| ▼ src | |
| ► core | |
| ► chemical | |
| ► carbohydrates | |
| carbohydrate_data_structures.hh | Data structure declarations for carbohdrates |
| 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 |
| LinkageType.hh | Enumerator definition for LinkageType |
| 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 |
| ► 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.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 |
| 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_ResidueType.cc | |
| RNA_ResidueType.fwd.hh | |
| RNA_ResidueType.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 |
| PeptoidRotamerLibrarySpecification.cc | The PeptoidRotamerLibrarySpecification class specifies building PeptoidRotamers |
| PeptoidRotamerLibrarySpecification.fwd.hh | Forward declaration of a class that specifies how to build a rotamer library from a Peptoid rotlib |
| PeptoidRotamerLibrarySpecification.hh | The PeptoidRotamerLibrarySpecification class says to build a rotamer library from a Peptoid rotlib |
| PeptoidRotamerLibrarySpecificationCreator.hh | Class for instantiating a particular PeptoidRotamerLibrarySpecification |
| 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 |
| 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 | |
| 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 | |
| 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 |
| 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.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.cc | |
| ResidueGraphTypes.hh | Graph structure for ResidueType |
| ResidueLoader.cc | |
| ResidueLoader.fwd.hh | Implementation of the Residue Loader |
| ResidueLoader.hh | |
| ResidueLoaderCreator.hh | |
| ResidueLoaderOptions.cc | Forward headers for the Residue Loader Options |
| ResidueLoaderOptions.fwd.hh | Forward headers for the Residue Loader Options |
| ResidueLoaderOptions.hh | Forward headers for the Residue Loader Options |
| ResidueLoaderOptionsCreator.hh | |
| 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 |
| 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 |
| 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 globally-accessible ResidueTypeSets |
| ResidueTypeSet.srlz.hh | Serialization and deserialization routines for when working with globally-accessible ResidueTypeSets |
| ResidueTypeSetCache.cc | |
| ResidueTypeSetCache.fwd.hh | |
| ResidueTypeSetCache.hh | |
| types.hh | |
| util.cc | Utilities for modifying and utilizing Residues 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 | |
| ► membrane | |
| Exceptions.hh | Exception Hierarchy for Membrane framework Code |
| LipidAccInfo.cc | Membrane Lipid Accessibility Data |
| LipidAccInfo.fwd.hh | Membrane Lipid Accessibility Data |
| LipidAccInfo.hh | Membrane Lipid Accessibility Data |
| MembraneInfo.cc | Information about the membrane bilayer and its relationship with the protein(s) |
| MembraneInfo.fwd.hh | Information about the membrane bilayer and its relationship with the protein(s) |
| MembraneInfo.hh | Information about the membrane bilayer and its relationship with the protein(s) |
| 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.hh | Created on: Jun 30, 2011 |
| ► parametric | |
| 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 | |
| ► 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 |
| SymmDataOptions.hh | Load the SymmData data-structure, which is used to configure symmetric poses |
| SymmDataOptionsCreator.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 |
| 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 | |
| ► 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 |
| ► 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 |
| 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 | |
| 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 | |
| ► graph | |
| ArrayPool.cc | ArrayPool class declaration and implementation |
| ArrayPool.fwd.hh | Forward declaration for ArrayPool classes |
| ArrayPool.hh | ArrayPool class declaration and implementation |
| DisjointSets.cc | |
| DisjointSets.fwd.hh | DisjointSets class forward declaration |
| DisjointSets.hh | |
| Graph.cc | Graph base classes |
| Graph.fwd.hh | Graph base class forward declarations |
| Graph.hh | Generic graph class header |
| graph_util.cc | |
| graph_util.hh | Generic graph class header |
| unordered_object_pool.fwd.hpp | |
| unordered_object_pool.hpp | |
| UpperEdgeGraph.fwd.hh | |
| UpperEdgeGraph.hh | Templated graph for fast edge additions |
| UpperEdgeGraph.srlz.hh | Templated graph for fast edge additions |
| ► 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 |
| 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 | |
| ► pose_stream | |
| ExtendedPoseInputStream.cc | |
| ExtendedPoseInputStream.hh | |
| LazySilentFilePoseInputStream.cc | |
| LazySilentFilePoseInputStream.fwd.hh | |
| LazySilentFilePoseInputStream.hh | |
| MetaPoseInputStream.cc | |
| 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 | |
| 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 | |
| import_pose_options_creator.hh | |
| PDBSilentStruct.cc | |
| PDBSilentStruct.hh | |
| PDBSilentStructCreator.cc | |
| PDBSilentStructCreator.hh | |
| PoseFromPDBLoader.cc | |
| PoseFromPDBLoader.fwd.hh | |
| PoseFromPDBLoader.hh | |
| PoseFromPDBLoaderCreator.hh | |
| ► indexed_structure_store | |
| ABEGOHashedFragmentStore.cc | A wrapper to allow me to load the hashed fragment store on the datacache |
| ABEGOHashedFragmentStore.fwd.hh | A wrapper to allow me to load the hashed fragment store on the datacache |
| ABEGOHashedFragmentStore.hh | A wrapper to allow me to load the hashed fragment store on the datacache |
| BinaryFragmentStoreBackend.cc | |
| BinaryFragmentStoreBackend.fwd.hh | |
| BinaryFragmentStoreBackend.hh | |
| FragmentLookup.cc | |
| FragmentLookup.fwd.hh | |
| FragmentLookup.hh | |
| FragmentStore.cc | |
| FragmentStore.fwd.hh | |
| FragmentStore.hh | |
| H5FragmentStoreBackend.cc | |
| H5FragmentStoreBackend.fwd.hh | |
| H5FragmentStoreBackend.hh | |
| StructureStoreManager.cc | |
| StructureStoreManager.fwd.hh | |
| StructureStoreManager.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 | |
| ► 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.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 |
| 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) |
| ► 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.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 |
| SilentFileLoader.cc | |
| SilentFileLoader.fwd.hh | Forward Header for Loader for constructing a pose from a silent file |
| SilentFileLoader.hh | Load a silent file from an input stream and a SilentFileOptions object |
| SilentFileLoaderCreator.hh | |
| 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 |
| SilentFileOptionsCreator.hh | |
| 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 HEADER record in the PDB format |
| HeaderInformation.fwd.hh | Information stored in the HEADER record in the PDB format |
| HeaderInformation.hh | Information stored in the HEADER record 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 | |
| ► 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 |
| ► 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 |
| 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 |
| 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 |
| ► 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 | |
| RotamerLibrary.cc | |
| RotamerLibrary.fwd.hh | RotamerLibrary forward declarations and typedefs |
| RotamerLibrary.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 | |
| SingleResidueDunbrackLibraryCreator.hh | Class for instantiating a particular SingleResidueRotamerLibrary |
| ► 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 | |
| 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 |
| 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 | |
| ► 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 |
| SymmetricRotamerSetFactory.cc | |
| SymmetricRotamerSetFactory.fwd.hh | |
| SymmetricRotamerSetFactory.hh | Residue Set Factory 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 | |
| RotamerSetsBase.cc | |
| RotamerSetsBase.fwd.hh | |
| RotamerSetsBase.hh | |
| 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 | |
| WaterAnchorInfo.cc | |
| WaterAnchorInfo.fwd.hh | |
| WaterAnchorInfo.hh | |
| WaterPackingInfo.cc | |
| WaterPackingInfo.fwd.hh | |
| WaterPackingInfo.hh | |
| ► rotamers | |
| RotamericSingleResiduePeptoidLibrary.fwd.hh | |
| RotamericSingleResiduePeptoidLibrary.hh | |
| RotamericSingleResiduePeptoidLibrary.tmpl.hh | |
| 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 |
| SingleResiduePeptoidLibrary.cc | |
| SingleResiduePeptoidLibrary.fwd.hh | SingleResiduePeptoidLibrary forward declarations and typedefs |
| SingleResiduePeptoidLibrary.hh | SingleResiduePeptoidLibrary class |
| SingleResiduePeptoidLibraryCreator.cc | |
| SingleResiduePeptoidLibraryCreator.fwd.hh | Forward declaration of a class that instantiates a particular Peptoid rotlib |
| SingleResiduePeptoidLibraryCreator.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 | |
| 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 |
| 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 | |
| ReplicateTask.cc | |
| ReplicateTask.fwd.hh | Forward declaration for ReplicateTask |
| ReplicateTask.hh | |
| ReplicateTaskCreator.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 |
| 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 | |
| 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 | |
| ClashBasedRepackShellSelector.cc | The ClashBasedRepackShellSelector identifies all residues that clash with at least one rotamer of a design position |
| ClashBasedRepackShellSelector.fwd.hh | Forward declaration of a class that identifies all residues that clash with at least one rotamer of a design position |
| ClashBasedRepackShellSelector.hh | The ClashBasedRepackShellSelector identifies all residues that clash with at least one rotamer of a design position |
| ClashBasedRepackShellSelectorCreator.hh | The ClashBasedRepackShellSelector 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 |
