| VoxelSetIterator.cc | Implementation of the VoxelSetIterator class |
| VoxelSetIterator.fwd.hh | |
| VoxelSetIterator.hh | Forward declaration for iterator to traverse the 64 bins each hit covers |
| ► matdes | |
| BuildingBlockInterfaceOperation.cc | |
| BuildingBlockInterfaceOperation.fwd.hh | Restrict design to only residues at inter-building block interfaces |
| BuildingBlockInterfaceOperation.hh | Restrict design to only residues at inter-building block interfaces |
| BuildingBlockInterfaceOperationCreator.hh | |
| ClashCheckFilter.cc | Checks to see if any residues defined by the TaskOperations have clashing CA/CBs between interfaces (building block aware) |
| ClashCheckFilter.fwd.hh | |
| ClashCheckFilter.hh | Header file for ClashCheckFilter class |
| ClashCheckFilterCreator.hh | FilterCreator for the ClashCheckFilter |
| ExtractSubposeMover.cc | Extract primary component associated with symdofs and all neighboring components. Note: Currently just dumps extracted PDB and does not modify pose |
| ExtractSubposeMover.fwd.hh | |
| ExtractSubposeMover.hh | Extract primary component associated with symdofs and all neighboring components |
| ExtractSubposeMoverCreator.hh | |
| GetRBDOFValues.cc | Returns the translation and angle for movable jump |
| GetRBDOFValues.fwd.hh | |
| GetRBDOFValues.hh | Header file for GetRBDOFValues class |
| GetRBDOFValuesCreator.hh | FilterCreator for the GetRBDOFValues |
| InterfacePackingFilter.cc | |
| InterfacePackingFilter.fwd.hh | Forward declaration for InterfacePackingFilter |
| InterfacePackingFilter.hh | Calculates the RosettaHoles score for the atoms within a user-defined cutoff distance (default = 9.0) of the subpose interface. Filters based on lower and upper thresholds, which are set to -/+5 by default |
| InterfacePackingFilterCreator.hh | FilterCreators for the InterfacePackingFilter |
| MatDesGreedyOptMutationMover.cc | |
| MatDesGreedyOptMutationMover.fwd.hh | This is a modified version of Chris King's GreedyOptMutationMover with additional functionality that is currently not compatible with all of the ParetoOpt functionality. Please note that this has been checked into master in its current state in response to requests from others to use this modified version of Chris King's GreedyOptMutationMover. Although this is still a somewhat developmental piece of code, it has currently been left in src/protocols/matdes/ to avoid issues with intra-library level dependencies |
| MatDesGreedyOptMutationMover.hh | This is a modified version of Chris King's GreedyOptMutationMover with additional functionality that is currently not compatible with all of the ParetoOpt functionality. Please note that this has been checked into master in its current state in response to requests from others to use this modified version of Chris King's GreedyOptMutationMover. Although this is still a somewhat developmental piece of code, it has currently been left in src/protocols/matdes/ to avoid issues with intra-library level dependencies |
| MatDesGreedyOptMutationMoverCreator.hh | |
| MatDesPointMutationCalculator.cc | |
| MatDesPointMutationCalculator.fwd.hh | This is a modified version of chris king's PointMutationCalculator with additional functionality that is currently not compatible with all of the ParetoOpt functionality. please note that this has been checked into master in its current state in response to requests from others to use this modified version of chris king's GreedyOptMutationMover. although this is still a somewhat developmental piece of code, it has currently been left in src/protocols/matdes/ to avoid issues with intra-library level dependencies |
| MatDesPointMutationCalculator.hh | This is a modified version of chris king's PointMutationCalculator with additional functionality that is currently not compatible with all of the ParetoOpt functionality. please note that this has been checked into master in its current state in response to requests from others to use this modified version of chris king's GreedyOptMutationMover. although this is still a somewhat developmental piece of code, it has currently been left in src/protocols/matdes/ to avoid issues with intra-library level dependencies |
| MotifHitsRotamersOperation.cc | |
| MotifHitsRotamersOperation.fwd.hh | |
| MotifHitsRotamersOperation.hh | |
| OligomericAverageDegreeFilter.cc | Calculates AverageDegree within the context of an unbound oligomer |
| OligomericAverageDegreeFilter.fwd.hh | |
| OligomericAverageDegreeFilter.hh | Header file for OligomericAverageDegreeFilter class |
| OligomericAverageDegreeFilterCreator.hh | FilterCreator for the OligomericAverageDegreeFilter |
| SchemePlaceMotifsMover.cc | |
| SchemePlaceMotifsMover.fwd.hh | |
| SchemePlaceMotifsMover.hh | |
| SchemePlaceMotifsMoverCreator.hh | |
| SymDofMover.cc | |
| SymDofMover.fwd.hh | |
| SymDofMover.hh | |
| SymDofMoverCreator.hh | |
| SymDofMoverSampler.cc | |
| SymDofMoverSampler.hh | |
| SymUnsatHbondFilter.cc | Determine the number of unsatified hydrogen bonds at an interface Works with both symmetric and asymmetric poses |
| SymUnsatHbondFilter.fwd.hh | |
| SymUnsatHbondFilter.hh | Definition of filter class SymUnsatHbondFilter |
| SymUnsatHbondFilterCreator.hh | FilterCreators for the SymUnsatHbondFilterCreator |
| ► md | |
| CartesianMD.cc | |
| CartesianMD.fwd.hh | |
| CartesianMD.hh | Cartesian MD |
| CartesianMDCreator.hh | |
| MDBase.cc | Initialization for MD |
| MDBase.fwd.hh | Initialization for MD |
| MDBase.hh | Initialization for MD |
| MDConstants.hh | Protocols/md package type declarations |
| Rattle.hh | Rattle bond length constrainer for CartesianMD |
| thermostat.hh | Thermostat for MD simulation |
| ► mean_field | |
| AAMatrix.cc | |
| AAMatrix.fwd.hh | |
| AAMatrix.hh | |
| AAProb.cc | |
| AAProb.fwd.hh | |
| AAProb.hh | |
| DesignMeanField.cc | |
| DesignMeanField.fwd.hh | |
| DesignMeanField.hh | |
| EnergiesByTaskCalculator.cc | |
| EnergiesByTaskCalculator.hh | |
| FlexBBDesignMeanField.cc | |
| FlexBBDesignMeanField.fwd.hh | |
| FlexBBDesignMeanField.hh | |
| FlexBBMeanField.cc | |
| FlexBBMeanField.fwd.hh | |
| FlexBBMeanField.hh | |
| GenMeanFieldMover.cc | |
| GenMeanFieldMover.fwd.hh | Forward declaration for GenMeanFieldMover |
| GenMeanFieldMover.hh | Reports to Tracer a probability distribution per rotamer, per repackable/designable res, based on a mean-field method can also report entropy per residue or per all repackable/designable res if some residues are designable, will report logo plot as well |
| GenMeanFieldMoverCreator.hh | FilterCreators for the GenMeanFieldMover |
| jagged_array.functions.hh | Some useful functions for jagged_array |
| jagged_array.fwd.hh | Protocols::mean_field::jagged_array forward declarations |
| jagged_array.hh | |
| MeanField.cc | |
| MeanField.fwd.hh | |
| MeanField.hh | |
| MeanFieldFactory.cc | |
| MeanFieldFactory.fwd.hh | Mean field calculator factory class forward declaration |
| MeanFieldFactory.hh | Mean field calculator class declaration |
| ResHashMap.cc | |
| ResHashMap.fwd.hh | |
| ResHashMap.hh | |
| RotMatrix.cc | |
| RotMatrix.fwd.hh | |
| RotMatrix.hh | |
| RotProb.cc | |
| RotProb.fwd.hh | |
| RotProb.hh | |
| ► medal | |
| MedalExchangeMover.cc | |
| MedalExchangeMover.fwd.hh | |
| MedalExchangeMover.hh | |
| MedalMain.cc | |
| MedalMain.hh | |
| MedalMover.cc | |
| MedalMover.fwd.hh | |
| MedalMover.hh | |
| util.cc | |
| util.hh | |
| ► membrane | |
| ► benchmark | |
| MakeCanonicalHelix.cc | Creates an ideal a-helix from sequence given a range of residues |
| MakeCanonicalHelix.fwd.hh | Creates an ideal a-helix from sequence given a range of residues |
| MakeCanonicalHelix.hh | Creates an ideal a-helix from sequence given a range of residues |
| MakeCanonicalHelixCreator.hh | Creates an ideal a-helix from sequence given a range of residues |
| SampleTiltAngles.cc | Calculates the energy at all possible tilt angles (0->180 degrees) |
| SampleTiltAngles.fwd.hh | Calculates the energy at all possible tilt angles (0->180 degrees) |
| SampleTiltAngles.hh | Calculates the energy at all possible tilt angles (0->180 degrees) |
| SampleTiltAnglesCreator.hh | Calculates the energy at all possible tilt angles (0->180 degrees) |
| ► geometry | |
| Embedding.cc | |
| Embedding.fwd.hh | |
| Embedding.hh | Methods for Computing Membrane Embeddings |
| EmbeddingDef.cc | Basic Embedding Definitions for Membrane Embedding |
| EmbeddingDef.fwd.hh | Basic Embedding Definitions for Membrane Embedding |
| EmbeddingDef.hh | Basic Embedding Definitions for Membrane Embedding |
| ► scoring | |
| FaWaterToBilayerEnergy.cc | Implicit Lipid Membrane Model Water-to-Bilayer transfer energy (one-body) |
| FaWaterToBilayerEnergy.fwd.hh | |
| FaWaterToBilayerEnergy.hh | Implicit Lipid Membrane Model Water-to-Bilayer transfer energy (one-body) |
| FaWaterToBilayerEnergyCreator.hh | Water to Bilayer transfer free energy for atom groups derived from Moon & Fleming thermodynamic side chain hydrophobicity scale |
| MEnvAtomParams.cc | A container for storing memrbane environemnt parameters and derivatives |
| MEnvAtomParams.fwd.hh | A container for storing memrbane environemnt parameters and derivatives |
| MEnvAtomParams.hh | A container for storing memrbane environemnt parameters and derivatives |
| ► symmetry | |
| SymmetricAddMembraneMover.cc | Add Membrane Representation to a Symmetric starting pose |
| SymmetricAddMembraneMover.fwd.hh | Add Membrane Representation to a Symmetric starting pose |
| SymmetricAddMembraneMover.hh | |
| SymmetricAddMembraneMoverCreator.hh | Add Membrane Representation to a Symmetric starting pose |
| util.cc | Quick calculations for symmetrizing membrane proteins |
| util.hh | Quick calculations for symmetrizing membrane proteins |
| ► visualize | |
| VisualizeEmbeddingMover.cc | |
| VisualizeEmbeddingMover.fwd.hh | |
| VisualizeEmbeddingMover.hh | |
| VisualizeEmbeddingMoverCreator.hh | |
| VisualizeMembraneMover.cc | |
| VisualizeMembraneMover.fwd.hh | |
| VisualizeMembraneMover.hh | |
| VisualizeMembraneMoverCreator.hh | |
| AddMembraneMover.cc | Initialize the RosettaMP framework by adding representations of the membrane environemnt to the conformation data held by the pose |
| AddMembraneMover.fwd.hh | Initialize the RosettaMP framework by adding representations of the membrane environemnt to the conformation data held by the pose |
| AddMembraneMover.hh | Initialize the RosettaMP framework by adding representations of the membrane environemnt to the conformation data held by the pose |
| AddMembraneMoverCreator.hh | |
| AddMembraneSpanConstraint.cc | |
| AddMembraneSpanConstraint.fwd.hh | |
| AddMembraneSpanConstraint.hh | |
| AddMembraneSpanConstraintCreator.hh | Add membrane span constraint |
| AddMembraneSpanTermZConstraint.cc | |
| AddMembraneSpanTermZConstraint.fwd.hh | |
| AddMembraneSpanTermZConstraint.hh | |
| AddMembraneSpanTermZConstraintCreator.hh | Add membrane span constraint |
| AddMPLigandMover.cc | Add "single" ligand to to membrane pose |
| AddMPLigandMover.fwd.hh | Add "single" ligand to to membrane pose |
| AddMPLigandMover.hh | Add "single" ligand to to membrane pose |
| AddMPLigandMoverCreator.hh | Add "single" ligand to to membrane pose |
| AqueousPoreFinder.cc | Compute the center, major radius and minor radius of an ellipsoidal aqueous pore |
| AqueousPoreFinder.fwd.hh | Compute the center, major axis and minor axis of an ellipsoidal aqueous pore |
| AqueousPoreFinder.hh | Compute the center, major axis and minor axis of an ellipsoidal aqueous pore |
| AqueousPoreFinderCreator.hh | Compute the center, major axis and minor axis of an ellipsoidal aqueous pore |
| FlipMover.cc | |
| FlipMover.fwd.hh | |
| FlipMover.hh | |
| FlipMoverCreator.hh | Flips a span or protein in the membrane (Rosetta Scripts Hook) |
| MembranePositionFromTopologyMover.cc | Computes and sets the initial position of the membrane |
| MembranePositionFromTopologyMover.fwd.hh | Computes and sets the initial position of the membrane |
| MembranePositionFromTopologyMover.hh | Computes and sets the initial position of the membrane |
| MembranePositionFromTopologyMoverCreator.hh | Compute the Initial Position of the membrane |
| MPLipidAccessibility.cc | Mover that computes which residues are lipid accessible and puts that information into the B-factors: 50 is lipid accessible, 0 is lipid INaccessible |
| MPLipidAccessibility.fwd.hh | Mover that computes which residues are lipid accessible and puts that information into the B-factors: 50 is lipid accessible, 0 is lipid INaccessible |
| MPLipidAccessibility.hh | Mover that computes which residues are lipid accessible and puts that information into the B-factors: 50 is lipid accessible, 0 is lipid INaccessible |
| MPLipidAccessibilityCreator.hh | Mover that computes which residues are lipid accessible and puts that information into the B-factors: 50 is lipid accessible, 0 is lipid INaccessible |
| MPQuickRelaxMover.cc | |
| MPQuickRelaxMover.fwd.hh | |
| MPQuickRelaxMover.hh | |
| MPQuickRelaxMoverCreator.hh | |
| OptimizeMembranePositionMover.cc | |
| OptimizeMembranePositionMover.fwd.hh | |
| OptimizeMembranePositionMover.hh | |
| OptimizeMembranePositionMoverCreator.hh | |
| OptimizeProteinEmbeddingMover.cc | |
| OptimizeProteinEmbeddingMover.fwd.hh | |
| OptimizeProteinEmbeddingMover.hh | |
| OptimizeProteinEmbeddingMoverCreator.hh | |
| RandomMembranePositionMover.cc | Random membrane position mover |
| RandomMembranePositionMover.fwd.hh | Random membrane position mover |
| RandomMembranePositionMover.hh | Random membrane position mover |
| SetMembranePositionMover.cc | Sets the membrane position normal and center Last Modified: 7/4/15 |
| SetMembranePositionMover.fwd.hh | Sets the membrane position normal and center |
| SetMembranePositionMover.hh | Sets the membrane position normal and center |
| SetMembranePositionMoverCreator.hh | Sets the membrane position normal and center |
| SpinAroundPartnerMover.cc | Spins the downstream partner around the upstream partner |
| SpinAroundPartnerMover.fwd.hh | Spins the downstream partner around the upstream partner |
| SpinAroundPartnerMover.hh | Spins the downstream partner around the upstream partner |
| SpinAroundPartnerMoverCreator.hh | Spins the downstream partner around the upstream partner |
| TiltMover.cc | Tilts a protein in the membrane (Rosetta Scripts Hook) |
| TiltMover.fwd.hh | Tilts a protein in the membrane (Rosetta Scripts Hook) |
| TiltMover.hh | Tilts a protein in the membrane (Rosetta Scripts Hook) |
| TiltMoverCreator.hh | Tilts a protein in the membrane (Rosetta Scripts Hook) |
| TransformIntoMembraneMover.cc | Transform a pose into a membrane coordinate frame |
| TransformIntoMembraneMover.fwd.hh | Transform a pose into a membrane coordinate frame |
| TransformIntoMembraneMover.hh | Transform a pose into a membrane coordinate frame |
| TransformIntoMembraneMoverCreator.hh | Transform a pose into a membrane coordinate frame |
| TranslationRotationMover.cc | |
| TranslationRotationMover.fwd.hh | |
| TranslationRotationMover.hh | |
| TranslationRotationMoverCreator.hh | |
| util.cc | Utility methods for working with proteins in the membrane Several groups of utilities for working in the memrbane environment |
| util.hh | Utility methods for working with proteins in the membrane Several groups of utilities for working in the memrbane environment |
| ► membrane_benchmark | |
| MembraneEnergyLandscapeSampler.cc | Sample a protein energy landscape as a function of orientation in the membrane |
| MembraneEnergyLandscapeSampler.fwd.hh | Sample all points on a 2D membrane energy landscape given implicit model and protein dimensions |
| MembraneEnergyLandscapeSampler.hh | Sample all points on a 2D membrane energy landscape given implicit model and protein dimensions |
| MembraneEnergyLandscapeSamplerCreator.hh | Sample all points on a 2D membrane energy landscape given implicit model and protein dimensions |
| PeptideOrientationMover.cc | Orient a peptide to a specific orientation relative to the membrane |
| PeptideOrientationMover.fwd.hh | |
| PeptideOrientationMover.hh | Orient a peptide to a specific orientation relative to the membrane |
| PeptideOrientationMoverCreator.hh | Orient a peptide to a specific orientation relative to the membrane |
| ► metal_interface | |
| AddZincSiteConstraints.cc | Adds metal binding site geometry constraints to pose |
| AddZincSiteConstraints.fwd.hh | AddZincSiteConstraints protocol-mover forward declarations header |
| AddZincSiteConstraints.hh | Adds metal binding site geometry constraints to pose |
| FindClosestAtom.cc | |
| FindClosestAtom.hh | Finds the closest atom in a given residue to a point (usually a zinc atom) |
| MatchGrafter.cc | Takes a scaffold protein and a match pdb from RosettaMatch, grafts the match onto the protein. For zinc homodimer design, it can then combine two grafted poses by overlaying the zinc atoms |
| MatchGrafter.fwd.hh | MatchGrafter protocol-mover forward declarations header |
| MatchGrafter.hh | Takes a scaffold protein and a match pdb from RosettaMatch, grafts the match onto the protein. For zinc homodimer design, it can then combine two grafted poses by overlaying the zinc atoms |
| MetalSiteResidue.cc | Stores data that describes a metal-coordinating residue |
| MetalSiteResidue.fwd.hh | MetalSiteResidue protocol-mover forward declarations header |
| MetalSiteResidue.hh | Stores data that describes a metal-coordinating residue |
| ZincHeterodimerMover.cc | ZincHeterodimerMover methods implemented - see apps/pilot/rjha/README for details |
| ZincHeterodimerMover.fwd.hh | ZincHeterodimerMover protocol-mover forward declarations header |
| ZincHeterodimerMover.hh | ZincHeterodimerMover protocol main mover |
| ZincSiteFinder.cc | |
| ZincSiteFinder.fwd.hh | ZincSiteFinder protocol-mover forward declarations header |
| ZincSiteFinder.hh | |
| ► minimization_packing | |
| ► symmetry | |
| SymMinMover.cc | |
| SymMinMover.fwd.hh | MinMover forward declarations header |
| SymMinMover.hh | |
| SymMinMoverCreator.hh | |
| SymPackRotamersMover.cc | |
| SymPackRotamersMover.fwd.hh | |
| SymPackRotamersMover.hh | |
| SymPackRotamersMoverCreator.hh | |
| SymRotamerTrialsMover.cc | |
| SymRotamerTrialsMover.fwd.hh | |
| SymRotamerTrialsMover.hh | |
| SymRotamerTrialsMoverCreator.hh | |
| TaskAwareSymMinMover.cc | |
| TaskAwareSymMinMover.fwd.hh | |
| TaskAwareSymMinMover.hh | Minimize only those residues specified by a set of TaskOperations in a symmetric pose |
| TaskAwareSymMinMoverCreator.hh | |
| BoltzmannRotamerMover.cc | Implementation of BoltzmannRotamerMover class and functions |
| BoltzmannRotamerMover.fwd.hh | |
| BoltzmannRotamerMover.hh | Definition of BoltzmannRotamerMover class and functions |
| BoltzmannRotamerMoverCreator.hh | This class will create instances of protocols::moves::Mover BoltzmannRotamerMover for the protocols::moves::MoverFactory |
| DisulfideOptimizationMover.cc | A Mover to jointly optimize the geometry of a pair of disulfide-bonded residues |
| DisulfideOptimizationMover.fwd.hh | A Mover to jointly optimize the geometry of a pair of disulfide-bonded residues |
| DisulfideOptimizationMover.hh | A Mover to jointly optimize the geometry of a pair of disulfide-bonded residues |
| DisulfideOptimizationMoverCreator.hh | A Mover to jointly optimize the geometry of a pair of disulfide-bonded residues |
| GreenPacker.cc | Packing mover that makes extensive reuse of rotamer pair energies class definition |
| GreenPacker.fwd.hh | Packing mover that makes extensive reuse of rotamer pair energies class forward declaration |
| GreenPacker.hh | Packing mover that makes extensive reuse of rotamer pair energies class declaration |
| MinMover.cc | Method definitions for MinMover |
| MinMover.fwd.hh | MinMover forward declarations header |
| MinMover.hh | Class definition for MinMover |
| MinMoverCreator.hh | |
| MinPackMover.cc | Implementation of the MinPackMover class; a wrapper class for invoking core::pack::min_pack |
| MinPackMover.fwd.hh | Forward declaration of the mover class to both pack and minimize rotamers |
| MinPackMover.hh | Protocols::moves::Mover class to invoke core::pack::min_pack |
| MinPackMoverCreator.hh | This class will create instances of protocols::moves::Mover MinPackMover for the protocols::moves::MoverFactory |
| PackRotamersMover.cc | |
| PackRotamersMover.fwd.hh | |
| PackRotamersMover.hh | |
| PackRotamersMoverCreator.hh | |
| PackRotamersMoverLazy.cc | |
| PackRotamersMoverLazy.fwd.hh | |
| PackRotamersMoverLazy.hh | |
| PackRotamersMoverLazyCreator.hh | |
| PertMinMover.cc | Roberto Chica inspired random perturbation followed by minimization |
| PertMinMover.fwd.hh | Random perturbation, followed by minimization |
| PertMinMover.hh | Roberto Chica inspired random perturbation followed by minimization |
| PertMinMoverCreator.hh | Random perturbation, followed by minimization |
| RepackSidechainsMover.cc | |
| RepackSidechainsMover.fwd.hh | |
| RepackSidechainsMover.hh | |
| RepackSidechainsMoverCreator.hh | |
| RotamerizeMover.cc | Definitions of class methods for RotamerizeMover |
| RotamerizeMover.fwd.hh | Forward declarations for rotamerizing |
| RotamerizeMover.hh | |
| RotamerTrialsMinMover.cc | Protocols::moves::Mover for Rotamer-Trials with Minimization (based on RotamerTrialsMover) |
| RotamerTrialsMinMover.fwd.hh | |
| RotamerTrialsMinMover.hh | Wrapper mover for Rotamer-Trials with Minimization (based on RotamerTrialsMover) |
| RotamerTrialsMinMoverCreator.hh | This class will create instances of RotamerTrialsMinMover for the protocols::moves::MoverFactory |
| RotamerTrialsMover.cc | |
| RotamerTrialsMover.fwd.hh | |
| RotamerTrialsMover.hh | |
| RotamerTrialsMoverCreator.hh | This class will create instances of protocols::moves::Mover SidechainMCMover for the protocols::moves::MoverFactory |
| SaneMinMover.cc | |
| SaneMinMover.fwd.hh | |
| SaneMinMover.hh | |
| SaneMinMoverCreator.hh | |
| SetReturningPackRotamersMover.cc | A pack mover which returns not just the best packer solution, but all nloop solutions |
| SetReturningPackRotamersMover.fwd.hh | |
| SetReturningPackRotamersMover.hh | A PackRotamers mover which returns a set of packed poses for when ndruns/nloop is in use |
| TaskAwareMinMover.cc | TaskAwareMinMover methods implemented |
| TaskAwareMinMover.fwd.hh | TaskAwareMinMover forward declarations header |
| TaskAwareMinMover.hh | MinMover which updates MoveMap to mirror PackerTask |
| TaskAwareMinMoverCreator.hh | |
| ► monte_carlo | |
| GenericMonteCarloMover.cc | |
| GenericMonteCarloMover.fwd.hh | |
| GenericMonteCarloMover.hh | Perform a given mover and sample structures by MonteCarlo |
| GenericMonteCarloMoverCreator.hh | |
| GenericSimulatedAnnealer.cc | Perform a given mover and sample structures by MonteCarlo with gradual simulated annealing |
| GenericSimulatedAnnealer.fwd.hh | |
| GenericSimulatedAnnealer.hh | Perform a given mover and sample structures by MonteCarlo with simulated annealing of acceptance temperatures |
| GenericSimulatedAnnealerCreator.hh | This class will create instances of Mover GenericSimulatedAnnealer for the MoverFactory |
| MonteCarloInterface.cc | A MonteCarlo object for optimizing the interface dG as defined using InterfaceAnalyzer. The dG and Total energy can be weighted. This is so that the interface energy itself can be optimized through a protocol |
| MonteCarloInterface.fwd.hh | A MonteCarlo object for optimizing the interface dG as defined using InterfaceAnalyzer. The dG and Total energy can be weighted. This is so that the interface energy itself can be optimized through a protocol |
| MonteCarloInterface.hh | A MonteCarlo object for optimizing the interface dG as defined using InterfaceAnalyzer. The dG and Total energy can be weighted. This is so that the interface energy itself can be optimized through a protocol |
| MonteCarloRecover.cc | |
| MonteCarloRecover.fwd.hh | |
| MonteCarloRecover.hh | |
| MonteCarloRecoverCreator.hh | |
| MonteCarloReset.cc | |
| MonteCarloReset.fwd.hh | |
| MonteCarloReset.hh | Perform a given mover and sample structures by MonteCarlo |
| MonteCarloResetCreator.hh | |
| MonteCarloTest.cc | |
| MonteCarloTest.fwd.hh | |
| MonteCarloTest.hh | Perform a given mover and sample structures by MonteCarlo |
| MonteCarloTestCreator.hh | |
| ResetBaselineMover.cc | |
| ResetBaselineMover.fwd.hh | Switch the chain order |
| ResetBaselineMover.hh | Switch the chain order |
| ResetBaselineMoverCreator.hh | |
| ► motif_grafting | |
| ► movers | |
| MotifGraftCreator.hh | |
| MotifGraftMover.cc | |
| MotifGraftMover.hh | |
| ► motifs | |
| BuildPosition.cc | Position where motifs are built in MotifSearch |
| BuildPosition.fwd.hh | Forward declaration for position where motifs are built in MotifSearch |
| BuildPosition.hh | Class declaration for position where motifs are built in MotifSearch |
| IRCollection.cc | Implmentation of interaction motifs |
| IRCollection.fwd.hh | Forward declaration for sets of interaction motifis between residues |
| IRCollection.hh | Class declaration for collections of inverse rotamers |
| LigandMotifSearch.cc | Ligand motif searching protocol |
| LigandMotifSearch.fwd.hh | Forward declaration for interaction motif search protocol |
| LigandMotifSearch.hh | Class declaration for ligand motif searching protocol |
| Motif.cc | Implementation of interaction motifs |
| Motif.fwd.hh | Forward declaration for interaction motif between residues |
| Motif.hh | Header for interaction motif between residues |
| motif_utils.cc | Motif helper/conversion/io functions |
| motif_utils.hh | Header for motif helper/conversion/io functions |
| MotifDnaPacker.cc | |
| MotifDnaPacker.fwd.hh | |
| MotifDnaPacker.hh | |
| MotifDnaPackerCreator.hh | This class will create instances of Mover MotifDnaPacker for the MoverFactory |
| MotifHit.cc | Class that holds information about a motif in the context of the search |
| MotifHit.fwd.hh | Forward declaration for class that holds information about a motif in the context of the search |
| MotifHit.hh | Class declaration for class that holds information about a motif in the context of the search |
| MotifLibrary.cc | Implementation of interaction motifs |
| MotifLibrary.fwd.hh | Forward declaration for sets of interaction motifis between residues |
| MotifLibrary.hh | Class declaration for sets of interaction motifs between residues |
| MotifSearch.cc | Motif searching protocol |
| MotifSearch.fwd.hh | Forward declaration for interaction motif search protocol |
| MotifSearch.hh | Class declaration for motif searching protocol |
| SingleMotif.cc | |
| SingleMotif.fwd.hh | Forward declaration for interaction motif between residues |
| SingleMotif.hh | Header for interaction motif between residues |
| ► moves | |
| ChangeFoldTreeMover.fwd.hh | |
| ChangeFoldTreeMover.hh | ChangeFoldTreeMover |
| CompositionMover.cc | |
| CompositionMover.fwd.hh | |
| CompositionMover.hh | |
| CyclicMover.cc | |
| CyclicMover.fwd.hh | |
| CyclicMover.hh | |
| DsspMover.cc | Performs dssp and set secondary structure to pose |
| DsspMover.fwd.hh | |
| DsspMover.hh | Header file of DsspMover.cc |
| DsspMoverCreator.hh | |
| DualMonteCarlo.cc | |
| DualMonteCarlo.fwd.hh | "dual" MonteCarlo header - wraps MonteCarlo to allow for centroid MonteCarlo scoring of a fullatom pose (or other similar situations) |
| DualMonteCarlo.hh | "dual" MonteCarlo wraps MonteCarlo to allow for centroid MonteCarlo scoring of a fullatom pose (or other similar situations) |
| FilterMover.cc | |
| FilterMover.fwd.hh | |
| FilterMover.hh | |
| FilterReportAsPoseExtraScoresMover.cc | This Mover runs a Filter and dumps the report_sm value to Pose's extra scores (for later JD reporting) To do the same for all filters, use WriteFiltersToPose |
| FilterReportAsPoseExtraScoresMover.fwd.hh | This Mover runs a Filter and dumps the report_sm value to Pose's extra scores (for later JD reporting) |
| FilterReportAsPoseExtraScoresMover.hh | This Mover runs a Filter and dumps the report_sm value to Pose's extra scores (for later JD reporting) |
| FilterReportAsPoseExtraScoresMoverCreator.hh | This Mover runs a Filter and dumps the report_sm value to Pose's extra scores (for later JD reporting) |
| FilterReporterMover.cc | A FilterMover that also calls report() on apply() |
| FilterReporterMover.fwd.hh | A FilterMover that also calls report() on apply() |
| FilterReporterMover.hh | A FilterMover that also calls report() on apply() |
| IfMover.cc | |
| IfMover.hh | |
| IfMoverCreator.hh | |
| IteratedConvergenceMover.cc | Implementation of IteratedConvergenceMover, class to repeatedly apply a submover until filter convergence is reached |
| IteratedConvergenceMover.fwd.hh | Forward declaration of the mover class to repeatedly apply a submover until filter convergence is reached |
| IteratedConvergenceMover.hh | Mover class to repeatedly apply a submover until filter convergence is reached |
| IteratedConvergenceMoverCreator.hh | This class will create instances of Mover IteratedConvergenceMover for the MoverFactory |
| JumpOutMover.cc | |
| JumpOutMover.fwd.hh | |
| JumpOutMover.hh | JumpOutMover |
| MonteCarlo.cc | |
| MonteCarlo.fwd.hh | |
| MonteCarlo.hh | |
| MonteCarlo.tmpl.hh | Implentation for MonteCarlo template functions |
| MonteCarloExceptionConverge.fwd.hh | |
| MonteCarloExceptionConverge.hh | |
| MonteCarloStatus.cc | |
| MonteCarloStatus.hh | |
| MoveMapMover.cc | Implementation file for MoveMapMover |
| MoveMapMover.fwd.hh | |
| MoveMapMover.hh | A MoveMapMover is nothing more than a mover that has a function that sets its movemap |
| Mover.cc | Method code and full headers for Mover– keeps heavily-included Mover.hh small and concise to maximize compiling efficiency and to make the class definitions easier to read |
| Mover.fwd.hh | |
| Mover.hh | : A mover is an object that can apply a conformational change to a pose |
| mover_schemas.cc | |
