| ▼ src | |
| ▼ core | |
| ► chemical | |
| ► carbohydrates | |
| CarbohydrateInfo.cc | Method definitions for CarbohydrateInfo |
| CarbohydrateInfo.fwd.hh | Forward declarations for CarbohydrateInfo |
| CarbohydrateInfo.hh | Declarations and simple accessor/mutator definitions for CarbohydrateInfo |
| database_io.cc | Database input/output function definitions for carbohydrate-specific data |
| database_io.hh | Database input/output function declarations for carbohydrate-specific data |
| ► 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 |
| ► orbitals | |
| AssignOrbitals.cc | |
| AssignOrbitals.hh | |
| ICoorOrbitalData.cc | |
| 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 | |
| ► 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 | |
| ► 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 | Method definitions for chemical::Atom |
| Atom.fwd.hh | Class declaration for chemical::Atom |
| Atom.hh | Class 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 |
| 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 | Support functions for class Bond; functions that should not be included as part of the class |
| bond_support.hh | Support functions for class Bond; functions that should not be included as part of the class |
| ChemicalManager.cc | |
| ChemicalManager.fwd.hh | Chemical manager class header |
| ChemicalManager.hh | |
| ElectronConfiguration.cc | The data for the BCL electron configuration |
| ElectronConfiguration.fwd.hh | |
| ElectronConfiguration.hh | The data for the BCL electron configuration |
| 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 | |
| icoor_support.cc | External support for manipulating the ResidueType's icoor/ideal_xyz |
| icoor_support.hh | |
| IdealBondLengthSet.cc | |
| IdealBondLengthSet.fwd.hh | |
| IdealBondLengthSet.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 | Declaration of class to represent the chemical bond between two ResidueConnections from one conformation::Residue to another |
| residue_io.cc | Helper methods for ResidueType input/output |
| residue_io.hh | |
| residue_support.cc | Support functions for class residue; functions that should not be included as part of the class |
| residue_support.hh | Support functions for class residue; functions that should not be included as part of the class |
| ResidueConnection.cc | |
| 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 | Graph structure for ResidueType |
| ResidueGraphTypes.hh | Graph structure for ResidueType |
| ResidueLoader.cc | Implementation of the Residue Loader |
| ResidueLoader.fwd.hh | Forward headers for the Residue Loader |
| ResidueLoader.hh | Headers for the Residue Loader |
| 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 |
| ResidueSelector.cc | |
| ResidueSelector.fwd.hh | |
| ResidueSelector.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 |
| ResidueTypeKinWriter.cc | Class to write kinemage-formatted output for Residue and chemical |
| ResidueTypeKinWriter.fwd.hh | Class to write kinemage-formatted output for ResidueType |
| ResidueTypeKinWriter.hh | Class to write kinemage-formatted output for ResidueType |
| ResidueTypeSet.cc | ResidueTypeSet class |
| ResidueTypeSet.fwd.hh | |
| ResidueTypeSet.hh | |
| 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 |
| RingConformerSet.cc | Method definitions for RingConformerSet |
| RingConformerSet.fwd.hh | Forward declarations for RingConformerSet |
| RingConformerSet.hh | Declarations and simple accessor/mutator definitions for RingConformerSet |
| types.hh | Rosetta project type declarations |
| 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 |
| ► 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 | MembraneInfo - Membrane Pose Definition Object |
| MembraneInfo.fwd.hh | MembraneInfo - Membrane Pose Definition Object |
| MembraneInfo.hh | MembraneInfo - Membrane Pose Definition Object |
| MembraneParams.hh | Membrane Params Enum - map Atom indices to atom types |
| Span.cc | Object for describing start and end of a transmembrane span |
| Span.fwd.hh | Object for describing start and end of a transmembrane span |
| Span.hh | Object for describing start and end of a transmembrane span |