| 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 |
| ► 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 | |
| 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 | |
| BasePair.cc | |
| BasePair.fwd.hh | |
| BasePair.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_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_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 | |
| util.cc | |
| util.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 |
| annotated_sequence.cc | Utility functions for making poses from sequences |
| annotated_sequence.hh | |
| 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 |
| ResidueIndexDescription.cc | Two 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 | Two 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 | Two 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 |
| util.cc | Pose class utilities |
| util.hh | Pose utilities |
| util.tmpl.hh | |
| 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 |
| AACompositionEnergy.cc | An EnergyMethod that penalizes deviation from a desired amino acid composition |
| AACompositionEnergy.fwd.hh | Forward declarations for an EnergyMethod that penalizes deviation from a desired amino acid composition |
| AACompositionEnergy.hh | Headers for an EnergyMethod that penalizes deviation from a desired amino acid composition |
| AACompositionEnergyCreator.hh | Creator for an EnergyMethod that penalizes deviation from a desired amino acid composition |
| 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 |
| ► aa_repeat_energy | |
| AARepeatEnergy.cc | An EnergyMethod that penalizes stretches of a repeating amino acid (e.g. poly-Q sequences) |
| AARepeatEnergy.fwd.hh | Forward declarations for an EnergyMethod that penalizes stretches of a repeating amino acid (e.g. poly-Q sequences) |
| AARepeatEnergy.hh | Headers for an EnergyMethod that penalizes stretches of a repeating amino acid (e.g. poly-Q sequences) |
| AARepeatEnergyCreator.hh | Creator for an EnergyMethod that penalizes stretches of a repeating amino acid (e.g. poly-Q sequences) |
| ► 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 |
| ► 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 |
| 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 |
| ► 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 | |
| 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 | |
| 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 | |
| ResidueTypeConstraint.cc | |
| ResidueTypeConstraint.fwd.hh | |
| ResidueTypeConstraint.hh | |
| ResidueTypeLinkingConstraint.cc | |
| ResidueTypeLinkingConstraint.fwd.hh | Constrainting two residues to be the same type, based on |
| ResidueTypeLinkingConstraint.hh | |
| 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 | |
| XtalMLEnergy.cc | ML target |
| XtalMLEnergy.hh | ML target |
| XtalMLEnergyCreator.hh | ML target |
| ► 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 | |
| CentroidDisulfideEnergy.cc | Centroid Disulfide Energy class implementation |
| CentroidDisulfideEnergy.fwd.hh | Centroid Disulfide Energy class forward declaration |
| CentroidDisulfideEnergy.hh | Centroid Disulfide Energy class declaration |
| CentroidDisulfideEnergyContainer.cc | |
| CentroidDisulfideEnergyContainer.fwd.hh | |
| CentroidDisulfideEnergyContainer.hh | Disulfide Energy Container class declaration |
| CentroidDisulfideEnergyCreator.hh | Declaration for the class that connects CentroidDisulfideEnergy with the ScoringManager |
| 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 |
| DisulfideMatchingEnergy.cc | Centroid Disulfide Energy class implementation |
| DisulfideMatchingEnergy.fwd.hh | Centroid Disulfide Energy class forward declaration |
| DisulfideMatchingEnergy.hh | Centroid Disulfide Energy class declaration |
| DisulfideMatchingEnergyContainer.cc | |
| DisulfideMatchingEnergyContainer.fwd.hh | |
| DisulfideMatchingEnergyContainer.hh | Disulfide Energy Container class declaration |
| DisulfideMatchingEnergyCreator.hh | Declaration for the class that connects DisulfideMatchingEnergy with the ScoringManager |
| DisulfideMatchingPotential.cc | |
| DisulfideMatchingPotential.fwd.hh | |
| DisulfideMatchingPotential.hh | Centroid Disulfide Energy Potentials |
| FullatomDisulfideEnergy.cc | Disulfide Energy class implementation |
| FullatomDisulfideEnergy.fwd.hh | Disulfide Energy class forward declaration |
| FullatomDisulfideEnergy.hh | |
| FullatomDisulfideEnergyContainer.cc | |
| FullatomDisulfideEnergyContainer.fwd.hh | |
| FullatomDisulfideEnergyContainer.hh | Disulfide Energy Container class declaration |
| FullatomDisulfideEnergyCreator.hh | Declaration for the class that connects FullatomDisulfideEnergy with the ScoringManager |
| 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 |
| DNAChiEnergy.cc | DNA Chi torsion energy method implementation |
| DNAChiEnergy.fwd.hh | DNA Chi torsion energy method forward declaration |
| DNAChiEnergy.hh | Energy term for simple DNA chi torsion |
| DNAChiEnergyCreator.hh | Declaration for the class that connects DNAChiEnergy with the ScoringManager |
| DNATorsionEnergy.cc | |
| DNATorsionEnergy.fwd.hh | |
| DNATorsionEnergy.hh | Statistically derived rotamer pair potential class declaration |
| DNATorsionEnergyCreator.hh | Declaration for the class that connects DNATorsionEnergy with the ScoringManager |
| 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 | |
| ElecAtom.cc | |
| ElecAtom.fwd.hh | |
| ElecAtom.hh | |
| FA_ElecEnergy.cc | |
| FA_ElecEnergy.fwd.hh | |
| FA_ElecEnergy.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_ElecEnergyCreator.hh | Declaration for the class that connects FA_ElecEnergy 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 |
| GroupElec.cc | |
| GroupElec.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 |
| ► electron_density | |
| ElecDensAllAtomCenEnergy.cc | |
| ElecDensAllAtomCenEnergy.hh | |
| ElecDensAllAtomCenEnergyCreator.hh | Declaration for the class that connects ElecDensAllAtomCenEnergy with the ScoringManager |
| ElecDensCenEnergy.cc | |
| ElecDensCenEnergy.hh | |
| ElecDensCenEnergyCreator.hh | Declaration for the class that connects ElecDensCenEnergy with the ScoringManager |
| ElecDensEnergy.cc | |
| ElecDensEnergy.hh | |
| ElecDensEnergyCreator.hh | Declaration for the class that connects ElecDensEnergy with the ScoringManager |
| ElectronDensity.cc | |
| ElectronDensity.fwd.hh | |
| ElectronDensity.hh | |
| ElectronDensityLoader.cc | |
| ElectronDensityLoader.fwd.hh | |
| ElectronDensityLoader.hh | |
| ElectronDensityLoaderCreator.hh | Header for ElectronDensityLoader Creator for the load-time factory registration scheme |
| ElectronDensityOptions.cc | |
| ElectronDensityOptions.fwd.hh | |
| ElectronDensityOptions.hh | |
| ElectronDensityOptionsCreator.hh | Header for ElectronDensityOptions Creator for the load-time factory registration scheme |
| FastDensEnergy.cc | |
| FastDensEnergy.hh | |
| FastDensEnergyCreator.hh | Declaration for the class that connects FastDensEnergy with the ScoringManager |
| SplineInterp.cc | |
| SplineInterp.hh | |
| util.cc | |
| util.hh | |
| xray_scattering.cc | |
| xray_scattering.hh | |
| ► electron_density_atomwise | |
| ElecDensAtomwiseEnergy.cc | Elec_dens_atomwise scoring method implementation |
| ElecDensAtomwiseEnergy.fwd.hh | Elec_dens_atomwise energy method forward declaration |
| ElecDensAtomwiseEnergy.hh | Declaration for elec_dens_atomwise scoring method |
| ElecDensAtomwiseEnergyCreator.hh | |
| ElectronDensityAtomwise.cc | Elec_dens_atomwise scoring method implementation |
| ElectronDensityAtomwise.hh | Scoring a structure against an electron density map |
| ► 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 |
| 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 | |
| FACTSEnergy.cc | |
| FACTSEnergy.fwd.hh | |
| FACTSEnergy.hh | |
| FACTSEnergyCreator.hh | |
| 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 |
| FiberDiffractionEnergy.cc | |
| FiberDiffractionEnergy.hh | FiberDiffraction scoring and derivatives (all-atom) |
| FiberDiffractionEnergyCreator.hh | Energy Creator for FiberDiffractionEnergy |
| FiberDiffractionEnergyDens.cc | |
| FiberDiffractionEnergyDens.hh | FiberDiffractionDens scoring (low-resolution, electron density based) |
| FiberDiffractionEnergyDensCreator.hh | Energy Creator for FiberDiffractionEnergyDens |
| FiberDiffractionEnergyGpu.cc | |
| FiberDiffractionEnergyGpu.hh | |
| FiberDiffractionEnergyGpuCreator.hh | |
| FiberDiffractionKernelGpu.hh | FiberDiffraction kernel module for GPU computations |
| FiberDiffractionLoader.cc | Options for constructing fiber diffraction layer lines |
| FiberDiffractionLoader.fwd.hh | Fiber diffraction data forward creator |
| FiberDiffractionLoader.hh | Options for constructing fiber diffraction layer lines |
| FiberDiffractionLoaderCreator.hh | Fiber diffraction data creator |
| FiberDiffractionOptions.cc | Options for fiber diffraction data |
| FiberDiffractionOptions.fwd.hh | Options for fiber diffraction data |
| FiberDiffractionOptions.hh | Options for fiber diffraction data |
| FiberDiffractionOptionsCreator.hh | Options for fiber diffraction data |
| 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 |
| 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 | |
| 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 | |
| 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 | |
| ContextDependentGeometricSolEnergy.cc | |
| ContextDependentGeometricSolEnergy.fwd.hh | |
| ContextDependentGeometricSolEnergy.hh | |
| ContextDependentGeometricSolEnergyCreator.hh | Declaration for the class that connects GeometricSolEnergy with the ScoringManager |
| ContextIndependentGeometricSolEnergy.cc | |
| ContextIndependentGeometricSolEnergy.fwd.hh | |
| ContextIndependentGeometricSolEnergy.hh | |
| ContextIndependentGeometricSolEnergyCreator.hh | |
| DatabaseOccSolEne.cc | Database containing params for OccludedHbondSolEnergy |
| DatabaseOccSolEne.fwd.hh | Database containing params for OccludedHbondSolEnergy |
| DatabaseOccSolEne.hh | Database containing params for OccludedHbondSolEnergy |