| mover_schemas.hh | |
| MoverApplyingMover.cc | Implementation file for MoverApplyingMover |
| MoverApplyingMover.fwd.hh | |
| MoverApplyingMover.hh | A MoverApplyingMover is nothing more than a mover that applies another (variable) mover |
| MoverContainer.cc | Apply functions for classes of type MoverContainer |
| MoverContainer.fwd.hh | MoverContainer forward declarations header |
| MoverContainer.hh | Base class for containers of movers such as SequenceMover |
| MoverContainerCreator.hh | |
| MoverCreator.cc | |
| MoverCreator.hh | Base class for MoverCreators for the Mover load-time factory registration scheme |
| MoverFactory.cc | |
| MoverFactory.fwd.hh | |
| MoverFactory.hh | |
| MoverForPoseList.cc | |
| MoverForPoseList.fwd.hh | |
| MoverForPoseList.hh | : In addition to applying to a pose, this mover can apply to a vector1 of poses |
| MoverStatistics.cc | Keeps track of the acceptance_rate of a Mover |
| MoverStatistics.hh | Keeps track of the acceptance_rate of a Mover |
| MoverStatus.cc | |
| MoverStatus.hh | Return status enum for Movers |
| NullMover.cc | |
| NullMover.fwd.hh | |
| NullMover.hh | |
| OutputMovers.cc | File to contain classes that deal with output and pdb dumping |
| OutputMovers.fwd.hh | OutputMovers forward declarations header |
| OutputMovers.hh | File to contain classes that deal with output and pdb dumping |
| PyMOLMover.cc | Send infromation to PyMOL |
| PyMOLMover.fwd.hh | |
| PyMOLMover.hh | Send infromation to PyMOL |
| PyMOLMoverCreator.hh | |
| RampingMover.cc | Mover class for ramping the repulsive term of a score function over the course of several apply() evaluations |
| RampingMover.fwd.hh | |
| RampingMover.hh | |
| RampingMoverCreator.hh | This class will create instances of Mover RampingMover for the MoverFactory |
| RepeatMover.cc | Method definitions for RepeatMover |
| RepeatMover.fwd.hh | |
| RepeatMover.hh | Declarations and simple accessor/mutator definitions for RepeatMover |
| ReplicaExchangeMC.cc | Implementing a Recplica Exchange Monte Carlo Mover |
| ReplicaExchangeMC.fwd.hh | Implementing a Recplica Exchange Monte Carlo Mover |
| ReplicaExchangeMC.hh | Implementing a Recplica Exchange Monte Carlo Mover |
| ResId.cc | |
| ResId.fwd.hh | |
| ResId.hh | A simple base class providing common access to a residue identity for movers and filters. The anticipated usage is to derive movers and filters multiply, from the relevant base class and from ResId and make these movers/filters use the residue id encapsulated in this class |
| SimulatedTempering.cc | |
| SimulatedTempering.fwd.hh | |
| SimulatedTempering.hh | |
| StructureRestrictor.cc | Lookup relevant chains for a structure in a table |
| StructureRestrictor.fwd.hh | Lookup relevant chains for a structure in a table |
| StructureRestrictor.hh | Lookup relevant chains for a structure in a table |
| TrialCounter.cc | |
| TrialCounter.fwd.hh | |
| TrialCounter.hh | |
| TrialMover.cc | |
| TrialMover.fwd.hh | TrialMover forward declarations header |
| TrialMover.hh | |
| util.cc | |
| util.hh | |
| VectorPoseMover.cc | Designates a mover that can be passed multiple poses by the VectorPoseJobDistributor Any movers deriving from this subclass can then act on all of the input poses simultaneously Only accessible through recon application |
| VectorPoseMover.fwd.hh | Used for movers that require multiple poses to act upon. Only accessible through recon application |
| VectorPoseMover.hh | Designates a mover that can be passed multiple poses by the VectorPoseJobDistributor Any movers deriving from this subclass can then act on all of the input poses simultaneously Only accessible through recon application |
| WhileMover.cc | |
| WhileMover.fwd.hh | |
| WhileMover.hh | |
| ► mpi_refinement | |
| Clusterer.cc | |
| Clusterer.hh | |
| MPI_Refine_Emperor.cc | |
| MPI_Refine_Emperor.hh | |
| MPI_Refine_Master.cc | |
| MPI_Refine_Master.hh | |
| MPI_Refinement.cc | |
| MPI_Refinement.hh | |
| MultiObjective.cc | |
| MultiObjective.fwd.hh | |
| MultiObjective.hh | |
| Scheduler.cc | |
| Scheduler.hh | |
| Serial_Refine.cc | |
| Serial_Refine.hh | |
| StructAvrgMover.cc | |
| StructAvrgMover.hh | |
| util.cc | |
| util.hh | |
| WorkUnit_Aggressive.cc | |
| WorkUnit_Aggressive.hh | |
| WorkUnit_Loop.cc | |
| WorkUnit_Loop.hh | |
| WorkUnit_Relax.cc | |
| WorkUnit_Relax.hh | |
| WorkUnit_Sampler.cc | |
| WorkUnit_Sampler.hh | |
| ► multistage_rosetta_scripts | |
| ► cluster | |
| ► metrics | |
| JumpMetric.cc | |
| JumpMetric.fwd.hh | |
| JumpMetric.hh | Stores the 6-dimensions of a given jump |
| JumpMetricCreator.hh | |
| SequenceMetric.cc | |
| SequenceMetric.fwd.hh | |
| SequenceMetric.hh | Stores the amino acid sequence of the pose or subset of the pose. Distance is the number of mutations |
| SequenceMetricCreator.hh | |
| ClusterMetric.cc | Auto-generated serialization template functions |
| ClusterMetric.fwd.hh | |
| ClusterMetric.hh | |
| ClusterMetricCreator.hh | |
| ClusterMetricFactory.cc | Class for instantiating arbitrary Cluster Metrics from a string |
| ClusterMetricFactory.hh | Class for instantiating arbitrary Cluster Metrics from a string |
| ClusterMetricRegistrator.hh | Declaration of the template class for registrating ClusterMetricCreators with the ClusterMetricFactory |
| KMedoids.cc | |
| KMedoids.hh | Clustering algorithm used in multistage_rosetta_scripts |
| KMedoidsOnTheFly.cc | |
| KMedoidsOnTheFly.hh | Clustering algorithm used in multistage_rosetta_scripts |
| util.cc | |
| util.hh | |
| MRSJob.cc | |
| MRSJob.fwd.hh | |
| MRSJob.hh | JD3 job class to be used by Multistage Rosetta Scripts (MRS) |
| MRSJobQueen.cc | Queen for JD3 multistep protocol |
| MRSJobQueen.fwd.hh | |
| MRSJobQueen.hh | Derived Job Queen for Multistage Rosetta Scripts |
| MRSJobQueenChecker.cc | |
| MRSJobQueenChecker.fwd.hh | |
| MRSJobQueenChecker.hh | This class is derived from the MRSJobQueen and is intended to be a "dry run" equivalent - used to check conditions of the run without doing heavy computation |
| MRSJobSummary.cc | The implementation for class protocols::multistage_rosetta_scripts::MRSJobSummary's methods |
| MRSJobSummary.fwd.hh | The declaration for class protocols::multistage_rosetta_scripts::MRSJobSummary |
| MRSJobSummary.hh | The definition for class protocols::multistage_rosetta_scripts::MRSJobSummary |
| TagManager.cc | |
| TagManager.fwd.hh | |
| TagManager.hh | This class was designed to help the MRSJobQueen handle tags for many input jobs |
| ► multistate_design | |
| MetricCalculatorFitnessFunction.cc | |
| MetricCalculatorFitnessFunction.fwd.hh | |
| MetricCalculatorFitnessFunction.hh | |
| MultiStateAggregateFunction.cc | |
| MultiStateAggregateFunction.fwd.hh | |
| MultiStateAggregateFunction.hh | |
| MultiStateEntity.cc | |
| MultiStateEntity.fwd.hh | |
| MultiStateEntity.hh | |
| MultiStateFitnessFunction.cc | |
| MultiStateFitnessFunction.fwd.hh | |
| MultiStateFitnessFunction.hh | |
| MultiStatePacker.cc | |
| MultiStatePacker.fwd.hh | |
| MultiStatePacker.hh | |
| PackingState.cc | |
| PackingState.fwd.hh | |
| PackingState.hh | For multistate design that is based on (re)use of packer information (RotamerSets and InteractionGraph) |
| PartitionAggregateFunction.cc | |
| PartitionAggregateFunction.fwd.hh | |
| PartitionAggregateFunction.hh | |
| SingleState.cc | |
| SingleState.fwd.hh | |
| SingleState.hh | |
| SingleStateEntityData.cc | |
| SingleStateEntityData.fwd.hh | |
| SingleStateEntityData.hh | |
| SingleStateFitnessFunction.cc | |
| SingleStateFitnessFunction.fwd.hh | |
| SingleStateFitnessFunction.hh | |
| util.cc | Collection of useful utilities for setting up and using a GeneticAlgorithm with multistate design |
| util.hh | |
| ► ncbb | |
| ► a3b_hbs | |
| A3BHbsMover.cc | A3BHbsMover methods implemented |
| A3BHbsMover.fwd.hh | HbsMover forward declarations header |
| A3BHbsMover.hh | |
| A3BHbsPatcher.cc | |
| A3BHbsPatcher.fwd.hh | A3BHbsPatcher forward declarations header |
| A3BHbsPatcher.hh | |
| A3BHbsRandomSmallMover.cc | A3BHbsRandomSmallMover methods implemented |
| A3BHbsRandomSmallMover.fwd.hh | A3BHbsRandomSmallMover forward declarations header |
| A3BHbsRandomSmallMover.hh | |
| ► hbs | |
| HbsPatcher.cc | HbsPatcher methods implemented |
| HbsPatcher.fwd.hh | HbsPatcher forward declarations header |
| HbsPatcher.hh | |
| ► oop | |
| OopCreatorMover.cc | |
| OopCreatorMover.fwd.hh | |
| OopCreatorMover.hh | |
| OopCreatorMoverCreator.fwd.hh | |
| OopCreatorMoverCreator.hh | |
| OopDockDesignProtocol.cc | |
| OopDockDesignProtocol.fwd.hh | |
| OopDockDesignProtocol.hh | |
| OopDockDesignProtocolCreator.fwd.hh | |
| OopDockDesignProtocolCreator.hh | |
| OopMover.cc | OopMover methods implemented |
| OopMover.fwd.hh | OopMover forward declarations header |
| OopMover.hh | |
| OopPatcher.cc | OopPatcher methods implemented |
| OopPatcher.fwd.hh | OopPatcher forward declarations header |
| OopPatcher.hh | |
| OopPuckMover.cc | OopPuckMover methods implemented |
| OopPuckMover.fwd.hh | OopPuckMover forward declarations header |
| OopPuckMover.hh | |
| OopRandomPuckMover.cc | OopRandomPuckMover methods implemented |
| OopRandomPuckMover.fwd.hh | OopRandomPuckMover forward declarations header |
| OopRandomPuckMover.hh | |
| OopRandomSmallMover.cc | OopRandomSmallMover methods implemented |
| OopRandomSmallMover.fwd.hh | OopRandomSmallMover forward declarations header |
| OopRandomSmallMover.hh | |
| ► triazolamer | |
| TriazolamerMover.cc | TriazolamerMover methods implemented |
| TriazolamerMover.fwd.hh | TriazolamerMover forward declarations header |
| TriazolamerMover.hh | |
| TriazolamerRandomSmallMover.cc | TriazolamerRandomSmallMover methods implemented |
| TriazolamerRandomSmallMover.fwd.hh | TriazolamerRandomSmallMover forward declarations header |
| TriazolamerRandomSmallMover.hh | |
| NcbbDockDesignProtocol.cc | |
| NcbbDockDesignProtocol.fwd.hh | |
| NcbbDockDesignProtocol.hh | |
| NcbbDockDesignProtocolCreator.fwd.hh | |
| NcbbDockDesignProtocolCreator.hh | |
| PeptideStapleMover.cc | Peptide Staples are covalent links between i/i+[4,7] residues in a helix. Applying a PeptideStapleMover creates one of these links |
| PeptideStapleMover.fwd.hh | |
| PeptideStapleMover.hh | Definition of classes for placing peptide staples in the pose |
| ResidueReplacementRebuildMover.cc | A simple method to mutate a pose fairly destructively, and barely recover |
| ResidueReplacementRebuildMover.fwd.hh | A simple method to mutate a pose fairly destructively, and barely recover |
| ResidueReplacementRebuildMover.hh | A simple method to mutate a pose fairly destructively, and barely recover |
| ResidueReplacementRebuildMoverCreator.hh | A simple method to mutate a pose fairly destructively, and barely recover |
| SecStructFinder.cc | |
| SecStructFinder.fwd.hh | |
| SecStructFinder.hh | |
| SecStructFinderCreator.fwd.hh | |
| SecStructFinderCreator.hh | |
| SecStructMinimizeMover.cc | |
| SecStructMinimizeMover.fwd.hh | |
| SecStructMinimizeMover.hh | |
| SecStructMinimizeMoverCreator.fwd.hh | |
| SecStructMinimizeMoverCreator.hh | |
| SecStructMinimizeMultiFunc.cc | |
| SecStructMinimizeMultiFunc.hh | |
| util.cc | |
| util.hh | |
| ► neighbor | |
| Neighborhood.cc | |
| Neighborhood.hh | |
| ► network | |
| cloud.cc | |
| cloud.hh | : RosettaCloud integration |
| hal.cc | : HAL implementaion |
| hal.hh | : HAL implementaion |
| hal.util.hh | : HAL util implementaion |
| signals.hh | : Signal description for network layer |
| ui_mover.cc | : UIMover, apply to send in-progress results to UI |
| ui_mover.fwd.hh | : UIMover, apply to send in-progress results to UI |
| ui_mover.hh | : UIMover, apply to send in-progress results to UI |
| util.cc | : various supplemental declarations for network layer |
| util.hh | : various supplemental declarations for network layer |
| ► nmr | |
| ► pcs | |
| PCSEnergy.cc | Implementation of class PCSEnergy |
| PCSEnergy.fwd.hh | Forward declaration for PCSEnergy.hh |
| PCSEnergy.hh | Class that calculates energy from NMR pseudocontact shift data |
| PCSEnergyCreator.hh | Declaration for the class that connects PCSEnergy with the ScoringManager |
| PCSLigandTransformMover.cc | Implementation of PCSLigandTransformMover |
| PCSLigandTransformMover.fwd.hh | Forward declaration for PCSLigandTransformMover |
| PCSLigandTransformMover.hh | Finds a ligand position and orientation that minimizes experimental PCS data through a grid search. The pose found by PCSLigandTransformMover can be used as starting position for subsequent ligand docking |
| PCSLigandTransformMoverCreator.hh | This class will create instances of PCSLigandTransformMover for the MoverFactory |
| PCSTensorOptimizer.cc | Implementation of class PCSTensorOptimizer |
| PCSTensorOptimizer.fwd.hh | Forward declaration for PCSTensorOptimizer.hh |
| PCSTensorOptimizer.hh | Class that performs optimization of the lanthanide coordinates and other components of the PCSTensor in the laboratory frame. Used in combination with PCS grid search and SVD |
| ► pre | |
| PREEnergy.cc | Implementation of class PREEnergy |
| PREEnergy.fwd.hh | Forward declaration for PREEnergy.hh |
| PREEnergy.hh | Class that calculates energy from NMR paramagnetic relaxation enhancement data |
| PREEnergyCreator.hh | Declaration for the class that connects PREEnergy with the ScoringManager |
| PREMover.cc | Mover that converts NMR PRE rates into CB-CB atom pair distances and assigns them as atom pair constraints to the pose. In case of degenerate spins (e.g. degenerate protons or symmetric spins) an AmbiguousNMRDistanceConstraint is created. As constraints function a SplineFunc is fitted to a PRE distance histogram. By default, the histogram file is read from the spinlabel database and the generated spline potential converts the HN PRE distances into CB-CB distance constraints. Alternatively, the user can provide a different histogram file to generate CB-CB distance constraints from PRE rates collected for a different type of PRE nucleus e.g. 15N or 1HA |
| PREMover.fwd.hh | Forward declaration for PREMover |
| PREMover.hh | Mover that converts NMR PRE rates into CB-CB atom pair distances and assigns them as atom pair constraints to the pose. In case of degenerate spins (e.g. degenerate protons or symmetric spins) an AmbiguousNMRDistanceConstraint is created. As constraints function a SplineFunc is fitted to a PRE distance histogram. By default, the histogram file is read from the spinlabel database and the generated spline potential converts the HN PRE distances into CB-CB distance constraints. Alternatively, the user can provide a different histogram file to generate CB-CB distance constraints from PRE rates collected for a different type of PRE nucleus e.g. 15N or 1HA or a different spinlabel type |
| PREMoverCreator.hh | This class will create instances of PREMover for the MoverFactory |
| ► rdc | |
| RDCEnergy.cc | Implementation of class RDCEnergy |
| RDCEnergy.fwd.hh | Forward declaration for RDCEnergy.hh |
| RDCEnergy.hh | Class that calculates energy from NMR residual dipolar couplings |
| RDCEnergyCreator.hh | Declaration for the class that connects RDCEnergy with the ScoringManager |
| nmrspinlabel_util.cc | Utility functions for working with NMRSpinlabel class used both in PCSEnergy and PREEnergy |
| nmrspinlabel_util.hh | Utility functions for working with NMRSpinlabel class used both in PCSEnergy and PREEnergy |
| ParaNMRScoreMover.cc | Implementation file of ParaNMRScoreMover |
| ParaNMRScoreMover.fwd.hh | Forward declaration for ParaNMRScoreMover |
| ParaNMRScoreMover.hh | Evaluate pose with paramagnetic NMR data. Print table of experimental and predicted values to file. Write scores and q-factors to scorefile |
| ParaNMRScoreMoverCreator.hh | This class will create instances of ParaNMRScoreMover for the MoverFactory |
| ► noesy_assign | |
| CovalentCompliance.cc | |
| CovalentCompliance.hh | |
| CrossPeak.cc | |
| CrossPeak.fwd.hh | |
| CrossPeak.hh | |
| CrossPeakInfo.cc | |
| CrossPeakInfo.fwd.hh | |
| CrossPeakInfo.hh | |
| CrossPeakList.cc | |
| CrossPeakList.fwd.hh | |
| CrossPeakList.hh | |
| CrossPeakList.impl.hh | |
| DistanceScoreMover.cc | |
| DistanceScoreMover.fwd.hh | |
| DistanceScoreMover.hh | |
| Exceptions.hh | |
| FloatingResonance.cc | |
| FloatingResonance.fwd.hh | |
| FloatingResonance.hh | |
| FoldResonance.fwd.hh | |
| FoldResonance.hh | |
| FragsToAtomDist.cc | |
| FragsToAtomDist.fwd.hh | |
| FragsToAtomDist.hh | |
| LabelResonance.cc | |
| LabelResonance.fwd.hh | |
| LabelResonance.hh | |
| MethylNames.cc | |
| MethylNames.hh | |
| NoesyModule.cc | Main hook-up for the automatic NOESY assignment module |
| NoesyModule.fwd.hh | |
| NoesyModule.hh | Main hook-up for the automatic NOESY assignment module |
| NoesyModule.impl.hh | |
| PeakAssignment.cc | |
| PeakAssignment.fwd.hh | |
| PeakAssignment.hh | |
| PeakAssignmentOptionKeys.hh | |
| PeakAssignmentParameters.cc | |
| PeakAssignmentParameters.hh | |
| PeakAssignmentResidueMap.cc | |
| PeakAssignmentResidueMap.fwd.hh | |
| PeakAssignmentResidueMap.hh | |
| PeakCalibrator.cc | |
| PeakCalibrator.fwd.hh | |
| PeakCalibrator.hh | |
| PeakFileFormat.cc | |
| PeakFileFormat.fwd.hh | |
| PeakFileFormat.hh | |
| PeakFileFormat_Sparky.cc | |
| PeakFileFormat_Sparky.hh | |
| PeakFileFormat_xpk.cc | |
| PeakFileFormat_xpk.hh | |
| ProtonResonance.cc | |
| ProtonResonance.fwd.hh | |
| ProtonResonance.hh | |
| Resonance.cc | |
| Resonance.fwd.hh | |
| Resonance.hh | |
| ResonanceList.cc | |
| ResonanceList.fwd.hh | |
| ResonanceList.hh | Table with atomID - chemical shift mapping |
| StructureDependentPeakCalibrator.cc | |
| StructureDependentPeakCalibrator.hh | |
| StructureIndependentPeakCalibrator.cc | |
| StructureIndependentPeakCalibrator.hh | |
| util.cc | |
| util.hh | |
| ► nonlocal | |
| BiasedFragmentMover.cc | |
| BiasedFragmentMover.fwd.hh | |
| BiasedFragmentMover.hh | |
| Chunk.cc | |
| Chunk.fwd.hh | |
| Chunk.hh | |
| HelixRotate.cc | |
| HelixRotate.fwd.hh | |
| HelixRotate.hh | |
| Policy.fwd.hh | |
| Policy.hh | |
| PolicyFactory.cc | |
| PolicyFactory.hh | |
| Region.cc | |
| Region.fwd.hh | |
| Region.hh | |
| SheetTranslate.cc | |
| SheetTranslate.fwd.hh | |
| SheetTranslate.hh | |
| SimpleTreeBuilder.cc | |
| SimpleTreeBuilder.fwd.hh | |
| SimpleTreeBuilder.hh | |
| SingleFragmentMover.cc | |
| SingleFragmentMover.fwd.hh | |
| SingleFragmentMover.hh | |
| SingleFragmentMoverCreator.cc | |
| SingleFragmentMoverCreator.hh | |
| SmoothPolicy.cc | |
| SmoothPolicy.hh | |
| StarTreeBuilder.cc | |
| StarTreeBuilder.fwd.hh | |
| StarTreeBuilder.hh | |
| TreeBuilder.fwd.hh | |
| TreeBuilder.hh | |
| TreeBuilderFactory.cc | |
| TreeBuilderFactory.hh | |
| UniformPolicy.cc | |
| UniformPolicy.hh | |
| util.cc | |
| util.hh | |
| ► normalmode | |
| NormalMode.cc | |
| NormalMode.hh | Initialization for NormalMode |
| NormalModeMinimizer.cc | High-level atom tree minimizer class |
| NormalModeMinimizer.fwd.hh | Protocols::normalmode::NormalModeMinimizer forward declarations |
| NormalModeMinimizer.hh | |
| NormalModeMinimizerCreator.hh | |
| NormalModeMultiFunc.cc | |
| NormalModeMultiFunc.hh | |
| NormalModeRelaxMover.cc | Normal Mode Perturbation + Relax |
| NormalModeRelaxMover.fwd.hh | Initialization for NormalMode |
| NormalModeRelaxMover.hh | Initialization for NormalMode |
| NormalModeRelaxMoverCreator.hh | |
| ► optimize_weights | |
| DDGBindOptEData.cc | |
| DDGBindOptEData.fwd.hh | Forward header for a optE position data class that holds interface ddG information |
| DDGBindOptEData.hh | Header file for OptEPositionData class that hold interface ddG information |
| DGBindOptEData.cc | Implementation of the OptEPositionData class that handles interface ddG optimization |
| DGBindOptEData.fwd.hh | |
| DGBindOptEData.hh | |
| IterativeOptEDriver.cc | Implementation of iterative weight fitting protocol |
| IterativeOptEDriver.fwd.hh | Forward declaration of iterative weight fitting protocol |
| IterativeOptEDriver.hh | A class for optimizing weights in an iterative weight fitting, sequence recovery test protocol |
| NestedEnergyTermOptEData.cc | |
| NestedEnergyTermOptEData.fwd.hh | Forward header for some special optE position data classes |
| NestedEnergyTermOptEData.hh | Classes to store by-energy-term rotamer data for optE, when using the unfolded state energy term |
| OptEData.cc | |
| OptEData.fwd.hh | Forward declarations for OptE data structures |
| OptEData.hh | |
| OptEMultifunc.cc | |
| OptEMultifunc.fwd.hh | |
| OptEMultifunc.hh | |
| PNatLigPoseOptEData.cc | |
| PNatLigPoseOptEData.fwd.hh | |
| PNatLigPoseOptEData.hh | |
| ► pack_daemon | |
| DynamicAggregateFunction.cc | |
| DynamicAggregateFunction.fwd.hh | |
| DynamicAggregateFunction.hh | Declaration for a file-driven definition for the active states in a multistate design and the set of mathematical expressions that together define the fitness function for the sequence being designed |
| EntityCorrespondence.cc | Implementation for class EntityCorrespondence |
| EntityCorrespondence.fwd.hh | |
| EntityCorrespondence.hh | Forward declaration for class EntityCorrespondence |
| MultistateAggregateFunction.cc | Implementation for class MultistateAggregateFunction to work with the PackDeamon classes (not to be confused with J. Ashworth's MultiStateAggregateFunction class) |
| MultistateAggregateFunction.fwd.hh | Forward declaration of class MultistateAggregateFunction |
| MultistateAggregateFunction.hh | Declaration for class MultistateAggregateFunction to work with the PackDeamon classes (not to be confused with J. Ashworth's MultiStateAggregateFunction class) |
| MultistateFitnessFunction.cc | Implementation of the class MultistateFitnessFunction |
| MultistateFitnessFunction.fwd.hh | Forward declaration of class MultistateFitnessFunction |
| MultistateFitnessFunction.hh | Declaration for class MultistateFitnessFunction to work with the PackDeamon classes (not to be confused with J. Ashworth's MultiStateFitnessFunction class) |
| PackDaemon.cc | Implementation for class PackDaemon |
| PackDaemon.fwd.hh | |
| PackDaemon.hh | Declaration for class PackDaemon |
| util.cc | Utility functions for working with the multistate-design classes |
| util.hh | Declaration for utility functions for working with the multistate-design classes |
| ► pack_interface | |
| ProteinProteinInterfaceUpweighterTaskOperation.cc | Upweight the interface energies |
| ProteinProteinInterfaceUpweighterTaskOperation.fwd.hh | |
| ProteinProteinInterfaceUpweighterTaskOperation.hh | Upweight protein interface energies |
| ProteinProteinInterfaceUpweighterTaskOperationCreator.hh | |
| ► parser | |
| BluePrint.cc | |
| BluePrint.fwd.hh | |
| BluePrint.hh | |
| ConstraintGeneratorLoader.cc | |
| ConstraintGeneratorLoader.hh | Declartion of the XML parser's ConstraintGeneratorLoader class for adding named ConstraintGenerators to the basic::datacache::DataMap |
| ConstraintGeneratorLoaderCreator.hh | Creator classes for the default DataLoader classes, TaskOperationLoader and ScoreFunctionLoader |
| DatabaseSessionLoader.cc | |
| DatabaseSessionLoader.hh | Declartion of the XML parser's DatabaseSessionLoader class for adding named DatabaseSessions to the basic::datacache::DataMap |
| DatabaseSessionLoaderCreator.hh | |
| DataLoader.cc | Implementation of the XML parser's DataLoader base class (ctor & dstor) |
| DataLoader.fwd.hh | Forward declartion of the XML parser's DataLoader class |
| DataLoader.hh | Declartion of the XML parser's DataLoader class |
| DataLoaderCreator.cc | Creator class for the parser's DataLoader classes |
| DataLoaderCreator.hh | Creator class for the parser's DataLoader classes |
| DataLoaderFactory.cc | Implementation of the factory class for the parser's DataLoader classes |
| DataLoaderFactory.hh | Factory class for the parser's DataLoader classes |
| FragmentReader.cc | |
| FragmentReader.fwd.hh | |
| FragmentReader.hh | |
| FragSetLoader.cc | |
| FragSetLoader.hh | Declartion of the XML parser's FragSetLoader class for adding named FragSets to the basic::datacache::DataMap |
| JumpSelectorLoader.cc | |
| JumpSelectorLoader.hh | Declartion of the XML parser's JumpSelectorLoader class for adding named JumpSelectors to the basic::datacache::DataMap |
| JumpSelectorLoaderCreator.hh | |
| MonteCarloLoader.cc | |
| MonteCarloLoader.hh | Declartion of the XML parser's MonteCarloLoader class for adding named ScoreFunctions to the basic::datacache::DataMap |
| MoveMapFactoryLoader.cc | Implementation of the XML parser's DataLoader class for MoveMaps |
| MoveMapFactoryLoader.hh | Declartion of the XML parser's MoveMapFactoryLoader class |
| MoveMapFactoryLoaderCreator.hh | |
| PackerPaletteLoader.cc | XML parsing for PackerPalettes |
| PackerPaletteLoader.hh | Declartion of the XML parser's PackerPaletteLoader class for adding named PackerPalettes to the basic::datacache::DataMap |
| PackerPaletteLoaderCreator.hh | Creator classes for PackerPaletteLoader class |
| ResidueSelectorLoader.cc | |
| ResidueSelectorLoader.hh | Declartion of the XML parser's ResidueSelectorLoader class for adding named ResidueSelectors to the basic::datacache::DataMap |
| ResidueSelectorLoaderCreator.hh | |
| ResLvlTaskOperationLoader.cc | |
| ResLvlTaskOperationLoader.hh | Declartion of the XML parser's ResLvlTaskOperationLoader class |
| ScoreFunctionLoader.cc | |
| ScoreFunctionLoader.hh | Declartion of the XML parser's ScoreFunctionLoader class for adding named ScoreFunctions to the basic::datacache::DataMap |
| SimpleMetricLoader.cc | |
| SimpleMetricLoader.hh | Declartion of the XML parser's SimpleMetricLoader class for adding named SimpleMetrics to the basic::datacache::DataMap |
| SimpleMetricLoaderCreator.hh | |
| StandardLoaderCreators.hh | |
| TaskOperationLoader.cc | |
| TaskOperationLoader.hh | Declartion of the XML parser's TaskOperationLoader class |
| ► pb_potential | |
| SetupPoissonBoltzmannPotential.cc | |
| SetupPoissonBoltzmannPotential.fwd.hh | |
| SetupPoissonBoltzmannPotential.hh | |
| SetupPoissonBoltzmannPotentialCreator.hh | |
| ► pdbinfo_manipulations | |
| AlignPDBInfoToSequences.cc | Realign poses to sequences after losing pdb_info |
| AlignPDBInfoToSequences.fwd.hh | Realign poses to sequences after losing pdb_info |
| AlignPDBInfoToSequences.hh | Realign poses to sequences after losing pdb_info |
| AlignPDBInfoToSequencesCreator.hh | Realign poses to sequences after losing pdb_info |
| AlignPDBInfoToSequencesUtil.cc | Helper functions for AlignPDBInfoToSequences |
| AlignPDBInfoToSequencesUtil.hh | Helper functions for AlignPDBInfoToSequences |
| ► peptide_deriver | |
| PeptideDeriverBasicStreamOutputter.cc | Outputs a Peptiderive report to a stream in a basic, easily parsable format |
| PeptideDeriverBasicStreamOutputter.fwd.hh | Outputs a Peptiderive report to a stream in a basic, easily parsable format |
| PeptideDeriverBasicStreamOutputter.hh | Outputs a Peptiderive report to a stream in a basic, easily parsable format |
| PeptideDeriverFilter.cc | A filter that, for each dimer in a pose, outputs the peptide which contributes most to the interface |
| PeptideDeriverFilter.fwd.hh | A filter that, for each dimer in a pose, outputs the peptide which contributes most to the interface |
| PeptideDeriverFilter.hh | A filter that, for each dimer in a pose, outputs the peptide which contributes most to the interface |
| PeptideDeriverFilterCreator.cc | Creator class for PeptideDeriverFilterCreator |
| PeptideDeriverFilterCreator.fwd.hh | Creator class for PeptideDeriverFilterCreator |
| PeptideDeriverFilterCreator.hh | Creator class for PeptideDeriverFilterCreator |
| PeptideDeriverMarkdownStreamOutputter.cc | Outputs a Markdown formatted Peptiderive report to a stream |
| PeptideDeriverMarkdownStreamOutputter.fwd.hh | Outputs a Markdown formatted Peptiderive report to a stream |
| PeptideDeriverMarkdownStreamOutputter.hh | Outputs a Markdown formatted Peptiderive report to a stream |
| PeptideDeriverOutputter.cc | Abstract base class for handling calculation outputs from PeptideDeriverFilter |
| PeptideDeriverOutputter.fwd.hh | Abstract base class for handling calculation outputs from PeptideDeriverFilter |
| PeptideDeriverOutputter.hh | Abstract base class for handling calculation outputs from PeptideDeriverFilter |
| PeptideDeriverOutputterContainer.cc | Container class which holds a list of PeptideDeriverOutputter instances and delegates calls to those |
| PeptideDeriverOutputterContainer.fwd.hh | Container class which holds a list of PeptideDeriverOutputter instances and delegates calls to those |
| PeptideDeriverOutputterContainer.hh | Container class which holds a list of PeptideDeriverOutputter instances and delegates calls to those |
| PeptideDeriverPoseOutputter.cc | Outputs poses at different points of the Peptiderive protocol, according to the given set of options |
| PeptideDeriverPoseOutputter.fwd.hh | Outputs poses at different points of the Peptiderive protocol, according to the given set of options |
| PeptideDeriverPoseOutputter.hh | Outputs poses at different points of the Peptiderive protocol, according to the given set of options |
| ► pmut_scan | |
| AlterSpecDisruptionDriver.cc | A protocol that tries to find interface-disrupting mutations as phase 1 of an altered-specificity protocol |
| AlterSpecDisruptionDriver.hh | A protocol that tries to find interface-disrupting mutations as phase 1 of an altered-specificity protocol |
| Mutant.cc | A helper class for the point mut scan protocol which holds data about mutants |
| Mutant.fwd.hh | Forward declaration for Mutant.hh |
| Mutant.hh | A helper class for the point mut scan protocol |
| PointMutScanDriver.cc | A protocol that tries to find stability enhancing mutations |
| PointMutScanDriver.hh | A protocol that tries to find stability enhancing mutations |
| ► pockets | |
| DarcParticleSwarmMinimizer.cc | |
| DarcParticleSwarmMinimizer.fwd.hh | |
| DarcParticleSwarmMinimizer.hh | |