| SpanningTopology.cc | Transmembrane Spans Object |
| SpanningTopology.fwd.hh | Membrane Spanning Topology Data |
| SpanningTopology.hh | Transmembrane Spans Object |
| types.hh | Default values for membrane code |
| util.cc | Utility functions for membrane things |
| util.hh | Utility functions for membrane things |
| ► 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 | Prototypes and method declarations for the Parameters class, a class for holding parameters for parametric backbone generation |
| 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 | Prototypes and method declarations for the ParametersSet class, a class for holding sets of parameters for parametric backbone generation |
| ► 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.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 | |
| 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 | Symmetry conformation container |
| SymmetricConformation.fwd.hh | |
| SymmetricConformation.hh | Symmetry conformation container |
| SymmetryInfo.cc | |
| SymmetryInfo.fwd.hh | |
| SymmetryInfo.hh | |
| SymSlideInfo.cc | Class to store ingformation about symmetrical dofs |
| SymSlideInfo.fwd.hh | |
| SymSlideInfo.hh | SymSlideInfo data container |
| util.cc | Utility functions for handling of symmetric conformations |
| util.hh | Utility functions for handling with symmetric conformations |
| VirtualCoordinate.cc | VirtualCoordinate container |
| VirtualCoordinate.fwd.hh | |
| VirtualCoordinate.hh | Symmetry data container |
| 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 | Forward headers for find_neighbors.hh |
| find_neighbors.hh | Sets up the residue neighbor information |
| 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.fwd.hh | Classes to work with UpperEdgeGraph for fast neighbor detection |
| PointGraphData.hh | Classes to work with UpperEdgeGraph for fast neighbor detection |
| ppo_torsion_bin.cc | Functions for assigning and manipulating the phi/psi/omega torsion bins |
| ppo_torsion_bin.fwd.hh | An enumeration to represent a binning of the phi/psi/omega torsions |
| ppo_torsion_bin.hh | An enumeration to represent a binning of the phi/psi/omega torsions |
| 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 | Class to write kinemage-formatted output for Residue and Conformation |
| 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 | Abstract base class for a class that holds disembodied Residues (ie not contained within a Pose) as Rotamers |
| 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 | An environment that automatically distributes rights to shared degrees of freedom (e.g. fold tree) |
| EnvCore.cc | |
| EnvCore.fwd.hh | Definition of the EnvCore class |
| EnvCore.hh | Low compile-level functions of Environment |
| EnvExcnBase.hh | A special kind of exception for the bad stuff that can happen in exceptions |
| 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 | A class that is used to express a mover-specific DoF-unlock on a ProtectedPose. Its destruction expresses a re-locking |
| 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 | Forward declaration for core::fragment::picking_old::concepts::Librarian |
| 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 | Reading/writing of Vall libraries |
| 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 | Set of fragments for a certain alignment frame |
| BBTorsionAndAnglesSRFD.cc | |
| BBTorsionAndAnglesSRFD.hh | SRFD that remembers torsion angles as well as arbitrary bond angles SO LONG AS THOSE ANGLES ARE ONLY THE N-CA-C BOND ANGLE. CANNOT REPRESENT BOND ANGLES TO PREVIOUS OR NEXT RESIDUES |
| BBTorsionSRFD.cc | |
| BBTorsionSRFD.fwd.hh | Set of fragments for a certain alignment frame |
| BBTorsionSRFD.hh | A fragment as list of SingleResidue Data |
| ConstantLengthFragSet.cc | Set of fragments for a certain alignment frame |
| ConstantLengthFragSet.fwd.hh | Set of fragments for a certain alignment frame |
| ConstantLengthFragSet.hh | Yields a simple implementation of a fragset |
| ConstantLengthFragSetIterator_.hh | Yields a simple implementation of a fragset |