| ExactOccludedHbondSolEnergy.cc | |
| ExactOccludedHbondSolEnergy.fwd.hh | |
| ExactOccludedHbondSolEnergy.hh | Solvation model based on penalizing potential for Hbonding to solvent |
| ExactOccludedHbondSolEnergyCreator.hh | Declaration for the class that connects ExactOccludedHbondSolEnergy with the ScoringManager |
| GeometricSolEnergyEvaluator.cc | |
| GeometricSolEnergyEvaluator.fwd.hh | |
| GeometricSolEnergyEvaluator.hh | Geometric solvation energy |
| non_scorefxn_exact_model.cc | |
| non_scorefxn_exact_model.hh | |
| OccludedHbondSolEnergy.cc | Solvation model based on penalizing potential for Hbonding to solvent |
| OccludedHbondSolEnergy.fwd.hh | Solvation model based on penalizing potential for Hbonding to solvent |
| OccludedHbondSolEnergy.hh | Solvation model based on penalizing potential for Hbonding to solvent |
| OccludedHbondSolEnergy_onebody.cc | Solvation model based on penalizing potential for Hbonding to solvent |
| OccludedHbondSolEnergy_onebody.fwd.hh | Solvation model based on penalizing potential for Hbonding to solvent |
| OccludedHbondSolEnergy_onebody.hh | Solvation model based on penalizing potential for Hbonding to solvent |
| OccludedHbondSolEnergy_onebodyCreator.hh | Declaration for the class that connects OccludedHbondSolEnergy_onebody with the ScoringManager |
| OccludedHbondSolEnergyCreator.hh | Declaration for the class that connects OccludedHbondSolEnergy with the ScoringManager |
| ► hackaro | |
| HackAroEnergy.cc | |
| HackAroEnergy.fwd.hh | |
| HackAroEnergy.hh | |
| HackAroEnergyCreator.hh | |
| ► hbonds | |
| ► 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 |
| 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 |
| 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 | |
| Loop.cc | |
| Loop.fwd.hh | |
| Loop.hh | |
| LoopCloseEnergy.cc | Cost of bringing two chains together |
| LoopCloseEnergy.hh | |
| LoopCloseEnergyCreator.hh | Declaration for the class that connects LoopCloseEnergy with the ScoringManager |
| LoopCycle.cc | |
| LoopCycle.fwd.hh | |
| LoopCycle.hh | |
| LoopGraph.cc | |
| LoopGraph.fwd.hh | |
| LoopGraph.hh | |
| LoopScoreInfo.cc | |
| LoopScoreInfo.fwd.hh | |
| LoopScoreInfo.hh | |
| ► magnesium | |
| MgEnergy.cc | |
| MgEnergy.fwd.hh | |
| MgEnergy.hh | |
| MgEnergyCreator.hh | Declaration for the class that connects MgEnergy with the ScoringManager |
| MgKnowledgeBasedPotential.cc | |
| MgKnowledgeBasedPotential.fwd.hh | |
| MgKnowledgeBasedPotential.hh | Information on which atoms to use for computing clashes |
| 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 |
| 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 | |
| FaMPEnvEnergy.cc | |
| FaMPEnvEnergy.fwd.hh | LK-Type Membrane Environment Energy |
| FaMPEnvEnergy.hh | LK-Type Membrane Environment Energy |
| FaMPEnvEnergyCreator.hh | Membrane Environment Energy |
| FaMPEnvSmoothEnergy.cc | |
| FaMPEnvSmoothEnergy.fwd.hh | Fullatom Smoothed Membrane Environment Energy |
| FaMPEnvSmoothEnergy.hh | Fullatom Smoothed Membrane Environment Energy |
| FaMPEnvSmoothEnergyCreator.hh | Fullatom Smoothed Membrane Environment Energy |
| FaMPSolvEnergy.cc | LK-Type Membrane Solvation Energy |
| FaMPSolvEnergy.fwd.hh | |
| FaMPSolvEnergy.hh | LK-Type Membrane Solvation Energy |
| FaMPSolvEnergyCreator.hh | LK-Type Membrane Solvation Energy |
| MembraneData.cc | Membrane Scorefunction Statistics Class |
| MembraneData.fwd.hh | Membrane Base Potential |
| MembraneData.hh | Membrane Scorefunction Statistics Class |
| 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 | Membrane Environemnt Energy |
| MPLipoEnergy.cc | Membrane Lipophibicity Term |
| MPLipoEnergy.fwd.hh | Membrane Lipophibicity Term |
| MPLipoEnergy.hh | Membrane Lipophibicity Term |
| MPLipoEnergyCreator.hh | |
| 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 |
| MPPairEnergy.cc | Membrane Residue Pair Energy Term |
| MPPairEnergy.fwd.hh | Membrane Residue Pair Energy Term |
| MPPairEnergy.hh | Membrane Residue Pair Energy Term |
| MPPairEnergyCreator.hh | Membrane Residue Pair Energy Term Creator |
| 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 | |
| ► carbohydrates | |
| SugarBackboneEnergy.cc | |
| SugarBackboneEnergy.fwd.hh | Forward declarations for SugarBackboneEnergy |
| SugarBackboneEnergy.hh | Method definitions for SugarBackboneEnergy and SugarBackboneEnergyCreator |
| SugarBackboneEnergyCreator.hh | Method declarations for SugarBackboneEnergyCreator |
| ► dfire | |
| DFIRE_Energy.cc | |
| DFIRE_Energy.fwd.hh | |
| DFIRE_Energy.hh | |
| DFIRE_EnergyCreator.hh | |
| DFIRE_Potential.cc | |
| DFIRE_Potential.fwd.hh | |
| DFIRE_Potential.hh | DFIRE Potential class declaration |
| BurialEnergy.cc | |
| BurialEnergy.hh | Energy term use for scoring predicted burial |
| BurialEnergyCreator.hh | Declaration for the class that connects BurialEnergy with the ScoringManager |
| CartBondedParameters.hh | |
| 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 | |
| chainbreak_util.cc | Utility functions for scoring chainbreaks |
| chainbreak_util.hh | Utility functions for scoring chainbreaks |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| FreeDOF_Options.cc | |
| FreeDOF_Options.fwd.hh | |
| FreeDOF_Options.hh | |
| 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 |
| 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 | |
| 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 |
| 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 |
| LinearChainbreakEnergy.cc | |
| 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 |
| 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 |
| 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 |
| Methods.hh | Energy Method enumeration |
| 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 |
| 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 |
| 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 |
| 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 | |
| NMerSVMEnergy.fwd.hh | SVMerence energy method forward declaration |
| NMerSVMEnergy.hh | SVMerence energy method implementation |
| NMerSVMEnergyCreator.hh | Declaration for the class that connects NMerSVMEnergy with the ScoringManager |
| 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 |
| OneBodyEnergy.cc | |
| OneBodyEnergy.fwd.hh | |
| OneBodyEnergy.hh | |
| 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 | PH Score (kT = 0.59 at 298 K) based on the chemical potential of the protonated/deprotonated residues. It indirectly contributes to a change in rotamer probabilities of protonated/deprotonated residues in the Dunbrack energy depending on the value of pH |
| pHEnergyCreator.hh | Declaration for the class that connects pHEnergy with the ScoringManager |
| 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 |
| PyEnergyMethodRegisterer.hh | EnergyMethod factory registration and creation 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_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 |
| SA_Energy.cc | Sa energy function definition |
| SA_Energy.hh | Statistically derived rotamer pair potential class declaration |
| SA_EnergyCreator.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 |
| 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 |
| 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 | |
| SSElementMotifContactEnergyCreator.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 |
| 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 | |
| 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 |
| 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 |
| util.cc | Utility methods for scoring |
| util.hh | Utility methods for scoring |
| VdWTinkerEnergy.cc | VdW treatment using buffered 14-7 approach in Tinker/Amoeba |
| VdWTinkerEnergy.fwd.hh | |
| VdWTinkerEnergy.hh | VdW replacement using buffered 14-7 approach in Tinker/Amoeba |
| VdWTinkerEnergyCreator.hh | Declaration for the class that connects VdWTinkerEnergy with the ScoringManager |
| WaterAdductHBondEnergy.cc | |
| WaterAdductHBondEnergy.fwd.hh | |
| WaterAdductHBondEnergy.hh | Energy potential for water mediated hydrogen bonds involving adduct-placed water molecules |
| WaterAdductHBondEnergyCreator.hh | Declaration for the class that connects WaterAdductHBondEnergy with the ScoringManager |
| WaterAdductIntraEnergy.cc | |
| WaterAdductIntraEnergy.fwd.hh | |
| WaterAdductIntraEnergy.hh | Energetic offset/cost for placing a water adduct on an amino or nucleic acid |
| WaterAdductIntraEnergyCreator.hh | Declaration for the class that connects WaterAdductIntraEnergy with the ScoringManager |
| 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 |
| 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 | |
| ► 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 | |
| ► 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 |
| HolesEnergy.cc | |
| HolesEnergy.hh | Packing Score |
| HolesEnergyCreator.hh | Declaration for the class that connects HolesEnergy with the ScoringManager |
| 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 | |
| SurfEnergy.cc | Packing Score |
| SurfEnergy.hh | Packing Score |
| SurfEnergyCreator.hh | Declaration for the class that connects SurfEnergy with the ScoringManager |
| SurfVolEnergy.cc | Packing Score |
| SurfVolEnergy.hh | Packing Score |
| SurfVolEnergyCreator.hh | Declaration for the class that connects SurfVolEnergy with the ScoringManager |
| ► 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 | |
| ► rna | |
| ► chemical_shift | |
| 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 | Declaration for the class that connects RNA_ChemicalShiftEnergy with the ScoringManager |
| 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_ChemicalMappingEnergy.cc | Statistically derived base-base energy |
| RNA_ChemicalMappingEnergy.fwd.hh | |
| RNA_ChemicalMappingEnergy.hh | Statistically derived chemical mapping score |
| RNA_ChemicalMappingEnergyCreator.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 | Declaration for the class that connects RNA_DataBackboneEnergy with the ScoringManager |
| RNA_DataInfo.cc | |