| Fingerprint.cc | Protocols::pockets::Fingerprint functions |
| Fingerprint.fwd.hh | Protocols::pockets::Fingerprint forward declarations header |
| Fingerprint.hh | |
| FingerprintMultifunc.cc | |
| FingerprintMultifunc.fwd.hh | Protocols::pockets::FingerprintMultifunc forward declarations |
| FingerprintMultifunc.hh | Fingerprint multifunction class |
| GenPharmacophore.cc | |
| GenPharmacophore.fwd.hh | |
| GenPharmacophore.hh | |
| PocketConstraint.cc | |
| PocketConstraint.fwd.hh | Core::grid::Pockets::PocketConstraint forward declarations header |
| PocketConstraint.hh | |
| PocketConstraintCreator.hh | |
| PocketExemplarMultifunc.cc | |
| PocketExemplarMultifunc.fwd.hh | Protocols::pockets::PocketExemplarMultifunc forward declarations |
| PocketExemplarMultifunc.hh | Pocket multifunction class |
| PocketGrid.cc | Protocols::pockets::PocketGrid functions |
| PocketGrid.fwd.hh | Protocols::pockets::PocketGrid forward declarations header |
| PocketGrid.hh | Protocols::pockets::PocketGrid header |
| util.cc | Protocols::pockets::util functions |
| ► pose_creation | |
| ExtendedPoseMover.cc | |
| ExtendedPoseMover.fwd.hh | |
| ExtendedPoseMover.hh | |
| ExtendedPoseMoverCreator.cc | |
| ExtendedPoseMoverCreator.hh | |
| HelixFromSequence.cc | Generates a (transmembrane) helix from a fasta file containing the sequence |
| HelixFromSequence.fwd.hh | Generates a (transmembrane) helix from a fasta file containing the sequence |
| HelixFromSequence.hh | Generates a (transmembrane) helix from a fasta file containing the sequence |
| HelixFromSequenceCreator.hh | Generates a (transmembrane) helix from a fasta file containing the sequence |
| LoadPDBMover.cc | Simple mover that loads a pdb from file and replaces the current pdb with it. Useful for checkpointing |
| LoadPDBMover.fwd.hh | Switch the chain order |
| LoadPDBMover.hh | Switch the chain order |
| LoadPDBMoverCreator.hh | |
| MakeJunctionsMover.cc | Reads in a file that contains a descriptions of the junctions. Then goes through that file making 1 junction at a time |
| MakeJunctionsMover.fwd.hh | |
| MakeJunctionsMover.hh | |
| MakeJunctionsMoverCreator.hh | |
| MakePolyXMover.cc | Convert pose to poly XXX: any amino acid, default poly Ala |
| MakePolyXMover.fwd.hh | Convert pose to poly XXX: any amino acid, default poly Ala |
| MakePolyXMover.hh | Header file of MakePolyXMover.cc |
| MakePolyXMoverCreator.hh | This class will create instances of protocols::moves::Mover MakePolyXMover for the protocols::moves::MoverFactory |
| MergePDBatOverlapMover.cc | This class combines two pdbs with a known overlap |
| MergePDBatOverlapMover.fwd.hh | |
| MergePDBatOverlapMover.hh | This class combines two pdbs with a known overlap |
| MergePDBatOverlapMoverCreator.hh | This class combines two pdbs with a known overlap |
| MergePDBMover.cc | This class will allign & combine parts of the pdb |
| MergePDBMover.fwd.hh | |
| MergePDBMover.hh | This class will allign & combine parts of the pdb |
| MergePDBMoverCreator.hh | This class will allign & combine parts of the pdb |
| PoseFromSequenceMover.cc | A class for generating a pose from a sequence/fasta |
| PoseFromSequenceMover.fwd.hh | A class for generating a pose from a sequence/fasta |
| PoseFromSequenceMover.hh | A class for generating a pose from a sequence/fasta |
| PoseFromSequenceMoverCreator.hh | A class for generating a pose from a sequence/fasta |
| RepeatPropagationMover.cc | Can repeat both a symmetric, non symmetric & broken pose |
| RepeatPropagationMover.fwd.hh | |
| RepeatPropagationMover.hh | |
| RepeatPropagationMoverCreator.hh | |
| SliceToMiniProteinMover.cc | |
| SliceToMiniProteinMover.fwd.hh | |
| SliceToMiniProteinMover.hh | This mover chops a big protein into miniProteins |
| SliceToMiniProteinMoverCreator.hh | |
| ► pose_length_moves | |
| AnalyzeLoopModeling.cc | |
| AnalyzeLoopModeling.fwd.hh | Very simple mover to extend a pose (Could be done inside remodel) |
| AnalyzeLoopModeling.hh | |
| AnalyzeLoopModelingCreator.hh | |
| ConnectChainsMover.cc | |
| ConnectChainsMover.fwd.hh | Connects chains with native like loops |
| ConnectChainsMover.hh | Connects chains and returns the connection with lowest rmsd |
| ConnectChainsMoverCreator.hh | |
| FixAllLoopsMover.cc | |
| FixAllLoopsMover.fwd.hh | Very simple mover to extend a pose (Could be done inside remodel) |
| FixAllLoopsMover.hh | |
| FixAllLoopsMoverCreator.hh | |
| InsertResMover.cc | |
| InsertResMover.fwd.hh | Very simple mover to extend a pose (Could be done inside remodel) |
| InsertResMover.hh | Inserts ideal residues into pose. Useful for extending helices |
| InsertResMoverCreator.hh | |
| NearNativeLoopCloser.cc | |
| NearNativeLoopCloser.fwd.hh | Uses KIC/CCD and a fast Look back to close loops near native |
| NearNativeLoopCloser.hh | |
| NearNativeLoopCloserCreator.hh | |
| ► pose_metric_calculators | |
| CatPiCalculator.cc | |
| CatPiCalculator.hh | |
| ChargeCalculator.cc | |
| ChargeCalculator.hh | |
| ClashCountCalculator.cc | |
| ClashCountCalculator.hh | |
| DecomposeAndReweightEnergiesCalculator.cc | |
| DecomposeAndReweightEnergiesCalculator.hh | |
| ExplicitWaterUnsatisfiedPolarsCalculator.cc | |
| FragQualCalculator.cc | |
| FragQualCalculator.hh | |
| HPatchCalculator.cc | |
| HPatchCalculator.hh | |
| InterGroupNeighborsCalculator.cc | |
| InterGroupNeighborsCalculator.fwd.hh | |
| InterGroupNeighborsCalculator.hh | |
| MetricValueGetter.cc | |
| MetricValueGetter.fwd.hh | |
| MetricValueGetter.hh | |
| NeighborhoodByDistanceCalculator.cc | |
| NeighborhoodByDistanceCalculator.fwd.hh | |
| NeighborhoodByDistanceCalculator.hh | |
| NeighborsByDistanceCalculator.cc | |
| NeighborsByDistanceCalculator.fwd.hh | |
| NeighborsByDistanceCalculator.hh | |
| NonlocalContactsCalculator.cc | |
| NonlocalContactsCalculator.hh | |
| PackstatCalculator.cc | |
| PackstatCalculator.hh | |
| PiPiCalculator.cc | |
| PiPiCalculator.hh | |
| ResidueDecompositionByChainCalculator.cc | |
| ResidueDecompositionByChainCalculator.hh | |
| ResidueDecompositionCalculator.cc | |
| ResidueDecompositionCalculator.hh | |
| RotamerBoltzCalculator.cc | |
| RotamerBoltzCalculator.fwd.hh | |
| RotamerBoltzCalculator.hh | |
| RotamerRecovery.cc | |
| RotamerRecovery.hh | Compare the rotamer recovery between a native protein and a list of other proteins |
| SaltBridgeCalculator.cc | |
| SaltBridgeCalculator.hh | |
| SemiExplicitWaterUnsatisfiedPolarsCalculator.cc | |
| SemiExplicitWaterUnsatisfiedPolarsCalculator.hh | |
| SequenceComparison.cc | |
| SequenceComparison.hh | |
| SHOBuriedUnsatisfiedPolarsCalculator.cc | |
| SHOBuriedUnsatisfiedPolarsCalculator.fwd.hh | |
| SHOBuriedUnsatisfiedPolarsCalculator.hh | |
| SurfaceCalculator.cc | |
| SurfaceCalculator.hh | |
| ► pose_reporters | |
| BasicPosePropertyReporterCreators.hh | Collection of PosePropertySelector creators for basic pose reporters |
| BasicPosePropertyReporters.cc | |
| BasicPosePropertyReporters.hh | Collection of simple pose property reporters |
| ► pose_selectors | |
| BasicPoseSelectorCreators.hh | Collection of PoseSelector creators for basic selectors |
| BasicPoseSelectors.cc | |
| BasicPoseSelectors.hh | Collection of simple pose selectors |
| ClusterPoseSelector.cc | |
| ClusterPoseSelector.hh | Cluster pose selector using protocols::cluster |
| ClusterPoseSelectorCreator.hh | Creator for ClusterPoseSelector |
| ► protein_interface_design | |
| ► filters | |
| AtomicContactCountFilter.cc | |
| AtomicContactCountFilter.fwd.hh | Forward declaration for AtomicContactCountFilter |
| AtomicContactCountFilter.hh | |
| AtomicContactCountFilterCreator.hh | FilterCreators for the AtomicContactCountFilter |
| AverageDegreeFilter.cc | |
| AverageDegreeFilter.fwd.hh | Forward declaration for AverageDegreeFilter |
| AverageDegreeFilter.hh | |
| AverageDegreeFilterCreator.hh | FilterCreators for the AverageDegreeFilter |
| BindingStrainFilter.cc | |
| BindingStrainFilter.fwd.hh | Forward declaration for BindingStrainFilter |
| BindingStrainFilter.hh | |
| BindingStrainFilterCreator.hh | FilterCreators for the BindingStrainFilter |
| BoltzmannFilter.cc | |
| BoltzmannFilter.fwd.hh | Forward declaration for BoltzmannFilter |
| BoltzmannFilter.hh | |
| BoltzmannFilterCreator.hh | FilterCreators for the BoltzmannFilter |
| ClashWithTargetFilter.cc | ClashWithTarget filtering |
| ClashWithTargetFilter.hh | Clash check with Target using motifgrafting |
| ClashWithTargetFilterCreator.hh | FilterCreators for the ClashWithTargetFilter |
| DesignableResiduesFilter.cc | |
| DesignableResiduesFilter.fwd.hh | Forward declaration for DesignableResiduesFilter |
| DesignableResiduesFilter.hh | |
| DesignableResiduesFilterCreator.hh | FilterCreators for the DesignableResiduesFilter |
| DisulfideFilter.cc | |
| DisulfideFilter.hh | |
| DisulfideFilterCreator.hh | FilterCreators for the DisulfideFilter |
| FilterScan.cc | |
| FilterScan.fwd.hh | Forward declaration for FilterScanFilter |
| FilterScan.hh | |
| FilterScanCreator.hh | FilterCreators for the FilterScanFilter |
| FNatFilter.cc | Filtering on fraction of native contacts |
| FNatFilter.hh | Calculate L_RMSD using the method from protocols::docking::metrics |
| FNatFilterCreator.hh | FilterCreators for the FNatFilter |
| HbondsToAtomFilter.cc | |
| HbondsToAtomFilter.fwd.hh | Forward declaration for HbondsToAtomFilter |
| HbondsToAtomFilter.hh | Definition of filter classes for iterations of docking/design |
| HbondsToAtomFilterCreator.hh | FilterCreators for the filters defined in HbondsToAtomFilterCreator.hh |
| HbondsToResidueFilter.cc | |
| HbondsToResidueFilter.fwd.hh | Forward declaration for HbondsToResidueFilter |
| HbondsToResidueFilter.hh | Definition of filter classes for iterations of docking/design |
| HbondsToResidueFilterCreator.hh | FilterCreators for the filters defined in HbondsToResidueFilterCreator.hh |
| InterfaceHolesFilter.cc | Find packing defects at an interface using packstat score terms |
| InterfaceHolesFilter.hh | Find packing defects at an interface using packstat score terms |
| InterfaceHolesFilterCreator.hh | FilterCreators for the InterfaceHolesFilter |
| IRmsdFilter.cc | |
| IRmsdFilter.hh | Calculate I_RMSD using the method from protocols::docking::metrics |
| IRmsdFilterCreator.hh | FilterCreators for the IRmsdFilter |
| LRmsdFilter.cc | |
| LRmsdFilter.hh | Calculate L_RMSD using the method from protocols::docking::metrics |
| LRmsdFilterCreator.hh | FilterCreators for the LRmsdFilter |
| RelativeSegmentFilter.cc | |
| RelativeSegmentFilter.fwd.hh | Forward declaration for RelativeSegmentFilter |
| RelativeSegmentFilter.hh | |
| RelativeSegmentFilterCreator.hh | FilterCreators for the filters defined in RelativeSegmentFilterCreator.hh |
| RmsdFilter.cc | Rmsd filtering |
| RmsdFilter.hh | Find packing defects at an interface using packstat score terms |
| RmsdFilterCreator.hh | FilterCreators for the RmsdFilter |
| RmsdSimpleFilter.cc | Rmsd filtering |
| RmsdSimpleFilter.hh | Simply calculate RMSD, doesn't assume that poses are statick unmutable objects |
| RmsdSimpleFilterCreator.hh | FilterCreators for the RmsdSimpleFilter |
| SequenceRecoveryFilter.cc | |
| SequenceRecoveryFilter.fwd.hh | Forward declaration for SequenceRecoveryFilter |
| SequenceRecoveryFilter.hh | |
| SequenceRecoveryFilterCreator.hh | FilterCreators for the SequenceRecoveryFilter |
| SpecificResiduesNearInterfaceFilter.cc | |
| SpecificResiduesNearInterfaceFilter.fwd.hh | Forward header for SpecificResiduesNearInterface |
| SpecificResiduesNearInterfaceFilter.hh | |
| SpecificResiduesNearInterfaceFilterCreator.hh | Pass if a specific set of residues are near the interface |
| SSamountFilter.cc | SS fraction filtering |
| SSamountFilter.hh | Calculate SS fraction, doesn't assume that poses are statick unmutable objects |
| SSamountFilterCreator.hh | FilterCreators for the SSamountFilter |
| StubScoreFilter.cc | |
| StubScoreFilter.fwd.hh | Forward declaration for StubScoreFilter |
| StubScoreFilter.hh | |
| StubScoreFilterCreator.hh | FilterCreators for the StubScoreFilter |
| StubScoreLoopsFilter.cc | |
| StubScoreLoopsFilter.fwd.hh | Forward declaration for StubScoreLoopsFilter |
| StubScoreLoopsFilter.hh | |
| StubScoreLoopsFilterCreator.hh | FilterCreators for the StubScoreLoopsFilter |
| TorsionFilter.cc | |
| TorsionFilter.fwd.hh | |
| TorsionFilter.hh | |
| TorsionFilterCreator.hh | |
| ► movers | |
| AddChainBreak.cc | |
| AddChainBreak.hh | |
| AddChainBreakCreator.hh | Declaration of the MoverCreator class for the AddChainBreak |
| AddSidechainConstraintsToHotspots.cc | |
| AddSidechainConstraintsToHotspots.hh | |
| AddSidechainConstraintsToHotspotsCreator.hh | Declaration of the MoverCreator class for the AddSidechainConstraintsToHotspots |
| BackrubDDMover.cc | |
| BackrubDDMover.hh | Derived class from mover for dock design with backrub moves |
| BackrubDDMoverCreator.hh | Declaration of the MoverCreator class for the BackrubDDMover |
| BestHotspotCstMover.cc | |
| BestHotspotCstMover.hh | |
| BestHotspotCstMoverCreator.hh | Declaration of the MoverCreator class for the BestHotspotCstMover |
| BuildAlaPose.cc | |
| BuildAlaPose.fwd.hh | |
| BuildAlaPose.hh | |
| BuildAlaPoseCreator.hh | Declaration of the MoverCreator class for the BuildAlaPose |
| DesignMinimizeHbonds.cc | |
| DesignMinimizeHbonds.hh | |
| DesignMinimizeHbondsCreator.hh | Declaration of the MoverCreator class for the DesignMinimizeHbonds |
| DisulfideMover.cc | |
| DisulfideMover.hh | |
| DisulfideMoverCreator.hh | Declaration of the MoverCreator class for the DisulfideMover |
| DockAndRetrieveSidechains.cc | |
| DockAndRetrieveSidechains.hh | |
| DockAndRetrieveSidechainsCreator.hh | Declaration of the MoverCreator class for the DockAndRetrieveSidechains |
| DockWithHotspotMover.cc | |
| DockWithHotspotMover.fwd.hh | |
| DockWithHotspotMover.hh | |
| DockWithHotspotMoverCreator.hh | This class will create instances of protocols::moves::Mover DockWithHotspotMover for the protocols::moves::MoverFactory |
| FavorNativeResiduePreCycle.cc | |
| FavorNativeResiduePreCycle.hh | |
| FavorNativeResiduePreCycleCreator.hh | Declaration of the MoverCreator class for the FavorNativeResiduePreCycle |
| FavorNonNativeResiduePreCycle.cc | |
| FavorNonNativeResiduePreCycle.hh | |
| FavorNonNativeResiduePreCycleCreator.hh | |
| HotspotDisjointedFoldTreeMover.cc | |
| HotspotDisjointedFoldTreeMover.hh | |
| HotspotDisjointedFoldTreeMoverCreator.hh | Declaration of the MoverCreator class for the HotspotDisjointedFoldTreeMover |
| HotspotHasherMover.cc | |
| HotspotHasherMover.hh | |
| HotspotHasherMoverCreator.hh | Declaration of the MoverCreator class for the HotspotHasherMover |
| InterfaceRecapitulationMover.cc | |
| InterfaceRecapitulationMover.hh | |
| InterfaceRecapitulationMoverCreator.hh | Declaration of the MoverCreator class for the InterfaceRecapitulationMover |
| LoopFinder.cc | |
| LoopFinder.hh | Header for class to find loops (parseable options to control how loops are found) |
| LoopFinderCreator.hh | Declaration of the MoverCreator class for the LoopFinder |
| LoopLengthChange.cc | |
| LoopLengthChange.fwd.hh | |
| LoopLengthChange.hh | |
| LoopLengthChangeCreator.hh | Declaration of the MoverCreator class for the LoopLengthChange |
| LoopMoverFromCommandLine.cc | |
| LoopMoverFromCommandLine.fwd.hh | |
| LoopMoverFromCommandLine.hh | |
| LoopMoverFromCommandLineCreator.hh | |
| LoopOver.cc | |
| LoopOver.hh | |
| LoopOverCreator.hh | Declaration of the MoverCreator class for the LoopOver |
| LoopRemodel.cc | Parseable class to run loop perturbation or refinement between a given loop between start/end (inclusive). Intended to sample loop conformations at an interface |
| LoopRemodel.fwd.hh | |
| LoopRemodel.hh | Header for parseable class to run loop perturbation or refinement between a given loop between start/end (inclusive) |
| LoopRemodelCreator.hh | Declaration of the MoverCreator class for the LoopRemodel |
| MapHotspot.cc | |
| MapHotspot.hh | |
| MapHotspotCreator.hh | Declaration of the MoverCreator class for the MapHotspot |
| PatchdockTransform.cc | |
| PatchdockTransform.fwd.hh | |
| PatchdockTransform.hh | |
| PatchdockTransformCreator.hh | Declaration of the MoverCreator class for the PatchdockTransform |
| PeptideStapleDesignMover.cc | |
| PeptideStapleDesignMover.hh | |
| PeptideStapleDesignMoverCreator.hh | Declaration of the MoverCreator class for the PeptideStapleDesignMover |
| PlacementAuctionMover.cc | |
| PlacementAuctionMover.fwd.hh | Forward declations for PlacementAuctionMover |
| PlacementAuctionMover.hh | Definition of a class for making the placement auction used by PlaceSimultaneouslyMover |
| PlacementAuctionMoverCreator.hh | Declaration of the MoverCreator class for the PlacementAuctionMover |
| PlacementMinimizationMover.cc | |
| PlacementMinimizationMover.fwd.hh | Forward declations for PlacementMinimizationMover |
| PlacementMinimizationMover.hh | Definition of a class for making the placement auction used by PlaceSimultaneouslyMover |
| PlacementMinimizationMoverCreator.hh | Declaration of the MoverCreator class for the PlacementMinimizationMover |
| PlaceOnLoop.cc | |
| PlaceOnLoop.fwd.hh | |
| PlaceOnLoop.hh | |
| PlaceOnLoopCreator.hh | Declaration of the MoverCreator class for the PlaceOnLoop |
| PlaceSimultaneouslyMover.cc | |
| PlaceSimultaneouslyMover.hh | |
| PlaceSimultaneouslyMoverCreator.hh | Declaration of the MoverCreator class for the PlaceSimultaneouslyMover |
| PlaceStubMover.cc | |
| PlaceStubMover.fwd.hh | Forward declarations for PlaceStubMover |
| PlaceStubMover.hh | Definition of classes for grafting hotspots into a pose |
| PlaceStubMoverCreator.hh | Declaration of the MoverCreator class for the PlaceStubMover |
| PlaceUtils.cc | Collection of utility functions for placement classes |
| PlaceUtils.hh | |
| PrepackMover.cc | |
| PrepackMover.hh | |
| PrepackMoverCreator.hh | Declaration of the MoverCreator class for the PrepackMover |
| ProteinInterfaceMultiStateDesignMover.cc | |
| ProteinInterfaceMultiStateDesignMover.fwd.hh | |
| ProteinInterfaceMultiStateDesignMover.hh | |
| ProteinInterfaceMultiStateDesignMoverCreator.hh | Declaration of the MoverCreator class for the ProteinInterfaceMultiStateDesignMover |
| RandomMutation.cc | |
| RandomMutation.fwd.hh | |
| RandomMutation.hh | |
| RandomMutationCreator.hh | Declaration of the MoverCreator class for the RandomMutation |
| RepackMinimize.cc | |
| RepackMinimize.hh | |
| RepackMinimizeCreator.hh | Declaration of the MoverCreator class for the RepackMinimize |
| SaveAndRetrieveSidechains.cc | |
| SaveAndRetrieveSidechains.fwd.hh | |
| SaveAndRetrieveSidechains.hh | |
| SaveAndRetrieveSidechainsCreator.hh | Declaration of the MoverCreator class for the SaveAndRetrieveSidechains |
| SetAtomTree.cc | |
| SetAtomTree.hh | |
| SetAtomTreeCreator.hh | Declaration of the MoverCreator class for the SetAtomTree |
| SetTemperatureFactor.cc | |
| SetTemperatureFactor.fwd.hh | |
| SetTemperatureFactor.hh | |
| SetTemperatureFactorCreator.hh | Declaration of the MoverCreator class for the SetTemperatureFactor |
| SetupHotspotConstraintsLoopsMover.cc | |
| SetupHotspotConstraintsLoopsMover.fwd.hh | |
| SetupHotspotConstraintsLoopsMover.hh | |
| SetupHotspotConstraintsLoopsMoverCreator.hh | Declaration of the MoverCreator class for the SetupHotspotConstraintsLoopsMover |
| SetupHotspotConstraintsMover.cc | |
| SetupHotspotConstraintsMover.fwd.hh | |
| SetupHotspotConstraintsMover.hh | |
| SetupHotspotConstraintsMoverCreator.hh | Declaration of the MoverCreator class for the SetupHotspotConstraintsMover |
| ShoveResidueMover.cc | |
| ShoveResidueMover.hh | |
| ShoveResidueMoverCreator.hh | Declaration of the MoverCreator class for the ShoveResidueMover |
| SpinMover.cc | |
| SpinMover.hh | |
| SpinMoverCreator.hh | Declaration of the MoverCreator class for the SpinMover |
| SubroutineMover.cc | |
| SubroutineMover.fwd.hh | Forward declations for SubroutineMover |
| SubroutineMover.hh | Definition of a class for making the placement auction used by PlaceSimultaneouslyMover |
| SubroutineMoverCreator.hh | Declaration of the MoverCreator class for the SubroutineMover |
| TaskAwareCsts.cc | |
| TaskAwareCsts.fwd.hh | |
| TaskAwareCsts.hh | |
| TaskAwareCstsCreator.hh | Declaration of the MoverCreator class for the TaskAwareCsts |
| TopologyBrokerMover.cc | |
| TopologyBrokerMover.fwd.hh | |
| TopologyBrokerMover.hh | |
| TopologyBrokerMoverCreator.hh | This class will create instances of protocols::moves::Mover TopologyBrokerMover for the protocols::moves::MoverFactory |
| TryRotamers.cc | |
| TryRotamers.hh | |
| TryRotamersCreator.hh | Declaration of the MoverCreator class for the TryRotamers |
| VLB.cc | |
| VLB.hh | |
| VLBCreator.hh | Declaration of the MoverCreator class for the VLB |
| design_utils.cc | |
| design_utils.hh | |
| ParserJobInputter.cc | |
| ParserJobInputter.fwd.hh | |
| ParserJobInputter.hh | |
| ParserJobInputterCreator.hh | |
| PatchdockReader.fwd.hh | |
| read_patchdock.cc | |
| read_patchdock.hh | |
| ReportPSSMDifference.cc | |
| ReportPSSMDifference.fwd.hh | |
| ReportPSSMDifference.hh | |
| util.cc | |
| util.hh | |
| ► qsar | |
| ► scoring_grid | |
| AtrGrid.cc | |
| AtrGrid.fwd.hh | |
| AtrGrid.hh | |
| AtrGridCreator.hh | |
| ChargeGrid.cc | This is an implementation of equation 3 in Goodford, J. Med. Chem. 1985,28,849-857. doi:10.1021/jm00145a002 |
| ChargeGrid.fwd.hh | |
| ChargeGrid.hh | This is an implementation of equation 3 in Goodford, J. Med. Chem. 1985,28,849-857. doi:10.1021/jm00145a002 |
| ChargeGridCreator.hh | |
| ClassicGrid.cc | |
| ClassicGrid.fwd.hh | |
| ClassicGrid.hh | |
| ClassicGridCreator.hh | |
| ConstantScoreBase.fwd.hh | |
| ConstantScoreBase.hh | This is a base class for defining constant terms which are computed over an entire ligand rather than on a per atom basis The unneeded functions are stubbed out, everything left is pure virtual |
| GridBase.fwd.hh | |
| GridBase.hh | |
| GridCreator.cc | |
| GridCreator.hh | Base class for GridCreators for the Grid load time factory registration scheme |
| GridFactory.cc | |
| GridFactory.fwd.hh | |
| GridFactory.hh | |
| GridManager.cc | |
| GridManager.fwd.hh | |
| GridManager.hh | |
| GridSet.cc | A set of related grids |
| GridSet.fwd.hh | A set of related grids |
| GridSet.hh | A set of related grids |
| HbaGrid.cc | |
| HbaGrid.fwd.hh | |
| HbaGrid.hh | |
| HbaGridCreator.hh | |
| HbdGrid.cc | |
| HbdGrid.fwd.hh | |
| HbdGrid.hh | |
| HbdGridCreator.hh | |
| LigandPropertyScore.cc | |
| LigandPropertyScore.fwd.hh | |
| LigandPropertyScore.hh | |
| LigandPropertyScoreCreator.hh | |
| PCSMultiGrid.cc | Implementation of PCSMultiGrid |
| PCSMultiGrid.fwd.hh | Forward declaration for class PCSMultiGrid |
| PCSMultiGrid.hh | Class that setups a vector of scoring grids with PseudoContactShift (PCS) values |
| PCSMultiGridCreator.hh | Creator class for nested PCS scoring grid |
| PCSSingleGrid.cc | Implementation of PCSSingleGrid |
| PCSSingleGrid.fwd.hh | Forward declaration for class PCSSingleGrid |
| PCSSingleGrid.hh | Class that setups a single scoring grid with PseudoContactShift (PCS) values |
| PCSSingleGridCreator.hh | Creator class for simple PCS scoring grid |
| RepGrid.cc | |
| RepGrid.fwd.hh | |
| RepGrid.hh | |
| RepGridCreator.hh | |
| schema_util.cc | Utility functions for defining XML Schema for scoring grids |
| schema_util.hh | Utility functions for defining XML Schema for scoring grids |
| ScoreNormalization.cc | Header file for Score Normalization methods |
| ScoreNormalization.fwd.hh | Report data to database |
| ScoreNormalization.hh | Header file for Score Normalization methods |
| ScoringGridLoader.cc | |
| ScoringGridLoader.fwd.hh | |
| ScoringGridLoader.hh | |
| ScoringGridLoaderCreator.hh | Creator classes for the default DataLoader classes, TaskOperationLoader and ScoreFunctionLoader |
| ShapeGrid.cc | |
| ShapeGrid.fwd.hh | |
| ShapeGrid.hh | |
| ShapeGridCreator.hh | |
| SingleGrid.cc | |
| SingleGrid.fwd.hh | |
| SingleGrid.hh | |
| SiteGrid.cc | |
| SiteGrid.fwd.hh | |
| SiteGrid.hh | |
| SiteGridCreator.hh | |
| SolvationGrid.cc | |
| SolvationGrid.fwd.hh | |
| SolvationGrid.hh | |
| SolvationGridCreator.hh | |
| SolvationMetaGrid.cc | |
| SolvationMetaGrid.fwd.hh | |
| SolvationMetaGrid.hh | |
| SolvationMetaGridCreator.hh | |
| VdwGrid.cc | |
| VdwGrid.fwd.hh | |
| VdwGrid.hh | |
| VdwGridCreator.hh | |
| qsarMap.cc | |
| qsarMap.fwd.hh | |
| qsarMap.hh | |
| qsarMover.cc | |
| qsarMover.fwd.hh | |
| qsarMover.hh | |
| qsarMoverCreator.hh | |
| qsarOptFunc.cc | |
| qsarOptFunc.fwd.hh | |
| qsarOptFunc.hh | |
| RenderGridsToKinemage.cc | |
| RenderGridsToKinemage.fwd.hh | |
| RenderGridsToKinemage.hh | |
| RenderGridsToKinemageCreator.hh | |
| ► quantum_annealing | |
| ExternalPackerResultLoader.cc | A mover that reads the result of an externally-called packer, and applies it to a pose to generate a structure |
| ExternalPackerResultLoader.fwd.hh | A mover that reads the result of an externally-called packer, and applies it to a pose to generate a structure |
| ExternalPackerResultLoader.hh | A mover that reads the result of an externally-called packer, and applies it to a pose to generate a structure |
| ExternalPackerResultLoaderCreator.hh | A mover that reads the result of an externally-called packer, and applies it to a pose to generate a structure |
| InteractionGraphSummaryMetric.cc | A simple metric that allows an InteractionGraph to be written out in a format that external annealers (including quantum annealers) can read |
| InteractionGraphSummaryMetric.fwd.hh | A simple metric that allows an InteractionGraph to be written out in a format that external annealers (including quantum annealers) can read |
| InteractionGraphSummaryMetric.hh | A simple metric that allows an InteractionGraph to be written out in a format that external annealers (including quantum annealers) can read |
| InteractionGraphSummaryMetricCreator.hh | A simple metric that allows an InteractionGraph to be written out in a format that external annealers (including quantum annealers) can read |
| ► rbsegment_relax | |
| AutoRBRelaxMover.cc | |
| AutoRBRelaxMover.hh | |
| FragInsertAndAlignMover.cc | |
| FragInsertAndAlignMover.hh | |
| IdealizeHelices.cc | Protocols for folding into density |
| IdealizeHelices.hh | |
| IdealizeHelicesCreator.hh | |
| MakeStarTopology.cc | Protocols for folding into density |
| MakeStarTopology.hh | |
| MakeStarTopologyCreator.hh | |
| OptimizeThreading.cc | Protocols for folding into density |
| OptimizeThreading.hh | |
| OptimizeThreadingCreator.hh | |
| RBSegment.cc | |
| RBSegment.fwd.hh | |
| RBSegment.hh | |
| RBSegmentMover.cc | |
| RBSegmentMover.hh | |
| RBSegmentRelax.cc | RBSegmentRelax protocol |
| RBSegmentRelax.hh | RBSegmentRelax protocol |
| RBSegmentRelax_main.cc | |
| RBSegmentRelax_main.hh | |
| util.cc | |
| util.hh | |
| ► recces | |
| ► options | |
| RECCES_Options.cc | |
| RECCES_Options.fwd.hh | |
| RECCES_Options.hh | |
| ► params | |
| RECCES_Parameters.cc | |
| RECCES_Parameters.fwd.hh | |
| RECCES_Parameters.hh | |
| ► sampler | |
| ► rna | |
| MC_RNA_KIC_Sampler.cc | Sample and torsions and close an RNA loop |
| MC_RNA_KIC_Sampler.fwd.hh | Sample torsions and close an RNA loop |
| MC_RNA_KIC_Sampler.hh | Sample and torsions and close an RNA loop |
| MC_RNA_MultiSuite.cc | Markov chain sampler for mulitple RNA suite |
| MC_RNA_MultiSuite.fwd.hh | Markov chain sampler for mulitple RNA suite |
| MC_RNA_MultiSuite.hh | Markov chain sampler for mulitple RNA suite |
| MC_RNA_OneJump.cc | |
| MC_RNA_OneJump.fwd.hh | |
| MC_RNA_OneJump.hh | |
| MC_RNA_Sugar.cc | Markov chain sampler for sugar pucker |
| MC_RNA_Sugar.fwd.hh | Markov chain sampler for sugar pucker |
| MC_RNA_Sugar.hh | Markov chain sampler for sugar pucker |
| MC_RNA_Suite.cc | Markov chain sampler for RNA suite |
| MC_RNA_Suite.fwd.hh | Markov chain sampler for RNA suite |
| MC_RNA_Suite.hh | Markov chain sampler for RNA suite |
| MC_Any.cc | |
| MC_Any.fwd.hh | |
| MC_Any.hh | Chooses at random between samplers (rather than running all of them) |
| MC_Comb.cc | Ensemble of Markov chain samplers for modeler combinatorially |
| MC_Comb.fwd.hh | Ensemble of Markov chain samplers for modeler combinatorially |
| MC_Comb.hh | Ensemble of Markov chain samplers for modeler combinatorially |
| MC_Loop.cc | |
| MC_Loop.fwd.hh | |
| MC_Loop.hh | |
| MC_OneTorsion.cc | Markov chain sampler for one torsion |
| MC_OneTorsion.fwd.hh | Markov chain sampler for one torsion |
| MC_OneTorsion.hh | Markov chain sampler for one torsion |
| MC_Sampler.fwd.hh | Abstract Base Class for Markov chain rotamer sampler |
| MC_Sampler.hh | Abstract Base Class for Markov chain rotamer sampler |
| util.cc | |
| util.hh | |
| ► scratch | |
| thermal_sampler.cc | |
| thermal_sampler.hh | |
| ThermalMinimizer.cc | |
| ThermalMinimizer.fwd.hh | Use a simulated tempering simulation to refine a pose |
| ThermalMinimizer.hh | Use a simulated tempering simulation to refine a pose |
| ThermalMinimizerCreator.hh | Use a simulated tempering simulation to refine a pose |
| ThermalSamplingMover.cc | Use a simulated tempering simulation to refine a pose |
| ThermalSamplingMover.fwd.hh | Use a simulated tempering simulation to refine a pose |
| ThermalSamplingMover.hh | Use a simulated tempering simulation to refine a pose |
| ThermalSamplingMoverCreator.hh | Use a simulated tempering simulation to refine a pose |
| Histogram.cc | |
| Histogram.fwd.hh | |
| Histogram.hh | Light-weight histogram class used to save data for simulated tempering |
| RECCES_Mover.cc | Fast Monte Carlo, using MC_Sampler & simulated tempering |
| RECCES_Mover.fwd.hh | |
| RECCES_Mover.hh | |
| setup_util.cc | |
| setup_util.hh | |
| stdev_util.cc | Encodes 'reasonable' assumptions about sampling stdevs |
| stdev_util.hh | |
| util.cc | |
| util.hh | Util functions for RECCES and thermal_sampler |
| ► recon_design | |