| FragCache.fwd.hh | Set of fragments for a certain alignment frame |
| FragCache.hh | Set of fragments for a certain alignment frame |
| FragData.cc | Collection classes of the FragData and SingleResidueFragData class hirachy |
| FragData.fwd.hh | Set of fragments for a certain alignment frame |
| FragData.hh | A fragment as list of SingleResidue Data |
| FragID.cc | Set of fragments for a certain alignment frame |
| FragID.fwd.hh | Set of fragments for a certain alignment frame |
| FragID.hh | Set of fragments for a certain alignment frame |
| FragID_Iterator.cc | |
| FragID_Iterator.fwd.hh | Set of fragments |
| FragID_Iterator.hh | Set of fragments |
| FragmentIO.cc | Set of fragments for a certain alignment frame |
| FragmentIO.hh | |
| FragmentRmsd.cc | |
| FragmentRmsd.fwd.hh | |
| FragmentRmsd.hh | |
| FragSet.cc | Set of fragments for a certain alignment frame |
| FragSet.fwd.hh | Set of fragments for a certain alignment frame |
| FragSet.hh | Set of fragments |
| FragSetCollection.cc | Set of fragments for a certain alignment frame |
| FragSetCollection.fwd.hh | Set of fragments for a certain alignment frame |
| FragSetCollection.hh | Set of fragments |
| Frame.cc | Set of fragments for a certain alignment frame |
| Frame.fwd.hh | Set of fragments for a certain alignment frame |
| Frame.hh | Set of fragments for a certain alignment frame |
| FrameIterator.cc | |
| FrameIterator.fwd.hh | |
| FrameIterator.hh | |
| FrameIteratorWorker_.fwd.hh | Set of fragments |
| FrameIteratorWorker_.hh | Set of fragments |
| FrameList.cc | Collection classes of the FragData and SingleResidueFragData class hirachy |
| FrameList.fwd.hh | Forward declarations for class FrameList |
| FrameList.hh | Set of fragments for a certain alignment frame |
| FrameListIterator_.hh | Yields a simple implementation of a fragset |
| 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 | Set of fragments for a certain alignment frame |
| JumpingFrame.fwd.hh | Forward declarations for fragment stuff |
| JumpingFrame.hh | Set of fragments for a certain alignment frame |
| JumpSRFD.cc | A fragment that changes a RigidBody Transform ( Jump ) |
| JumpSRFD.fwd.hh | Set of fragments for a certain alignment frame |
| JumpSRFD.hh | A fragment as list of SingleResidue Data |
| OrderedFragSet.cc | Set of fragments for a certain alignment frame |
| OrderedFragSet.fwd.hh | Set of fragments for a certain alignment frame |
| OrderedFragSet.hh | Yields a simple implementation of a fragset |
| OrderedFragSetIterator_.hh | Yields a simple implementation of a fragset |
| 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 | Collection classes of the FragData and SingleResidueFragData class hirachy |
| SecstructSRFD.hh | A fragment as list of SingleResidue Data |
| SingleResidueFragData.cc | Collection classes of the FragData and SingleResidueFragData class hirachy |
| SingleResidueFragData.fwd.hh | Set of fragments for a certain alignment frame |
| SingleResidueFragData.hh | A fragment as list of SingleResidue Data |
| util.cc | |
| util.hh | |
| ► graph | |
| ArrayPool.fwd.hh | Forward declaration for ArrayPool classes |
| ArrayPool.hh | ArrayPool class declaration and implementation |
| DisjointSets.cc | Generic graph class header |
| DisjointSets.fwd.hh | DisjointSets class forward declaration |
| DisjointSets.hh | Generic graph class header |
| Graph.cc | Graph base classes |
| Graph.fwd.hh | Graph base class forward declarations |
| Graph.hh | Generic graph class header |
| graph_util.cc | Generic graph class header |
| graph_util.hh | Generic graph class header |
| unordered_object_pool.fwd.hpp | |
| unordered_object_pool.hpp | |
| UpperEdgeGraph.fwd.hh | Templated graph for fast edge additions |
| UpperEdgeGraph.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 | |
| AtomID_Map.fwd.hh | Core::id::AtomID_Map forward declarations |
| AtomID_Map.hh | Map from Atom identifiers to contained values class |
| AtomID_Mask.fwd.hh | Id::AtomID_Mask forward declarations header |
| AtomID_Mask.hh | Map from Atom identifiers to booleans |
| 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 | 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) |