| RNA_DataInfo.fwd.hh | |
| RNA_DataInfo.hh | |
| 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 | |
| RG_Energy_RNA.cc | |
| RG_Energy_RNA.hh | |
| RG_Energy_RNACreator.hh | Declaration for the class that connects RG_Energy_RNA with the ScoringManager |
| RNA_AtomVDW.cc | |
| RNA_AtomVDW.fwd.hh | |
| RNA_AtomVDW.hh | Information on which atoms to use for computing clashes |
| RNA_BulgeEnergy.cc | |
| RNA_BulgeEnergy.fwd.hh | |
| RNA_BulgeEnergy.hh | Score function class |
| RNA_BulgeEnergyCreator.hh | |
| RNA_CentroidInfo.cc | |
| RNA_CentroidInfo.fwd.hh | |
| RNA_CentroidInfo.hh | |
| RNA_EnergyMethodOptions.cc | |
| RNA_EnergyMethodOptions.fwd.hh | |
| RNA_EnergyMethodOptions.hh | |
| RNA_FilteredBaseBaseInfo.cc | |
| RNA_FilteredBaseBaseInfo.fwd.hh | |
| RNA_FilteredBaseBaseInfo.hh | |
| RNA_FullAtomStackingEnergy.cc | |
| RNA_FullAtomStackingEnergy.fwd.hh | |
| RNA_FullAtomStackingEnergy.hh | |
| RNA_FullAtomStackingEnergyCreator.hh | Declaration for the class that connects RNA_FullAtomStackingEnergy with the ScoringManager |
| 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 | Van der waals over aromatics |
| RNA_LJ_BaseEnergyCreator.hh | Declaration for the class that connects RNA_LJ_BaseEnergy with the ScoringManager |
| RNA_LowResolutionPotential.cc | |
| RNA_LowResolutionPotential.fwd.hh | |
| RNA_LowResolutionPotential.hh | |
| RNA_PairwiseLowResolutionEnergy.cc | Statistically derived rotamer pair potential class implementation |
| RNA_PairwiseLowResolutionEnergy.fwd.hh | |
| RNA_PairwiseLowResolutionEnergy.hh | Statistically derived rotamer pair potential class declaration |
| RNA_PairwiseLowResolutionEnergyCreator.hh | Declaration for the class that connects RNA_PairwiseLowResolutionEnergy with the ScoringManager |
| RNA_RawBaseBaseInfo.cc | |
| RNA_RawBaseBaseInfo.fwd.hh | |
| RNA_RawBaseBaseInfo.hh | |
| RNA_ScoringInfo.cc | |
| RNA_ScoringInfo.fwd.hh | |
| RNA_ScoringInfo.hh | |
| RNA_ScoringUtil.cc | |
| RNA_ScoringUtil.hh | |
| RNA_SugarCloseEnergy.cc | |
| RNA_SugarCloseEnergy.fwd.hh | |
| RNA_SugarCloseEnergy.hh | Statistically derived rotamer pair potential class declaration |
| RNA_SugarCloseEnergyCreator.hh | |
| RNA_SuiteEnergy.cc | |
| RNA_SuiteEnergy.fwd.hh | |
| RNA_SuiteEnergy.hh | |
| RNA_SuiteEnergyCreator.hh | Declaration for the class that connects RNA_ChemicalMappingEnergy with the ScoringManager |
| RNA_SuitePotential.cc | |
| RNA_SuitePotential.fwd.hh | |
| RNA_SuitePotential.hh | |
| RNA_TorsionEnergy.cc | |
| RNA_TorsionEnergy.fwd.hh | |
| RNA_TorsionEnergy.hh | Statistically derived rotamer pair potential class declaration |
| RNA_TorsionEnergyCreator.hh | Declaration for the class that connects RNA_TorsionEnergy with the ScoringManager |
| RNA_TorsionPotential.cc | |
| RNA_TorsionPotential.fwd.hh | |
| RNA_TorsionPotential.hh | |
| RNA_VDW_Energy.cc | Statistically derived clash check for RNA |
| RNA_VDW_Energy.fwd.hh | |
| RNA_VDW_Energy.hh | Statistically derived rotamer pair potential class declaration |
| RNA_VDW_EnergyCreator.hh | Declaration for the class that connects RNA_VDW_Energy with the ScoringManager |
| StackElecEnergy.cc | FA_Elec, but just 'perpendicular' to bases... trying to separate from H-bonds & geom_sol |
| StackElecEnergy.fwd.hh | |
| StackElecEnergy.hh | |
| StackElecEnergyCreator.hh | Declaration for the class that connects StackElecEnergy with the ScoringManager |
| ► 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 | |
| FastSAXSEnergy.cc | |
| FastSAXSEnergy.hh | |
| FastSAXSEnergyCreator.hh | Energy Creator for FastSAX scoring of Stovgaard et al (BMC Bioinf. 2010) |
| 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 |
| SAXSEnergy.cc | FastSAX scoring of Stovgaard et al (BMC Bioinf. 2010) |
| SAXSEnergy.hh | FastSAX scoring of Stovgaard et al (BMC Bioinf. 2010) |
| SAXSEnergyCEN.hh | |
| SAXSEnergyCreator.hh | Declaration for the class that connects SAXSEnergyCreator with the ScoringManager |
| 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 | |
| SinXOverX.cc | |
| SinXOverX.hh | |
| ► sc | |
| 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.cc | |
| 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 |
| ► 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 | |
| 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_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 | |
| 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_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 |
| ScoreFunction.cc | ScoreFunction class definition |
| 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 | |
| ► select | |
| ► 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 |
| 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 |
| 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 | |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | |
| 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 |
| ► 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 | |
| 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 |
| 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 |
| 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 | Small bundle of utilities for dealing with sequences |
| util.hh | |
| ► 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 |
| svn_version.cc | |
| svn_version.hh | |
| 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 | |
| ClearCompositionConstraintsMover.cc | Clears all AACompositionConstraints from a pose |
| ClearCompositionConstraintsMover.fwd.hh | Forward declarations for the ClearCompositionConstraintsMover |
| ClearCompositionConstraintsMover.hh | Headers for the ClearCompositionConstraintsMover |
| ClearCompositionConstraintsMoverCreator.hh | |
| ► 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 | |
| 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 |
| 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 |
| PackStatMover.cc | |
| PackStatMover.fwd.hh | Created on: Jan 25, 2012 |
| PackStatMover.hh | |
| 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 |
| ► 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 | |
| AntibodyDesignProtocol.cc | Handles the Antibody Design Protocol |
| AntibodyDesignProtocol.fwd.hh | Handles all loading of CDR, Framework, and cluster/dmap info from database file |
| AntibodyDesignProtocol.hh | Handles the Antibody Design Protocol |
| AntibodyDesignProtocolCreator.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 | |
| util.cc | |
| util.hh | Utility functions for antibody design namespace |
| ► grafting | |
| antibody_sequence.cc | |
| antibody_sequence.hh | |
| 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 |
| regex_based_cdr_detection.cc | |
| regex_based_cdr_detection.hh | RegEx based detection of CRS's |
| 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 |
| util.cc | Helpers for antibody grafting code |
| util.hh | Helpers for antibody grafting code |
| ► snugdock | |
| SnugDock.cc | |
| SnugDock.fwd.hh | Forward declaration |
| SnugDock.hh | |
| 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 |
| 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 | |
| ModelCDRH3.cc | Models CDR H3 loop using loop modeling |
| ModelCDRH3.fwd.hh | |
| ModelCDRH3.hh | |
| RefineBetaBarrel.cc | Build a homology model of an antibody |
| RefineBetaBarrel.fwd.hh | Forward declaration |
| RefineBetaBarrel.hh | Build a homology model of an antibody |
| RefineOneCDRLoop.cc | Build a homology model of an antibody |
| RefineOneCDRLoop.fwd.hh | |
| RefineOneCDRLoop.hh | Build a homology model of an antibody |
| RefineOneCDRLoopCentroid.cc | Build a homology model of an antibody |
| RefineOneCDRLoopCentroid.fwd.hh | |
| RefineOneCDRLoopCentroid.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 |
| ► 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 |
| ► 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 | |
| GlycanRelaxMover.cc | Main mover for Glycan Relax, which optimizes glycans in a pose |
| GlycanRelaxMover.fwd.hh | Main mover for Glycan Relax, which optimizes glycans in a pose |
| GlycanRelaxMover.hh | Main mover for Glycan Relax, which optimizes glycans in a pose |
| GlycanRelaxMoverCreator.hh | Main mover for Glycan Relax, which optimizes glycans in a pose |
| LinkageConformerMover.cc | 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.fwd.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.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 |
| 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 |
| 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 | |
| ► cluster | |
| APCluster.cc | |
| APCluster.fwd.hh | |
| APCluster.hh | |
| cluster.cc | |
| cluster.hh | |
| ► coarse_rna | |
| 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 | Forward declarations header |
| MultipleDomainMover.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 |
| ► 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 | |
| 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 | |
| ► 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 | |
| ► cyclic_peptide | |
| CreateAngleConstraint.cc | Add angle constraints to the current pose conformation |
| CreateAngleConstraint.hh | Add angle constraints to the current pose conformation |
| CreateAngleConstraintCreator.hh | |
| CreateDistanceConstraint.cc | Add distance constraints to the current pose conformation |
| CreateDistanceConstraint.hh | Add distance constraints to the current pose conformation |
| CreateDistanceConstraintCreator.hh | |
| CreateTorsionConstraint.cc | Add torsion constraints to the current pose conformation |
| CreateTorsionConstraint.hh | Add torsion constraints to the current pose conformation |
| CreateTorsionConstraintCreator.hh | |
| 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 | |
| PeptideStubMover.cc | Add constraints to the current pose conformation |
| PeptideStubMover.fwd.hh | Defines owning pointers for PeptideStubMover mover class |
| PeptideStubMover.hh | Add constraints to the current pose conformation |
| PeptideStubMoverCreator.hh | |
| 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 | |