| FindConsensusSequence.cc | Takes in multiple poses from the VectorPoseJobDistributor and finds the consensus sequence that optimizes energy of all input poses. Used in conjuction with MSDMover at the end of a protocol to make sure that you end up with one multistate solution. Only accessible through recon application |
| FindConsensusSequence.fwd.hh | Finds the consensus sequence that optimizes energy of all input poses. Used in RECON msd application |
| FindConsensusSequence.hh | Takes in multiple poses from the VectorPoseJobDistributor and finds the consensus sequence that optimizes energy of all input poses. Used in conjuction with MSDMover at the end of a protocol to make sure that you end up with one multistate solution. Only accessible through recon application |
| FindConsensusSequenceCreator.hh | Multistate design mover used for RECON msd application |
| FitnessFilter.cc | Returns the sum of energy of input poses. Only accessible through recon application |
| FitnessFilter.fwd.hh | |
| FitnessFilter.hh | Returns the sum of energy of input poses. Only accessible through recon application |
| FitnessFilterCreator.hh | FilterCreators for the FitnessFilterCreator |
| MSDMover.cc | Multistate design mover used for RECON multistate design Takes in multiple poses, applies residue linking constraints based on sequence of all input poses and runs a design submover that has been specified in the tag Only accessible through recon application |
| MSDMover.fwd.hh | Multistate design mover used for RECON MSD application |
| MSDMover.hh | Multistate design mover used for RECON multistate design Takes in multiple poses, applies residue linking constraints based on sequence of all input poses and runs a design submover that has been specified in the tag Only accessible through recon application |
| MSDMoverCreator.hh | Multistate design mover used for RECON MSD application. Only accessible through recon application |
| recon_util.cc | Utility functions for the recon_design namespace |
| recon_util.hh | |
| ► relax | |
| ► loop_closure | |
| FASelectSlidingWindowLoopClosure.cc | |
| FASelectSlidingWindowLoopClosure.fwd.hh | Fwd headers for FASelectSlidingWindowLoopClosure |
| FASelectSlidingWindowLoopClosure.hh | |
| ► membrane | |
| MPFastRelaxMover.cc | Membrane Fast Relax Protocol - Relax with minimization of mem position |
| MPFastRelaxMover.fwd.hh | Membrane Fast Relax Protocol - Relax with minimization of mem position |
| MPFastRelaxMover.hh | Membrane Fast Relax Protocol - Relax with minimization of mem position |
| MPFastRelaxMoverCreator.hh | Membrane Fast Relax Protocol - Relax with minimization of mem position |
| MPMutateRelaxMover.cc | |
| MPMutateRelaxMover.fwd.hh | |
| MPMutateRelaxMover.hh | |
| MPMutateRelaxMoverCreator.hh | |
| MPRangeRelaxMover.cc | |
| MPRangeRelaxMover.fwd.hh | |
| MPRangeRelaxMover.hh | Relaxes a membrane protein by relaxing in ranges |
| util.cc | |
| util.hh | Utility functions for the MPMutateRelaxMover |
| AcceptToBestMover.cc | Mover equivalent of the accept_to_best command |
| AcceptToBestMover.fwd.hh | |
| AcceptToBestMover.hh | Mover equivalent of the accept_to_best command |
| AcceptToBestMoverCreator.hh | |
| AtomCoordinateCstMover.cc | Add coordinate constraints to a pose, as for the relax protocol |
| AtomCoordinateCstMover.fwd.hh | |
| AtomCoordinateCstMover.hh | Coordinate constraints for relax, etc |
| AtomCoordinateCstMoverCreator.hh | |
| CentroidRelax.cc | |
| CentroidRelax.fwd.hh | |
| CentroidRelax.hh | Centroid-based relax, using Frank Dimaio's updated centroid statistics |
| ClassicRelax.cc | |
| ClassicRelax.hh | |
| cst_util.cc | |
| cst_util.hh | Set of functions for adding constraints used in relax |
| FastRelax.cc | The FastRelax Protocol |
| FastRelax.fwd.hh | |
| FastRelax.hh | The FastRelax Protocol |
| FastRelaxCreator.hh | |
| LocalRelax.cc | A relax protocol that iteratively cart relaxes clustered subsets of residues |
| LocalRelax.fwd.hh | |
| LocalRelax.hh | A relax protocol that iteratively cart relaxes clustered subsets of residues |
| LocalRelaxCreator.hh | |
| MiniRelax.cc | |
| MiniRelax.fwd.hh | Forward declaration for MiniRelax class |
| MiniRelax.hh | |
| Ramady.cc | Header for the Rana energy repair code, Ramady |
| Ramady.hh | Header for the Rana energy repair code, Ramady |
| RangeRelaxMover.cc | |
| RangeRelaxMover.fwd.hh | |
| RangeRelaxMover.hh | Relaxes the protein by relaxing in ranges |
| relax_main.cc | |
| relax_main.hh | |
| RelaxProtocolBase.cc | |
| RelaxProtocolBase.fwd.hh | |
| RelaxProtocolBase.hh | |
| RelaxScriptManager.cc | A singleton class for managing relax scripts, to ensure that they are loaded once and only once from disk |
| RelaxScriptManager.fwd.hh | A singleton class for managing relax scripts, to ensure that they are loaded once and only once from disk |
| RelaxScriptManager.hh | |
| RepeatProteinRelax.cc | Allows the protein to maintain symmetry during internal relax |
| RepeatProteinRelax.fwd.hh | |
| RepeatProteinRelax.hh | |
| RepeatProteinRelaxCreator.hh | |
| util.cc | Initialization protocols for relax and utility functions |
| util.hh | Initialization protocols for relax and utility functions |
| WorkUnit_BatchRelax.cc | |
| WorkUnit_BatchRelax.hh | |
| ► residue_optimization | |
| MetapatchEnumeration.cc | |
| MetapatchEnumeration.fwd.hh | Forward declaration for a class that enumerates all metapatched variants |
| MetapatchEnumeration.hh | Class that enumerates all metapatched variants |
| ► residue_selectors | |
| HBondSelector.cc | |
| HBondSelector.fwd.hh | |
| HBondSelector.hh | A ResidueSelector that selects residues forming hydrogen bonds with specified residues. By default it ignores backbone-backbone hydrogen bonds |
| HBondSelectorCreator.hh | Creator for HBondSelector class |
| LigandMetalContactSelector.cc | |
| LigandMetalContactSelector.fwd.hh | This residue selector takes a selector or residue number of a ligand and returns any residues in contact with metal atoms in the ligand |
| LigandMetalContactSelector.hh | This residue selector takes a selector or residue number of a ligand and returns any residues in contact with metal atoms in the ligand |
| LigandMetalContactSelectorCreator.hh | This residue selector takes a selector or residue number of a ligand and returns any residues in contact with metal atoms in the ligand |
| NativeSelector.cc | |
| NativeSelector.fwd.hh | |
| NativeSelector.hh | A ResidueSelector that applies a given residue selector to the native pose |
| NativeSelectorCreator.hh | Creator for NativeSelector class |
| StoredResidueSubsetSelector.cc | |
| StoredResidueSubsetSelector.fwd.hh | Forward declaration of a class that selects residues using a previously stored residue subset |
| StoredResidueSubsetSelector.hh | The StoredResidueSubsetSelector selects residues using a previously stored residue subset |
| StoredResidueSubsetSelectorCreator.hh | |
| StoreResidueSubsetMover.cc | The StoreResidueSubsetMover allows you to create a at some point during a RosettaScripts run and save it for access later during the same run. Can be useful for mutating/analyzing a particular set of residues using many different movers/filters |
| StoreResidueSubsetMover.fwd.hh | |
| StoreResidueSubsetMover.hh | |
| StoreResidueSubsetMoverCreator.hh | |
| TaskSelector.cc | |
| TaskSelector.fwd.hh | Forward declaration of a class that selects residues using their names |
| TaskSelector.hh | The TaskSelector selects residues using a string containing residue names |
| TaskSelectorCreator.hh | |
| ► rigid | |
| PoseMembraneRigidBodyMover.cc | |
| PoseMembraneRigidBodyMover.hh | |
| RB_geometry.cc | |
| RB_geometry.hh | |
| rigid_body_moves.cc | |
| rigid_body_moves.hh | |
| RigidBodyMotionMover.cc | |
| RigidBodyMotionMover.fwd.hh | |
| RigidBodyMotionMover.hh | |
| RigidBodyMover.cc | |
| RigidBodyMover.fwd.hh | RigidBodyMover forward declarations header |
| RigidBodyMover.hh | |
| RigidBodyMoverCreator.hh | This class will create instances of Movers SmallMover and ShearMover for the MoverFactory |
| RollMover.cc | |
| RollMover.fwd.hh | RollMover forward declarations header |
| RollMover.hh | |
| RollMoverCreator.hh | This class will create instances of Mover RollMover for the MoverFactory |
| RotateJumpAxisMover.cc | RotateJumpAxisMover methods implemented |
| RotateJumpAxisMover.fwd.hh | RotateJumpAxisMover forward declarations header |
| RotateJumpAxisMover.hh | RotateJumpAxisMover header |
| UniformRigidBodyCM.cc | |
| UniformRigidBodyCM.fwd.hh | Definition of the UniformRigidBodyCM class |
| UniformRigidBodyCM.hh | |
| UniformRigidBodyCMCreator.hh | This class will create instances of Mover UniformRigidBodyCM for the MoverFactory |
| UniformRigidBodyMover.cc | |
| UniformRigidBodyMover.fwd.hh | Definition of the FragmentJumpCM class |
| UniformRigidBodyMover.hh | |
| UniformRigidBodyMoverCreator.hh | This class will create instances of Mover UniformRigidBodyMover for the MoverFactory |
| ► rna | |
| ► denovo | |
| ► coarse | |
| CoarseRNA_DeNovoProtocol.cc | |
| CoarseRNA_DeNovoProtocol.hh | |
| CoarseRNA_Fragments.cc | |
| CoarseRNA_Fragments.hh | |
| CoarseRNA_LoopCloser.cc | |
| CoarseRNA_LoopCloser.fwd.hh | |
| CoarseRNA_LoopCloser.hh | |
| MultipleDomainMover.cc | |
| MultipleDomainMover.fwd.hh | |
| MultipleDomainMover.hh | |
| ► movers | |
| RNA_DeNovoMasterMover.cc | Fragment insertions, jump moves, docking, 'chunk' moves, and RNA-protein docking |
| RNA_DeNovoMasterMover.fwd.hh | |
| RNA_DeNovoMasterMover.hh | |
| RNA_DeNovoProtocolMover.cc | |
| RNA_DeNovoProtocolMover.fwd.hh | |
| RNA_DeNovoProtocolMover.hh | |
| RNA_DeNovoProtocolMoverCreator.hh | This class will create instances of the RNA_DeNovoProtocolMover for the MoverFactory |
| RNA_FragmentMover.cc | |
| RNA_FragmentMover.fwd.hh | |
| RNA_FragmentMover.hh | |
| RNA_HelixMover.cc | Protocols that are specific to RNA_HelixMover |
| RNA_HelixMover.fwd.hh | |
| RNA_HelixMover.hh | |
| RNA_Minimizer.cc | |
| RNA_Minimizer.fwd.hh | |
| RNA_Minimizer.hh | |
| RNA_Relaxer.cc | |
| RNA_Relaxer.fwd.hh | |
| RNA_Relaxer.hh | |
| RNP_HighResMover.cc | Protocols that are specific to RNP_HighResMover |
| RNP_HighResMover.fwd.hh | |
| RNP_HighResMover.hh | |
| ► output | |
| RNA_FragmentMonteCarloOutputter.cc | Running output of jumps/scores during rna_denovo/farfar |
| RNA_FragmentMonteCarloOutputter.fwd.hh | |
| RNA_FragmentMonteCarloOutputter.hh | |
| RNA_DeNovoPoseInitializer.cc | |
| RNA_DeNovoPoseInitializer.fwd.hh | |
| RNA_DeNovoPoseInitializer.hh | |
| RNA_DeNovoProtocol.cc | |
| RNA_DeNovoProtocol.hh | |
| RNA_DeNovoProtocolCreator.hh | This class will create instances of the RNA_DeNovoProtocol for the MoverFactory |
| RNA_FragmentMonteCarlo.cc | Fragment Assembly of RNA (FARNA) with full-atom refinement (FARFAR) |
| RNA_FragmentMonteCarlo.fwd.hh | |
| RNA_FragmentMonteCarlo.hh | |
| util.cc | |
| util.hh | |
| ► movers | |
| ERRASER2Protocol.cc | Run a single-threaded, checkpoint free, RosettaScripts accessible ERRASER2 job |
| ERRASER2Protocol.fwd.hh | Run a single-threaded, checkpoint free, RosettaScripts accessible ERRASER2 job |
| ERRASER2Protocol.hh | Run a single-threaded, checkpoint free, RosettaScripts accessible ERRASER2 job |
| ERRASER2ProtocolCreator.hh | Run a single-threaded, checkpoint free, RosettaScripts accessible ERRASER2 job |
| ErraserMinimizerMover.cc | |
| ErraserMinimizerMover.fwd.hh | |
| ErraserMinimizerMover.hh | |
| ErraserMinimizerMoverCreator.hh | This class will create instances of Mover ErraserMinimizerMover for the MoverFactory |
| RNA_DeNovoOptimizer.cc | |
| RNA_DeNovoOptimizer.fwd.hh | |
| RNA_DeNovoOptimizer.hh | |
| RNA_LoopCloser.cc | |
| RNA_LoopCloser.fwd.hh | |
| RNA_LoopCloser.hh | |
| RNAIdealizeMover.cc | Slowly accomodate movement from non-ideal to ideal bond lengths and angles by repeated minimization |
| RNAIdealizeMover.fwd.hh | Slowly accomodate movement from non-ideal to ideal bond lengths and angles by repeated minimization |
| RNAIdealizeMover.hh | Slowly accomodate movement from non-ideal to ideal bond lengths and angles by repeated minimization |
| RNAIdealizeMoverCreator.hh | Slowly accomodate movement from non-ideal to ideal bond lengths and angles by repeated minimization |
| RNAThreadAndMinimizeMover.cc | Thread a new sequence over a given RNA scaffold and do a little optimization |
| RNAThreadAndMinimizeMover.fwd.hh | Thread a new sequence over a given RNA scaffold and do a little optimization |
| RNAThreadAndMinimizeMover.hh | Thread a new sequence over a given RNA scaffold and do a little optimization |
| RNAThreadAndMinimizeMoverCreator.hh | Thread a new sequence over a given RNA scaffold and do a little optimization |
| ► setup | |
| RNA_CSA_JobDistributor.cc | |
| RNA_CSA_JobDistributor.fwd.hh | |
| RNA_CSA_JobDistributor.hh | |
| RNA_JobDistributor.fwd.hh | |
| RNA_JobDistributor.hh | |
| RNA_MonteCarloJobDistributor.cc | |
| RNA_MonteCarloJobDistributor.fwd.hh | |
| RNA_MonteCarloJobDistributor.hh | |
| AlignmentEnergy.cc | An RMSD-type energy to a reference pose, complete with derivatives hacked out of coordinate constraints |
| AlignmentEnergy.fwd.hh | An RMSD-type energy to a reference pose, complete with derivatives hacked out of coordinate constraints |
| AlignmentEnergy.hh | An RMSD-type energy to a reference pose, complete with derivatives hacked out of coordinate constraints |
| AlignmentEnergyCreator.hh | |
| util.hh | |
| ► rosetta_scripts | |
| AdditionalOutputWrapper.cc | This mover wraps another mover to obtain additional output from it via regular call to apply(). A new instance is created for each call to get_additional_output() on this wrapper |
| AdditionalOutputWrapper.hh | |
| AdditionalOutputWrapperCreator.hh | This class will create instances of Mover AdditionalOutputWrapper for the MoverFactory |
| MultipleOutputWrapper.cc | This mover wraps another mover or a ROSETTASCRIPTS block to obtain additional, |
| MultipleOutputWrapper.hh | This mover wraps another mover or a ROSETTASCRIPTS block to obtain additional, |
| MultipleOutputWrapperCreator.hh | This class will create instances of Mover MultipleOutputWrapper for the MoverFactory |
| MultiplePoseMover.cc | This mover accepts multiple poses from a previous mover, performs selection using a provided pose selector, applies contained ROSETTASCRIPTS protocol (ParsedProtocol), and output multiple poses to the next mover of JD2 |
| MultiplePoseMover.hh | This mover accepts multiple poses from a previous mover, performs selection using a provided pose selector, applies contained ROSETTASCRIPTS protocol (ParsedProtocol), and output multiple poses to the next mover of JD2 |
| MultiplePoseMoverCreator.hh | This class will create instances of Mover MultiplePoseMover for the MoverFactory |
| ParsedProtocol.cc | A mover that applies a protocol parsed from a ROSETTASCRIPTS script |
| ParsedProtocol.fwd.hh | Forward declarations for ParsedProtocol |
| ParsedProtocol.hh | |
| ParsedProtocolCreator.hh | This class will create instances of Mover DockDesign for the MoverFactory |
| PosePropertyReporter.cc | |
| PosePropertyReporter.fwd.hh | |
| PosePropertyReporter.hh | Base class for pose selectors used by MultiplePoseMover |
| PosePropertyReporterCreator.cc | Base class for PosePropertyReporters for the load-time factory registration scheme |
| PosePropertyReporterCreator.hh | Base class for PosePropertyReporters for the load-time factory registration scheme |
| PosePropertyReporterFactory.cc | Factory for PosePropertyReporters |
| PosePropertyReporterFactory.fwd.hh | Factory for PosePropertyReporters forward definitions |
| PosePropertyReporterFactory.hh | Factory for PosePropertyReporters |
| PoseSelector.cc | |
| PoseSelector.fwd.hh | Forward declarations for PoseSelector |
| PoseSelector.hh | Base class for pose selectors used by MultiplePoseMover |
| PoseSelectorCreator.cc | |
| PoseSelectorCreator.hh | Base class for PoseSelectors for the load-time factory registration scheme |
| PoseSelectorFactory.cc | Factory for PoseSelectors |
| PoseSelectorFactory.fwd.hh | |
| PoseSelectorFactory.hh | |
| RosettaScriptsJobQueen.cc | JD3 JobQueen for RosettaScripts class method implementation |
| RosettaScriptsJobQueen.hh | JD3 JobQueen for RosettaScripts class declaration |
| RosettaScriptsParser.cc | August 2008 job distributor as planned at RosettaCon08 - Interface base class Parser |
| RosettaScriptsParser.fwd.hh | |
| RosettaScriptsParser.hh | Header file for Parser class, part of August 2008 job distributor |
| SavePoseMover.cc | |
| SavePoseMover.fwd.hh | |
| SavePoseMover.hh | |
| SavePoseMoverCreator.hh | This class will create instances of Mover SavePoseMover for the MoverFactory |
| util.cc | |
| util.hh | |
| XmlObjects.cc | Class to load objects from xml |
| XmlObjects.fwd.hh | Class to load objects from xml |
| XmlObjects.hh | Class to load objects from xml |
| ► rotamer_recovery | |
| RotamerRecovery.cc | |
| RotamerRecovery.fwd.hh | Measure how well rosetta is a recovering the conformation of an experimentally validated structure |
| RotamerRecovery.hh | |
| RotamerRecoveryCreator.cc | Creator classes for components of the RotamerRecovery framework |
| RotamerRecoveryCreator.fwd.hh | |
| RotamerRecoveryCreator.hh | |
| RotamerRecoveryFactory.cc | Factory for creating RotamerRecoverys objects |
| RotamerRecoveryFactory.fwd.hh | Report atom-atom pair geometry and scores to rotamer_recovery Statistics Scientific Benchmark |
| RotamerRecoveryFactory.hh | Factory for creating RotamerRecovery objects |
| RotamerRecoveryMover.cc | A wrapper that measures how similar the rotamers are between before and after running the child mover |
| RotamerRecoveryMover.fwd.hh | Measure how well rosetta is a recovering the conformation of an experimentally validated structure |
| RotamerRecoveryMover.hh | A wrapper that measures how similar the rotamers are between before and after running the child mover |
| RotamerRecoveryMoverCreator.hh | This class will create instances of Mover ConstraintSetMover for the MoverFactory |
| RRComparer.cc | |
| RRComparer.fwd.hh | Measure how well rosetta is a recovering the conformation of an experimentally validated structure |
| RRComparer.hh | |
| RRComparerAutomorphicRMSD.cc | |
| RRComparerAutomorphicRMSD.fwd.hh | Measure how well rosetta is a recovering the conformation of an experimentally validated structure by measuing the minimum root mean squared deviation of sidechain atoms for all chemical atomorphic forms |
| RRComparerAutomorphicRMSD.hh | |
| RRComparerElecDensDiff.cc | |
| RRComparerElecDensDiff.fwd.hh | Measure rotamer recovery by change in sidechain electron density correlation |
| RRComparerElecDensDiff.hh | |
| RRProtocol.cc | |
| RRProtocol.fwd.hh | Manage how the rotamer recovery test should be preformed |
| RRProtocol.hh | |
| RRProtocolMinPack.cc | |
| RRProtocolMinPack.fwd.hh | Preform the rotamer recovery test by minimizing each residue in a fixed context |
| RRProtocolMinPack.hh | |
| RRProtocolMover.cc | Preform the rotamer recovery after applying mover |
| RRProtocolMover.fwd.hh | Preform the rotamer recovery after applying mover |
| RRProtocolMover.hh | Preform the rotamer recovery after applying mover |
| RRProtocolPackRotamers.cc | |
| RRProtocolPackRotamers.fwd.hh | Preform the rotamer recovery test using the pack_rotamers discrete optimization algorithm |
| RRProtocolPackRotamers.hh | |
| RRProtocolReferenceStructure.cc | Preform the rotamer recovery against a reference structure |
| RRProtocolReferenceStructure.fwd.hh | Preform the rotamer recovery after applying mover |
| RRProtocolReferenceStructure.hh | Preform the rotamer recovery against a reference structure |
| RRProtocolRelax.cc | Perform the rotamer recovery test using the FastRelax protocol |
| RRProtocolRelax.fwd.hh | Perform the rotamer recovery test using the FastRelax protocol |
| RRProtocolRelax.hh | |
| RRProtocolRotamerTrials.cc | |
| RRProtocolRotamerTrials.fwd.hh | Preform the rotamer recovery test by determining the lowest energy (discrete) rotamer for each residue in a fixed context |
| RRProtocolRotamerTrials.hh | |
| RRProtocolRTMin.cc | |
| RRProtocolRTMin.fwd.hh | Preform the rotamer recovery test by minimizing each residue in a fixed context |
| RRProtocolRTMin.hh | |
| RRReporter.cc | |
| RRReporter.fwd.hh | |
| RRReporter.hh | |
| RRReporterHuman.cc | |
| RRReporterHuman.fwd.hh | Report how well rosetta is a recovering the conformation of an experimentally validated structure in a human readable format |
| RRReporterHuman.hh | |
| RRReporterSQLite.cc | |
| RRReporterSQLite.fwd.hh | Report Rotamer Recovery to an SQLite database |
| RRReporterSQLite.hh | |
| ► RotamerDump | |
| RotamerDumpMover.cc | |
| RotamerDumpMover.fwd.hh | |
| RotamerDumpMover.hh | |
| ► rpc | |
| rpc.cc | |
| rpc.fwd.hh | JSON_RPC base classes |
| rpc.hh | |
| ► sasa_scores | |
| sasapack.cc | |
| sasapack.hh | Sasapack and other scores that are normalized by residue sasa |
| ► score_filters | |
| GeometryFilter.cc | |
| GeometryFilter.fwd.hh | |
| GeometryFilter.hh | Definition of filter class GeometryFilter |
| GeometryFilterCreator.hh | FilterCreators for the GeometryFilterCreator |
| ScoreCutoffFilter.cc | |
| ScoreCutoffFilter.fwd.hh | |
| ScoreCutoffFilter.hh | Header file for ScoreCutoffFitler class |
| ScoreCutoffFilterCreator.hh | FilterCreator for the ScoreCutoffFilter |
| ScoreTypeFilter.cc | |
| ScoreTypeFilter.fwd.hh | |
| ScoreTypeFilter.hh | Definition of filter class ScoreTypeFilter |
| ScoreTypeFilterCreator.hh | FilterCreators for the ScoreTypeFilter |
| ► scoring | |
| ► methods | |
| ► pcs | |
| GridSearchIterator.cc | |
| GridSearchIterator.fwd.hh | |
| GridSearchIterator.hh | |
| PseudocontactShiftData.cc | |
| PseudocontactShiftData.fwd.hh | |
| PseudocontactShiftData.hh | |
| PseudocontactShiftEnergy.cc | |
| PseudocontactShiftEnergy.fwd.hh | |
| PseudocontactShiftEnergy.hh | |
| PseudocontactShiftEnergyCreator.hh | Declaration for the class that connects PseudocontactShiftEnergy with the ScoringManager |
| PseudocontactShiftInput.cc | |
| PseudocontactShiftInput.fwd.hh | |
| PseudocontactShiftInput.hh | |
| PseudocontactShiftTensor.cc | |
| PseudocontactShiftTensor.fwd.hh | |
| PseudocontactShiftTensor.hh | |
| TensorsOptimizer.cc | |
| TensorsOptimizer.fwd.hh | |
| TensorsOptimizer.hh | |
| ► pcs2 | |
| GridSearchIteratorCA.cc | |
| GridSearchIteratorCA.fwd.hh | |
| GridSearchIteratorCA.hh | |
| PcsDataCenter.cc | |
| PcsDataCenter.fwd.hh | |
| PcsDataCenter.hh | Hold the PCS data on which the SVD will be applyed |
| PcsDataCenterManager.cc | |
| PcsDataCenterManager.fwd.hh | |
| PcsDataCenterManager.hh | |
| PcsDataCenterManagerSingleton.cc | |
| PcsDataCenterManagerSingleton.fwd.hh | |
| PcsDataCenterManagerSingleton.hh | |
| PcsDataLanthanide.cc | |
| PcsDataLanthanide.fwd.hh | |
| PcsDataLanthanide.hh | |
| PcsEnergy.cc | |
| PcsEnergy.fwd.hh | |
| PcsEnergy.hh | |
| PcsEnergyCreator.hh | Declaration for the class that connects PcsEnergyCreator with the ScoringManager |
| PcsEnergyParameter.cc | |
| PcsEnergyParameter.fwd.hh | |
| PcsEnergyParameter.hh | |
| PcsEnergyParameterManager.cc | |
| PcsEnergyParameterManager.fwd.hh | |
| PcsEnergyParameterManager.hh | |
| PcsGridSearchParameter.cc | |
| PcsGridSearchParameter.fwd.hh | |
| PcsGridSearchParameter.hh | |
| PcsGridSearchParameterManager.cc | |
| PcsGridSearchParameterManager.fwd.hh | |
| PcsGridSearchParameterManager.hh | |
| PcsInputCenter.cc | |
| PcsInputCenter.fwd.hh | Christophe Schmitz |
| PcsInputCenter.hh | This class hold the information for each paramagnetic center Multiple data set with different lanthanide can be measured for each paramagnetic center |
| PcsInputCenterManager.cc | Singleton that hold everything about the input PCS This avoid multiple reading of the input file |
| PcsInputCenterManager.fwd.hh | Christophe Schmitz |
| PcsInputCenterManager.hh | Singleton that hold everything about the input PCS This avoid multiple reading of the input files |
| PcsInputFile.cc | Read all input from a .npc input file, and hold the data in the class One file per lanthanide data |
| PcsInputFile.fwd.hh | Read all input from a .npc input file, and hold the data in the class |
| PcsInputFile.hh | Read all input from a .npc input file, and hold the data in the class. One file per lanthanide data |
| PcsInputLine.cc | |
| PcsInputLine.fwd.hh | Class that hold a line data of the input file |
| PcsInputLine.hh | Class that hold a line data of the input file |
| PcsTensor.cc | Hold chi-tensor information of PCS |
| PcsTensor.fwd.hh | |
| PcsTensor.hh | Hold chi-tensor information of PCS |
| TensorsOptimizer.cc | |
| TensorsOptimizer.fwd.hh | |
| TensorsOptimizer.hh | |
| TensorsOptimizerFix.cc | |
| TensorsOptimizerFix.fwd.hh | |
| TensorsOptimizerFix.hh | |
| TensorsOptimizerSvd.cc | |
| TensorsOptimizerSvd.fwd.hh | |
| TensorsOptimizerSvd.hh | |
| ► pcsTs1 | |
| GridSearchIterator.cc | |
| GridSearchIterator.fwd.hh | |
| GridSearchIterator.hh | |
| PseudocontactShiftData.cc | |
| PseudocontactShiftData.fwd.hh | |
| PseudocontactShiftData.hh | |
| PseudocontactShiftEnergy.cc | |
| PseudocontactShiftEnergy.fwd.hh | |
| PseudocontactShiftEnergy.hh | |
| PseudocontactShiftEnergyCreator.hh | |
| PseudocontactShiftInput.cc | |
| PseudocontactShiftInput.fwd.hh | |
| PseudocontactShiftInput.hh | |
| PseudocontactShiftTensor.cc | |
| PseudocontactShiftTensor.fwd.hh | |
| PseudocontactShiftTensor.hh | |
| TensorsOptimizer.cc | |
| TensorsOptimizer.fwd.hh | |
| TensorsOptimizer.hh | |
| ► pcsTs2 | |
| GridSearchIterator.cc | |
| GridSearchIterator.fwd.hh | |
| GridSearchIterator.hh | |
| PseudocontactShiftData.cc | |
| PseudocontactShiftData.fwd.hh | |
| PseudocontactShiftData.hh | |
| PseudocontactShiftEnergy.cc | |
| PseudocontactShiftEnergy.fwd.hh | |
| PseudocontactShiftEnergy.hh | |
| PseudocontactShiftEnergyCreator.hh | |
| PseudocontactShiftInput.cc | |
| PseudocontactShiftInput.fwd.hh | |
| PseudocontactShiftInput.hh | |
| PseudocontactShiftTensor.cc | |
| PseudocontactShiftTensor.fwd.hh | |
| PseudocontactShiftTensor.hh | |
| TensorsOptimizer.cc | |
| TensorsOptimizer.fwd.hh | |
| TensorsOptimizer.hh | |
| ► pcsTs3 | |
| GridSearchIterator.cc | |
| GridSearchIterator.fwd.hh | |
| GridSearchIterator.hh | |
| PseudocontactShiftData.cc | |
| PseudocontactShiftData.fwd.hh | |
| PseudocontactShiftData.hh | |
| PseudocontactShiftEnergy.cc | |
| PseudocontactShiftEnergy.fwd.hh | |
| PseudocontactShiftEnergy.hh | |
| PseudocontactShiftEnergyCreator.hh | |
| PseudocontactShiftInput.cc | |
| PseudocontactShiftInput.fwd.hh | |
| PseudocontactShiftInput.hh | |
| PseudocontactShiftTensor.cc | |
| PseudocontactShiftTensor.fwd.hh | |
| PseudocontactShiftTensor.hh | |
| TensorsOptimizer.cc | |
| TensorsOptimizer.fwd.hh | |
| TensorsOptimizer.hh | |
| ► pcsTs4 | |
| GridSearchIterator.cc | |
| GridSearchIterator.fwd.hh | |
| GridSearchIterator.hh | |
| PseudocontactShiftData.cc | |
| PseudocontactShiftData.fwd.hh | |
| PseudocontactShiftData.hh | |
| PseudocontactShiftEnergy.cc | |
| PseudocontactShiftEnergy.fwd.hh | |
| PseudocontactShiftEnergy.hh | |
| PseudocontactShiftEnergyCreator.hh | |
| PseudocontactShiftInput.cc | |
| PseudocontactShiftInput.fwd.hh | |
| PseudocontactShiftInput.hh | |
| PseudocontactShiftTensor.cc | |
| PseudocontactShiftTensor.fwd.hh | |
| PseudocontactShiftTensor.hh | |
| TensorsOptimizer.cc | |
| TensorsOptimizer.fwd.hh | |
| TensorsOptimizer.hh | |
| ► saxs | |
| PDDFEnergy.cc | |
| PDDFEnergy.fwd.hh | Forward declaration of a PDDF energy term |
| PDDFEnergy.hh | |
| PDDFEnergyCreator.hh | Declaration for the class that connects PDDFEnergyCreator with the ScoringManager |
| EnsembleEnergy.cc | Function to subtract out individual reference energies during ensemble docking |
| EnsembleEnergy.hh | |
| EnsembleEnergyCreator.hh | Declaration for the class that connects EnsembleEnergy with the ScoringManager |
| InterchainEnvEnergy.cc | Statistically derived rotamer pair potentials |
| InterchainEnvEnergy.hh | |
| InterchainEnvEnergyCreator.hh | Declaration for the class that connects InterchainEnvEnergy with the ScoringManager |
| InterchainPairEnergy.cc | |
| InterchainPairEnergy.hh | |
| InterchainPairEnergyCreator.hh | |
| ResidualDipolarCouplingEnergyRigidSegments.cc | |
| ResidualDipolarCouplingEnergyRigidSegments.fwd.hh | |
| ResidualDipolarCouplingEnergyRigidSegments.hh | |
| ResidualDipolarCouplingEnergyRigidSegmentsCreator.hh | |
| SpecialRotamerEnergy.cc | |
| SpecialRotamerEnergy.fwd.hh | |
| SpecialRotamerEnergy.hh | Adds a bonus to any rotamer that is flagged |
| SpecialRotamerEnergyCreator.hh | Declaration for the class that connects SpecialRotamerEnergy with the ScoringManager |
| TargetClashEnergy.cc | |
| TargetClashEnergy.fwd.hh | |
| TargetClashEnergy.hh | |
| TargetClashEnergyCreator.hh | |
| ImplicitFastClashCheck.cc | |
| ImplicitFastClashCheck.fwd.hh | |
| ImplicitFastClashCheck.hh | |
| InterchainPotential.cc | Statistically derived rotamer pair potentials |
| InterchainPotential.fwd.hh | |
| InterchainPotential.hh | |
| Interface.cc | |
| Interface.fwd.hh | |
| Interface.hh | |
| InterfaceInfo.cc | Statistically derived rotamer pair potentials |
| InterfaceInfo.fwd.hh | |
| InterfaceInfo.hh | |
| ResidualDipolarCouplingRigidSegments.cc | |
| ResidualDipolarCouplingRigidSegments.fwd.hh | |
| ResidualDipolarCouplingRigidSegments.hh | |
| VDW_CachedRepScreenInfo.cc | |
| VDW_CachedRepScreenInfo.fwd.hh | |
| VDW_CachedRepScreenInfo.hh | |
| VDW_GridEnergy.cc | VDW_GridEnergy energy method implementation |
| VDW_GridEnergy.fwd.hh | Grid_vdw energy method forward declaration |
| VDW_GridEnergy.hh | VDW_GridEnergy energy method |
| VDW_GridEnergyCreator.hh | |
| ► seeded_abinitio | |
| CAcstGenerator.cc | |
| CAcstGenerator.hh | |
| CAcstGeneratorCreator.hh | |
| CloseFold.cc | |
| CloseFold.hh | |
| CloseFoldCreator.hh | |