| Exceptions.hh | Top-class (Organizer) of the TopologyBroker mechanism |
| JumpID.fwd.hh | Kinematics JumpID forward declarations header |
| JumpID.hh | |
| NamedAtomID.cc | Kinematics Atom identifier |
| NamedAtomID.fwd.hh | Kinematics AtomID forward declarations header |
| 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 | Kinematics Atom identifier |
| NamedStubID.fwd.hh | Kinematics AtomID forward declarations header |
| NamedStubID.hh | |
| SequenceMapping.cc | |
| SequenceMapping.fwd.hh | |
| SequenceMapping.hh | |
| TorsionID.cc | Kinematics Atom identifier |
| TorsionID.fwd.hh | Kinematics TorsionID forward declarations header |
| TorsionID.hh | Declarations for the TorsionID class |
| 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 | Silent-file format based on "diffs" of AtomTree DOFs |
| atom_tree_diff.hh | Silent-file format based on "diffs" of AtomTree DOFs |
| ► 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 | Representation of PDB files in a silent-file format |
| PDBSilentStruct.hh | Representation of rosetta++ protein silent-file structures |
| PDBSilentStructCreator.cc | |
| PDBSilentStructCreator.hh | Base class for BasicSilentStructCreators for the BasicSilentStruct load-time factory registration scheme |
| PoseFromPDBLoader.cc | |
| PoseFromPDBLoader.fwd.hh | |
| PoseFromPDBLoader.hh | |
| PoseFromPDBLoaderCreator.hh | |
| ► indexed_structure_store | |
| 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 | |
| ► pdb | |
| Field.cc | Each line of a PDB file is a Record which is divided into Fields |
| Field.fwd.hh | Each line of a PDB file is a Record which is divided into Fields |
| Field.hh | Each line of a PDB file is a Record which is divided into Fields |
| file_data.cc | Method definitions for FileData and related classes |
| file_data.fwd.hh | |
| file_data.hh | Declarations for FileData and related classes |
| file_data_fixup.cc | |
| file_data_fixup.fwd.hh | Various utilities to accomodated PDB input issues |
| file_data_fixup.hh | Various utilities to accomodated PDB input issues |
| file_data_options.cc | Definitions for FileDataOptions |
| file_data_options.fwd.hh | |
| file_data_options.hh | Declarations for FileDataOptions |
| 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 |
| pdb_dynamic_reader.cc | Method definitions for PDB Dynamic reader |
| pdb_dynamic_reader.hh | Declarations for PDB Dynamic reader |
| pdb_dynamic_reader_options.cc | Definitions for PDB_DReaderOptions |
| pdb_dynamic_reader_options.fwd.hh | |
| pdb_dynamic_reader_options.hh | Declarations for PDB_DReaderOptions |
| pose_io.cc | Method definitions for input/output functions for use with Pose |
| pose_io.hh | Method declarations for input/output functions for use with Pose |
| ► raw_data | |
| DecoyFileData.cc | Write decoys in "silent" format |
| DecoyFileData.hh | Output a decoy in "silent" format |
| DecoyStruct.cc | Protein-specific "silent" file reader and writer for mini |
| DecoyStruct.hh | Silent input file reader for mini |
| DisulfideFile.cc | A simple wrapper for a Disulfide File suitable for the -fix_disulf option |
| 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 | FileData base class |
| 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 | User input parameters for RNA structure inference |
| RNA_DataReader.fwd.hh | Pose forward declarations header |
| RNA_DataReader.hh | |
| ► sequence_comparation | |
| DesignContrast.cc | |
| DesignContrast.fwd.hh | |
| DesignContrast.hh | |
| ► serialization | |
| Pipe.cc | Quick typedef of a vector of PoseSP |
| Pipe.fwd.hh | Quick typedef of a vector of PoseSP |
| PipeMap.cc | Quick typedef of a map of strings to PipeSP |
| PipeMap.fwd.hh | Quick typedef of a map of strings to PipeSP |
| serialize_pose.cc | |
| serialize_pose.hh | |
| ► silent | |
| BasicSilentStructCreators.cc | Base class for SilentStructCreators for the SilentStruct load-time factory registration scheme |
| BasicSilentStructCreators.hh | Base class for BasicSilentStructCreators for the BasicSilentStruct load-time factory registration scheme |
| 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 | Representation of rosetta++ protein silent-file structures |