| 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 |
| ► ddg | |
| ddG_main.cc | |
| ddG_main.hh | |
| ddGData.cc | |
| ddGData.fwd.hh | |
| ddGData.hh | |
| ddGMover.cc | |
| ddGMover.hh | |
| ► denovo_design | |
| ► components | |
| 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 |
| NamedMover.cc | Named segment of residues |
| NamedMover.fwd.hh | |
| NamedMover.hh | NamedMover functions for building structures from components |
| Picker.cc | Auto-caching fragment picker |
| Picker.fwd.hh | Picker forward header |
| Picker.hh | Auto-caching fragment picker |
| Segment.cc | Named segment of residues |
| Segment.fwd.hh | |
| Segment.hh | Segment functions for building structures from components |
| StructureData.cc | |
| StructureData.fwd.hh | StructureData forward header |
| StructureData.hh | StructureData functions for building structures from components |
| ► connection | |
| BridgeChains.cc | The BridgeChains |
| BridgeChains.fwd.hh | BridgeChains forward header |
| BridgeChains.hh | The BridgeChains Protocol |
| BridgeChainsCreator.hh | |
| BridgeChainsOld.cc | |
| BridgeChainsOld.fwd.hh | |
| BridgeChainsOld.hh | |
| BridgeChainsOldCreator.hh | |
| Connection.cc | |
| Connection.fwd.hh | |
| Connection.hh | Connection classes for building structures from components |
| ConnectionCreators.hh | Creators for classes that connect chains |
| ExtendChain.cc | The BridgeChains |
| ExtendChain.fwd.hh | ExtendChain forward header |
| ExtendChain.hh | The ExtendChain Protocol |
| ExtendChainCreator.hh | |
| ► constraints | |
| CoordinateConstraintGenerator.cc | Coordinate constraint remodel constraint generator |
| CoordinateConstraintGenerator.fwd.hh | CoordinateConstraintGenerator forward header |
| CoordinateConstraintGenerator.hh | The CoordinateConstraintGenerator Protocol, for adding coordinate constraints |
| CoordinateConstraintGeneratorCreator.hh | |
| FileConstraintGenerator.cc | |
| FileConstraintGenerator.fwd.hh | |
| FileConstraintGenerator.hh | |
| FileConstraintGeneratorCreator.hh | This class will create instances of the ConstraintFileRCG mover |
| ► filters | |
| 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 |
| ► movers | |
| DisulfidizeMover.cc | The DisulfidizeMover |
| DisulfidizeMover.fwd.hh | |
| DisulfidizeMover.hh | The DisulfidizeMover Protocol |
| DisulfidizeMoverCreator.hh | |
| ► task_operations | |
| ConsensusLoopDesign.cc | Restrict loop residue identities to those commonly found in nature |
| ConsensusLoopDesign.fwd.hh | Restrict loop residue identities to those commonly found in nature |
| ConsensusLoopDesign.hh | Restrict loop residue identities to those commonly found in nature |
| ConsensusLoopDesignCreator.hh | |
| types.hh | |
| util.cc | -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*- |
| 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 | |
| ► 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 | |
| DockingHighResLegacy.cc | |
| DockingHighResLegacy.fwd.hh | Forward declarations for DockingHighResLegacy (high resolution docking protocol as it existed in mini before the GrayLab refactor) |
| DockingHighResLegacy.hh | |
| 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 | |
| DockingProtocol.cc | |
| DockingProtocol.fwd.hh | |
| DockingProtocol.hh | |
| DockingProtocolCreator.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 | |
| DockMinMover.cc | |
| DockMinMover.fwd.hh | Forward declarations for DockMinMover (high resolution min) docking |
| DockMinMover.hh | |
| 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 | |
| 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 | |
| ► 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 | |
| ► 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 | |
| ► farna | |
| ► base_pairs | |
| BasePairStep.cc | |
| BasePairStep.fwd.hh | |
| BasePairStep.hh | |
| RNA_BasePairHandler.cc | |
| RNA_BasePairHandler.fwd.hh | |
| RNA_BasePairHandler.hh | |
| ► fragments | |
| FullAtomRNA_Fragments.cc | |
| FullAtomRNA_Fragments.fwd.hh | |
| FullAtomRNA_Fragments.hh | |
| RNA_Fragments.cc | |
| RNA_Fragments.fwd.hh | |
| RNA_Fragments.hh | |
| RNA_FragmentsClasses.fwd.hh | |
| RNA_MatchType.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 | |
| ► movers | |
| RNA_FragmentMover.cc | |
| RNA_FragmentMover.fwd.hh | |
| RNA_FragmentMover.hh | |
| RNA_JumpMover.cc | |
| RNA_JumpMover.fwd.hh | |
| RNA_JumpMover.hh | |
| RNA_LoopCloser.cc | |
| RNA_LoopCloser.fwd.hh | |
| RNA_LoopCloser.hh | |
| RNA_Minimizer.cc | |
| RNA_Minimizer.fwd.hh | |
| RNA_Minimizer.hh | |
| RNA_Relaxer.cc | |
| RNA_Relaxer.fwd.hh | |
| RNA_Relaxer.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 | |
| ► secstruct | |
| RNA_SecStructInfo.cc | |
| RNA_SecStructInfo.fwd.hh | |
| RNA_SecStructInfo.hh | |
| ► setup | |
| RNA_DeNovoParameters.cc | |
| RNA_DeNovoParameters.fwd.hh | |
| RNA_DeNovoParameters.hh | |
| RNA_DeNovoPoseSetup.cc | |
| RNA_DeNovoPoseSetup.fwd.hh | |
| RNA_DeNovoPoseSetup.hh | |
| FARNA_Optimizer.cc | |
| FARNA_Optimizer.fwd.hh | |
| FARNA_Optimizer.hh | |
| RNA_DeNovoProtocol.cc | |
| RNA_DeNovoProtocol.hh | |
| RNA_FragmentMonteCarlo.cc | |
| RNA_FragmentMonteCarlo.fwd.hh | |
| RNA_FragmentMonteCarlo.hh | |
| util.cc | |
| util.hh | |
| ► 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 |
| 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 | |
| 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 | |
| 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 |
| 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 | |
| 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 |
| ► 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 |
| 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 |
| ► 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 mover |
| ► 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 | |
| ► 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 |
| RemoveConstraints.cc | |
| RemoveConstraints.hh | |
| RemoveConstraintsCreator.hh | This class will create instances of the RemoveConstraints 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 | |
| ► frag_movers | |
| FragSetFromH5Mover.cc | |
| FragSetFromH5Mover.fwd.hh | |
| FragSetFromH5Mover.hh | Pick fragments from the H5 database |
| FragSetFromH5MoverCreator.hh | |
| MergeFragSetMover.cc | |
| MergeFragSetMover.fwd.hh | |
| MergeFragSetMover.hh | |
| MergeFragSetMoverCreator.hh | |
| ReduceFragLengthMover.cc | |
| ReduceFragLengthMover.fwd.hh | |
| ReduceFragLengthMover.hh | |
| ReduceFragLengthMoverCreator.hh | |
| ► 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 |
| 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 |
| ► 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 |
| 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 |
| 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 |
| PerturbBundleOptions.cc | A class for options for the PerturbBundle mover |
| PerturbBundleOptions.fwd.hh | Owning pointers and whatnot for PerturbBundleOptions class |
| PerturbBundleOptions.hh | Prototypes and method declarations for the PerturbBundleOptions class |
| util.cc | Utility functions for helical bundle construction |
| util.hh | |
| ► helix_capper | |
| HelixNCapperMover.cc | Mover to find and fix poorly N-capped helices |
| HelixNCapperMover.hh | |
| ► hotspot_hashing | |
| ► movers | |
| PlaceProbeMover.cc | |
| 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 |
| ► 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 |
| ► 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() |
| ► 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/toolbox/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 | |
| ► parser | |
| BluePrint.cc | |
| BluePrint.fwd.hh | |
| BluePrint.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 |
| MonteCarloLoader.cc | |
| MonteCarloLoader.hh | Declartion of the XML parser's MonteCarloLoader class for adding named ScoreFunctions to the basic::datacache::DataMap |
| ResidueSelectorLoader.cc | |
| ResidueSelectorLoader.hh | Declartion of the XML parser's ResidueSelectorLoader class for adding named ResidueSelectors to the basic::datacache::DataMap |
| ResidueSelectorLoaderCreator.hh | |
| ScoreFunctionLoader.cc | |
| ScoreFunctionLoader.hh | Declartion of the XML parser's ScoreFunctionLoader class for adding named ScoreFunctions to the basic::datacache::DataMap |
| StandardLoaderCreators.hh | |
| TaskOperationLoader.cc | |
| TaskOperationLoader.hh | Declartion of the XML parser's TaskOperationLoader class |
| 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 |
| 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 | |
| JD2ResourceManager.cc | |
| JD2ResourceManager.fwd.hh | Forward header for the JD2ResourceManager |
| JD2ResourceManager.hh | |
| JD2ResourceManagerCreator.hh | |
| JD2ResourceManagerJobInputter.cc | |
| JD2ResourceManagerJobInputter.hh | |
| JD2ResourceManagerJobInputterCreator.hh | |
| 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 | |
| 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 |
| MSDJobDistributor.cc | Job distributor subclass for running restrained multistate design |
| MSDJobDistributor.fwd.hh | Job distributor for running constrained multistate design |
| MSDJobDistributor.hh | |
| 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 | |
| Parser.cc | August 2008 job distributor as planned at RosettaCon08 - Interface base class Parser |
| Parser.fwd.hh | Header file for Parser class, part of August 2008 job distributor |
| Parser.hh | Header file for Parser class, part of August 2008 job distributor |
| 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 | |
| ScoreMap.cc | A place to put some common functions for scoremap output |
| ScoreMap.hh | A place to put some common functions for scoremap output |
| 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 |
| 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 | |
| util.hh | August 2008 job distributor as planned at RosettaCon08 - Base class |
| ► jd3 | |
| ► job_distributors | |
| MPIWorkPartitionJobDistributor.hh | |
| MPIWorkPoolJobDistributor.hh | |
| MultiThreadedJobDistributor.hh | |