| CoordinateCst.cc | Allows to add coordinate constraints to the pose based on parsed spans or residues residues specified are parsed at runtime not at parse time, so it can be used somewhat used with length changes currently it only adds CA constraints, but hopefully at some time point others too |
| CoordinateCst.hh | |
| CoordinateCstCreator.hh | |
| DefineMovableLoops.cc | |
| DefineMovableLoops.hh | |
| DefineMovableLoopsCreator.hh | |
| GrowPeptides.cc | Different ways of growing peptide sequences |
| GrowPeptides.hh | |
| GrowPeptidesCreator.hh | |
| SeededAbinitio_util.cc | |
| SeededAbinitio_util.hh | |
| SeedFoldTree.cc | |
| SeedFoldTree.fwd.hh | |
| SeedFoldTree.hh | |
| SeedFoldTreeCreator.hh | |
| SeedSetupMover.cc | Mover to set up packer task and movemap for seededabinitio |
| SeedSetupMover.hh | |
| SeedSetupMoverCreator.hh | |
| SegmentHybridizer.cc | |
| SegmentHybridizer.hh | Repurposing logic and some functions from CartesianHybridze protocols for segment insertions and chain closure |
| SegmentHybridizerCreator.hh | |
| SwapSegment.cc | |
| SwapSegment.hh | |
| SwapSegmentCreator.hh | |
| util.cc | |
| util.hh | |
| ► sewing | |
| ► data_storage | |
| Basis.cc | Class for storing residue information needed to generate alignments |
| Basis.fwd.hh | Class for storing residue information needed to generate alignments |
| Basis.hh | Class for storing residue information needed to generate alignments |
| HashedSmartAssembly.cc | Assembly that makes use of the Hasher |
| HashedSmartAssembly.fwd.hh | Assembly that makes use of the Hasher |
| HashedSmartAssembly.hh | Assembly that makes use of the Hasher |
| LigandResidue.cc | |
| LigandResidue.fwd.hh | Minimal container for SEWING residues |
| LigandResidue.hh | |
| LigandSegment.cc | |
| LigandSegment.fwd.hh | |
| LigandSegment.hh | |
| SmartAssembly.cc | |
| SmartAssembly.fwd.hh | |
| SmartAssembly.hh | |
| SmartSegment.cc | |
| SmartSegment.fwd.hh | |
| SmartSegment.hh | |
| SmartSewingResidue.cc | Minimal container for SEWING residues |
| SmartSewingResidue.fwd.hh | Minimal container for SEWING residues |
| SmartSewingResidue.hh | Minimal container for SEWING residues |
| ► hashing | |
| AlignmentFileGeneratorMover.cc | Given a model file, edge file ,and one or more input structures, generates alignment files for use with AppendAssemblyMover |
| AlignmentFileGeneratorMover.fwd.hh | |
| AlignmentFileGeneratorMover.hh | Given a model file, edge file ,and one or more input structures, generates alignment files for use with AppendAssemblyMover |
| AlignmentFileGeneratorMoverCreator.hh | Given a model file, edge file ,and one or more input structures, generates alignment files for use with AppendAssemblyMover |
| AlignmentGenerator.cc | Determines all possible alignments for an edge given the two SewSegments involved. Also contains the mechanisms for reading an edge file |
| AlignmentGenerator.fwd.hh | Determines all possible alignments for an edge given the two SewSegments involved. Also contains the mechanisms for reading an edge file |
| AlignmentGenerator.hh | Determines all possible alignments for an edge given the two SewSegments involved. Also contains the mechanisms for reading an edge file |
| BasisMapGenerator.cc | Given a model file, edge file ,and one or more input structures, generates alignment files for use with AppendAssemblyMover |
| BasisMapGenerator.fwd.hh | Generates alignments for a given set of segments and stores them in a BasisMap |
| BasisMapGenerator.hh | Given a model file, edge file ,and one or more input structures, generates alignment files for use with AppendAssemblyMover |
| EdgeMapGenerator.cc | Class used to generate edge files for use with SEWING protocols |
| EdgeMapGenerator.fwd.hh | Class used to generate edge files for use with SMART_SEWING devel |
| EdgeMapGenerator.hh | Class used to generate edge files for use with SEWING protocols |
| Hasher.cc | A geometric hashing class used by the SEWING protocol |
| Hasher.fwd.hh | A geometric hashing class used by the SEWING protocol |
| Hasher.hh | A geometric hashing class used by the SEWING protocol |
| hasher_data.hh | Data storage for the Hasher |
| LigandBindingResPlacer.cc | |
| LigandBindingResPlacer.fwd.hh | Uses predetermined coordinate frames to place coordinating residues in SEWING proteins |
| LigandBindingResPlacer.hh | |
| ModelFileReader.cc | Reader of SEWING model files |
| ModelFileReader.fwd.hh | Reader of SEWING model files |
| ModelFileReader.hh | Reader of SEWING model files |
| ► movers | |
| AppendAssemblyMover.cc | AssemblyMover for adding to existing poses |
| AppendAssemblyMover.fwd.hh | AssemblyMover for adding to existing poses |
| AppendAssemblyMover.hh | AssemblyMover for adding to existing poses |
| AppendAssemblyMoverCreator.hh | AssemblyMover for adding to existing poses |
| AssemblyMover.cc | Interface for making Movers that deal with Assemblies |
| AssemblyMover.fwd.hh | Interface for making Movers that deal with Assemblies |
| AssemblyMover.hh | Interface for making Movers that deal with Assemblies |
| AssemblyMoverCreator.hh | Interface for making Movers that deal with Assemblies |
| LigandBindingAssemblyMover.cc | |
| LigandBindingAssemblyMover.fwd.hh | Subclass of AppendAssemlbyMover for building an assembly with new ligand contacts |
| LigandBindingAssemblyMover.hh | AssemblyMover for adding to existing poses |
| LigandBindingAssemblyMoverCreator.hh | AssemblyMover for adding contacts to ligands |
| ► requirements | |
| AssemblyRequirement.fwd.hh | Interface for making Requirements that deal with Assemblies |
| AssemblyRequirement.hh | Interface for making Requirements that deal with Assemblies |
| AssemblyRequirementCreator.fwd.hh | |
| AssemblyRequirementCreator.hh | |
| AssemblyRequirementFactory.cc | Factory for creating Requirements objects |
| AssemblyRequirementFactory.fwd.hh | Creates AssemblyScorers using AssemblyMovers |
| AssemblyRequirementFactory.hh | |
| ClashRequirement.cc | Requirement that an Assembly have less than a certain number of clashes |
| ClashRequirement.fwd.hh | Requirement that an Assembly have less than a certain number of clashes |
| ClashRequirement.hh | Requirement that an Assembly have less than a certain number of clashes |
| ClashRequirementCreator.fwd.hh | |
| ClashRequirementCreator.hh | Creates ClashRequirements for the AssemblyRequirementFactory |
| DsspSpecificLengthRequirement.cc | Requirement that the segments of an Assembly with a specific dssp code be within a certain range of lengths |
| DsspSpecificLengthRequirement.fwd.hh | Requirement that the segments of an Assembly with a specific dssp code be within a certain range of lengths |
| DsspSpecificLengthRequirement.hh | Requirement that the segments of an Assembly with a specific dssp code be within a certain range of lengths |
| DsspSpecificLengthRequirementCreator.fwd.hh | |
| DsspSpecificLengthRequirementCreator.hh | Creates DsspSpecificLengthRequirements for the AssemblyRequirementFactory |
| KeepLigandContactsRequirement.cc | Requirement that an Assembly have less than a certain number of clashes |
| KeepLigandContactsRequirement.fwd.hh | Requirement that an Assembly lose no more than a certain number of contacts during a conformer switch step |
| KeepLigandContactsRequirement.hh | Requirement that an Assembly lose no more than a certain number of ligand contacts during conformer switches |
| KeepLigandContactsRequirementCreator.fwd.hh | |
| KeepLigandContactsRequirementCreator.hh | Creates KeepLigandContactsRequirements for the AssemblyRequirementFactory |
| LengthInResiduesRequirement.cc | Requirement that an Assembly be within a certain range of lengths |
| LengthInResiduesRequirement.fwd.hh | Requirement that an Assembly be within a certain range of lengths |
| LengthInResiduesRequirement.hh | Requirement that an Assembly be within a certain range of lengths |
| LengthInResiduesRequirementCreator.fwd.hh | |
| LengthInResiduesRequirementCreator.hh | Creates LengthInResiduesRequirements for the AssemblyRequirementFactory |
| LigandAssemblyRequirement.cc | Interface for making Ligand specific Requirements for Assemblies |
| LigandAssemblyRequirement.fwd.hh | Interface for making ligand specific Requirements for Assemblies |
| LigandAssemblyRequirement.hh | Interface for making Ligand specific Requirements for Assemblies |
| LigandClashRequirement.cc | Assembly requirement that clash checks the assembly backbone with its bound ligands |
| LigandClashRequirement.fwd.hh | Assembly requirement that clash checks the assembly backbone with its bound ligands |
| LigandClashRequirement.hh | Assembly requirement that clash checks the assembly backbone with its bound ligands |
| LigandClashRequirementCreator.fwd.hh | |
| LigandClashRequirementCreator.hh | Creates LigandClashRequirements for the AssemblyRequirementFactory |
| NonTerminalStartingSegmentRequirement.cc | Requirement that an Assembly have less than a certain number of clashes |
| NonTerminalStartingSegmentRequirement.fwd.hh | Requirement that an Assembly have less than a certain number of clashes |
| NonTerminalStartingSegmentRequirement.hh | Requirement that an Assembly have less than a certain number of clashes |
| NonTerminalStartingSegmentRequirementCreator.fwd.hh | |
| NonTerminalStartingSegmentRequirementCreator.hh | Creates NonTerminalStartingSegmentRequirements for the AssemblyRequirementFactory |
| SizeInSegmentsRequirement.cc | Requirement that an Assembly be within a certain range of sizes |
| SizeInSegmentsRequirement.fwd.hh | Requirement that an Assembly be within a certain range of lengths |
| SizeInSegmentsRequirement.hh | Requirement that an Assembly be within a certain range of sizes |
| SizeInSegmentsRequirementCreator.fwd.hh | |
| SizeInSegmentsRequirementCreator.hh | Creates SizeInSegmentsRequirements for the AssemblyRequirementFactory |
| ► scoring | |
| AssemblyScorer.fwd.hh | Interface for making Requirements that deal with Assemblies |
| AssemblyScorer.hh | Interface for making Requirements that deal with Assemblies |
| AssemblyScorerCreator.fwd.hh | |
| AssemblyScorerCreator.hh | |
| AssemblyScorerFactory.cc | |
| AssemblyScorerFactory.fwd.hh | Creates AssemblyScorers using AssemblyMovers |
| AssemblyScorerFactory.hh | |
| InterModelMotifScorer.cc | |
| InterModelMotifScorer.fwd.hh | |
| InterModelMotifScorer.hh | |
| InterModelMotifScorerCreator.fwd.hh | |
| InterModelMotifScorerCreator.hh | |
| IntraDesignTerminusMotifScorer.cc | |
| IntraDesignTerminusMotifScorer.fwd.hh | |
| IntraDesignTerminusMotifScorer.hh | |
| IntraDesignTerminusMotifScorerCreator.fwd.hh | |
| IntraDesignTerminusMotifScorerCreator.hh | |
| LigandAssemblyScorer.cc | Interface for making Requirements that deal with Assemblies |
| LigandAssemblyScorer.fwd.hh | Interface for making ligand specific scorers for Assemblies |
| LigandAssemblyScorer.hh | Interface for making Requirements that deal with Assemblies |
| LigandScorer.cc | |
| LigandScorer.fwd.hh | |
| LigandScorer.hh | |
| LigandScorerCreator.fwd.hh | |
| LigandScorerCreator.hh | |
| MotifScorer.cc | |
| MotifScorer.fwd.hh | |
| MotifScorer.hh | |
| MotifScorerCreator.fwd.hh | |
| MotifScorerCreator.hh | |
| PartnerMotifScorer.cc | |
| PartnerMotifScorer.fwd.hh | |
| PartnerMotifScorer.hh | |
| PartnerMotifScorerCreator.fwd.hh | |
| PartnerMotifScorerCreator.hh | |
| SegmentContactOrderScorer.cc | Favors assemblies whose segments form contacts with segments distant in the assembly |
| SegmentContactOrderScorer.fwd.hh | |
| SegmentContactOrderScorer.hh | Favors assemblies whose segments form contacts with segments distant in the assembly |
| SegmentContactOrderScorerCreator.fwd.hh | |
| SegmentContactOrderScorerCreator.hh | |
| StartingNodeMotifScorer.cc | |
| StartingNodeMotifScorer.fwd.hh | |
| StartingNodeMotifScorer.hh | |
| StartingNodeMotifScorerCreator.fwd.hh | |
| StartingNodeMotifScorerCreator.hh | |
| SubsetPartnerMotifScorer.cc | |
| SubsetPartnerMotifScorer.fwd.hh | |
| SubsetPartnerMotifScorer.hh | |
| SubsetPartnerMotifScorerCreator.fwd.hh | |
| SubsetPartnerMotifScorerCreator.hh | |
| TerminusMotifScorer.cc | |
| TerminusMotifScorer.fwd.hh | |
| TerminusMotifScorer.hh | |
| TerminusMotifScorerCreator.fwd.hh | |
| TerminusMotifScorerCreator.hh | |
| TopNMotifScorer.cc | |
| TopNMotifScorer.fwd.hh | |
| TopNMotifScorer.hh | Returns the normalized motif score for only the best N segments |
| TopNMotifScorerCreator.fwd.hh | |
| TopNMotifScorerCreator.hh | |
| ► sic_dock | |
| ► scores | |
| MotifHashRigidScore.cc | |
| MotifHashRigidScore.fwd.hh | |
| MotifHashRigidScore.hh | |
| TrisBpyScore.cc | |
| TrisBpyScore.fwd.hh | |
| TrisBpyScore.hh | |
| designability_score.cc | |
| designability_score.hh | |
| loophash_util.cc | |
| loophash_util.hh | |
| read_biounit.cc | |
| read_biounit.hh | |
| RigidScore.cc | |
| RigidScore.fwd.hh | |
| RigidScore.hh | |
| Rose.cc | |
| Rose.fwd.hh | |
| Rose.hh | |
| SICFast.cc | |
| SICFast.fwd.hh | |
| SICFast.hh | |
| types.hh | |
| util.cc | |
| util.hh | |
| xyzStripeHashPoseWithMeta.fwd.hh | |
| xyzStripeHashPoseWithMeta.hh | |
| ► simple_ddg | |
| AlaScan.cc | |
| AlaScan.fwd.hh | |
| AlaScan.hh | Definition of filter class AlsScan |
| AlaScanCreator.hh | FilterCreators for the AlaScanCreator |
| ddG.cc | Implementation of the ddG class for computing interface delta dGs |
| ddG.fwd.hh | Forward declarations for ddG |
| ddG.hh | |
| ddGCreator.hh | |
| DdgFilter.cc | |
| DdgFilter.fwd.hh | |
| DdgFilter.hh | Definition of filter class DdgFilter |
| DdgFilterCreator.hh | FilterCreators for the DdgFilterCreator |
| DdGScan.cc | |
| DdGScan.fwd.hh | |
| DdGScan.hh | Definition of filter class DdGScan |
| DdGScanCreator.hh | FilterCreators for the DdGScanCreator |
| InterfaceBindingEnergyDensityFilter.cc | Implementation of the binding-energy-density filter |
| InterfaceBindingEnergyDensityFilter.fwd.hh | Forward declaration and typedefs for InterfaceBindingEnergyDensityFilter |
| InterfaceBindingEnergyDensityFilter.hh | Filter class for looking at the dGbind/dSASA ratio |
| InterfaceBindingEnergyDensityFilterCreator.hh | FilterCreators for the InterfaceBindingEnergyDensityFilterCreator |
| SSElementBisectddGFilter.cc | |
| SSElementBisectddGFilter.fwd.hh | Filter for the interconnection between secondary elements |
| SSElementBisectddGFilter.hh | Disconnects a protein by secondary structure elements and calculates the DDG between the elements |
| SSElementBisectddGFilterCreator.hh | |
| ► simple_filters | |
| AbinitioBaseFilter.cc | |
| AbinitioBaseFilter.hh | Header file for AbinitioBaseFilter.cc |
| AngleToVectorFilter.cc | |
| AngleToVectorFilter.fwd.hh | |
| AngleToVectorFilter.hh | |
| AngleToVectorFilterCreator.hh | FilterCreators for the AngleToVectorFilter |
| AtomicContactFilter.cc | |
| AtomicContactFilter.hh | |
| AtomicContactFilterCreator.hh | FilterCreator for the AtomicContactFilter |
| AtomicDistanceFilter.cc | |
| AtomicDistanceFilter.hh | Filter for looking at specific atom distances |
| AtomicDistanceFilterCreator.hh | FilterCreator for the AtomicDistanceFilter |
| AveragePathLengthFilter.cc | Filter on the average covalent path length between residues, including disulfides |
| AveragePathLengthFilter.fwd.hh | Filter on the average covalent path length between residues, including disulfides |
| AveragePathLengthFilter.hh | Filter on the average covalent path length between residues, including disulfides |
| AveragePathLengthFilterCreator.hh | FilterCreators for the AveragePathLengthFilter |
| BatchNrEvaluator.cc | |
| BatchNrEvaluator.hh | |
| BuriedSurfaceAreaFilter.cc | Calculates buried surface area (exposed surface area minus total surface area, on a per-residue basis). Accepts a residue selector to allow buried subsets to be considered |
| BuriedSurfaceAreaFilter.fwd.hh | Forward declarations and owning pointer typedefs for the BuriedSurfaceAreaFilter |
| BuriedSurfaceAreaFilter.hh | Headers for the BuriedSurfaceAreaFilter |
| BuriedSurfaceAreaFilterCreator.hh | Creator for the BuriedSurfaceAreaFilter |
| BuriedUnsatHbondFilter.cc | Filter to report buried polar atoms that are not satisfied by hydrogen bonds |
| BuriedUnsatHbondFilter.fwd.hh | |
| BuriedUnsatHbondFilter.hh | Filter to report buried polar atoms that are not satisfied by hydrogen bonds |
| BuriedUnsatHbondFilterCreator.hh | FilterCreators for the BuriedUnsatHbondFilterCreator |
| CamShiftEvaluator.cc | |
| CamShiftEvaluator.hh | |
| CamShiftEvaluatorCreator.cc | |
| CamShiftEvaluatorCreator.hh | Header for CamShiftEvaluatorCreator |
| ChainBreakFilter.cc | |
| ChainBreakFilter.fwd.hh | |
| ChainBreakFilter.hh | |
| ChainBreakFilterCreator.hh | FilterCreators for the ChainBreakFilter |
| ChainCountFilter.cc | |
| ChainCountFilter.fwd.hh | FilterCreator for the ChainCountFilter |
| ChainCountFilter.hh | Count the amount of chains in a pose |
| ChainCountFilterCreator.hh | FilterCreator for the ChainCountFilter |
| ChiWellRmsdEvaluator.cc | |
| ChiWellRmsdEvaluator.hh | |
| ChiWellRmsdEvaluatorCreator.cc | |
| ChiWellRmsdEvaluatorCreator.hh | Header for ChiWellRmsdEvaluatorCreator |
| COFilter.cc | Runs reject or accept filters on pose |
| COFilter.hh | |
| ContactMapEvaluator.cc | |
| ContactMapEvaluator.hh | |
| ContactMapEvaluatorCreator.cc | |
| ContactMapEvaluatorCreator.hh | Header for ContactMapEvaluatorCreator |
| ContactMolecularSurfaceFilter.cc | Filter structures by weighted contact molecular surface area |
| ContactMolecularSurfaceFilter.fwd.hh | Filter structures by weighted contact molecular surface area |
| ContactMolecularSurfaceFilter.hh | Header file for ContactMolecularSurfaceFilter class |
| ContactMolecularSurfaceFilterCreator.hh | FilterCreator for the ContactMolecularSurfaceFilter |
| DeltaFilter.cc | |
| DeltaFilter.fwd.hh | Forward declaration for DeltaFilter |
| DeltaFilter.hh | Reports the average degree of connectivity of interface residues |
| DeltaFilterCreator.hh | FilterCreators for the DeltaFilter |
| DisulfideEntropyFilter.cc | Filter on the entropic effect of disulfide linkage |
| DisulfideEntropyFilter.fwd.hh | Filter on the entropic effect of disulfide linkage |
| DisulfideEntropyFilter.hh | Filter on the entropic effect of disulfide linkage |
| DisulfideEntropyFilterCreator.hh | FilterCreators for the DisulfideEntropyFilter |
| DomainInterfaceFilter.cc | Implementation of DomainInterfaceFilter which checks whether a defined region of a protein is part of an interface with a pre-defined other domain of the protein |
| DomainInterfaceFilter.fwd.hh | Forward declaration for DomainInterfaceFilter which checks if a query region is part of an an interface with a pre-defined other domain of a protein |
| DomainInterfaceFilter.hh | Header file for DomainInterfaceFilter which checks whether a defined region of a protein is buried in an interface by evaluating the number of non-water neighbors of all residues |
| EnergyPerResidueFilter.cc | |
| EnergyPerResidueFilter.fwd.hh | |
| EnergyPerResidueFilter.hh | Definition of filter class EnergyPerResidueFilter |
| EnergyPerResidueFilterCreator.hh | FilterCreators for the EnergyPerResidueFilterCreator |
| EvaluatedTrialMover.cc | |
| EvaluatedTrialMover.hh | |
| ExpiryFilter.cc | |
| ExpiryFilter.fwd.hh | |
| ExpiryFilter.hh | Simple filter that tests whether a file exists. Useful to test whether we're recovering from a checkpoint |
| ExpiryFilterCreator.hh | FilterCreators for the ExpiryFilter |
| ExternalEvaluator.cc | |
| ExternalEvaluator.hh | |
| ExtraScoreEvaluatorCreator.cc | |
| ExtraScoreEvaluatorCreator.hh | Header for ExtraScoreEvaluatorCreator |
| FileExistFilter.cc | |
| FileExistFilter.fwd.hh | |
| FileExistFilter.hh | Simple filter that tests whether a file exists. Useful to test whether we're recovering from a checkpoint |
| FileExistFilterCreator.hh | FilterCreators for the FileExistFilter |
| FileRemoveFilter.cc | |
| FileRemoveFilter.fwd.hh | |
| FileRemoveFilter.hh | Simple filter that tests whether a file exists. Useful to test whether we're recovering from a checkpoint |
| FileRemoveFilterCreator.hh | FilterCreators for the FileRemoveFilter |
| HelixHelixAngleFilter.cc | HelixHelixAngleFilter computes wither the crossing angle or distance between two TMs |
| HelixHelixAngleFilter.fwd.hh | Return the matching (%) between span file determined topology and of the actual pose |
| HelixHelixAngleFilter.hh | HelixHelixAngleFilter computes wither the crossing angle or distance between two TMs |
| HelixHelixAngleFilterCreator.hh | FilterCreators for the HelixHelixAngleFilterCreator |
| HolesFilter.cc | |
| HolesFilter.fwd.hh | Filter structures by will's hole score |
| HolesFilter.hh | Header file for HolesFilter class |
| HolesFilterCreator.hh | FilterCreator for the HolesFilter |
| InterfaceHbondsFilter.cc | Counts the number of hydrogen bonds across an interface defined by a jump, the salt |
| InterfaceHbondsFilter.fwd.hh | Forward declaration for InterfaceHbondsFilter |
| InterfaceHbondsFilter.hh | Counts the number of cross interface hydrogen bonds |
| InterfaceHbondsFilterCreator.hh | FilterCreators for the InterfaceHbondsFilter |
| InterfaceHydrophobicResidueContactsFilter.cc | Counts the number of hydrophobic residues on the target that have at least a certain hydrophobic score |
| InterfaceHydrophobicResidueContactsFilter.fwd.hh | Forward declaration for InterfaceHydrophobicResidueContactsFilter |
| InterfaceHydrophobicResidueContactsFilter.hh | Counts the number of hydrophobic residues on the target that have at least a certain hydrophobic score |
| InterfaceHydrophobicResidueContactsFilterCreator.hh | FilterCreators for the InterfaceHydrophobicResidueContactsFilter |
| InterfaceSasaFilter.cc | |
| InterfaceSasaFilter.fwd.hh | |
| InterfaceSasaFilter.hh | Definition of filter class InterfaceSasaFilter |
| InterfaceSasaFilterCreator.hh | FilterCreators for the InterfaceSasaFilterCreator |
| InterRepeatContactFilter.cc | |
| InterRepeatContactFilter.fwd.hh | |
| InterRepeatContactFilter.hh | |
| InterRepeatContactFilterCreator.hh | |
| IntraRepeatContactFilter.cc | |
| IntraRepeatContactFilter.fwd.hh | |
| IntraRepeatContactFilter.hh | |
| IntraRepeatContactFilterCreator.hh | |
| JScoreEvaluator.cc | |
| JScoreEvaluator.hh | |
| JScoreEvaluatorCreator.cc | |
| JScoreEvaluatorCreator.hh | Header for JScoreEvaluatorCreator |
| JumpEvaluator.cc | |
| JumpEvaluator.hh | |
| JumpNrEvaluatorCreator.cc | |
| JumpNrEvaluatorCreator.hh | Header for JumpNrEvaluatorCreator |
| LeastNativeLike9merFilter.cc | |
| LeastNativeLike9merFilter.fwd.hh | |
| LeastNativeLike9merFilter.hh | Find the rmsd to the worst 9mer in the chain |
| LeastNativeLike9merFilterCreator.hh | |
| LongestContinuousApolarSegmentFilter.cc | This filter computes the longest continuous stretch of apolar residues within a pose or selection |
| LongestContinuousApolarSegmentFilter.fwd.hh | This filter computes the longest continuous stretch of polar residues within a pose or selection |
| LongestContinuousApolarSegmentFilter.hh | This filter computes the longest continuous stretch of polar residues within a pose or selection |
| LongestContinuousApolarSegmentFilterCreator.hh | This filter computes the longest continuous stretch of polar residues within a pose or selection |
| LongestContinuousPolarSegmentFilter.cc | This filter computes the longest continuous stretch of polar residues within a pose or selection |
| LongestContinuousPolarSegmentFilter.fwd.hh | This filter computes the longest continuous stretch of polar residues within a pose or selection |
| LongestContinuousPolarSegmentFilter.hh | This filter computes the longest continuous stretch of polar residues within a pose or selection |
| LongestContinuousPolarSegmentFilterCreator.hh | This filter computes the longest continuous stretch of polar residues within a pose or selection |
| MembAccesResidueLipophilicityFilter.cc | Return the matching (%) between span file determined topology and of the actual pose |
| MembAccesResidueLipophilicityFilter.fwd.hh | Return the matching (%) between span file determined topology and of the actual pose |
| MembAccesResidueLipophilicityFilter.hh | Calcualtes the overall lipophilicity of the pose for each residue exposed to the ocre, the dsTbL membrane insertion energy is computed, and multiplied by the relative SASA of that residue. this amounts, generally speaking, ot the energy of isnertion of the protein, in that conformation. useful for filtering poses that are not hydrophobic enough |
| MembAccesResidueLipophilicityFilterCreator.hh | FilterCreators for the MembAccesResidueLipophilicityFilterCreator |
| MotifScoreFilter.cc | Scores poses using will's motifScore |
| MotifScoreFilter.fwd.hh | |
| MotifScoreFilter.hh | |
| MotifScoreFilterCreator.hh | |
| MPSpanAngleFilter.cc | Calculates the angle between the TM span and the membrane normal |
| MPSpanAngleFilter.fwd.hh | Calculates the angle between the TM span and the membrane normal |
| MPSpanAngleFilter.hh | Definition of filter class MPSpanAngleFilter |
| MPSpanAngleFilterCreator.hh | |
| MutationsFilter.cc | |
| MutationsFilter.fwd.hh | Forward declaration for MutationsFilter |
| MutationsFilter.hh | A filter to return the number of mutated positions within a given set of designable resdues |
| MutationsFilterCreator.hh | FilterCreators for the MutationsFilter |
| NativeEvaluatorCreator.cc | |
| NativeEvaluatorCreator.hh | Header for NativeEvaluatorCreator |
| NeighborTypeFilter.cc | |
| NeighborTypeFilter.fwd.hh | |
| NeighborTypeFilter.hh | Definition of filter class InterfaceSasaFilter |
| NeighborTypeFilterCreator.hh | FilterCreators for the NeighborTypeFilterCreator |
| NetChargeFilter.cc | |
| NetChargeFilter.fwd.hh | |
| NetChargeFilter.hh | Definition of filter class NetChargeFilter |
| NetChargeFilterCreator.hh | FilterCreators for the NetChargeFilterCreator |
| NMerPSSMEnergyFilter.cc | |
| NMerPSSMEnergyFilter.fwd.hh | |
| NMerPSSMEnergyFilter.hh | Definition of filter class NMerPSSMEnergyFilter |
| NMerPSSMEnergyFilterCreator.hh | FilterCreators for the NMerPSSMEnergyFilter |
| NMerSVMEnergyFilter.cc | |
| NMerSVMEnergyFilter.fwd.hh | |
| NMerSVMEnergyFilter.hh | Definition of filter class NMerSVMEnergyFilter |
| NMerSVMEnergyFilterCreator.hh | FilterCreators for the NMerSVMEnergyFilter |
| NonSequentialNeighborsFilter.cc | |
| NonSequentialNeighborsFilter.fwd.hh | |
| NonSequentialNeighborsFilter.hh | Simple filter that tests whether a file exists. Useful to test whether we're recovering from a checkpoint |
| NonSequentialNeighborsFilterCreator.hh | FilterCreators for the NonSequentialNeighborsFilter |
| PackerNeighborGraphFilter.cc | |
| PackerNeighborGraphFilter.hh | Header file for packer neighbor graph based filter |
| PackStatFilter.cc | |
| PackStatFilter.fwd.hh | |
| PackStatFilter.hh | Header file for PackStatFilter class |
| PackStatFilterCreator.hh | FilterCreator for the PackStatFilter |
| PalesEvaluator.cc | |
| PalesEvaluator.hh | |
| PalesEvaluatorCreator.cc | |
| PalesEvaluatorCreator.hh | Header for PalesEvaluatorCreator |
| PDDFScoreFilter.cc | Runs reject or accept filters on pose |
| PDDFScoreFilter.fwd.hh | |
| PDDFScoreFilter.hh | |
| PoolEvaluatorCreator.cc | |
| PoolEvaluatorCreator.hh | Header for PoolEvaluatorCreator |
| PoseCommentFilter.cc | |
| PoseCommentFilter.fwd.hh | |
| PoseCommentFilter.hh | |
| PoseCommentFilterCreator.hh | FilterCreators for the PoseCommentFilter |
| PoseInfoFilter.cc | |
| PoseInfoFilter.hh | Filter for outputing information about the pose |
| PoseInfoFilterCreator.hh | FilterCreator for the PoseInfoFilter |
| PoseMetricEvaluator.fwd.hh | Forward header for PoseMetricEvaluator |
| PoseMetricEvaluator.hh | |
| PredictedBurialEvaluator.cc | |
| PredictedBurialEvaluator.hh | |
| PredictedBurialFnEvaluatorCreator.cc | |
| PredictedBurialFnEvaluatorCreator.hh | Header for PredictedBurialFnEvaluatorCreator |
| RangeFilter.cc | |
| RangeFilter.fwd.hh | |
| RangeFilter.hh | Range filter evaluates if the return value of a particular filter is between a specific range |
| RangeFilterCreator.hh | FilterCreator for the RangeFilter |
| RDC_Evaluator.cc | |
| RDC_Evaluator.fwd.hh | |
| RDC_Evaluator.hh | |
| RdcEvaluatorCreator.cc | |
| RdcEvaluatorCreator.hh | Header for RdcEvaluatorCreator |
| RdcSelectEvaluatorCreator.cc | |
| RdcSelectEvaluatorCreator.hh | Header for RdcSelectEvaluatorCreator |
| RdcTargetEvaluatorCreator.cc | |
| RdcTargetEvaluatorCreator.hh | Header for RdcTargetEvaluatorCreator |
| ReadPoseExtraScoreFilter.cc | |
| ReadPoseExtraScoreFilter.fwd.hh | |
| ReadPoseExtraScoreFilter.hh | Definition of filter class ReadPoseExtraScoreFilter |
| ReadPoseExtraScoreFilterCreator.hh | FilterCreators for the ReadPoseExtraScoreFilter |
| RepeatParameterFilter.cc | Can filter a pose for the rise, run and omega. Many of the functions have been stolen from RepeatGlobalFrame but made const to work with filter obejcts |
| RepeatParameterFilter.fwd.hh | Forward declaration for RepeatParameterFilter |
| RepeatParameterFilter.hh | Simple filter that tests whether a file exists. Useful to test whether we're recovering from a checkpoint |
| RepeatParameterFilterCreator.hh | |
| ReportFilter.cc | |
| ReportFilter.fwd.hh | |
| ReportFilter.hh | Simple filter that tests whether a file exists. Useful to test whether we're recovering from a checkpoint |
| ReportFilterCreator.hh | FilterCreators for the ReportFilter |
| ResidueBurialFilter.cc | |
| ResidueBurialFilter.fwd.hh | |
| ResidueBurialFilter.hh | Definition of filter class ResidueBurialFilter |
| ResidueBurialFilterCreator.hh | FilterCreator for the ResidueBurialFilter |
| ResidueChiralityFilter.cc | Checks the chirality of a specific residues, whether it is D or L |
| ResidueChiralityFilter.fwd.hh | Return the matching (%) between span file determined topology and of the actual pose |
| ResidueChiralityFilter.hh | Checks the chirality of a specific residues, whether it is D or L |
| ResidueChiralityFilterCreator.hh | FilterCreators for the ResidueChiralityFilterCreator |