| RigidBodySilentStruct.hh | Representation of rosetta++ protein silent-file structures |
| 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 | Silent input file reader for mini |
| SilentEnergy.hh | Simple class for managing energies in SilentStruct objects |
| SilentFileData.cc | Silent input file reader for mini |
| SilentFileData.fwd.hh | Silent input file reader for mini |
| SilentFileData.hh | Silent input file reader for mini |
| SilentFileLoader.cc | Load a silent file from an input stream and a SilentFileOptions object |
| 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 | Creator for loader for constructing a pose from a silent file |
| SilentFileOptions.cc | Options for constructing a pose from a silent file |
| 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 | Creator for options for constructing a pose from a silent file |
| SilentStruct.cc | Silent input file reader for mini |
| SilentStruct.fwd.hh | Silent input file reader for mini |
| SilentStruct.hh | Silent input file reader for mini |
| SilentStructCreator.cc | Base class for SilentStructCreators for the SilentStruct load-time factory registration scheme |
| SilentStructCreator.fwd.hh | Base class for SilentStructCreators for the SilentStruct load-time factory registration scheme |
| 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 |
| ► 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.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 | AtomTree/Conformation communication vector class forward declaration |
| ResidueCoordinateChangeList.fwd.hh | AtomTree/Conformation communication vector class forward declaration |
| ResidueCoordinateChangeList.hh | AtomTree/Conformation communication vector class forward declaration |
| 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 | Atom tree minimization functions |
| sym_atom_tree_minimize.hh | Atom tree minimization functions |
| SymAtomTreeMinimizer.cc | High-level atom tree minimizer class for symmetrical minimization |
| SymAtomTreeMinimizer.fwd.hh | High-level atom tree minimizer class for symmetrical minimization |
| SymAtomTreeMinimizer.hh | High-level atom tree minimizer class for symmetrical minimization |
| SymAtomTreeMultifunc.cc | |
| SymAtomTreeMultifunc.hh | Atom tree multifunction class for symmetrical minimization |
| SymMinimizerMap.cc | MinimizerMap for symmetric minimization implementation |
| SymMinimizerMap.fwd.hh | MinimizerMap for symmetric minimization forward declaration |
| SymMinimizerMap.hh | MinimizerMap for symmetric minimization |
| 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 | Atom tree multifunction class |
| AtomTreeMultifunc.fwd.hh | Core::optimization::AtomTreeMultifunc forward declarations |
| AtomTreeMultifunc.hh | Atom tree multifunction class |
| cartesian_minimize.cc | Atom tree minimization functions |
| cartesian_minimize.hh | Atom tree minimization functions |
| CartesianMinimizer.cc | High-level Cartesian minimizer class |
| CartesianMinimizer.fwd.hh | Core::optimization::CartesianMinimizer forward declarations |
| CartesianMinimizer.hh | |
| CartesianMinimizerMap.cc | Kinematics |
| 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 | Kinematics |
| DOF_Node.hh | Kinematics |
| 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 | Kinematics |
| 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 | Minimizer class |
| NelderMeadSimplex.hh | Simple low-level minimizer class |
| NumericalDerivCheckResult.cc | Declaration for nuerical derivative check results classes |
| 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 | Annealer Factory class forward declaration |
| 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 | Packer's standard annealer class declaration |
| FixbbCoupledRotamerSimAnnealer.hh | Packer's standard annealer class declaration |
| FixbbLinkingRotamerSimAnnealer.cc | Packer's standard simulated annealing class implementation |
| FixbbLinkingRotamerSimAnnealer.fwd.hh | Packer's standard annealer class declaration |
| 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 | CenRot version of centroid dunbrack energy |