| ► 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 |
| SilentFilePoseInputter.hh | |
| util.cc | |
| util.hh | |
| ► pose_outputters | |
| PDBPoseOutputter.cc | |
| PDBPoseOutputter.fwd.hh | |
| PDBPoseOutputter.hh | |
| 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 |
| 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 |
| 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 |
| 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 | |
| JobResult.hh | The declaration for class protocols::jd3::JobResult |
| 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 class protocols::jd3::LarvalJob |
| MoverAndPoseJob.cc | The class method definitions for MoverAndPoseJob and PoseJobResult |
| MoverAndPoseJob.fwd.hh | The declaration of classes MoverAndPoseJob and PoseJobResult |
| MoverAndPoseJob.hh | The definition of class protocols::jd3::MoverAndPoseJob, which applies a Mover to a Pose in its run() method |
| 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 |
| PoseInputterFactory.hh | |
| PoseOutputter.cc | Definition of the PoseOutputter class's methods |
| PoseOutputter.fwd.hh | Declaration of the PoseOutputter class |
| PoseOutputter.hh | Definition of the PoseOutputter class |
| SilentFilePoseInputter.hh | |
| StandardJobQueen.cc | StandardJobQueen class's method definitions |
| StandardJobQueen.fwd.hh | Class declaration for StandardJobQueen |
| StandardJobQueen.hh | Class declaration for StandardJobQueen |
| ► 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 | |
| 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 |
| ► ligand_docking | |
| ► 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 |
| 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 | |
| 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 |
| 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_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 | |
| LoopBuilder.cc | |
| LoopBuilder.fwd.hh | |
| LoopBuilder.hh | |
| LoopBuilderCreator.hh | |
| LoopModeler.cc | |
| LoopModeler.fwd.hh | |
| LoopModeler.hh | |
| LoopModelerCreator.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 |
| LoopHashLibraryOptions.hh | Load the Loop Hash library using the resource manager |
| LoopHashLibraryOptionsCreator.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 |
| FASelectSlidingWindowLoopClosure.cc | |
| FASelectSlidingWindowLoopClosure.fwd.hh | Fwd headers for FASelectSlidingWindowLoopClosure |
| FASelectSlidingWindowLoopClosure.hh | |
| 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 | |
| ► 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 |
| 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 | |
| LoopsFileFallbackConfiguration.fwd.hh | Forward hearder for OptionsSystemFallback class |
| LoopsFileFallbackConfiguration.hh | |
| LoopsFileFallbackConfigurationCreator.hh | |
| 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 | |
| LoopsFileOptions.cc | |
| LoopsFileOptions.fwd.hh | LoopsFileOptions forward declarations header |
| LoopsFileOptions.hh | |
| LoopsFileOptionsCreator.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 | |
| ► make_rot_lib | |
| MakeRotLib.cc | |
| MakeRotLib.hh | |
| 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 |
| 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 |
| ► 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 |
| ► 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 | |
| AddMembraneMover.fwd.hh | |
| AddMembraneMover.hh | Initialize the RosettaMP Framework by adding membrane representations to the pose |
| AddMembraneMoverCreator.hh | |
| 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 |
| 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 |
| MPMutateRelaxMover.cc | |
| MPMutateRelaxMover.fwd.hh | |
| MPMutateRelaxMover.hh | |
| MPMutateRelaxMoverCreator.hh | |
| 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 |
| ► 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 | |
| ► 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 | |
| ConstraintGenerator.cc | |
| ConstraintGenerator.fwd.hh | |
| ConstraintGenerator.hh | Abstract base class that generates constraints |
| 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 | |
| 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 |
| 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 | |
| VectorPoseMover.fwd.hh | |
| VectorPoseMover.hh | |
| 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 | |
| ► 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 | |
| ► 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 | |
| NcbbDockDesignProtocol.cc | |
| NcbbDockDesignProtocol.fwd.hh | |
| NcbbDockDesignProtocol.hh | |
| NcbbDockDesignProtocolCreator.fwd.hh | |
| NcbbDockDesignProtocolCreator.hh | |
| 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 | |
| ► 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 |
| ► 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 |
| ► pb_potential | |
| SetupPoissonBoltzmannPotential.cc | |
| SetupPoissonBoltzmannPotential.fwd.hh | |
| SetupPoissonBoltzmannPotential.hh | |
| SetupPoissonBoltzmannPotentialCreator.hh | |
| ► 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 |
| ► pose_length_moves | |
| 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 | |
| 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_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 | |
| DockDesignFilterFactory.cc | |
| DockDesignFilterFactory.fwd.hh | |
| DockDesignFilterFactory.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 | |
| GridInitMover.cc | |
| GridInitMover.fwd.hh | |
| GridInitMover.hh | |
| GridInitMoverCreator.hh | |
| GridManager.cc | |
| GridManager.fwd.hh | |
| GridManager.hh | |
| 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 | |
| RepGrid.cc | |
| RepGrid.fwd.hh | |
| RepGrid.hh | |
| RepGridCreator.hh | |
| 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 | |
| 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 | |
| ► 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 | |
| ► relax | |
| ► 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 |
| MPRangeRelaxMover.cc | |
| MPRangeRelaxMover.fwd.hh | |
| MPRangeRelaxMover.hh | Relaxes a membrane protein by relaxing in ranges |
| 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 | |
| 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 | |
| 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 |
| ► 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 | |
| RosettaScriptsParser.cc | August 2008 job distributor as planned at RosettaCon08 - Interface base class Parser |
| 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 | |
| ► 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 |
| ► 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 |
| 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 | |
| ► 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 | |
| ► 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 | |
| GlobalLengthRequirement.cc | |
| GlobalLengthRequirement.fwd.hh | |
| GlobalLengthRequirement.hh | Require that all segments of the specified secondary structure(s) are between the given min and max size |
| GlobalLengthRequirementCreator.hh | |
| GlobalRequirement.fwd.hh | |
| GlobalRequirement.hh | An interface for all SEWING requirements concerning an entire assembly |
| IntraSegmentRequirement.fwd.hh | |
| IntraSegmentRequirement.hh | An interface for all SEWING requirements concerning a single SewSegment |
| RequirementCreator.fwd.hh | |
| RequirementCreator.hh | Forward Header for base class for RequirementCreators for the Requirement load-time factory registration scheme |
| RequirementFactory.cc | Factory for creating Requirements objects |
| RequirementFactory.fwd.hh | |
| RequirementFactory.hh | |
| RequirementSet.cc | |
| RequirementSet.fwd.hh | |
| RequirementSet.hh | A container for all SEWING requirements |
| ResidueRetentionRequirement.cc | |
| ResidueRetentionRequirement.fwd.hh | |
| ResidueRetentionRequirement.hh | A container for all SEWING requirements |
| ResidueRetentionRequirementCreator.hh | |
| SegmentDsspRequirement.cc | |
| SegmentDsspRequirement.fwd.hh | |
| SegmentDsspRequirement.hh | A requirement on the seconday structure of a given SewSegment |
| SegmentDsspRequirementCreator.hh | |
| SegmentLengthRequirement.cc | |
| SegmentLengthRequirement.fwd.hh | |
| SegmentLengthRequirement.hh | A requirement on the total number of residues for a given SewSegment |
| SegmentLengthRequirementCreator.hh | |
| AddStartnodeFragments.cc | |
| AddStartnodeFragments.fwd.hh | |
| AddStartnodeFragments.hh | A Mover that uses loophash to find fragments that can bridge a gap with minimal modifications to the original pose |
| AddStartnodeFragmentsCreator.hh | |
| AppendAssemblyMover.cc | |
| AppendAssemblyMover.fwd.hh | |
| AppendAssemblyMover.hh | A Mover that uses loophash to find fragments that can bridge a gap with minimal modifications to the original pose |
| AppendAssemblyMoverCreator.hh | |
| AssemblyConstraintsMover.cc | |
| AssemblyConstraintsMover.fwd.hh | |
| AssemblyConstraintsMover.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 |
| AssemblyConstraintsMoverCreator.hh | |
| AssemblyMover.cc | |
| AssemblyMover.fwd.hh | |
| AssemblyMover.hh | |
| AssemblyMoverCreator.hh | |
| EnumerateAssemblyMover.cc | Enumerate every possible assembly exhaustively |
| EnumerateAssemblyMover.fwd.hh | |
| EnumerateAssemblyMover.hh | |
| EnumerateAssemblyMoverCreator.hh | |
| GivenPathAssemblyMover.cc | |
| GivenPathAssemblyMover.fwd.hh | |
| GivenPathAssemblyMover.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 |
| GivenPathAssemblyMoverCreator.hh | |
| GreedyAssemblyMover.cc | |
| GreedyAssemblyMover.fwd.hh | |
| GreedyAssemblyMover.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 |
| GreedyAssemblyMoverCreator.hh | |
| LoophashAssemblyMover.cc | Derived from AssemblyMover, this mover generates an assembly and then uses Loophash segments to connect any broken segments resulting from the assembly process |
| LoophashAssemblyMover.fwd.hh | |