| ResidueCountFilter.cc | Filter on the total number of residues in the structure |
| ResidueCountFilter.fwd.hh | Filter on the total number of residues in the structure |
| ResidueCountFilter.hh | Filter on the total number of residues in the structure |
| ResidueCountFilterCreator.hh | FilterCreators for the ResidueCountFilter |
| ResidueDepthFilter.cc | |
| ResidueDepthFilter.fwd.hh | |
| ResidueDepthFilter.hh | |
| ResidueDepthFilterCreator.hh | FilterCreator for the ResidueDepthFilter |
| ResidueDistanceFilter.cc | |
| ResidueDistanceFilter.fwd.hh | |
| ResidueDistanceFilter.hh | Definition of filter class ResidueDistanceFilter |
| ResidueDistanceFilterCreator.hh | FilterCreator for the ResidueDistanceFilter |
| ResidueIEFilter.cc | |
| ResidueIEFilter.fwd.hh | |
| ResidueIEFilter.hh | Definition of filter class ResidueIEFilter |
| ResidueIEFilterCreator.hh | FilterCreators for the ResidueIEFilterCreator |
| ResidueLipophilicityFilter.cc | Returns the value calculated by the energy term mp_res_lipo. useful for understanding and debugging this energy term. use the output_file tag to print a full table of parameters from within the energy term |
| ResidueLipophilicityFilter.fwd.hh | Returns the value calculated by the energy term mp_res_lipo. useful for understanding and debugging this energy term. use the output_file tag to print a full table of parameters from within the energy term |
| ResidueLipophilicityFilter.hh | Definition of filter class ResidueLipophilicityFilter |
| ResidueLipophilicityFilterCreator.hh | FilterCreators for the ResidueLipophilicityFilterCreator |
| ResidueSelectionDistanceFilter.cc | |
| ResidueSelectionDistanceFilter.fwd.hh | |
| ResidueSelectionDistanceFilter.hh | Loops over the residues in a residue selector and reports the average distance |
| ResidueSelectionDistanceFilterCreator.hh | FilterCreator for the ResidueSelectionDistanceFilter |
| ResidueSetChainEnergyFilter.cc | |
| ResidueSetChainEnergyFilter.fwd.hh | |
| ResidueSetChainEnergyFilter.hh | Definition of filter class ResidueSetChainEnergyFilter |
| ResidueSetChainEnergyFilterCreator.hh | FilterCreators for the ResidueSetChainEnergyFilter |
| ResiduesInInterfaceFilter.cc | |
| ResiduesInInterfaceFilter.fwd.hh | |
| ResiduesInInterfaceFilter.hh | Reports to Tracer which residues are designable in a taskfactory |
| ResiduesInInterfaceFilterCreator.hh | FilterCreators for the ResiduesInInterfaceFilter |
| RGFilter.cc | Runs reject or accept filters on pose |
| RGFilter.hh | |
| RmsdEvaluator.cc | |
| RmsdEvaluator.hh | |
| RmsdEvaluatorCreator.cc | |
| RmsdEvaluatorCreator.hh | Header for RmsdEvaluatorCreator |
| RmsdTargetEvaluatorCreator.cc | |
| RmsdTargetEvaluatorCreator.hh | Header for RmsdTargetEvaluatorCreator |
| SaveResfileToDiskFilter.cc | Outputs a resfile based on a given set of taskoperations |
| SaveResfileToDiskFilter.fwd.hh | |
| SaveResfileToDiskFilter.hh | Header file for SaveResfileToDiskFilter class |
| SaveResfileToDiskFilterCreator.hh | FilterCreator for the SaveResfileToDiskFilter |
| SAXSScoreFilter.cc | Runs reject or accept filters on pose |
| SAXSScoreFilter.fwd.hh | |
| SAXSScoreFilter.hh | |
| ScoreEvaluator.cc | |
| ScoreEvaluator.hh | |
| SecretionPredictionFilter.cc | |
| SecretionPredictionFilter.fwd.hh | Filter for greasy helices https://www.nature.com/articles/nature06387 |
| SecretionPredictionFilter.hh | Filter for greasy helices https://www.nature.com/articles/nature06387 |
| SecretionPredictionFilterCreator.hh | |
| SequenceDistanceFilter.cc | |
| SequenceDistanceFilter.fwd.hh | |
| SequenceDistanceFilter.hh | |
| SequenceDistanceFilterCreator.hh | FilterCreators for the SequenceDistanceFilter |
| ShapeComplementarityFilter.cc | |
| ShapeComplementarityFilter.fwd.hh | |
| ShapeComplementarityFilter.hh | Header file for ShapeComplementarityFilter class |
| ShapeComplementarityFilterCreator.hh | FilterCreator for the ShapeComplementarityFilter |
| SheetFilter.cc | Runs reject or accept filters on pose |
| SheetFilter.hh | |
| SidechainRmsdFilter.cc | A filter based on automorphic sidechain RMSD |
| SidechainRmsdFilter.fwd.hh | A filter based on automorphic sidechain RMSD |
| SidechainRmsdFilter.hh | A filter based on automorphic sidechain RMSD |
| SidechainRmsdFilterCreator.hh | |
| SimpleHbondsToAtomFilter.cc | Simple filter for detercting Hbonds to atom with energy < energy cutoff |
| SimpleHbondsToAtomFilter.fwd.hh | Simple filter for detercting Hbonds to atom with energy < energy cutoff |
| SimpleHbondsToAtomFilter.hh | Simple filter for detercting Hbonds to atom with energy < energy cutoff |
| SimpleHbondsToAtomFilterCreator.hh | Simple filter for detercting Hbonds to atom with energy < energy cutoff |
| SimpleMetricFilter.cc | A filter takes any RealMetric and applies a set cutoff to filter the model |
| SimpleMetricFilter.fwd.hh | A filter takes any RealMetric and applies a set cutoff to filter the model |
| SimpleMetricFilter.hh | A filter takes any RealMetric and applies a set cutoff to filter the model |
| SimpleMetricFilterCreator.hh | A filter takes any RealMetric and applies a set cutoff to filter the model |
| SpanTopologyMatchPoseFilter.cc | Return the matching (%) between span file determined topology and of the actual pose |
| SpanTopologyMatchPoseFilter.fwd.hh | Return the matching (%) between span file determined topology and of the actual pose |
| SpanTopologyMatchPoseFilter.hh | Definition of filter class SpanTopologyMatchPoseFilter |
| SpanTopologyMatchPoseFilterCreator.hh | FilterCreators for the SpanTopologyMatchPoseFilterCreator |
| SSElementLengthFilter.cc | |
| SSElementLengthFilter.fwd.hh | Filter structures by longest,shortest or avg length of a given secondary structure type |
| SSElementLengthFilter.hh | Filter structures by longest,shortest or avg length of a given secondary structure type |
| SSElementLengthFilterCreator.hh | |
| SSElementMotifContactFilter.cc | |
| SSElementMotifContactFilter.fwd.hh | Filter for the interconnection between secondary elements |
| SSElementMotifContactFilter.hh | Reports either the average ss-contact or the worst ss-contacting element |
| SSElementMotifContactFilterCreator.hh | |
| SSMotifFinderFilter.cc | |
| SSMotifFinderFilter.fwd.hh | |
| SSMotifFinderFilter.hh | |
| SSMotifFinderFilterCreator.hh | FilterCreators for the SSMotifFinderFilter |
| StemFinderFilter.cc | |
| StemFinderFilter.fwd.hh | |
| StemFinderFilter.hh | |
| StemFinderFilterCreator.hh | FilterCreators for the StemFinderFilter |
| StructuralSimilarityEvaluator.cc | |
| StructuralSimilarityEvaluator.fwd.hh | Forward declaration for StructuralSimilarityEvaluator class |
| StructuralSimilarityEvaluator.hh | |
| StructureSimilarityEvaluatorCreator.cc | |
| StructureSimilarityEvaluatorCreator.hh | Header for StructureSimilarityEvaluatorCreator |
| SymmetricMotifFilter.cc | |
| SymmetricMotifFilter.hh | |
| SymmetricMotifFilterCreator.hh | |
| TaskAwareSASAFilter.cc | Calculates SASA for a set of residues defined by TaskOperations |
| TaskAwareSASAFilter.fwd.hh | |
| TaskAwareSASAFilter.hh | Header file for TaskAwareSASAFilter class |
| TaskAwareSASAFilterCreator.hh | FilterCreator for the TaskAwareSASAFilter |
| TaskAwareScoreTypeFilter.cc | |
| TaskAwareScoreTypeFilter.fwd.hh | Forward declaration for TaskAwareScoreTypeFilter |
| TaskAwareScoreTypeFilter.hh | |
| TaskAwareScoreTypeFilterCreator.hh | FilterCreators for the TaskAwareScoreTypeFilter |
| TerminusDistanceFilter.cc | |
| TerminusDistanceFilter.fwd.hh | |
| TerminusDistanceFilter.hh | Definition of filter class TerminusDistanceFilter |
| TerminusDistanceFilterCreator.hh | FilterCreators for the TerminusDistanceFilterCreator |
| TMsAACompFilter.cc | Return the matching (%) between span file determined topology and of the actual pose |
| TMsAACompFilter.fwd.hh | Return the matching (%) between span file determined topology and of the actual pose |
| TMsAACompFilter.hh | Definition of filter class TMsAACompFilter |
| TMsAACompFilterCreator.hh | FilterCreators for the TMsAACompFilterCreator |
| TMsSpanMembraneFilter.cc | Return the matching (%) between span file determined topology and of the actual pose |
| TMsSpanMembraneFilter.fwd.hh | Return the matching (%) between span file determined topology and of the actual pose |
| TMsSpanMembraneFilter.hh | Definition of filter class TMsSpanMembraneFilter |
| TMsSpanMembraneFilterCreator.hh | FilterCreators for the TMsSpanMembraneFilterCreator |
| TotalSasaFilter.cc | |
| TotalSasaFilter.fwd.hh | |
| TotalSasaFilter.hh | Definition of filter class TotalSasaFilter |
| TotalSasaFilterCreator.hh | FilterCreators for the TotalSasaFilterCreator |
| ► simple_moves | |
| ► asym_fold_and_dock | |
| AsymFoldandDockMoveRbJumpMover.cc | |
| AsymFoldandDockMoveRbJumpMover.fwd.hh | |
| AsymFoldandDockMoveRbJumpMover.hh | |
| AsymFoldandDockMoveRbJumpMoverCreator.hh | |
| AsymFoldandDockRbTrialMover.cc | |
| AsymFoldandDockRbTrialMover.fwd.hh | |
| AsymFoldandDockRbTrialMover.hh | |
| AsymFoldandDockRbTrialMoverCreator.hh | |
| ► bb_sampler | |
| BBDihedralSampler.cc | This class functions to hold, access, and set independent and dependent dihedral data. It can act as a base class for particular types of data |
| BBDihedralSampler.fwd.hh | |
| BBDihedralSampler.hh | This class functions to hold, access, and set independent and dependent dihedral data. It can act as a base class for particular types of data |
| SmallBBSampler.cc | A bb sampler that samples within a range of a starting angle. Similar to small mover |
| SmallBBSampler.fwd.hh | A bb sampler that samples within a range of a starting angle. Similar to small mover |
| SmallBBSampler.hh | A bb sampler that samples within a range of a starting angle. Similar to small mover |
| SugarBBSampler.cc | Sample dihdrals using sugar_bb data |
| SugarBBSampler.fwd.hh | |
| SugarBBSampler.hh | |
| ► bin_transitions | |
| InitializeByBins.cc | This mover takes a stretch of backbone and initializes its mainchain torsions based on the probabilities of transitions from one torsion bin to another |
| InitializeByBins.fwd.hh | |
| InitializeByBins.hh | |
| InitializeByBinsCreator.hh | This class will create instances of protocols::moves::Mover InitializeByBins for the protocols::moves::MoverFactory |
| PerturbByBins.cc | This mover takes a stretch of backbone and perturbs its mainchain torsions based on the probabilities of transitions from one torsion bin to another |
| PerturbByBins.fwd.hh | |
| PerturbByBins.hh | |
| PerturbByBinsCreator.hh | This class will create instances of protocols::moves::Mover PerturbByBins for the protocols::moves::MoverFactory |
| ► chiral | |
| ChiralMover.cc | ChiralMover methods implemented |
| ChiralMover.fwd.hh | ChiralMover forward declarations header |
| ChiralMover.hh | |
| ► rational_mc | |
| RationalMonteCarlo.cc | |
| RationalMonteCarlo.fwd.hh | |
| RationalMonteCarlo.hh | |
| ► sidechain_moves | |
| JumpRotamerSidechainMover.cc | |
| JumpRotamerSidechainMover.fwd.hh | |
| JumpRotamerSidechainMover.hh | Definition of JumpRotamerSidechainMover class and functions |
| JumpRotamerSidechainMoverCreator.hh | This class will create instances of protocols::moves::Mover JumpRotamerSidechainMover for the protocols::moves::MoverFactory |
| PerturbChiSidechainMover.cc | |
| PerturbChiSidechainMover.fwd.hh | |
| PerturbChiSidechainMover.hh | Definition of PerturbChiSidechainMover class and functions |
| PerturbChiSidechainMoverCreator.hh | This class will create instances of protocols::moves::Mover PerturbChiSidechainMover for the protocols::moves::MoverFactory |
| PerturbRotamerSidechainMover.cc | |
| PerturbRotamerSidechainMover.fwd.hh | |
| PerturbRotamerSidechainMover.hh | Definition of PerturbRotamerSidechainMover class and functions |
| PerturbRotamerSidechainMoverCreator.hh | This class will create instances of protocols::moves::Mover PerturbRotamerSidechainMover for the protocols::moves::MoverFactory |
| SetChiMover.cc | A mover to change one chi angle |
| SetChiMover.fwd.hh | A mover to change one chi angle |
| SetChiMover.hh | A mover to change one chi angle |
| SetChiMoverCreator.hh | A mover to change one chi angle |
| SidechainMCMover.cc | Implementation of SidechainMCMover class and functions |
| SidechainMCMover.fwd.hh | |
| SidechainMCMover.hh | Definition of SidechainMCMover class and functions |
| SidechainMCMoverCreator.hh | This class will create instances of protocols::moves::Mover SidechainMCMover for the protocols::moves::MoverFactory |
| SidechainMover.cc | Implementation of SidechainMover class and functions |
| SidechainMover.fwd.hh | |
| SidechainMover.hh | Definition of SidechainMover class and functions |
| SidechainMoverBase.cc | Implementation of JumpRotamerSidechainMover class and functions |
| SidechainMoverBase.fwd.hh | |
| SidechainMoverBase.hh | Definition of SidechainMoverBase class and functions |
| SidechainMoverCreator.hh | This class will create instances of protocols::moves::Mover SidechainMover for the protocols::moves::MoverFactory |
| AddCavitiesMover.cc | |
| AddCavitiesMover.hh | |
| AddChainMover.cc | |
| AddChainMover.fwd.hh | Add chain to an existing pose (as a new chain) |
| AddChainMover.hh | Switch the chain order |
| AddChainMoverCreator.hh | |
| AddJobPairData.cc | A really simple mover that takes some data in through xml and appends it to the pose |
| AddJobPairData.fwd.hh | Forward Header file for the AddJobPairData Mover |
| AddJobPairData.hh | Header file for the AddJobPairData Mover |
| AddJobPairDataCreator.hh | MoverCreator definitions for the AddJobPairData mover |
| AddPDBInfoMover.cc | |
| AddPDBInfoMover.fwd.hh | Forward header file for AddPDBInfoMover |
| AddPDBInfoMover.hh | |
| AddPDBInfoMoverCreator.hh | |
| AddResidueCouplingConstraint.cc | |
| AddResidueCouplingConstraint.fwd.hh | |
| AddResidueCouplingConstraint.hh | |
| AddResidueCouplingConstraintCreator.hh | |
| AddResidueLabelMover.cc | |
| AddResidueLabelMover.fwd.hh | |
| AddResidueLabelMover.hh | |
| AddResidueLabelMoverCreator.hh | This class will create instances of AddResidueLabelMover for the MoverFactory |
| AlignChainMover.cc | |
| AlignChainMover.fwd.hh | |
| AlignChainMover.hh | Switch the chain order |
| AlignChainMoverCreator.hh | |
| BackboneMover.cc | Method definitions for SmallMover and ShearMover |
| BackboneMover.fwd.hh | BackboneMover forward declarations header |
| BackboneMover.hh | Declarations and simple accessor/mutator definitions for SmallMover and ShearMover |
| BackboneMoverCreator.hh | This class will create instances of protocols::moves::Movers SmallMover and ShearMover for the protocols::moves::MoverFactory |
| BBConRotMover.cc | |
| BBConRotMover.fwd.hh | |
| BBConRotMover.hh | |
| BBDihedralSamplerMover.cc | |
| BBDihedralSamplerMover.fwd.hh | Mover interface to BBDihedralSampler |
| BBDihedralSamplerMover.hh | Mover interface to BBDihedralSampler |
| BBDihedralSamplerMoverCreator.hh | Mover interface to BBDihedralSampler |
| BBGaussianMover.cc | |
| BBGaussianMover.fwd.hh | Gaussian Perturbation to backbone |
| BBGaussianMover.hh | |
| BBGaussianMoverCreator.hh | |
| ChainSplitMover.cc | |
| ChainSplitMover.fwd.hh | Forward declaration of ChainSplitMover which splits a pose into two chains at a given cutpoint |
| ChainSplitMover.hh | Declaration of ChainSplitMover which splits a pose into two chains at a given cutpoint |
| ChangeAndResetFoldTreeMover.cc | |
| ChangeAndResetFoldTreeMover.fwd.hh | |
| ChangeAndResetFoldTreeMover.hh | Basic Mover used for setting up atomic protocols |
| ChangeAndResetFoldTreeMoverCreator.hh | |
| CombinePoseMover.cc | |
| CombinePoseMover.fwd.hh | |
| CombinePoseMover.hh | |
| ConcatenatePosesMover.cc | Links supplied Poses by their termini |
| ConcatenatePosesMover.fwd.hh | Links supplied Poses by their termini |
| ConcatenatePosesMover.hh | Links supplied Poses by their termini |
| ConcatenatePosesMoverCreator.hh | Links supplied Poses by their termini |
| ConstrainToIdealMover.cc | Adds to your pose constraints suitable for idealization of bond lengths and angles |
| ConstrainToIdealMover.fwd.hh | ConstrainToIdealMover forward declarations header |
| ConstrainToIdealMover.hh | Adds to your pose constraints suitable for idealization of bond lengths and angles |
| ContingentAcceptMover.cc | |
| ContingentAcceptMover.fwd.hh | Switch the chain order |
| ContingentAcceptMover.hh | Switch the chain order |
| ContingentAcceptMoverCreator.hh | |
| ConvertRealToVirtualMover.cc | Mover for switching a residue type to all virtual |
| ConvertRealToVirtualMover.fwd.hh | Mover for switching a residue type to all virtual |
| ConvertRealToVirtualMover.hh | Mover for switching a residue type to all virtual |
| ConvertRealToVirtualMoverCreator.hh | Mover for switching a residue type to all virtual |
| ConvertVirtualToRealMover.cc | Mover for switching virtual residues back to real residues |
| ConvertVirtualToRealMover.fwd.hh | Mover for switching virtual residues back to real residues |
| ConvertVirtualToRealMover.hh | Mover for switching virtual residues back to real residues |
| ConvertVirtualToRealMoverCreator.hh | |
| CopyDofMover.cc | |
| CopyDofMover.fwd.hh | |
| CopyDofMover.hh | |
| CopyRotamerMover.cc | A mover to copy a rotamer (residue identity and conformation) from one position in a pose to another |
| CopyRotamerMover.fwd.hh | A mover to copy a rotamer (residue identity and conformation) from one position in a pose to another |
| CopyRotamerMover.hh | A mover to copy a rotamer (residue identity and conformation) from one position in a pose to another |
| CopyRotamerMoverCreator.hh | A mover to copy a rotamer (residue identity and conformation) from one position in a pose to another |
| CoupledMover.cc | Implementation of CoupledMover class and functions |
| CoupledMover.fwd.hh | |
| CoupledMover.hh | Definition of CoupledMover class and functions |
| CoupledMoverCreator.hh | This class will create instances of protocols::moves::Mover CoupledMover for the protocols::moves::MoverFactory |
| CutChainMover.cc | |
| CutChainMover.fwd.hh | |
| CutChainMover.hh | |
| CutChainMoverCreator.hh | |
| CyclizationMover.cc | |
| CyclizationMover.fwd.hh | |
| CyclizationMover.hh | Implimentation file for CyclizationMover |
| DeleteChainMover.cc | |
| DeleteChainMover.fwd.hh | Add chain to an existing pose (as a new chain) |
| DeleteChainMover.hh | Delete the chain specified by chain number |
| DeleteChainMoverCreator.hh | |
| DeleteChainsMover.cc | |
| DeleteChainsMover.fwd.hh | Forward declations for DeleteChainsMover |
| DeleteChainsMover.hh | Delete a chain from a pose |
| DeleteChainsMoverCreator.hh | Declaration of the protocols::moves::MoverCreator class for the DeleteChainsMover |
| DisulfideInsertionMover.cc | Mover that closes a receptor bound peptide by an added disulfide bond |
| DisulfideInsertionMover.fwd.hh | Forward header file for DisulfideInsertionMover |
| DisulfideInsertionMover.hh | Header file for DisulfideInsertionMover |
| DisulfideInsertionMoverCreator.cc | Creator class for DisulfideInsertionMover |
| DisulfideInsertionMoverCreator.fwd.hh | Creator class for DisulfideInsertionMover |
| DisulfideInsertionMoverCreator.hh | Creator class for DisulfideInsertionMover |
| DME_FilterMover.cc | |
| DME_FilterMover.hh | |
| DOFHistogramRecorder.cc | |
| DOFHistogramRecorder.fwd.hh | Forward declarations for class DOFHistogramRecorder |
| DOFHistogramRecorder.hh | |
| DumpPdb.cc | |
| DumpPdb.fwd.hh | Forward header file for DumpPdb |
| DumpPdb.hh | |
| DumpPdbCreator.hh | |
| DumpSingleResidueRotamers.cc | Given a residue index, dump all of the rotamers to individual PDB files within 0-1 sd of the mean |
| DumpSingleResidueRotamers.fwd.hh | Given a residue index, dump all of the rotamers to individual PDB files within 0-1 sd of the mean |
| DumpSingleResidueRotamers.hh | Given a residue index, dump all of the rotamers to individual PDB files within 0-1 sd of the mean |
| DumpSingleResidueRotamersCreator.hh | Given a residue index, dump all of the rotamers to individual PDB files within 0-1 sd of the mean |
| ExplicitWaterMover.cc | Add explicit water molecules to surface of biomolecule |
| ExplicitWaterMover.fwd.hh | |
| ExplicitWaterMover.hh | |
| ExplicitWaterMoverCreator.hh | |
| FavorSequenceProfile.cc | Add a SequenceProfileConstraint to a pose |
| FavorSequenceProfile.hh | Add a SequenceProfileConstraint to a pose |
| FavorSequenceProfileCreator.hh | Declaration of the protocols::moves::MoverCreator class for the FavorSequenceProfile |
| FavorSymmetricSequence.cc | Apply constraints to enforce a symmetric sequence |
| FavorSymmetricSequence.fwd.hh | Apply constraints to enforce a symmetric sequence |
| FavorSymmetricSequence.hh | Apply constraints to enforce a symmetric sequence |
| FavorSymmetricSequenceCreator.hh | Apply constraints to enforce a symmetric sequence |
| FoldTreeFromMotif.cc | |
| FoldTreeFromMotif.fwd.hh | FoldTreeFromMotif forward declarations header |
| FoldTreeFromMotif.hh | |
| FoldTreeFromMotifCreator.hh | |
| FragmentMover.cc | |
| FragmentMover.fwd.hh | |
| FragmentMover.hh | |
| GunnCost.cc | |
| GunnCost.hh | |
| LoadUnboundRotMover.cc | LoadUnboundRotMover methods implemented |
| LoadUnboundRotMover.fwd.hh | |
| LoadUnboundRotMover.hh | |
| LoadUnboundRotMoverCreator.hh | |
| MembraneTopology.cc | |
| MembraneTopology.fwd.hh | |
| MembraneTopology.hh | |
| MembraneTopologyCreator.hh | |
| MissingDensityToJumpMover.cc | Implementation of mover that inserts a jump where there is gap in the pdb. This gap corresponds to missing density |
| MissingDensityToJumpMover.fwd.hh | Implementation of mover that inserts a jump where there is gap in the pdb. This gap corresponds to missing density |
| MissingDensityToJumpMover.hh | |
| ModifyVariantTypeMover.cc | Modify variant type to residues |
| ModifyVariantTypeMover.fwd.hh | |
| ModifyVariantTypeMover.hh | |
| ModifyVariantTypeMoverCreator.hh | |
| MutateResidue.cc | |
| MutateResidue.fwd.hh | |
| MutateResidue.hh | |
| MutateResidueCreator.hh | |
| PDBReloadMover.cc | |
| PDBReloadMover.fwd.hh | PDBReloadMover forward declarations header |
| PDBReloadMover.hh | |
| PDBReloadMoverCreator.hh | |
| PeriodicBoxMover.cc | Mover for running liquid simulation (or related other) |
| PeriodicBoxMover.fwd.hh | |
| PeriodicBoxMover.hh | Mover for running liquid simulation (and related others) |
| PeriodicBoxMoverCreator.hh | |
| PoseFromPoseResourceMover.cc | Mover that shuttles a Pose from a PoseResource into the DataMap when its parse_my_tag method is invoked |
| PoseFromPoseResourceMover.fwd.hh | Mover that shuttles a Pose from a PoseResource into the DataMap when its parse_my_tag method is invoked |
| PoseFromPoseResourceMover.hh | Mover that shuttles a Pose from a PoseResource into the DataMap when its parse_my_tag method is invoked |
| PoseFromPoseResourceMoverCreator.hh | Mover that shuttles a Pose from a PoseResource into the DataMap when its parse_my_tag method is invoked |
| ProlineFixMover.cc | |
| ProlineFixMover.fwd.hh | |
| ProlineFixMover.hh | |
| PSSM2BfactorMover.cc | |
| PSSM2BfactorMover.fwd.hh | Switch the chain order |
| PSSM2BfactorMover.hh | |
| PSSM2BfactorMoverCreator.hh | |
| RandomOmegaFlipMover.cc | |
| RandomOmegaFlipMover.fwd.hh | |
| RandomOmegaFlipMover.hh | |
| RandomOmegaFlipMoverCreator.hh | This class will create instances of RandomOmegaFlipMover for the MoverFactory |
| RandomTorsionMover.cc | |
| RandomTorsionMover.fwd.hh | |
| RandomTorsionMover.hh | |
| RandomTorsionMoverCreator.hh | This class will create instances of RandomTorsionMover for the MoverFactory |
| ReportEffectivePKA.cc | |
| ReportEffectivePKA.hh | |
| ReportEffectivePKACreator.hh | This class will create instances of Mover ReportEffectivePKA for the MoverFactory |
| ReportXYZ.cc | |
| ReportXYZ.fwd.hh | |
| ReportXYZ.hh | Adds the x,y,z of a selected residue to the score function |
| ReportXYZCreator.hh | |
| RepulsiveOnlyMover.cc | Calculate repulsive energy only for certain residues |
| RepulsiveOnlyMover.fwd.hh | |
| RepulsiveOnlyMover.hh | |
| ResetFoldTree.cc | |
| ResetFoldTree.fwd.hh | Eliminates the fold tree |
| ResetFoldTree.hh | Wipes out a fold tree making the first residue 0 and the last residue the length of the protein |
| ResetFoldTreeCreator.hh | |
| ResetFullModelInfoMover.cc | Ensure synchronized full model info |
| ResetFullModelInfoMover.fwd.hh | Ensure synchronized full model info |
| ResetFullModelInfoMover.hh | Ensure synchronized full model info |
| ResetFullModelInfoMoverCreator.hh | Ensure synchronized full model info |
| ResTypeFragmentMover.cc | |
| ResTypeFragmentMover.fwd.hh | |
| ResTypeFragmentMover.hh | |
| ReturnSidechainMover.cc | ReturnSidechainMover methods implemented |
| ReturnSidechainMover.fwd.hh | ReturnSidechainMover forward declarations header |
| ReturnSidechainMover.hh | Protocols::moves::Mover to "return" proper sidechains to a pose that was temporarily in centroid mode (can be used for any sidechain copying) |
| RingConformationMover.cc | Method definitions for RingConformationMover |
| RingConformationMover.fwd.hh | Forward declarations for RingConformationMover |
| RingConformationMover.hh | Declarations and simple accessor/mutator definitions for RingConformationMover |
| RingConformationMoverCreator.hh | Method declarations for RingConformationMoverCreator |
| SaveSequenceToCommentsMover.cc | Remove constraints from the current pose conformation |
| SaveSequenceToCommentsMover.fwd.hh | |
| SaveSequenceToCommentsMover.hh | Add constraints to the current pose conformation |
| SaveSequenceToCommentsMoverCreator.hh | Declaration of the MoverCreator class for the SaveSequenceToCommentsMover |
| ScoreMover.cc | Applies a ScoreFunction to a Pose. Also has CASP and loop modeling features |
| ScoreMover.fwd.hh | ScoreMover forward declarations header |
| ScoreMover.hh | |
| ScoreMoverCreator.hh | |
| SequenceProfileMover.cc | Moverization of code that was embedded in the parser |
| SequenceProfileMover.fwd.hh | |
| SequenceProfileMover.hh | BS mover to get around a stupid "mover" that was embedded in the parser |
| SequenceProfileMoverCreator.hh | |
| SetTorsion.cc | |
| SetTorsion.fwd.hh | |
| SetTorsion.hh | Sets the value of a desired torsion. Header files for the mover |
| SetTorsionCreator.hh | |
| SetupMetalsMover.cc | |
| SetupMetalsMover.fwd.hh | SetupMetalsMover forward declarations header |
| SetupMetalsMover.hh | Class definition for SetupMetalsMover |
| SetupMetalsMoverCreator.hh | |
| ShakeStructureMover.cc | |
| ShakeStructureMover.fwd.hh | |
| ShakeStructureMover.hh | |
| ShortBackrubMover.cc | Implementation of ShortBackrubMover class and functions |
| ShortBackrubMover.fwd.hh | |
| ShortBackrubMover.hh | Definition of ShortBackrubMover class and functions |
| ShortBackrubMoverCreator.hh | This class will create instances of protocols::moves::Mover ShortBackrubMover for the protocols::moves::MoverFactory |
| SimpleThreadingMover.cc | Very Simple class for threading a regional sequence onto a structure |
| SimpleThreadingMover.fwd.hh | |
| SimpleThreadingMover.hh | |
| SimpleThreadingMoverCreator.hh | |
| SmoothFragmentMover.cc | |
| SmoothFragmentMover.fwd.hh | |
| SmoothFragmentMover.hh | |
| StorePoseSnapshot.cc | Stores current residue indices in the pose as a ReferencePose. As residues are added or subtracted, this permits the user to set up movers based on the current residue indices rather than the modified indices of a future state |
| StorePoseSnapshot.fwd.hh | Owning pointers and whatnot for the StorePoseSnapshot mover class |
| StorePoseSnapshot.hh | Stores current residue indices in the pose as a ReferencePose. As residues are added or subtracted, this permits the user to set up movers based on the current residue indices rather than the modified indices of a future state. Header files for the mover |
| StorePoseSnapshotCreator.hh | This class will create instances of the protocols::simple_moves::StorePoseSnapshot mover for the protocols::moves::MoverFactory |
| StructProfileMover.cc | |
| StructProfileMover.fwd.hh | Quickly generates a structure profile |
| StructProfileMover.hh | Quickly generates a structure profile |
| StructProfileMoverCreator.hh | |
| SuperimposeMover.cc | |
| SuperimposeMover.fwd.hh | SuperimposeMover forward declarations header |
| SuperimposeMover.hh | |
| SuperimposeMoverCreator.hh | |
| SwitchChainOrderMover.cc | |
| SwitchChainOrderMover.fwd.hh | Switch the chain order |
| SwitchChainOrderMover.hh | Switch the chain order |
| SwitchChainOrderMoverCreator.hh | |
| SwitchResidueTypeSetMover.cc | Switch between residue type sets (e.g. centroid and all atom) |
| SwitchResidueTypeSetMover.fwd.hh | Switch between residue type sets (e.g. centroid and all atom) |
| SwitchResidueTypeSetMover.hh | Switch between residue type sets (e.g. centroid and all atom) |
| SwitchResidueTypeSetMoverCreator.hh | |
| SymmetricFragmentMover.cc | |
| SymmetricFragmentMover.fwd.hh | |
| SymmetricFragmentMover.hh | |
| TailsScoreMover.cc | |
| TailsScoreMover.hh | |
| TorsionDOFMover.cc | TorsionDOFMover methods implemented |
| TorsionDOFMover.fwd.hh | TorsionDOFMover forward declarations header |
| TorsionDOFMover.hh | TorsionDOFMover header |
| TorsionSetMover.cc | |
| TorsionSetMover.fwd.hh | |
| TorsionSetMover.hh | |
| Tumble.cc | Add constraints to the current pose conformation |
| Tumble.hh | Declaration of the MoverCreator class for the Tumble |
| TumbleCreator.hh | |
| UniformPositionMover.cc | |
| UniformPositionMover.fwd.hh | Apply a uniform (deterministic move) to a given position |
| UniformPositionMover.hh | Apply a uniform (deterministic move) to a given position |
| VirtualRootMover.cc | Manipulate virtual roots on poses. This is a seperate mover mainly to be RosettaScriptable |
| VirtualRootMover.fwd.hh | VirtualRootMover forward declarations header |
| VirtualRootMover.hh | Manipulate virtual roots on poses |