| CenRotDunEnergy.hh | CenRot version of centroid Dunbrack energy |
| CenRotDunEnergyCreator.hh | CenRot version of centroid Dunbrack Energy |
| SingleResidueCenrotLibrary.cc | |
| SingleResidueCenrotLibrary.fwd.hh | |
| SingleResidueCenrotLibrary.hh | |
| ChiSet.fwd.hh | Typedefs and forward declarations for class DunbrackRotamer |
| ChiSet.hh | Typedefs and forward declarations for class DunbrackRotamer |
| 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 | Dunbrack energy method forward declaration |
| DunbrackEnergy.hh | |
| DunbrackEnergyCreator.hh | Declaration for the class that connects DunbrackEnergy with the ScoringManager |
| DunbrackRotamer.cc | |
| DunbrackRotamer.fwd.hh | Typedefs and forward declarations for class DunbrackRotamer |
| DunbrackRotamer.hh | Fixed-sized dunbrack rotamer object |
| RotamerConstraint.cc | |
| RotamerConstraint.fwd.hh | |
| RotamerConstraint.hh | |
| RotamericSingleResidueDunbrackLibrary.fwd.hh | Forward declaration of rotameric rotamer libraries from Jun08 |
| RotamericSingleResidueDunbrackLibrary.hh | Declaration of rotameric rotamer libraries from Jun08 (as opposed to semi-rotameric) |
| RotamericSingleResidueDunbrackLibrary.tmpl.hh | Declaration of rotameric rotamer libraries from Jun08 (as opposed to semi-rotameric) |
| RotamericSingleResiduePeptoidLibrary.fwd.hh | Forward declaration of rotameric peptoid rotamer libraries |
| RotamericSingleResiduePeptoidLibrary.hh | Declaration of rotameric peptoid rotamer libraries |
| RotamericSingleResiduePeptoidLibrary.tmpl.hh | Declaration of rotameric peptoid rotamer libraries |
| RotamerLibrary.cc | |
| RotamerLibrary.fwd.hh | RotamerLibrary forward declarations and typedefs |
| RotamerLibrary.hh | Rotamer Library classes and utility functions |
| RotamerLibraryScratchSpace.cc | Declaration of scratch space class for Dunbrack rotamer library |
| RotamerLibraryScratchSpace.fwd.hh | Forward declaration of scratch space class for Dunbrack rotamer library |
| RotamerLibraryScratchSpace.hh | Declaration of scratch space class for Dunbrack rotamer library |
| SemiRotamericSingleResidueDunbrackLibrary.cc | Implementation of semi-rotameric rotamer libraries from Jun08 |
| SemiRotamericSingleResidueDunbrackLibrary.fwd.hh | Forward declaration of semi-rotameric rotamer libraries from Jun08 |
| SemiRotamericSingleResidueDunbrackLibrary.hh | Declaration of semi-rotameric rotamer libraries from Jun08 |
| SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh | Implementation of semi-rotameric rotamer libraries from Jun08 |
| SingleLigandRotamerLibrary.cc | |
| SingleLigandRotamerLibrary.fwd.hh | SingleLigandRotamerLibrary forward declarations and typedefs |
| SingleLigandRotamerLibrary.hh | SingleLigandRotamerLibrary class |
| SingleResidueDunbrackLibrary.cc | |
| SingleResidueDunbrackLibrary.fwd.hh | SingleResidueDunbrackLibrary forward declarations and typedefs |
| SingleResidueDunbrackLibrary.hh | SingleResidueDunbrackLibrary class |
| SingleResiduePeptoidLibrary.cc | SingleResiduePeptoidLibrary class |
| SingleResiduePeptoidLibrary.fwd.hh | SingleResiduePeptoidLibrary forward declarations and typedefs |
| SingleResiduePeptoidLibrary.hh | SingleResiduePeptoidLibrary class |
| SingleResidueRotamerLibrary.cc | SingleResidueRotamerLibrary class |
| SingleResidueRotamerLibrary.fwd.hh | SingleResidueRotamerLibrary forward declarations and typedefs |
| SingleResidueRotamerLibrary.hh | SingleResidueRotamerLibrary virtual base class |
| ► 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 |
| DensePDInteractionGraph.cc | Dense Edge-Matrix, Pairwise Decomposable interaction graph class implementation |
| DensePDInteractionGraph.fwd.hh | Helper class for AminoAcidNeighborSparseMatrix forward declaration |
| 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 | HPatch energy method, a score based on exact SASA calculations and a new patch identification algorithm, forward header file |
| HPatchEnergy.hh | HPatch energy method, a score based on exact SASA calculations and a new patch identification algorithm, header file |
| HPatchEnergyCreator.hh | Declaration for the class that connects HPatchEnergy with the ScoringManager |