| LoophashAssemblyMover.hh | A Mover that uses loophash to find fragments that can bridge a gap with minimal modifications to the original pose |
| LoophashAssemblyMoverCreator.hh | |
| MonteCarloAssemblyMover.cc | Assembly substructures by MonteCarlo way |
| MonteCarloAssemblyMover.fwd.hh | |
| MonteCarloAssemblyMover.hh | Assembly substructures by MonteCarlo way |
| MonteCarloAssemblyMoverCreator.hh | |
| NodeConstraintAssemblyMover.cc | |
| NodeConstraintAssemblyMover.fwd.hh | |
| NodeConstraintAssemblyMover.hh | A Mover that combines Smotif models into a continuous protein design |
| NodeConstraintAssemblyMoverCreator.hh | |
| ReadNativeRotamersFileCreator.hh | |
| ReadRepeatNativeRotamersFileCreator.hh | |
| RehashAssemblyMover.cc | Derived from AssemblyMover, this mover generates an assembly and then uses Loophash segments to connect any broken segments resulting from the assembly process |
| RehashAssemblyMover.fwd.hh | |
| RehashAssemblyMover.hh | A Mover that uses more sewing to close gaps from discontinous assemblies |
| RehashAssemblyMoverCreator.hh | |
| RepeatAssemblyMover.cc | |
| RepeatAssemblyMover.fwd.hh | |
| RepeatAssemblyMover.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 |
| RepeatAssemblyMoverCreator.hh | |
| SewGraph.cc | |
| SewGraph.fwd.hh | |
| SewGraph.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 |
| ► scoring | |
| AssemblyScorer.fwd.hh | |
| AssemblyScorer.hh | |
| BlosumScorer.cc | |
| BlosumScorer.fwd.hh | |
| BlosumScorer.hh | |
| ClashScorer.cc | |
| ClashScorer.fwd.hh | |
| ClashScorer.hh | Identifies and scores backbone clashes in SEWING Assemblies |
| InterModelMotifScorer.cc | |
| InterModelMotifScorer.fwd.hh | |
| InterModelMotifScorer.hh | |
| MotifScorer.cc | |
| MotifScorer.fwd.hh | |
| MotifScorer.hh | |
| PartnerMotifScorer.cc | |
| PartnerMotifScorer.fwd.hh | |
| PartnerMotifScorer.hh | |
| ► util | |
| io.cc | |
| io.hh | |
| util.cc | |
| util.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_filters | |
| AbinitioBaseFilter.cc | |
| AbinitioBaseFilter.hh | Header file for AbinitioBaseFilter.cc |
| AlaScan.cc | |
| AlaScan.fwd.hh | |
| AlaScan.hh | Definition of filter class AlsScan |
| AlaScanCreator.hh | FilterCreators for the AlaScanCreator |
| 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 | |
| BuriedUnsatHbondFilter.cc | |
| BuriedUnsatHbondFilter.fwd.hh | |
| BuriedUnsatHbondFilter.hh | Definition of filter class BuriedUnsatHbondFilter |
| BuriedUnsatHbondFilterCreator.hh | FilterCreators for the BuriedUnsatHbondFilterCreator |
| CamShiftEvaluator.cc | |
| CamShiftEvaluator.hh | |
| CamShiftEvaluatorCreator.cc | |
| CamShiftEvaluatorCreator.hh | Header for CamShiftEvaluatorCreator |
| ChiWellRmsdEvaluator.cc | |
| ChiWellRmsdEvaluator.hh | |
| ChiWellRmsdEvaluatorCreator.cc | |
| ChiWellRmsdEvaluatorCreator.hh | Header for ChiWellRmsdEvaluatorCreator |
| COFilter.cc | Runs reject or accept filters on pose |
| COFilter.hh | |
| ConservedPosMutationFilter.cc | |
| ConservedPosMutationFilter.fwd.hh | |
| ConservedPosMutationFilter.hh | Header file for ConservedPosMutationFitler class |
| ConservedPosMutationFilterCreator.hh | FilterCreator for the ConservedPosMutationFilter |
| ConstraintScoreCutoffFilter.cc | |
| ConstraintScoreCutoffFilter.fwd.hh | |
| ConstraintScoreCutoffFilter.hh | Header file for ConstraintScoreCutoffFitler class |
| ConstraintScoreCutoffFilterCreator.hh | FilterCreator for the ConstraintScoreCutoffFilter |
| ContactMapEvaluator.cc | |
| ContactMapEvaluator.hh | |
| ContactMapEvaluatorCreator.cc | |
| ContactMapEvaluatorCreator.hh | Header for ContactMapEvaluatorCreator |
| 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 |
| 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 |
| GeometryFilter.cc | |
| GeometryFilter.fwd.hh | |
| GeometryFilter.hh | Definition of filter class GeometryFilter |
| GeometryFilterCreator.hh | FilterCreators for the GeometryFilterCreator |
| 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 |
| 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 |
| 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 | |
| MotifScoreFilter.cc | Scores poses using will's motifScore |
| MotifScoreFilter.fwd.hh | |
| MotifScoreFilter.hh | |
| MotifScoreFilterCreator.hh | |
| MultipleSigmoidsFilter.cc | |
| MultipleSigmoidsFilter.fwd.hh | |
| MultipleSigmoidsFilter.hh | |
| MultipleSigmoidsFilterCreator.hh | FilterCreators for the MultipleSigmoidsFilter |
| 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 |
| OperatorFilter.cc | |
| OperatorFilter.fwd.hh | |
| OperatorFilter.hh | |
| OperatorFilterCreator.hh | FilterCreators for the OperatorFilter |
| 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.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 |
| 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 | |
| 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 |
| 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 |
| 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 |
| 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 |
| RotamerBoltzmannWeight.cc | |
| RotamerBoltzmannWeight.fwd.hh | |
| RotamerBoltzmannWeight.hh | Reports to Tracer which residues are designable in a taskfactory |
| RotamerBoltzmannWeightFilterCreator.hh | FilterCreators for the RotamerBoltzmannWeightFilter |
| SavePoseConstraintToFileFilter.cc | |
| SavePoseConstraintToFileFilter.hh | Filter for outputing information about the pose |
| SavePoseConstraintToFileFilterCreator.hh | FilterCreator for the SavePoseConstraintToFileFilter |
| 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 | |
| ScoreCutoffFilter.cc | |
| ScoreCutoffFilter.fwd.hh | |
| ScoreCutoffFilter.hh | Header file for ScoreCutoffFitler class |
| ScoreCutoffFilterCreator.hh | FilterCreator for the ScoreCutoffFilter |
| ScoreEvaluator.cc | |
| ScoreEvaluator.hh | |
| ScoreTypeFilter.cc | |
| ScoreTypeFilter.fwd.hh | |
| ScoreTypeFilter.hh | Definition of filter class ScoreTypeFilter |
| ScoreTypeFilterCreator.hh | FilterCreators for the ScoreTypeFilter |
| 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 | |
| SigmoidFilter.cc | |
| SigmoidFilter.fwd.hh | |
| SigmoidFilter.hh | |
| SigmoidFilterCreator.hh | FilterCreators for the SigmoidFilter |
| 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 |
| TotalSasaFilter.cc | |
| TotalSasaFilter.fwd.hh | |
| TotalSasaFilter.hh | Definition of filter class TotalSasaFilter |
| TotalSasaFilterCreator.hh | FilterCreators for the TotalSasaFilterCreator |
| ► simple_moves | |
| ► 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 | |
| ► asym_fold_and_dock | |
| AsymFoldandDockMoveRbJumpMover.cc | |
| AsymFoldandDockMoveRbJumpMover.fwd.hh | |
| AsymFoldandDockMoveRbJumpMover.hh | |
| AsymFoldandDockRbTrialMover.cc | |
| AsymFoldandDockRbTrialMover.fwd.hh | |
| AsymFoldandDockRbTrialMover.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 | |
| 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 | |
| ► hbs | |
| HbsPatcher.cc | HbsPatcher methods implemented |
| HbsPatcher.fwd.hh | HbsPatcher forward declarations header |
| HbsPatcher.hh | |
| ► oop | |
| 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 | |
| ► 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 |
| ► 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 | |
| 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 | |
| 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 | |
| SymShakeStructureMover.cc | |
| SymShakeStructureMover.fwd.hh | |
| SymShakeStructureMover.hh | |
| TaskAwareSymMinMover.cc | |
| TaskAwareSymMinMover.fwd.hh | |
| TaskAwareSymMinMover.hh | Minimize only those residues specified by a set of TaskOperations in a symmetric pose |
| TaskAwareSymMinMoverCreator.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 | |
| 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 | |
| AddConstraintsToCurrentConformationMover.cc | Add constraints to the current pose conformation |
| AddConstraintsToCurrentConformationMover.hh | Add constraints to the current pose conformation |
| AddConstraintsToCurrentConformationMoverCreator.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 |
| 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 | |
| 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 |
| 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 | |
| ClearConstraintsMover.cc | Add constraints to the current pose conformation |
| ClearConstraintsMover.hh | Add constraints to the current pose conformation |
| ClearConstraintsMoverCreator.hh | |
| CombinePoseMover.cc | |
| CombinePoseMover.fwd.hh | |
| CombinePoseMover.hh | |
| ConsensusDesignMover.cc | Cc file for ConsensusDesignMover |
| ConsensusDesignMover.fwd.hh | Fwd.hh file for ConsensusDesignMover |
| ConsensusDesignMover.hh | Header file for ConsensusDesignMover |
| ConsensusDesignMoverCreator.hh | |
| 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 |
| 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 | |
| ContingentAcceptMover.cc | |
| ContingentAcceptMover.fwd.hh | Switch the chain order |
| ContingentAcceptMover.hh | Switch the chain order |
| ContingentAcceptMoverCreator.hh | |
| CopyDofMover.cc | |
| CopyDofMover.fwd.hh | |
| CopyDofMover.hh | |
| 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 |
| ddG.cc | Implementation of the ddG class for computing interface delta dGs |
| ddG.fwd.hh | Forward declarations for ddG |
| ddG.hh | |
| ddGCreator.hh | |
| 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 |
| DesignRepackMover.cc | |
| DesignRepackMover.fwd.hh | Forward declations for DesignRepackMover |
| DesignRepackMover.hh | |
| DisulfideInsertionMover.cc | |
| 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.hh | |
| DumpPdbCreator.hh | |
| ExtendedPoseMover.cc | |
| ExtendedPoseMover.fwd.hh | |
| ExtendedPoseMover.hh | |
| ExtendedPoseMoverCreator.cc | |
| ExtendedPoseMoverCreator.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 |
| FindConsensusSequence.cc | Takes in multiple poses from the MSDJobDistributor and finds the consensus sequence that optimizes energy of all input poses |
| FindConsensusSequence.fwd.hh | Finds the consensus sequence that optimizes energy of all input poses |