| VirtualRootMoverCreator.hh | |
| WobbleMover.cc | |
| WobbleMover.hh | |
| WriteFiltersToPose.cc | Writes all filter results to the pose file |
| WriteFiltersToPose.fwd.hh | |
| WriteFiltersToPose.hh | Writes all filter results to the pose file |
| WriteFiltersToPoseCreator.hh | This class will create instances of Mover WriteFiltersToPose for the MoverFactory |
| WriteSSEMover.cc | Writes SSE assignation from DSSP or prediction from PSIPRED as REMARK |
| WriteSSEMover.fwd.hh | Writes SSE assignation from DSSP or prediction from PSIPRED as REMARK |
| WriteSSEMover.hh | Writes SSE assignation from DSSP or prediction from PSIPRED as REMARK |
| WriteSSEMoverCreator.hh | Writes SSE assignation from DSSP or prediction from PSIPRED as REMARK |
| ► simple_pose_metric_calculators | |
| BuriedUnsatisfiedPolarsCalculator.cc | |
| BuriedUnsatisfiedPolarsCalculator.hh | |
| NumberHBondsCalculator.cc | |
| NumberHBondsCalculator.hh | |
| ► simple_task_operations | |
| InterfaceTaskOperation.cc | Base class for TaskOperations that will work with docking to define an interface |
| InterfaceTaskOperation.fwd.hh | |
| InterfaceTaskOperation.hh | Base class for TaskOperations that will work with docking to define an interface |
| RestrictToInterface.cc | When passed to a PackerTask, pack/design is limited to the protein interface |
| RestrictToInterface.fwd.hh | |
| RestrictToInterface.hh | When passed to a PackerTask, pack/design is limited to the interface |
| RestrictToInterfaceCreator.hh | |
| RestrictToLoops.cc | |
| RestrictToLoops.fwd.hh | |
| RestrictToLoops.hh | |
| RestrictToLoopsAndNeighbors.cc | |
| RestrictToLoopsAndNeighbors.fwd.hh | Forward declaration of the RestrictToLoopsAndNeighbors class |
| RestrictToLoopsAndNeighbors.hh | This class allows the selection for packing (and possibly design) of residues contained in a Loops object as well as the neighbors within a specified cutoff distance, with the default and maximum cutoff at 10.0 A |
| RestrictToLoopsAndNeighborsCreator.hh | Creator class for the RestrictToLoopsAndNeighbors TaskOperation |
| RestrictToLoopsCreator.hh | |
| ► sparta | |
| ANN.cc | |
| ANN.hh | |
| ChemicalShiftEvaluator.cc | |
| ChemicalShiftEvaluator.hh | |
| ChemicalShiftEvaluatorCreator.cc | |
| ChemicalShiftEvaluatorCreator.hh | |
| constants.hh | |
| GDB.cc | |
| GDB.hh | |
| main.cc | |
| PDB.cc | |
| PDB.hh | |
| Sparta.cc | |
| Sparta.hh | |
| SpartaUtil.cc | |
| SpartaUtil.hh | |
| util.cc | |
| util.hh | |
| ► splice | |
| AlignEndsMover.cc | |
| AlignEndsMover.fwd.hh | Switch the chain order |
| AlignEndsMover.hh | |
| AlignEndsMoverCreator.hh | This class will create instances of protocols::moves::Mover AlignEndsMover for the protocols::moves::MoverFactory |
| DesignInterfacesOperation.cc | |
| DesignInterfacesOperation.fwd.hh | |
| DesignInterfacesOperation.hh | |
| DesignInterfacesOperationCreator.hh | |
| FindEndpointsOperation.cc | |
| FindEndpointsOperation.fwd.hh | |
| FindEndpointsOperation.hh | |
| FindEndpointsOperationCreator.hh | |
| RBInMover.cc | |
| RBInMover.fwd.hh | Switch the chain order |
| RBInMover.hh | Get rigid body orientations vH antibody chains when vL is aligned |
| RBInMoverCreator.hh | This class will create instances of protocols::moves::Mover RBInMover for the protocols::moves::MoverFactory |
| RBOutMover.cc | |
| RBOutMover.fwd.hh | Create AB RBO DB |
| RBOutMover.hh | Get rigid body orientations vH antibody chains when vL is aligned |
| RBOutMoverCreator.hh | This class will create instances of protocols::moves::Mover RBOutMover for the protocols::moves::MoverFactory |
| RotLibOut.cc | Generate a database of rotamers from a list of pdbs |
| RotLibOut.fwd.hh | |
| RotLibOut.hh | Generate a database of rotamers from a list of pdbs in a text file. this is used |
| RotLibOutCreator.hh | This class will create instances of protocols::moves::Mover RotLibOut for the protocols::moves::MoverFactory |
| SampleRotamersFromPDB.cc | Given source PDBs limits the rotamer sampling to those found in equivalent positions in the PDB At initialization the taskoperation reads a database with allowed rotamers for each position and changes the Rotmer set accordingly |
| SampleRotamersFromPDB.fwd.hh | |
| SampleRotamersFromPDB.hh | |
| SampleRotamersFromPDBCreator.hh | |
| Splice.cc | |
| Splice.fwd.hh | Splice forward declarations header |
| Splice.hh | Not used anymore. samples BB conformation from a PDB and pallies it to the pose |
| SpliceCreator.hh | Declaration of the MoverCreator class for the Splice |
| SpliceIn.cc | |
| SpliceIn.fwd.hh | SpliceIn forward declarations header |
| SpliceIn.hh | |
| SpliceInAntibody.cc | |
| SpliceInAntibody.fwd.hh | SpliceInAntibody forward declarations header |
| SpliceInAntibody.hh | |
| SpliceInAntibodyCreator.hh | This class will create instances of protocols::moves::Mover SpliceInAntibody for the protocols::moves::MoverFactory |
| SpliceInCreator.hh | This class will create instances of protocols::moves::Mover SpliceIn for the protocols::moves::MoverFactory |
| SpliceInTail.cc | |
| SpliceInTail.fwd.hh | SpliceInTail forward declarations header |
| SpliceInTail.hh | |
| SpliceInTailCreator.hh | This class will create instances of protocols::moves::Mover SpliceInTail for the protocols::moves::MoverFactory |
| SpliceManager.cc | |
| SpliceManager.fwd.hh | Splice forward declarations header |
| SpliceManager.hh | |
| SpliceOut.cc | |
| SpliceOut.fwd.hh | SpliceOut forward declarations header |
| SpliceOut.hh | |
| SpliceOutAntibody.cc | |
| SpliceOutAntibody.fwd.hh | SpliceOutAntibody forward declarations header |
| SpliceOutAntibody.hh | |
| SpliceOutAntibodyCreator.hh | This class will create instances of protocols::moves::Mover SpliceOutAntibody for the protocols::moves::MoverFactory |
| SpliceOutCreator.hh | This class will create instances of protocols::moves::Mover SpliceOut for the protocols::moves::MoverFactory |
| SpliceOutTail.cc | |
| SpliceOutTail.fwd.hh | SpliceOutTail forward declarations header |
| SpliceOutTail.hh | |
| SpliceOutTailCreator.hh | This class will create instances of protocols::moves::Mover SpliceOutTail for the protocols::moves::MoverFactory |
| SpliceSegment.cc | |
| SpliceSegment.fwd.hh | Splice forward declarations header |
| SpliceSegment.hh | |
| TailSegmentMover.cc | |
| TailSegmentMover.fwd.hh | |
| TailSegmentMover.hh | |
| TailSegmentMoverCreator.hh | |
| util.cc | |
| util.hh | |
| ► ss_prediction | |
| SS_predictor.cc | |
| SS_predictor.fwd.hh | SS_predictor forward header |
| SS_predictor.hh | |
| ► star | |
| Extender.cc | |
| Extender.hh | |
| StarAbinitio.cc | |
| StarAbinitio.fwd.hh | |
| StarAbinitio.hh | |
| StarAbinitioMain.cc | |
| StarAbinitioMain.hh | |
| util.cc | |
| util.hh | |
| ► stepwise | |
| ► legacy | |
| ► modeler | |
| ► protein | |
| StepWiseProteinMinimizer.cc | |
| StepWiseProteinMinimizer.fwd.hh | |
| StepWiseProteinMinimizer.hh | |
| StepWiseProteinPoseSetup.cc | |
| StepWiseProteinPoseSetup.fwd.hh | |
| StepWiseProteinPoseSetup.hh | |
| util.cc | |
| util.hh | |
| ► rna | |
| RNA_AnalyticLoopCloser.cc | |
| RNA_AnalyticLoopCloser.fwd.hh | |
| RNA_AnalyticLoopCloser.hh | |
| StepWiseRNA_Clusterer.cc | |
| StepWiseRNA_Clusterer.hh | |
| StepWiseRNA_Minimizer.cc | |
| StepWiseRNA_Minimizer.fwd.hh | |
| StepWiseRNA_Minimizer.hh | |
| StepWiseRNA_PoseSelection.cc | |
| StepWiseRNA_PoseSelection.fwd.hh | |
| StepWiseRNA_PoseSelection.hh | |
| StepWiseRNA_PoseSetup.cc | |
| StepWiseRNA_PoseSetup.fwd.hh | |
| StepWiseRNA_PoseSetup.hh | |
| StepWiseRNA_PoseSetupFromCommandLine.cc | |
| StepWiseRNA_PoseSetupFromCommandLine.hh | |
| StepWiseRNA_WorkingParametersSetup.cc | |
| StepWiseRNA_WorkingParametersSetup.hh | |
| util.cc | |
| util.fwd.hh | |
| util.hh | |
| ► screener | |
| ProteinAtrRepScreener.cc | |
| ProteinAtrRepScreener.fwd.hh | |
| ProteinAtrRepScreener.hh | |
| RNA_AtrRepScreener.cc | |
| RNA_AtrRepScreener.fwd.hh | |
| RNA_AtrRepScreener.hh | |
| SimplePoseSelection.cc | |
| SimplePoseSelection.fwd.hh | |
| SimplePoseSelection.hh | |
| SimpleRMSD_Screener.cc | |
| SimpleRMSD_Screener.fwd.hh | |
| SimpleRMSD_Screener.hh | |
| ► modeler | |
| ► align | |
| StepWiseClusterer.cc | |
| StepWiseClusterer.fwd.hh | |
| StepWiseClusterer.hh | |
| StepWiseLegacyClusterer.cc | |
| StepWiseLegacyClusterer.fwd.hh | |
| StepWiseLegacyClusterer.hh | |
| StepWiseLegacyClustererSilentBased.cc | |
| StepWiseLegacyClustererSilentBased.fwd.hh | |
| StepWiseLegacyClustererSilentBased.hh | |
| StepWisePoseAligner.cc | |
| StepWisePoseAligner.fwd.hh | |
| StepWisePoseAligner.hh | |
| util.cc | |
| util.hh | |
| ► movemap | |
| util.cc | |
| util.hh | |
| ► options | |
| StepWiseBasicModelerOptions.cc | |
| StepWiseBasicModelerOptions.fwd.hh | |
| StepWiseBasicModelerOptions.hh | |
| StepWiseModelerOptions.cc | |
| StepWiseModelerOptions.fwd.hh | |
| StepWiseModelerOptions.hh | |
| StepWiseProteinModelerOptions.cc | |
| StepWiseProteinModelerOptions.fwd.hh | |
| StepWiseProteinModelerOptions.hh | |
| StepWiseRNA_ModelerOptions.cc | |
| StepWiseRNA_ModelerOptions.fwd.hh | |
| StepWiseRNA_ModelerOptions.hh | |
| ► packer | |
| SideChainCopier.cc | |
| SideChainCopier.fwd.hh | |
| SideChainCopier.hh | |
| StepWiseMasterPacker.cc | |
| StepWiseMasterPacker.fwd.hh | |
| StepWiseMasterPacker.hh | |
| StepWisePacker.cc | |
| StepWisePacker.fwd.hh | |
| StepWisePacker.hh | |
| util.cc | |
| util.hh | |
| ► polar_hydrogens | |
| PolarHydrogenPacker.cc | |
| PolarHydrogenPacker.fwd.hh | |
| PolarHydrogenPacker.hh | |
| util.cc | |
| util.hh | |
| ► precomputed | |
| PrecomputedLibraryMover.cc | |
| PrecomputedLibraryMover.fwd.hh | |
| PrecomputedLibraryMover.hh | |
| ► protein | |
| ► checker | |
| ProteinAtrRepChecker.cc | |
| ProteinAtrRepChecker.fwd.hh | |
| ProteinAtrRepChecker.hh | |
| ► loop_close | |
| StepWiseProteinCCD_Closer.cc | |
| StepWiseProteinCCD_Closer.fwd.hh | |
| StepWiseProteinCCD_Closer.hh | |
| StepWiseProteinCCD_MultiPoseCloser.cc | |
| StepWiseProteinCCD_MultiPoseCloser.fwd.hh | |
| StepWiseProteinCCD_MultiPoseCloser.hh | |
| StepWiseProteinKIC_LoopBridger.cc | |
| StepWiseProteinKIC_LoopBridger.hh | |
| util.cc | |
| util.hh | |
| InputStreamWithResidueInfo.cc | |
| InputStreamWithResidueInfo.fwd.hh | |
| InputStreamWithResidueInfo.hh | |
| MainChainTorsionSet.cc | |
| MainChainTorsionSet.hh | |
| StepWiseProteinBackboneSampler.cc | |
| StepWiseProteinBackboneSampler.hh | |
| util.cc | |
| util.hh | |
| ► rna | |
| ► bulge | |
| BulgeApplyMover.cc | |
| BulgeApplyMover.fwd.hh | |
| BulgeApplyMover.hh | |
| BulgeUnApplyMover.cc | |
| BulgeUnApplyMover.fwd.hh | |
| BulgeUnApplyMover.hh | |
| ► checker | |
| RNA_AtrRepChecker.cc | |
| RNA_AtrRepChecker.fwd.hh | |
| RNA_AtrRepChecker.hh | |
| RNA_BaseCentroidChecker.cc | |
| RNA_BaseCentroidChecker.fwd.hh | |
| RNA_BaseCentroidChecker.hh | |
| RNA_ChainClosableGeometryChecker.cc | |
| RNA_ChainClosableGeometryChecker.fwd.hh | |
| RNA_ChainClosableGeometryChecker.hh | |
| RNA_ChainClosureChecker.cc | |
| RNA_ChainClosureChecker.fwd.hh | |
| RNA_ChainClosureChecker.hh | |
| RNA_VDW_BinChecker.cc | Very fast version of VWD repulsion screening |
| RNA_VDW_BinChecker.fwd.hh | |
| RNA_VDW_BinChecker.hh | |
| ► o2prime | |
| O2PrimePacker.cc | |
| O2PrimePacker.fwd.hh | |
| O2PrimePacker.hh | |
| ► phosphate | |
| MultiPhosphateSampler.cc | |
| MultiPhosphateSampler.fwd.hh | |
| MultiPhosphateSampler.hh | |
| PhosphateMove.cc | |
| PhosphateMove.fwd.hh | |
| PhosphateMove.hh | |
| PhosphateMover.cc | |
| PhosphateMover.fwd.hh | |
| PhosphateMover.hh | |
| util.cc | |
| util.hh | |
| ► rigid_body | |
| FloatingBaseClasses.hh | |
| util.cc | |
| util.hh | |
| ► sugar | |
| SugarInstantiateMover.cc | |
| SugarInstantiateMover.fwd.hh | |
| SugarInstantiateMover.hh | |
| SugarModeling.cc | |
| SugarModeling.fwd.hh | |
| SugarModeling.hh | |
| SugarVirtualizeMover.cc | |
| SugarVirtualizeMover.fwd.hh | |
| SugarVirtualizeMover.hh | |
| util.cc | |
| util.hh | |
| VirtualSugarJustInTimeInstantiator.cc | |
| VirtualSugarJustInTimeInstantiator.fwd.hh | |
| VirtualSugarJustInTimeInstantiator.hh | |
| VirtualSugarSampler.cc | |
| VirtualSugarSampler.hh | |
| VirtualSugarSamplerFromStringList.cc | |
| VirtualSugarSamplerFromStringList.fwd.hh | |
| VirtualSugarSamplerFromStringList.hh | |
| StepWiseRNA_Classes.hh | |
| StepWiseRNA_CombineLongLoopFilterer.cc | |
| StepWiseRNA_CombineLongLoopFilterer.fwd.hh | |
| StepWiseRNA_CombineLongLoopFilterer.hh | |
| StepWiseRNA_OutputData.cc | Output silent_file_data functions for Stepwise Assembly RNA |
| StepWiseRNA_OutputData.hh | |
| StepWiseRNA_ResidueInfo.cc | |
| StepWiseRNA_ResidueInfo.hh | |
| util.cc | Util functions for Stepwise Assembly RNA |
| util.hh | |
| ► working_parameters | |
| StepWiseBasicWorkingParameters.cc | |
| StepWiseBasicWorkingParameters.fwd.hh | |
| StepWiseBasicWorkingParameters.hh | |
| StepWiseWorkingParameters.cc | |
| StepWiseWorkingParameters.fwd.hh | |
| StepWiseWorkingParameters.hh | |
| util.cc | |
| util.hh | |
| constraint_util.cc | |
| constraint_util.hh | |
| output_util.cc | |
| output_util.hh | |
| scoring_util.cc | |
| scoring_util.hh | |
| StepWiseConnectionSampler.cc | |
| StepWiseConnectionSampler.fwd.hh | |
| StepWiseConnectionSampler.hh | |
| StepWiseMinimizer.cc | |
| StepWiseMinimizer.fwd.hh | |
| StepWiseMinimizer.hh | |
| StepWiseModeler.cc | |
| StepWiseModeler.fwd.hh | |
| StepWiseModeler.hh | |
| util.cc | |
| util.hh | |
| ► monte_carlo | |
| ► mover | |
| ► options | |
| StepWiseMoveSelectorOptions.cc | |
| StepWiseMoveSelectorOptions.fwd.hh | |
| StepWiseMoveSelectorOptions.hh | |
| AddMover.cc | |
| AddMover.fwd.hh | |
| AddMover.hh | |
| AddMoverCreator.fwd.hh | |
| AddMoverCreator.hh | |
| AddOrDeleteMover.cc | |
| AddOrDeleteMover.fwd.hh | |
| AddOrDeleteMover.hh | |
| DeleteMover.cc | |
| DeleteMover.fwd.hh | |
| DeleteMover.hh | |
| DeleteMoverCreator.fwd.hh | |
| DeleteMoverCreator.hh | |
| FromScratchMover.cc | |
| FromScratchMover.fwd.hh | |
| FromScratchMover.hh | |
| FromScratchMoverCreator.fwd.hh | |
| FromScratchMoverCreator.hh | |
| ResampleMover.cc | |
| ResampleMover.fwd.hh | |
| ResampleMover.hh | |
| ResampleMoverCreator.fwd.hh | |
| ResampleMoverCreator.hh | |
| StepWiseMasterMover.cc | |
| StepWiseMasterMover.fwd.hh | |
| StepWiseMasterMover.hh | |
| StepWiseMove.cc | |
| StepWiseMove.fwd.hh | |
| StepWiseMove.hh | |
| StepWiseMoveSelector.cc | |
| StepWiseMoveSelector.fwd.hh | |
| StepWiseMoveSelector.hh | |
| TransientCutpointHandler.cc | |
| TransientCutpointHandler.fwd.hh | |
| TransientCutpointHandler.hh | |
| VaryLoopLengthMover.cc | In stepwise design, vary desired loop lengths by updating FullModelParameters |
| VaryLoopLengthMover.fwd.hh | In stepwise design, vary desired loop lengths by updating FullModelParameters |
| VaryLoopLengthMover.hh | In stepwise design, vary desired loop lengths by updating FullModelParameters |
| ► options | |
| StepWiseMonteCarloOptions.cc | |
| StepWiseMonteCarloOptions.fwd.hh | |
| StepWiseMonteCarloOptions.hh | |
| ► rna | |
| RNA_AddDeleteMonteCarlo.cc | |
| RNA_AddDeleteMonteCarlo.fwd.hh | |
| RNA_AddDeleteMonteCarlo.hh | |
| RNA_O2PrimeMover.cc | |
| RNA_O2PrimeMover.fwd.hh | |
| RNA_O2PrimeMover.hh | |
| RNA_TorsionMover.cc | |
| RNA_TorsionMover.fwd.hh | |
| RNA_TorsionMover.hh | |
| ► submotif | |
| SubMotifLibrary.cc | |
| SubMotifLibrary.fwd.hh | |
| SubMotifLibrary.hh | |
| StepWiseMonteCarlo.cc | |
| StepWiseMonteCarlo.fwd.hh | |
| StepWiseMonteCarlo.hh | |
| util.cc | |
| util.hh | |
| ► options | |
| StepWiseBasicOptions.cc | |
| StepWiseBasicOptions.fwd.hh | |
| StepWiseBasicOptions.hh | |
| ► sampler | |
| ► copy_dofs | |
| CopyDofStepWiseSampler.cc | |
| CopyDofStepWiseSampler.fwd.hh | |
| CopyDofStepWiseSampler.hh | |
| ResidueAlternativeSet.cc | |
| ResidueAlternativeSet.fwd.hh | |
| ResidueAlternativeSet.hh | |
| ResidueAlternativeStepWiseSampler.cc | |
| ResidueAlternativeStepWiseSampler.fwd.hh | |
| ResidueAlternativeStepWiseSampler.hh | |
| ResidueAlternativeStepWiseSamplerComb.cc | |
| ResidueAlternativeStepWiseSamplerComb.fwd.hh | |
| ResidueAlternativeStepWiseSamplerComb.hh | |
| ResidueListStepWiseSampler.cc | |
| ResidueListStepWiseSampler.fwd.hh | |
| ResidueListStepWiseSampler.hh | |
| ► input_streams | |
| InputStreamStepWiseSampler.cc | |
| InputStreamStepWiseSampler.fwd.hh | |
| InputStreamStepWiseSampler.hh | |
| ► jump | |
| JumpStepWiseSampler.cc | |
| JumpStepWiseSampler.fwd.hh | |
| JumpStepWiseSampler.hh | |
| ► protein | |
| ProteinBetaAntiParallelStepWiseSampler.cc | |
| ProteinBetaAntiParallelStepWiseSampler.fwd.hh | |
| ProteinBetaAntiParallelStepWiseSampler.hh | |
| ProteinFragmentStepWiseSampler.cc | |
| ProteinFragmentStepWiseSampler.fwd.hh | |
| ProteinFragmentStepWiseSampler.hh | |
| ProteinMainChainStepWiseSampler.cc | |
| ProteinMainChainStepWiseSampler.fwd.hh | |
| ProteinMainChainStepWiseSampler.hh | |
| util.cc | |
| util.hh | |
| ► rigid_body | |
| EulerAngles.cc | |
| EulerAngles.fwd.hh | |
| EulerAngles.hh | |
| RigidBodyStepWiseSampler.cc | |
| RigidBodyStepWiseSampler.fwd.hh | |
| RigidBodyStepWiseSampler.hh | |
| RigidBodyStepWiseSamplerValueRange.cc | |
| RigidBodyStepWiseSamplerValueRange.fwd.hh | |
| RigidBodyStepWiseSamplerValueRange.hh | |
| RigidBodyStepWiseSamplerWithResidueAlternatives.cc | |
| RigidBodyStepWiseSamplerWithResidueAlternatives.fwd.hh | |
| RigidBodyStepWiseSamplerWithResidueAlternatives.hh | |
| RigidBodyStepWiseSamplerWithResidueList.cc | |
| RigidBodyStepWiseSamplerWithResidueList.fwd.hh | |
| RigidBodyStepWiseSamplerWithResidueList.hh | |
| ► rna | |
| RNA_ChiStepWiseSampler.cc | Generate glycosidic chi rotamers for RNA |
| RNA_ChiStepWiseSampler.fwd.hh | Generate glycosidic chi rotamers for RNA |
| RNA_ChiStepWiseSampler.hh | Generate glycosidic chi rotamers for RNA |
| RNA_KIC_Sampler.cc | Sample and torsions and close an RNA loop |
| RNA_KIC_Sampler.fwd.hh | Sample and torsions and close an RNA loop |
| RNA_KIC_Sampler.hh | |
| RNA_KinematicCloser.cc | Close a RNA loop with Kinematic Closer (KIC) |
| RNA_KinematicCloser.fwd.hh | Close a RNA loop with Kinematic Closer (KIC) |
| RNA_KinematicCloser.hh | Close a RNA loop with Kinematic Closer (KIC) |
| RNA_NucleosideStepWiseSampler.cc | Generate rotamers for one RNA nucleoside (pucker + glycosidic chi) |
| RNA_NucleosideStepWiseSampler.fwd.hh | Generate rotamers for one RNA nucleoside (pucker + glycosidic chi) |
| RNA_NucleosideStepWiseSampler.hh | Generate rotamers for one RNA nucleoside (pucker + glycosidic chi) |
| RNA_SugarStepWiseSampler.cc | Generate sugar pucker rotamers for RNA |
| RNA_SugarStepWiseSampler.fwd.hh | Generate sugar pucker rotamers for RNA |
| RNA_SugarStepWiseSampler.hh | Generate sugar pucker rotamers for RNA |
| RNA_SuiteStepWiseSampler.cc | Generate rotamers for one RNA suite (from residue i to i+1) |
| RNA_SuiteStepWiseSampler.fwd.hh | Generate rotamers for one RNA suite (from residue i to i+1) |
| RNA_SuiteStepWiseSampler.hh | Generate rotamers for one RNA suite (from residue i to i+1) |
| util.cc | |
| util.hh | |
| ► screener | |
| RNA_TorsionScreener.cc | Screener checking whether the rna torsions are resonable |
| RNA_TorsionScreener.fwd.hh | |
| RNA_TorsionScreener.hh | |
| StepWiseSampler.fwd.hh | |
| StepWiseSampler.hh | |
| StepWiseSamplerComb.cc | Aggregate of multiple rotamer samplers for modeler combinatorially |
| StepWiseSamplerComb.fwd.hh | Aggregate of multiple rotamer samplers for modeler combinatorially |
| StepWiseSamplerComb.hh | Aggregate of multiple rotamer samplers for modeler combinatorially |
| StepWiseSamplerOneDOF.cc | Generate rotamer for one DOF angle |
| StepWiseSamplerOneDOF.fwd.hh | Generate rotamer for one DOF angle |
| StepWiseSamplerOneDOF.hh | Generate rotamer for one DOF angle |
| StepWiseSamplerOneTorsion.cc | Generate rotamer for one torsion angle |
| StepWiseSamplerOneTorsion.fwd.hh | Generate rotamer for one torsion angle |
| StepWiseSamplerOneTorsion.hh | Generate rotamer for one torsion angle |
| StepWiseSamplerOneValue.cc | |
| StepWiseSamplerOneValue.fwd.hh | Generate rotamer for one torsion angle |
| StepWiseSamplerOneValue.hh | Base class for StepWiseSamplerOneValue |
| StepWiseSamplerOneValueComb.cc | Aggregate of multiple rotamer samplers for modeler combinatorially |
| StepWiseSamplerOneValueComb.fwd.hh | Aggregate of multiple rotamer samplers for modeler combinatorially |
| StepWiseSamplerOneValueComb.hh | Aggregate of multiple rotamer samplers for modeler combinatorially |
| StepWiseSamplerRingConformer.cc | Generate rotamer for one torsion angle |
| StepWiseSamplerRingConformer.fwd.hh | Generate rotamer for one torsion angle |
| StepWiseSamplerRingConformer.hh | Generate rotamer for one torsion angle |
| StepWiseSamplerSized.cc | Aggregate multiple samplers for modeler from any one of them |
| StepWiseSamplerSized.fwd.hh | Abstract Base Class for Sampler generator with finite size |
| StepWiseSamplerSized.hh | Abstract Base Class for Sampler sampler with finite size |
| StepWiseSamplerSizedAny.cc | Aggregate multiple samplers for modeler from any one of them |
| StepWiseSamplerSizedAny.fwd.hh | Aggregate multiple samplers for modeler from any one of them |
| StepWiseSamplerSizedAny.hh | Aggregate multiple samplers for modeler from any one of them |
| StepWiseSamplerSizedComb.cc | Aggregate of multiple rotamer samplers for modeler combinatorially |
| StepWiseSamplerSizedComb.fwd.hh | Aggregate of multiple rotamer samplers for modeler combinatorially |
| StepWiseSamplerSizedComb.hh | Aggregate of multiple rotamer samplers for modeler combinatorially |
| ► screener | |
| AlignRMSD_Screener.cc | |
| AlignRMSD_Screener.fwd.hh | |
| AlignRMSD_Screener.hh | |
| AnchorSugarScreener.cc | |
| AnchorSugarScreener.fwd.hh | |
| AnchorSugarScreener.hh | |
| BaseBinMapUpdater.cc | |
| BaseBinMapUpdater.fwd.hh | |
| BaseBinMapUpdater.hh | |
| BaseCentroidScreener.cc | |
| BaseCentroidScreener.fwd.hh | |
| BaseCentroidScreener.hh | |
| BulgeApplier.cc | |
| BulgeApplier.fwd.hh | |
| BulgeApplier.hh | |
| CentroidDistanceScreener.cc | |
| CentroidDistanceScreener.fwd.hh | |
| CentroidDistanceScreener.hh | |
| FastForwardToNextResidueAlternative.cc | |
| FastForwardToNextResidueAlternative.fwd.hh | |
| FastForwardToNextResidueAlternative.hh | |
| FastForwardToNextRigidBody.cc | |
| FastForwardToNextRigidBody.fwd.hh | |
| FastForwardToNextRigidBody.hh | |
| IntegrationTestBreaker.cc | |
| IntegrationTestBreaker.fwd.hh | |
| IntegrationTestBreaker.hh | |
| O2PrimeScreener.cc | |
| O2PrimeScreener.fwd.hh | |
| O2PrimeScreener.hh | |
| PackScreener.cc | |
| PackScreener.fwd.hh | |
| PackScreener.hh | |
| PartitionContactScreener.cc | |
| PartitionContactScreener.fwd.hh | |
| PartitionContactScreener.hh | |
| PhosphateScreener.cc | |
| PhosphateScreener.fwd.hh | |
| PhosphateScreener.hh | |
| PoseSelectionScreener.cc | |
| PoseSelectionScreener.fwd.hh | |
| PoseSelectionScreener.hh | |
| ProteinCCD_ClosureScreener.cc | |
| ProteinCCD_ClosureScreener.fwd.hh | |
| ProteinCCD_ClosureScreener.hh | |
| ResidueContactScreener.cc | |
| ResidueContactScreener.fwd.hh | |
| ResidueContactScreener.hh | |
| RNA_ChainClosableGeometryResidueBasedScreener.cc | |
| RNA_ChainClosableGeometryResidueBasedScreener.fwd.hh | |
| RNA_ChainClosableGeometryResidueBasedScreener.hh | |
| RNA_ChainClosableGeometryScreener.cc | |
| RNA_ChainClosableGeometryScreener.fwd.hh | |
| RNA_ChainClosableGeometryScreener.hh | |
| RNA_ChainClosableGeometryStubBasedScreener.cc | |
| RNA_ChainClosableGeometryStubBasedScreener.fwd.hh | |
| RNA_ChainClosableGeometryStubBasedScreener.hh | |
| RNA_ChainClosureScreener.cc | |
| RNA_ChainClosureScreener.fwd.hh | |
| RNA_ChainClosureScreener.hh | |
| SampleApplier.cc | |
| SampleApplier.fwd.hh | |
| SampleApplier.hh | |
| Scorer.cc | |
| Scorer.fwd.hh | |
| Scorer.hh | |
| StepWiseResiduePairScreener.cc | |
| StepWiseResiduePairScreener.fwd.hh | |
| StepWiseResiduePairScreener.hh | |
| StepWiseScreener.cc | |
| StepWiseScreener.fwd.hh | |
| StepWiseScreener.hh | |
| StepWiseScreenerType.hh | |
| StubApplier.cc | |
| StubApplier.fwd.hh | |
| StubApplier.hh | |
| StubDistanceScreener.cc | |
| StubDistanceScreener.fwd.hh | |
| StubDistanceScreener.hh | |
| SugarInstantiator.cc | |
| SugarInstantiator.fwd.hh | |
| SugarInstantiator.hh | |
| TagDefinition.cc | |
| TagDefinition.fwd.hh | |
| TagDefinition.hh | |
| util.cc | |
| util.hh | |
| VDW_BinScreener.cc | |
| VDW_BinScreener.fwd.hh | |
| VDW_BinScreener.hh | |
| ► setup | |
| util.cc | |
| util.hh | |
| StepWiseSampleAndScreen.cc | |
| StepWiseSampleAndScreen.fwd.hh | |
| StepWiseSampleAndScreen.hh | |
| ► struct_fragment | |
| StructFragmentMover.cc | Creating fragments from supplied structures |
| StructFragmentMover.fwd.hh | Creating fragments from supplied structures |
| StructFragmentMover.hh | Creating fragments from supplied structures |
| StructFragmentMoverCreator.hh | Creating fragments from supplied structures |
| ► surface_docking | |
| CentroidRelaxMover.cc | |
| CentroidRelaxMover.fwd.hh | |
| CentroidRelaxMover.hh | <add a="" description="" of="" the="" class>=""> |
| FullatomRelaxMover.cc | |
| FullatomRelaxMover.fwd.hh | |
| FullatomRelaxMover.hh | |
| SurfaceDockingProtocol.cc | |
| SurfaceDockingProtocol.fwd.hh | |
| SurfaceDockingProtocol.hh | |
| SurfaceOrientMover.cc | |
| SurfaceOrientMover.fwd.hh | |
| SurfaceOrientMover.hh | <add a="" description="" of="" the="" class>=""> |
| SurfaceParameters.cc | |
| SurfaceParameters.fwd.hh | |
| SurfaceParameters.hh | |
| SurfaceVectorFallbackConfiguration.cc | |
| SurfaceVectorLoader.cc | |
| SurfaceVectorLoader.fwd.hh | |
| SurfaceVectorLoader.hh | |
| SurfaceVectorLoaderCreator.hh | |
| ► switches | |
| GraftSwitchMover.cc | Mover to graft a fucntional sequence optimally on a helical LOCKR type latch |
| GraftSwitchMover.fwd.hh | |
| GraftSwitchMover.hh | |
| GraftSwitchMoverCreator.hh | |
| ► symmetric_docking | |
| ► membrane | |
| MPSymDockMover.cc | Membrane symmetric docking protocol |
| MPSymDockMover.fwd.hh | Membrane symmetric docking protocol |
| MPSymDockMover.hh | Membrane symmetric docking protocol |
| MPSymDockMoverCreator.hh | |
| SymDockBaseProtocol.cc | |
| SymDockBaseProtocol.hh | |
| SymDockingHiRes.cc | |
| SymDockingHiRes.fwd.hh | |
| SymDockingHiRes.hh | |
| SymDockingLowRes.cc | |
| SymDockingLowRes.fwd.hh | |
| SymDockingLowRes.hh | |
| SymDockProtocol.cc | Symmetric Protein-Protein Docking Protocol |
| SymDockProtocol.fwd.hh | |
| SymDockProtocol.hh | Symmetric Protein-Protein Docking Protocol |
| SymDockProtocolCreator.hh | Declaration of the MoverCreator class for the SymDockProtocol |
| SymFoldandDockCreators.hh | |
| SymFoldandDockMoveRbJumpMover.cc | |
| SymFoldandDockMoveRbJumpMover.fwd.hh | |
| SymFoldandDockMoveRbJumpMover.hh | |
| SymFoldandDockRbTrialMover.cc | |
| SymFoldandDockRbTrialMover.fwd.hh | |
| SymFoldandDockRbTrialMover.hh | |
| SymFoldandDockSlideTrialMover.cc | |
| SymFoldandDockSlideTrialMover.fwd.hh | |
| SymFoldandDockSlideTrialMover.hh | |
| SymRestrictTaskForDocking.cc | When passed to a PackerTask, pack/design is limited to the protein interface |
| SymRestrictTaskForDocking.fwd.hh | |
| SymRestrictTaskForDocking.hh | When passed to a PackerTask, pack/design is limited to the interface |
| SymSidechainMinMover.cc | |
| SymSidechainMinMover.fwd.hh | |
| SymSidechainMinMover.hh | |
| ► symmetry | |
| DetectSymmetryMover.cc | Automatical detection and setup of the symmetry machinery from an assymetric pose made of symmetric chains. Only works with cyclic simmetries |
| DetectSymmetryMover.fwd.hh | |
| DetectSymmetryMover.hh | Automatical detection and setup of the symmetry machinery from an asymetric pose made of symmetric chains. Only works with cyclic simmetries |
| DetectSymmetryMoverCreator.hh | |
| SetupForSequenceSymmetryMover.cc | |
| SetupForSequenceSymmetryMover.fwd.hh | |
| SetupForSequenceSymmetryMover.hh | |
| SetupForSequenceSymmetryMoverCreator.hh | |
| SetupForSymmetryMover.cc | |
| SetupForSymmetryMover.fwd.hh | |
| SetupForSymmetryMover.hh | |
| SetupForSymmetryMoverCreator.hh | |
| SetupNCSMover.cc | Sets up NCS restraints |
| SetupNCSMover.fwd.hh | Sets up NCS restraints |
| SetupNCSMover.hh | Sets up NCS restraints |
| SetupNCSMoverCreator.hh | Protocols::moves::MoverCreator for SetupNCSMover |
| SymDockingInitialPerturbation.cc | |
| SymDockingInitialPerturbation.hh | |
| SymmetricRMSMover.cc | |
| SymmetricRMSMover.fwd.hh | |
| SymmetricRMSMover.hh | |
| SymShakeStructureMover.cc | |
| SymShakeStructureMover.fwd.hh | |
| SymShakeStructureMover.hh | |
| ► task_operations | |
| AlignedThreadOperation.cc | |
| AlignedThreadOperation.fwd.hh | |
| AlignedThreadOperation.hh | TaskOperation class that restricts a chain to repacking |
| AlignedThreadOperationCreator.hh | |
| ConservativeDesignOperation.cc | |
| ConservativeDesignOperation.fwd.hh | |
| ConservativeDesignOperation.hh | |
| ConservativeDesignOperationCreator.hh | |
| CrystalContactsOperation.cc | Exclude crystal contacts from design |
| CrystalContactsOperation.fwd.hh | Exclude crystal contacts from design |
| CrystalContactsOperation.hh | Exclude crystal contacts from design |
| CrystalContactsOperationCreator.hh | Exclude crystal contacts from design |
| DatabaseThread.cc | Picks a sequence from database by start and end position on the pose |
| DatabaseThread.fwd.hh | |
| DatabaseThread.hh | TaskOperation class that restricts a chain to repacking |
| DatabaseThreadCreator.hh | |
| DesignAroundOperation.cc | |
| DesignAroundOperation.fwd.hh | |
| DesignAroundOperation.hh | |
| DesignAroundOperationCreator.hh | |
| DsspDesignOperation.cc | Design residues with selected amino acids depending on DSSP secondary structure assignment. All functionality here is included in the LayerDesign task operation, but this filter has significantly reduced overhead by avoiding slow SASA calculations |
| DsspDesignOperation.fwd.hh | |