| 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 | Interaction graph base class header |
| 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 | |
| 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 |
| 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 | Sparse matrix index class to work with AminoAcidNeighborSparseMatrix class |
| SurfaceEnergy.cc | |
| SurfaceEnergy.fwd.hh | Forward header file for SurfaceEnergy; Not really a CD1B energy; this class is needed for optE |
| SurfaceEnergy.hh | Header file for SurfaceEnergy; Not really a CD1B energy; this class is needed for optE |
| SurfaceEnergyCreator.hh | Declaration for the class that connects SurfaceEnergy with the ScoringManager |
| 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 | Class which keeps reads the residue hydrophobic ASA database file and calculates surface residue energies |
| SurfacePotential.hh | Class which keeps reads the residue hydrophobic ASA database file and calculates surface residue energies |
| 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 | Rotamer set implementation class for symmetric packing forward declarations |
| SymmetricRotamerSet_.hh | Rotamer set implementation class for symmetric packing |
| SymmetricRotamerSetFactory.cc | Residue Set Factory class for symmetric packing |
| SymmetricRotamerSetFactory.fwd.hh | Residue Set Facotry class forward declaration |
| SymmetricRotamerSetFactory.hh | Residue Set Factory class for symmetric packing |
| SymmetricRotamerSets.cc | RotamerSets class implementation, for symmetric packing |
| SymmetricRotamerSets.fwd.hh | RotamerSets class declaration, for symmetric packing |
| SymmetricRotamerSets.hh | RotamerSets class declaration, for symmetric packing |
| AddResiduesRotamerSetOperation.cc | Transform a vector of residues onto the backbone of the appropriate pose position and add the transformed residues to the rotamer set |
| AddResiduesRotamerSetOperation.hh | Transform a vector of residues onto the backbone of the appropriate pose position and add the transformed residues to the rotamer set |
| bb_independent_rotamers.cc | Bunch of utility functions used in enzdes |
| bb_independent_rotamers.hh | Build rotamers for residue type given neutral beckbone |
| BumpSelector.cc | Bump selector class implementation |
| BumpSelector.hh | Bump selector class implementation |
| ContinuousRotamerSet.cc | Implementation of the ContinuousRotamerSet and ContinuousRotamerSets classes |
| ContinuousRotamerSet.fwd.hh | Forward declaration of the ContinuousRotamerSet class |
| ContinuousRotamerSet.hh | Declaration for the class which desribes rotamers statistically instead of as discrete samples For use in stochastic packing (see Feng & Dokholyan, 2006) |
| FixbbRotamerSets.cc | Fixed-backbone Residue Sets interface class implementation |
| FixbbRotamerSets.fwd.hh | Fixed-backbone Residue Sets interface class foward declarations |
| FixbbRotamerSets.hh | Fixed-backbone Residue Sets interface class declaration |
| rna_rotamer_building_functions.cc | RNA nucleotide rotamer set class implementation |
| rna_rotamer_building_functions.hh | Rotamer set implementation class |
| rotamer_building_functions.cc | Amino acid rotamer set class implementation |
| rotamer_building_functions.hh | Rotamer set implementation class |
| RotamerCouplings.fwd.hh | Residue set class forward declarations |
| RotamerCouplings.hh | Residue set class forward declarations |
| RotamerLinks.fwd.hh | Residue set class forward declarations |
| RotamerLinks.hh | Residue set class forward declarations |
| RotamerSet.cc | Residue Set class |
| RotamerSet.fwd.hh | Residue set class forward declarations |
| RotamerSet.hh | Residue Set class |
| 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 | Residue Set Factory class |
| 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 class implementation |
| RotamerSets.fwd.hh | Residue Sets class foward declarations |
| RotamerSets.hh | RotamerSets class declaration |
| RotamerSetsBase.cc | Residue Sets Base class implementation |
| RotamerSetsBase.fwd.hh | Residue Sets Base class foward declarations |
| RotamerSetsBase.hh | RotamerSets base class declaration |