| FindConsensusSequence.hh | Takes in multiple poses from the MSDJobDistributor and finds the consensus sequence that optimizes energy of all input poses |
| FindConsensusSequenceCreator.hh | Multistate design mover used for constrained MSD application |
| ForceDisulfidesMover.cc | |
| ForceDisulfidesMover.fwd.hh | ForceDisulfidesMover forward declarations header |
| ForceDisulfidesMover.hh | |
| ForceDisulfidesMoverCreator.hh | |
| FragmentMover.cc | |
| FragmentMover.fwd.hh | |
| FragmentMover.hh | |
| GenericMonteCarloMover.cc | |
| GenericMonteCarloMover.fwd.hh | |
| GenericMonteCarloMover.hh | Perform a given mover and sample structures by MonteCarlo |
| GenericMonteCarloMoverCreator.hh | |
| 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 |
| GunnCost.cc | |
| GunnCost.hh | |
| 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 | |
| LoadUnboundRotMover.cc | LoadUnboundRotMover methods implemented |
| LoadUnboundRotMover.fwd.hh | |
| LoadUnboundRotMover.hh | |
| LoadUnboundRotMoverCreator.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 |
| MembraneTopology.cc | |
| MembraneTopology.fwd.hh | |
| MembraneTopology.hh | |
| MembraneTopologyCreator.hh | |
| 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 |
| 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 |
| 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 | |
| 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 | |
| MSDMover.cc | Multistate design mover used for restrained multistate design |
| MSDMover.fwd.hh | Multistate design mover used for constrained MSD application |
| MSDMover.hh | Multistate design mover used for restrained multistate design |
| MSDMoverCreator.hh | Multistate design mover used for constrained MSD application |
| MutateResidue.cc | |
| MutateResidue.fwd.hh | |
| MutateResidue.hh | |
| MutateResidueCreator.hh | |
| PackRotamersMover.cc | |
| PackRotamersMover.fwd.hh | |
| PackRotamersMover.hh | |
| PackRotamersMoverCreator.hh | |
| PackRotamersMoverLazy.cc | |
| PackRotamersMoverLazy.fwd.hh | |
| PackRotamersMoverLazy.hh | |
| PackRotamersMoverLazyCreator.hh | |
| PDBReloadMover.cc | |
| PDBReloadMover.fwd.hh | PDBReloadMover forward declarations header |
| PDBReloadMover.hh | |
| PDBReloadMoverCreator.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 |
| 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 | |
| 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 |
| RepackSidechainsMover.cc | |
| RepackSidechainsMover.fwd.hh | |
| RepackSidechainsMover.hh | |
| RepackSidechainsMoverCreator.hh | |
| RepeatPropagationMover.cc | Can repeat both a symmetric, non symmetric & broken pose |
| RepeatPropagationMover.fwd.hh | |
| RepeatPropagationMover.hh | |
| RepeatPropagationMoverCreator.hh | |
| ReportEffectivePKA.cc | |
| ReportEffectivePKA.hh | |
| ReportEffectivePKACreator.hh | This class will create instances of Mover ReportEffectivePKA for the MoverFactory |
| RepulsiveOnlyMover.cc | Calculate repulsive energy only for certain residues |
| RepulsiveOnlyMover.fwd.hh | |
| RepulsiveOnlyMover.hh | |
| ResetBaselineMover.cc | |
| ResetBaselineMover.fwd.hh | Switch the chain order |
| ResetBaselineMover.hh | Switch the chain order |
| ResetBaselineMoverCreator.hh | |
| 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 |
| 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 |
| 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 | |
| ScoreMover.cc | |
| 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 | |
| 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 |
| SetTorsion.cc | |
| SetTorsion.fwd.hh | |
| SetTorsion.hh | Sets the value of a desired torsion. Header files for the mover |
| SetTorsionCreator.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 | |
| TaskAwareMinMover.cc | TaskAwareMinMover methods implemented |
| TaskAwareMinMover.fwd.hh | TaskAwareMinMover forward declarations header |
| TaskAwareMinMover.hh | MinMover which updates MoveMap to mirror PackerTask |
| TaskAwareMinMoverCreator.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 | |
| ► 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 | |
| ► 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 | |
| util.cc | |
| util.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 | |
| VDW_CachedRepScreenInfo.cc | |
| VDW_CachedRepScreenInfo.fwd.hh | |
| VDW_CachedRepScreenInfo.hh | |
| VDW_Grid.cc | |
| VDW_Grid.fwd.hh | |
| VDW_Grid.hh | |
| VDW_RepScreenInfo.cc | |
| VDW_RepScreenInfo.fwd.hh | |
| VDW_RepScreenInfo.hh | |
| ► helix | |
| RNA_HelixAssembler.cc | |
| RNA_HelixAssembler.fwd.hh | |
| RNA_HelixAssembler.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 | |
| file_util.cc | |
| file_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 | |
| AddOrDeleteMover.cc | |
| AddOrDeleteMover.fwd.hh | |
| AddOrDeleteMover.hh | |
| DeleteMover.cc | |
| DeleteMover.fwd.hh | |
| DeleteMover.hh | |
| FromScratchMover.cc | |
| FromScratchMover.fwd.hh | |
| FromScratchMover.hh | |
| ResampleMover.cc | |
| ResampleMover.fwd.hh | |
| ResampleMover.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 | |
| ► 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_MC_MultiSuite.cc | Markov chain sampler for mulitple RNA suite |
| RNA_MC_MultiSuite.fwd.hh | Markov chain sampler for mulitple RNA suite |
| RNA_MC_MultiSuite.hh | Markov chain sampler for mulitple RNA suite |
| RNA_MC_Sugar.cc | Markov chain sampler for sugar pucker |
| RNA_MC_Sugar.fwd.hh | Markov chain sampler for sugar pucker |
| RNA_MC_Sugar.hh | Markov chain sampler for sugar pucker |
| RNA_MC_Suite.cc | Markov chain sampler for RNA suite |
| RNA_MC_Suite.fwd.hh | Markov chain sampler for RNA suite |
| RNA_MC_Suite.hh | Markov chain sampler for RNA suite |
| 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 | |
| JumpStepWiseSampler.cc | |
| JumpStepWiseSampler.fwd.hh | |
| JumpStepWiseSampler.hh | |
| 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_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_StepWiseSampler.fwd.hh | Abstract Base Class for Markov chain rotamer sampler |
| MC_StepWiseSampler.hh | Abstract Base Class for Markov chain rotamer sampler |
| NoOpStepWiseSampler.cc | |
| NoOpStepWiseSampler.fwd.hh | |
| NoOpStepWiseSampler.hh | |
| StepWiseSamplerAny.cc | Aggregate multiple samplers for modeler from any one of them |
| StepWiseSamplerAny.fwd.hh | Aggregate multiple samplers for modeler from any one of them |
| StepWiseSamplerAny.hh | Aggregate multiple samplers for modeler from any one of them |
| StepWiseSamplerBase.fwd.hh | Abstract Base Class for StepWiseSampler generator |
| StepWiseSamplerBase.hh | Abstract Base Class for StepWiseSampler generator |
| 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 |
| 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 |
| StepWiseSamplerSized.cc | Aggregate multiple samplers for modeler from any one of them |
| StepWiseSamplerSized.fwd.hh | Abstract Base Class for StepWiseSampler generator with finite size |
| StepWiseSamplerSized.hh | Abstract Base Class for StepWiseSampler 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 |
| StepWiseSamplerType.hh | |
| ► 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 | |
| FullModelInfoSetupFromCommandLine.cc | |
| FullModelInfoSetupFromCommandLine.fwd.hh | |
| FullModelInfoSetupFromCommandLine.hh | |
| StepWiseCSA_JobDistributor.cc | |
| StepWiseCSA_JobDistributor.fwd.hh | |
| StepWiseCSA_JobDistributor.hh | |
| StepWiseJobDistributor.fwd.hh | |
| StepWiseJobDistributor.hh | |
| StepWiseMonteCarloJobDistributor.cc | |
| StepWiseMonteCarloJobDistributor.fwd.hh | |
| StepWiseMonteCarloJobDistributor.hh | |
| util.cc | |
| util.hh | |
| StepWiseSampleAndScreen.cc | |
| StepWiseSampleAndScreen.fwd.hh | |
| StepWiseSampleAndScreen.hh | |
| ► 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 | |
| SurfaceVectorFallbackConfiguration.fwd.hh | Forward header for OptionsSystemFallback class |
| SurfaceVectorFallbackConfiguration.hh | |
| SurfaceVectorFallbackConfigurationCreator.hh | |
| SurfaceVectorLoader.cc | |
| SurfaceVectorLoader.fwd.hh | |
| SurfaceVectorLoader.hh | |
| SurfaceVectorLoaderCreator.hh | |
| SurfaceVectorOptions.cc | |
| SurfaceVectorOptions.fwd.hh | SurfaceVectorOptions forward declarations header |
| SurfaceVectorOptions.hh | |
| SurfaceVectorOptionsCreator.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 | |
| ► 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 |
| ► pose_metric_calculators | |
| BuriedUnsatisfiedPolarsCalculator.cc | |
| BuriedUnsatisfiedPolarsCalculator.hh | |
| 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 | |
| NumberHBondsCalculator.cc | |
| NumberHBondsCalculator.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 | |
| ► 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 | |
| ► 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 | |
| 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 |
| 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 |
| 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 | |
| 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 | |
| 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 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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/toolbox/task_operations/STMStoredTask.cc), but has been replaced by the StoreCompoundTaskMover (protocols/toolbox/task_operations/StoreCompoundTaskMover.cc), which is much more flexible. It is being moved out of devel/matdes/ into protocols/toolbox/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 | |
| AtomID_Mapper.cc | |
| AtomID_Mapper.fwd.hh | |
| AtomID_Mapper.hh | |
| AtomLevelDomainMap.cc | |
| AtomLevelDomainMap.fwd.hh | AtomLevelDomainMap forward declarations header |
| AtomLevelDomainMap.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 | |
| 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.hh | A few functions test how PyRosetta handle boost ReturnValuePolicy |
| 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 | |
| ► 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