| DsspDesignOperation.hh | Design residues with selected amino acids depending on DSSP secondary structure assignment. All functionality here is included in the LayerDesign task operation, but this filter has significantly reduced overhead by avoiding slow SASA calculations |
| DsspDesignOperationCreator.hh | |
| DsspDesignOperationTests.fwd.hh | |
| ImportUnboundRotamersOperation.cc | Import unbound (or native) rotamers into Rosetta! |
| ImportUnboundRotamersOperation.fwd.hh | |
| ImportUnboundRotamersOperation.hh | Rotamer set operation forward declaration |
| ImportUnboundRotamersOperationCreator.hh | |
| InteractingRotamerExplosion.cc | |
| InteractingRotamerExplosion.fwd.hh | |
| InteractingRotamerExplosion.hh | TaskOperation class that oversamples rotamers interacting with a certain target |
| InteractingRotamerExplosionCreator.hh | |
| JointSequenceOperation.cc | Set designable residues to those observed in a set of structures |
| JointSequenceOperation.fwd.hh | |
| JointSequenceOperation.hh | Set every position to be designable to residues observed in a set of structures |
| JointSequenceOperationCreator.hh | |
| LimitAromaChi2Operation.cc | Eliminate aromatic rotamers, of which chi2 are around 0, 180 degree. Chi2=0, 180 rotamers of aromatic residues ( PHE, TYR, HIS ) are not observed in nature very much, however Rosetta really like them. This is really pathology. For design purpose, we don't need them actually |
| LimitAromaChi2Operation.fwd.hh | |
| LimitAromaChi2Operation.hh | Rotamer set operation forward declaration |
| LimitAromaChi2OperationCreator.hh | |
| LinkResidues.cc | |
| LinkResidues.fwd.hh | |
| LinkResidues.hh | TaskOperation class that restricts a chain to repacking |
| LinkResiduesCreator.hh | |
| ModifyAnnealer.cc | Task operation to set high and low temps for annealer as well as whether or not to do a quench step |
| ModifyAnnealer.fwd.hh | Task operation to set high and low temps for annealer as well as whether or not to do a quench step |
| ModifyAnnealer.hh | Task operation to set high and low temps for annealer as well as whether or not to do a quench step |
| ModifyAnnealerCreator.hh | |
| MutationSetDesignOperation.cc | |
| MutationSetDesignOperation.fwd.hh | |
| MutationSetDesignOperation.hh | Sample a set of mutations each time packer is generated |
| pHVariantTaskOperation.cc | A TaskOp that enables sampling of protonation variants during repacking. The ionizable sidechains considered are ASP, GLU, LYS, TYR, and HIS. All other posiitons are restricted to repacking. The -pH_mode commandline option is still currently required to initially read the variants into the database |
| pHVariantTaskOperation.fwd.hh | During repacking, allow interchangeability of protonated and deprotonated variants |
| pHVariantTaskOperation.hh | |
| pHVariantTaskOperationCreator.hh | |
| PreventChainFromRepackingOperation.cc | |
| PreventChainFromRepackingOperation.fwd.hh | |
| PreventChainFromRepackingOperation.hh | TaskOperation class that restricts a chain to repacking |
| PreventChainFromRepackingOperationCreator.hh | |
| PreventResiduesFromRepackingOperation.cc | |
| PreventResiduesFromRepackingOperation.fwd.hh | |
| PreventResiduesFromRepackingOperation.hh | TaskOperation class that prevents a vector of residues indices from repacking parsed as a string that is comma delimited "," |
| PreventResiduesFromRepackingOperationCreator.hh | |
| ProteinCoreResFilter.cc | |
| ProteinCoreResFilter.hh | |
| ProteinCoreResFilterCreator.hh | |
| ProteinInterfaceDesignOperation.cc | |
| ProteinInterfaceDesignOperation.fwd.hh | |
| ProteinInterfaceDesignOperation.hh | TaskOperation class that restricts a chain to repacking |
| ProteinInterfaceDesignOperationCreator.hh | |
| PruneBuriedUnsatsOperation.cc | Eliminate rotamers that contain a sidechain buried unsat and make no other sidechain h-bonds This is intended to speed up packing by eliminating useless polar rotamers. This can also help to reduce the number of buried unsats in designs because Rosetta can't pack them |
| PruneBuriedUnsatsOperation.fwd.hh | Forward declaration for PruneBuriedUnsatsOperation |
| PruneBuriedUnsatsOperation.hh | Eliminate rotamers that contain a sidechain buried unsat and make no other sidechain h-bonds This is intended to speed up packing by eliminating useless polar rotamers. This can also help to reduce the number of buried unsats in designs because Rosetta can't pack them |
| PruneBuriedUnsatsOperationCreator.hh | Creator for PruneBuriedUnsatsOperation |
| ReadResfileFromDB.cc | |
| ReadResfileFromDB.fwd.hh | Forward declaration of the ReadResfileFromDB class |
| ReadResfileFromDB.hh | Read a refile indexed by the input structure tag from a supplied relational database |
| ReadResfileFromDBCreator.hh | |
| ResfileCommandOperation.cc | Applies the equivalent of a resfile line (without the resnums) to residues specified in a residue selector |
| ResfileCommandOperation.fwd.hh | Applies the equivalent of a resfile line (without the resnums) to residues specified in a residue selector |
| ResfileCommandOperation.hh | |
| ResfileCommandOperationCreator.hh | |
| ResidueProbDesignOperation.cc | |
| ResidueProbDesignOperation.fwd.hh | |
| ResidueProbDesignOperation.hh | Uses a probability distribution to sample allowed residues at a position, adding those types to the packer - only if they are designable |
| ResidueProbDesignOperationCreator.hh | |
| RestrictByCalculatorsOperation.cc | A class that applies arbitrary calculators (whose calculations return std::set< core::Size >) to restrict a PackerTask |
| RestrictByCalculatorsOperation.fwd.hh | A class that applies arbitrary calculators (whose calculations return std::set< core::Size >) to restrict a PackerTask |
| RestrictByCalculatorsOperation.hh | A class that applies arbitrary calculators (whose calculations return std::set< core::Size >) to restrict a PackerTask |
| RestrictByCalculatorsOperationCreator.hh | |
| RestrictChainToRepackingOperation.cc | |
| RestrictChainToRepackingOperation.fwd.hh | |
| RestrictChainToRepackingOperation.hh | TaskOperation class that restricts a chain to repacking |
| RestrictChainToRepackingOperationCreator.hh | |
| RestrictIdentitiesAtAlignedPositions.cc | |
| RestrictIdentitiesAtAlignedPositions.fwd.hh | |
| RestrictIdentitiesAtAlignedPositions.hh | |
| RestrictIdentitiesAtAlignedPositionsCreator.hh | |
| RestrictIdentitiesOperation.cc | Restricts specified residue types to only repack, no design |
| RestrictIdentitiesOperation.fwd.hh | |
| RestrictIdentitiesOperation.hh | |
| RestrictIdentitiesOperationCreator.hh | |
| RestrictInterGroupVectorOperation.cc | |
| RestrictInterGroupVectorOperation.fwd.hh | |
| RestrictInterGroupVectorOperation.hh | Restricts design to only those residues between two groups of structures |
| RestrictInterGroupVectorOperationCreator.hh | |
| RestrictNativeResiduesOperation.cc | Restrict every residue in the current pose that is native to repacking. ie, only allow mutated positions to be designed |
| RestrictNativeResiduesOperation.fwd.hh | |
| RestrictNativeResiduesOperation.hh | Restrict every residue in the current pose that is native to repacking. ie, only allow mutated positions to be designed |
| RestrictNativeResiduesOperationCreator.hh | |
| RestrictNonSurfaceToRepackingOperation.cc | |
| RestrictNonSurfaceToRepackingOperation.fwd.hh | |
| RestrictNonSurfaceToRepackingOperation.hh | |
| RestrictNonSurfaceToRepackingOperationCreator.hh | |
| RestrictOperationsBase.cc | Base class for PoseMetricCalculator-using TaskOperations |
| RestrictOperationsBase.fwd.hh | Base class for PoseMetricCalculator-using TaskOperations |
| RestrictOperationsBase.hh | Base class for PoseMetricCalculator-using TaskOperations |
| RestrictResiduesToRepackingOperation.cc | |
| RestrictResiduesToRepackingOperation.fwd.hh | |
| RestrictResiduesToRepackingOperation.hh | TaskOperation class that restricts a vector of core::Size defined residues to repacking when parsed, it takes in a string and splits by "," |
| RestrictResiduesToRepackingOperationCreator.hh | |
| RestrictToAlignedSegments.cc | |
| RestrictToAlignedSegments.fwd.hh | |
| RestrictToAlignedSegments.hh | |
| RestrictToAlignedSegmentsCreator.hh | |
| RestrictToCDRH3Loop.cc | |
| RestrictToCDRH3Loop.fwd.hh | Forward declaration of the RestrictToCDRH3Loop class |
| RestrictToCDRH3Loop.hh | This class allows the selection for packing of the Antibody CDR-H3 loop by taking advantage of the PDB numbering schemes that are commonly used for Antibodies |
| RestrictToCDRH3LoopCreator.hh | |
| RestrictToInterfaceOperation.cc | TaskOperation class that finds an interface and leaves it mobile in the PackerTask |
| RestrictToInterfaceOperation.fwd.hh | Forward declaration of a TaskOperation class that finds an interface leaves it mobile in the PackerTask |
| RestrictToInterfaceOperation.hh | TaskOperation class that finds an interface and makes it mobile in the PackerTask |
| RestrictToInterfaceOperationCreator.hh | |
| RestrictToInterfaceVectorOperation.cc | TaskOperation class that finds an interface based on: core/select/util/interface_vector_calculate.hh and leaves it mobile in the PackerTask |
| RestrictToInterfaceVectorOperation.fwd.hh | Forward declaration of a TaskOperation class that finds an interface leaves it mobile in the PackerTask |
| RestrictToInterfaceVectorOperation.hh | TaskOperation class that finds an interface based on InterfaceVectorDefinition and leaves it mobile in the PackerTask. Serves mostly to wrap InterfaceVectorDefinition into a TaskOperation. see src/core/select/util/interface_vector_calculate.hh |
| RestrictToInterfaceVectorOperationCreator.hh | |
| RestrictToMoveMapChiOperation.cc | |
| RestrictToMoveMapChiOperation.fwd.hh | |
| RestrictToMoveMapChiOperation.hh | Makes it easier to use TF and MM in the same class |
| RestrictToMoveMapChiOperationCreator.hh | |
| RestrictToNeighborhoodOperation.cc | TaskOperation class that finds a neighborhood and leaves it mobile in the PackerTask |
| RestrictToNeighborhoodOperation.fwd.hh | Forward declaration of a TaskOperation class that finds a neighborhood; leaves it mobile in the PackerTask |
| RestrictToNeighborhoodOperation.hh | TaskOperation class that finds a neighborhood and makes it mobile in the PackerTask |
| RestrictToNeighborhoodOperationCreator.hh | |
| RestrictToTerminiOperation.cc | |
| RestrictToTerminiOperation.fwd.hh | Restrict to packing only the residues at either or both termini |
| RestrictToTerminiOperation.hh | |
| RestrictToTerminiOperationCreator.hh | |
| RetrieveStoredTaskOperation.cc | Retrieves a stored task from the pose's CacheableData. Must be used in conjunction with the StoredTaskMover. Allows storage/retrieval of a task so that particular sets of residues can be stably addressed throughout the entirety of a RosettaScripts protocol |
| RetrieveStoredTaskOperation.fwd.hh | |
| RetrieveStoredTaskOperation.hh | Retrieves a stored task from the pose's CacheableData. Must be used in conjunction with the StoredTaskMover. Allows storage/retrieval of a task so that particular sets of residues can be stably addressed throughout the entirety of a RosettaScripts protocol |
| RetrieveStoredTaskOperationCreator.hh | |
| SelectByDeltaScoreOperation.cc | |
| SelectByDeltaScoreOperation.fwd.hh | |
| SelectByDeltaScoreOperation.hh | |
| SelectByDeltaScoreOperationCreator.hh | |
| SelectByDensityFitOperation.cc | |
| SelectByDensityFitOperation.fwd.hh | |
| SelectByDensityFitOperation.hh | |
| SelectByDensityFitOperationCreator.hh | |
| SelectBySASAOperation.cc | |
| SelectBySASAOperation.fwd.hh | |
| SelectBySASAOperation.hh | |
| SelectBySASAOperationCreator.hh | |
| SelectResiduesWithinChain.cc | |
| SelectResiduesWithinChain.fwd.hh | |
| SelectResiduesWithinChain.hh | |
| SelectResiduesWithinChainCreator.hh | |
| SeqprofConsensusOperation.cc | Set designable residues to those observed in sequence profile |
| SeqprofConsensusOperation.fwd.hh | |
| SeqprofConsensusOperation.hh | |
| SeqprofConsensusOperationCreator.hh | |
| SequenceMotifTaskOperation.cc | A TaskOp that takes a regex-like pattern and turns it into a set of design residues. The string should identify what to do for each position. An X indicates any residue, and is the same as [A_Z]. Anything other than a charactor should be in []. The ^ denotes a not. An example Regex for glycosylation is NX[ST]. This would design an ASN into the first position, skip the second, and allow S and T mutations only at the third position. N[^P][ST] would denote that at the second position, we do not allow proline. Sets of charactors using _ can be denoted, even though this doesnt really help us in design. In the future one can imagine having sets of polars, etc. etc. This TaskOp is like a simple RESFILE in a string |
| SequenceMotifTaskOperation.fwd.hh | A TaskOp that takes a regex-like pattern and turns it into a set of design residues. The string should identify what to do for each position. An X indicates any residue, and is the same as [A_Z]. Anything other than a charactor should be in []. The ^ denotes a not. An example Regex for glycosylation is NX[ST]. This would design an ASN into the first position, skip the second, and allow S and T mutations only at the third position. N[^P][ST] would denote that at the second position, we do not allow proline. Sets of charactors using _ can be denoted, even though this doesnt really help us in design. In the future one can imagine having sets of polars, etc. etc. This TaskOp is like a simple RESFILE in a string |
| SequenceMotifTaskOperation.hh | |
| SequenceMotifTaskOperationCreator.hh | |
| SetIGTypeOperation.cc | Task operation to set interaction graph type (linmem, lazy or double lazy) |
| SetIGTypeOperation.fwd.hh | Task operation to set Interaction graph Type |
| SetIGTypeOperation.hh | Task operation to set interaction graph type (linear memory, lazy or double lazy) |
| SetIGTypeOperationCreator.hh | |
| STMStoredTask.cc | CacheableData wrapper for PackerTask storage |
| STMStoredTask.fwd.hh | |
| STMStoredTask.hh | |
| StoreCombinedStoredTasksMover.cc | The StoreCombinedStoredTasksMover HAS BEEN DEPRECATED. It was used to combine several STMStoredTasks (protocols/task_operations/STMStoredTask.cc), but has been replaced by the StoreCompoundTaskMover (protocols/task_operations/StoreCompoundTaskMover.cc), which is much more flexible. It is being moved out of devel/matdes/ into protocols/task_operations/ to support the publication King et al., Nature 2014 |
| StoreCombinedStoredTasksMover.fwd.hh | |
| StoreCombinedStoredTasksMover.hh | Headers for StoreCombinedStoredTasksMover class – DEPRECATED (see .cc file) |
| StoreCombinedStoredTasksMoverCreator.hh | |
| StoreCompoundTaskMover.cc | Combine tasks using boolean logic for residues that are packable or designable, assign new packing behavior to residues that match or do not match the specified criteria, and store the resulting task in the pose's cacheable data. TODO (Jacob): Add option to combine allowed amino acid sets |
| StoreCompoundTaskMover.fwd.hh | |
| StoreCompoundTaskMover.hh | |
| StoreCompoundTaskMoverCreator.hh | |
| StoreTaskMover.cc | The StoreTaskMover allows you to create a PackerTask at some point during a RosettaScripts run and save it for access later during the same run. Can be useful for mutating/analyzing a particular set of residues using many different movers/filters |
| StoreTaskMover.fwd.hh | |
| StoreTaskMover.hh | Headers for StoreTaskMover class |
| StoreTaskMoverCreator.hh | This class will create instances of Mover StoreTaskMover for the MoverFactory |
| ThreadSequenceOperation.cc | |
| ThreadSequenceOperation.fwd.hh | |
| ThreadSequenceOperation.hh | TaskOperation class that restricts a chain to repacking |
| ThreadSequenceOperationCreator.hh | |
| ► tcr | |
| grafting_util.cc | Grafting utility functions for protocols/tcr |
| grafting_util.hh | Grafting utility functions for protocols/tcr |
| modeling_util.cc | Modeling utility functions for protocols/tcr |
| modeling_util.hh | |
| TCRloopRefine.cc | TCR cdr loop modeling/refinement |
| TCRloopRefine.fwd.hh | TCR cdr loop modeling/refinement |
| TCRloopRefine.hh | Class for tcr CDR loop modeling/refinement |
| TCRmodel.cc | Class for the tcr modeling protocol |
| TCRmodel.fwd.hh | TCRmodel class forward declarations header |
| TCRmodel.hh | Class for the tcr modeling protocol |
| TCRseqInfo.cc | Class for parsing and numbering tcr a/b chain sequences |
| TCRseqInfo.fwd.hh | TCR cdr loop modeling/refinement |
| TCRseqInfo.hh | |
| template_util.cc | Template identification utility functions for protocols/tcr/TCRmodel |
| template_util.hh | Template identification utility functions for protocols/tcr/TCRmodel |
| util.cc | Utility functions for protocols/tcr |
| util.hh | Utility functions for protocols/tcr |
| ► testing | |
| BenchmarkBuildRotamersMover.cc | For benchmarking purposes only. Builds data required to run pack rotamers but does not do any sampling. Input pose is untouched |
| BenchmarkBuildRotamersMover.fwd.hh | |
| BenchmarkBuildRotamersMover.hh | For benchmarking purposes only. Builds data required to run pack rotamers but does not do any sampling. Input pose is untouched |
| BenchmarkBuildRotamersMoverCreator.hh | |
| ► toolbox | |
| ► match_enzdes_util | |
| AlignPoseToInvrotTreeMover.cc | |
| AlignPoseToInvrotTreeMover.fwd.hh | Forward declaration for inverse rotamer tree node base |
| AlignPoseToInvrotTreeMover.hh | Small class to setup an invrot tree in an existing pose |
| AllowedSeqposForGeomCst.cc | |
| AllowedSeqposForGeomCst.fwd.hh | Forward declaration for AllowedSeqposForGeomCst |
| AllowedSeqposForGeomCst.hh | |
| EnzConstraintIO.cc | |
| EnzConstraintIO.fwd.hh | |
| EnzConstraintIO.hh | |
| EnzConstraintParameters.cc | |
| EnzConstraintParameters.hh | |
| EnzCstTemplateRes.cc | |
| EnzCstTemplateRes.hh | |
| EnzdesCacheableObserver.cc | |
| EnzdesCacheableObserver.fwd.hh | |
| EnzdesCacheableObserver.hh | |
| EnzdesCstCache.cc | |
| EnzdesCstCache.fwd.hh | |
| EnzdesCstCache.hh | |
| EnzdesLoopsFile.cc | |
| EnzdesLoopsFile.fwd.hh | |
| EnzdesLoopsFile.hh | |
| EnzdesSeqRecoveryCache.cc | |
| EnzdesSeqRecoveryCache.fwd.hh | |
| EnzdesSeqRecoveryCache.hh | |
| ExternalGeomSampler.cc | |
| ExternalGeomSampler.fwd.hh | |
| ExternalGeomSampler.hh | |
| InvrotTarget.cc | |
| InvrotTarget.fwd.hh | Forward declaration for inverse rotamer target |
| InvrotTarget.hh | .hh file for inverse rotamer target |
| InvrotTree.cc | |
| InvrotTree.fwd.hh | Forward declaration for inverse rotamer tree node base |
| InvrotTree.hh | Class to hold inverse rotamers associated with theozyme / cstfile |
| InvrotTreeNode.cc | .cc file for inverse rotamer tree node |
| InvrotTreeNode.fwd.hh | Forward declaration for inverse rotamer target |
| InvrotTreeNode.hh | .hh file for inverse rotamer tree node |
| InvrotTreeNodeBase.cc | Forward declaration for inverse rotamer tree node base |
| InvrotTreeNodeBase.fwd.hh | Forward declaration for inverse rotamer tree node base |
| InvrotTreeNodeBase.hh | Forward declaration for inverse rotamer tree node base |
| LigandConformer.cc | Implementation for class to hold a ligand conformation |
| LigandConformer.fwd.hh | Forward declaration for a class to hold the geometry of a ligand conformation |
| LigandConformer.hh | Declaration of a class to hold a ligand conformation |
| MatchConstraintFileInfo.cc | |
| MatchConstraintFileInfo.fwd.hh | |
| MatchConstraintFileInfo.hh | |
| util_functions.cc | Bunch of utility functions |
| util_functions.hh | |
| ► pose_manipulation | |
| pose_manipulation.cc | |
| pose_manipulation.hh | Some general functions to manipulate poses. feel free to add your own |
| ► rigid_body | |
| util.cc | |
| util.hh | |
| ► rotamer_set_operations | |
| AddGood2BPairEnergyRotamers.cc | |
| AddGood2BPairEnergyRotamers.fwd.hh | |
| AddGood2BPairEnergyRotamers.hh | |
| RigidBodyMoveRotSetOps.cc | |
| RigidBodyMoveRotSetOps.fwd.hh | |
| RigidBodyMoveRotSetOps.hh | |
| SpecialRotamerRotSetOps.cc | |
| SpecialRotamerRotSetOps.fwd.hh | |
| SpecialRotamerRotSetOps.hh | |
| ► sample_around | |
| util.cc | |
| util.hh | |
| CalcInterNeighborGroup.cc | This is meant for finding interfaces between protein domains - like protein-protein interfaces but within a protein. It's more flexible than that, though. You define groups of residues within a protein (say, the N and C terminal domains). You then define which pairs of groups you are interested in. This calculator returns the union of the sets of residues at the interfaces between these domains/groups. This calculator contains a superset of the functionality of some of the other calculators, but is less efficient in simple cases. The pose does NOT have to have been scored |
| CalcInterNeighborGroup.fwd.hh | |
| CalcInterNeighborGroup.hh | This calculator is meant for finding interfaces between protein domains - like protein-protein interfaces but within a protein. It's more flexible than that, though. You define groups of residues within a protein (say, the N and C terminal domains). You then define which pairs of groups you are interested in. This calculator returns the union of the sets of residues at the interfaces between these domains/groups. This calculator contains a superset of the functionality of some of the other calculators, but is less efficient in simple cases. The pose does NOT have to have been scored |
| Cluster.cc | |
| Cluster.hh | |
| Cluster.impl.hh | Template implementation for clustering of silentstructs that are provided by iterators |
| DecoySetEvaluation.cc | |
| DecoySetEvaluation.fwd.hh | |
| DecoySetEvaluation.hh | |
| DecoySetEvaluation.impl.hh | |
| EnergyLandscapeEvaluator.cc | Evaluates a set of score/rms points |
| EnergyLandscapeEvaluator.fwd.hh | Evaluates a set of score/rms points |
| EnergyLandscapeEvaluator.hh | Evaluates a set of score/rms points |
| IGEdgeReweighters.cc | |
| IGEdgeReweighters.hh | |
| InteratomicVarianceMatrix.cc | |
| InteratomicVarianceMatrix.hh | |
| KCluster.cc | |
| KCluster.fwd.hh | |
| KCluster.hh | Fast clustering algorithm for large silent file |
| NetworkAlgorithms.cc | Calculate various network properties from poses |
| NetworkAlgorithms.fwd.hh | FOrward header for class that analyzes properties of residue networks |
| NetworkAlgorithms.hh | Computes network properties of a pose |
| PyReturnValuePolicyTest.cc | |
| PyReturnValuePolicyTest.hh | A few functions test how PyRosetta handle boost ReturnValuePolicy |
| SamplerPlusPlus.fwd.hh | Abstract Base Class for Sampler generator |
| SamplerPlusPlus.hh | Abstract Base Class for Sampler generator |
| SamplerPlusPlusType.hh | |
| superimpose.cc | |
| superimpose.hh | |
| ► topology_broker | |
| ► claims | |
| BBClaim.fwd.hh | |
| BBClaim.hh | |
| CutClaim.fwd.hh | |
| CutClaim.hh | |
| DofClaim.cc | |
| DofClaim.fwd.hh | |
| DofClaim.hh | |
| JumpClaim.fwd.hh | |
| JumpClaim.hh | |
| LegacyRootClaim.fwd.hh | |
| LegacyRootClaim.hh | |
| SequenceClaim.fwd.hh | |
| SequenceClaim.hh | |
| SymmetryClaim.fwd.hh | |
| SymmetryClaim.hh | |
| ► weights | |
| AbinitioMoverWeight.hh | |
| ConstAbinitioMoverWeight.hh | |
| LargeFragWeight.hh | |
| SmallFragWeight.hh | |
| SmoothFragWeight.hh | |
| AsymFoldandDockClaimer.cc | |
| AsymFoldandDockClaimer.fwd.hh | AsymFoldandDockClaimer forward declarations header |
| AsymFoldandDockClaimer.hh | |
| BasicJumpClaimer.cc | |
| BasicJumpClaimer.fwd.hh | The forward head for the BasicJumpClaimre |
| BasicJumpClaimer.hh | |
| ClaimerMessage.cc | |
| ClaimerMessage.fwd.hh | |
| ClaimerMessage.hh | |
| ConstraintClaimer.cc | |
| ConstraintClaimer.fwd.hh | |
| ConstraintClaimer.hh | |
| ConstraintEvaluatorWrapper.cc | |
| ConstraintEvaluatorWrapper.fwd.hh | |
| ConstraintEvaluatorWrapper.hh | |
| ConstraintEvaluatorWrapperCreator.cc | |
| ConstraintEvaluatorWrapperCreator.hh | |
| CoordConstraintClaimer.cc | |
| CoordConstraintClaimer.fwd.hh | |
| CoordConstraintClaimer.hh | |
| CutBiasClaimer.cc | |
| CutBiasClaimer.fwd.hh | |
| CutBiasClaimer.hh | |
| DensityScoringClaimer.cc | |
| DensityScoringClaimer.fwd.hh | |
| DensityScoringClaimer.hh | |
| DisulfJumpClaimer.cc | |
| DisulfJumpClaimer.fwd.hh | Protocols::topology_broker::DisulfJumpClaimer forward declarations header |
| DisulfJumpClaimer.hh | |
| Exceptions.hh | |
| FibrilModelingClaimer.cc | |
| FibrilModelingClaimer.fwd.hh | FibrilModelingClaimer forward declarations header |
| FibrilModelingClaimer.hh | |
| FoldandDockClaimer.cc | |
| FoldandDockClaimer.fwd.hh | FoldandDockClaimer forward declarations header |
| FoldandDockClaimer.hh | |
| FragmentClaimer.cc | |
| FragmentClaimer.fwd.hh | |
| FragmentClaimer.hh | |
| FragmentJumpClaimer.cc | |
| FragmentJumpClaimer.fwd.hh | |
| FragmentJumpClaimer.hh | |
| LoopFragmentClaimer.cc | |
| LoopFragmentClaimer.fwd.hh | |
| LoopFragmentClaimer.hh | |
| MembraneTopologyClaimer.cc | |
| MembraneTopologyClaimer.fwd.hh | Protocols::topology_broker::MembraneTopologyClaimer forward declarations header |
| MembraneTopologyClaimer.hh | |
| MetalloClaimer.cc | |
| MetalloClaimer.fwd.hh | |
| MetalloClaimer.hh | |
| PcsEnergyController.cc | |
| PcsEnergyController.fwd.hh | |
| PcsEnergyController.hh | |
| PseudocontactShiftEnergyController.cc | |
| PseudocontactShiftEnergyController.fwd.hh | |
| PseudocontactShiftEnergyController.hh | |
| PseudocontactShiftEnergyController_Ts1.cc | |
| PseudocontactShiftEnergyController_Ts1.fwd.hh | |
| PseudocontactShiftEnergyController_Ts1.hh | |
| PseudocontactShiftEnergyController_Ts2.cc | |
| PseudocontactShiftEnergyController_Ts2.fwd.hh | |
| PseudocontactShiftEnergyController_Ts2.hh | |
| PseudocontactShiftEnergyController_Ts3.cc | |
| PseudocontactShiftEnergyController_Ts3.fwd.hh | |
| PseudocontactShiftEnergyController_Ts3.hh | |
| PseudocontactShiftEnergyController_Ts4.cc | |
| PseudocontactShiftEnergyController_Ts4.fwd.hh | |
| PseudocontactShiftEnergyController_Ts4.hh | |
| RigidBodyRandomTMHMover.cc | |
| RigidBodyRandomTMHMover.fwd.hh | |
| RigidBodyRandomTMHMover.hh | |
| RigidChunkClaimer.cc | |
| RigidChunkClaimer.fwd.hh | |
| RigidChunkClaimer.hh | |
| SequenceClaimer.cc | |
| SequenceClaimer.fwd.hh | |
| SequenceClaimer.hh | |
| SequenceNumberResolver.cc | |
| SequenceNumberResolver.fwd.hh | |
| SequenceNumberResolver.hh | |
| StartStructClaimer.cc | |
| StartStructClaimer.fwd.hh | |
| StartStructClaimer.hh | |
| SymmetryClaimer.cc | |
| SymmetryClaimer.fwd.hh | SymmetryClaimer forward declaration header |
| SymmetryClaimer.hh | Basic Claimer for making Symmetry Claims |
| TemplateFragmentClaimer.cc | |
| TemplateFragmentClaimer.fwd.hh | |
| TemplateFragmentClaimer.hh | |
| TemplateJumpClaimer.cc | |
| TemplateJumpClaimer.fwd.hh | |
| TemplateJumpClaimer.hh | |
| TMHTopologySamplerClaimer.cc | |
| TMHTopologySamplerClaimer.fwd.hh | Protocols::topology_broker::TMHTopologySamplerClaimer forward declarations header |
| TMHTopologySamplerClaimer.hh | Source file for TMHTopologySamplerClaimer protocol |
| TopologyBroker.cc | |
| TopologyBroker.fwd.hh | |
| TopologyBroker.hh | |
| TopologyClaimer.cc | |
| TopologyClaimer.fwd.hh | |
| TopologyClaimer.hh | |
| TopologyClaimerFactory.cc | |
| TopologyClaimerFactory.hh | |
| util.cc | |
| util.hh | |
| ► trajectory | |
| DbTrajectoryReader.cc | |
| DbTrajectoryReader.fwd.hh | |
| DbTrajectoryReader.hh | |
| DbTrajectoryWriter.cc | |
| DbTrajectoryWriter.fwd.hh | |
| DbTrajectoryWriter.hh | |
| ► unfolded_state_energy_calculator | |
| UnfoldedStateEnergyCalculatorJobDistributor.cc | |
| UnfoldedStateEnergyCalculatorJobDistributor.fwd.hh | |
| UnfoldedStateEnergyCalculatorJobDistributor.hh | |
| UnfoldedStateEnergyCalculatorMover.cc | |
| UnfoldedStateEnergyCalculatorMover.fwd.hh | |
| UnfoldedStateEnergyCalculatorMover.hh | |
| UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.cc | |
| UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.fwd.hh | |
| UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.hh | |
| UnfoldedStateEnergyCalculatorUtil.cc | |
| UnfoldedStateEnergyCalculatorUtil.hh | |
| ► vardist_solaccess | |
| LoadVarSolDistSasaCalculatorMover.hh | |
| VarSolDRotamerDots.cc | |
| VarSolDRotamerDots.fwd.hh | |
| VarSolDRotamerDots.hh | VarSolDRotamerDots classes header file |
| ► viewer | |
| ConformationViewer.cc | |
| ConformationViewer.fwd.hh | |
| ConformationViewer.hh | |
| GraphicsState.hh | |
| marchingCubes.cc | |
| marchingCubes.hh | |
| SilentObserver.cc | |
| SilentObserver.fwd.hh | |
| SilentObserver.hh | |
| triangle.hh | |
| triangleIterator.cc | |
| triangleIterator.hh | |
| viewers.cc | |
| viewers.hh | |
| visualize.cc | |
| visualize.hh | |
| ► vip | |
| VIP_Mover.cc | Void Identification and Packing Mover. Identifies buried voids in an input structure and attempts to fill these using fixed backbone packing and the GOE energy |
| VIP_Mover.hh | |
| VIP_Report.cc | Prints information about changes implemented in vip mover |
| VIP_Report.hh | Class for reports from vip mover implementation |
| VIP_Utils.cc | Utility functions for VIP mover |
| VIP_Utils.hh | |
| ► wum | |
| DatabaseEntryWorkUnit.cc | A work unit that runs a database query, processes the results, and returns a string (presumably a database insert statement) |
| DatabaseEntryWorkUnit.fwd.hh | A work unit that runs a database query, processes the results, and returns a string (presumably a database insert statement) |
| DatabaseEntryWorkUnit.hh | |
| MoverList.cc | |
| MoverList.hh | |
| MPI_WorkUnitManager.cc | |
| MPI_WorkUnitManager.fwd.hh | |
| MPI_WorkUnitManager.hh | |
| MPI_WorkUnitManager_Slave.cc | |
| MPI_WorkUnitManager_Slave.hh | |
| SilentStructStore.cc | |
| SilentStructStore.fwd.hh | SilentStructStore class forward declarations header |
| SilentStructStore.hh | |
| WorkUnitBase.cc | |
| WorkUnitBase.fwd.hh | |
| WorkUnitBase.hh | |
| WorkUnitList.cc | |
| WorkUnitList.hh | |
| WorkUnitManager.cc | |
| WorkUnitManager.fwd.hh | |
| WorkUnitManager.hh | |
1.8.7