| RotamerSubset.cc | |
| RotamerSubset.fwd.hh | Rotamer set implementation class forward declarations |
| RotamerSubset.hh | Rotamer set implementation class |
| RotamerSubsets.cc | RotamerSets class implementation |
| RotamerSubsets.fwd.hh | Residue Subsets class foward declarations |
| RotamerSubsets.hh | RotamerSets class declaration |
| UnboundRotamersOperation.cc | |
| UnboundRotamersOperation.fwd.hh | |
| UnboundRotamersOperation.hh | |
| WaterAnchorInfo.cc | |
| WaterAnchorInfo.fwd.hh | |
| WaterAnchorInfo.hh | |
| WaterPackingInfo.cc | |
| WaterPackingInfo.fwd.hh | |
| WaterPackingInfo.hh | |
| ► scmin | |
| AtomTreeCollection.cc | Implementation for the classes holding sets of AtomTrees used during variuos packing+minimizing schemes |
| AtomTreeCollection.fwd.hh | Forward declaration for the classes holding sets of AtomTrees used during variuos packing+minimizing schemes |
| AtomTreeCollection.hh | Classes for 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 | |
| ► util | |
| interface_vector_calculate.cc | Calculates the residues at an interface between two protein chains or jump. The calculation is done in the following manner. First the point graph is used to find all residues within some big cutoff of residues on the other chain. For these residues near the interface, two metrics are used to decide if they are actually possible interface residues. The first metric is to iterate through all the side chain atoms in the residue of interest and check to see if their distance is less than the nearby atom cutoff, if so then they are an interface residue. If a residue does not pass that check, then two vectors are drawn, a CA-CB vector and a vector from CB to a CB atom on the neighboring chain. The dot product between these two vectors is then found and if the angle between them is less than some cutoff then they are classified as interface |
| interface_vector_calculate.hh | Calculates an interface definition based on a short distance |
| 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 | Declaration of the base class for ResFilter factory registration and creation |
| ResFilterCreators.hh | Declaration for the class that connects ResFilters with the ResFilterFactory |
| ResFilterFactory.cc | |
| ResFilterFactory.fwd.hh | |
| ResFilterFactory.hh | |
| ResFilterRegistrator.hh | |
| ResFilters.cc | Core-level (very general) classes that take a pose and a residue index, and return true or false |
| 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 | Declaration of the base class for ResLvlTaskOperation factory registration and creation |
| 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 | Declaration of the base class for TaskOperation factory registration and creation |
| TaskOperationCreators.hh | Declaration for the class that connects TaskOperations with the TaskOperationFactory |
| TaskOperationFactory.cc | |
| TaskOperationFactory.fwd.hh | |
| TaskOperationFactory.hh | |
| TaskOperationRegistrator.hh | |
| TaskOperations.cc | |
| TaskOperations.fwd.hh | Forward declaration of a class that performs an operation on a packer task, usually, by a PackerTaskFactory right after the task's construction |
| TaskOperations.hh | An operation to perform on a packer task – usually, by a PackerTaskFactory right after the task's construction This is an incomplete list. Freely define your own TaskOperation and hand it to a PackerTaskFactory |
| ► residue_selector | |
| 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 |
| 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 |
| InterGroupInterfaceByVectorSelector.cc | |
| InterGroupInterfaceByVectorSelector.fwd.hh | Forward declaration and owning_ptr typedefs for the InterGroupByVectorSelector |
| InterGroupInterfaceByVectorSelector.hh | |
| JumpDownstreamSelector.cc | The JumpDownstreamSelector selects residues downstream of a given jump in a FoldTree |
| 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 | The JumpUpstreamSelector selects residues downstream of a given jump in a FoldTree |
| 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 |
| NeighborhoodResidueSelector.cc | The NeighborhoodResidueSelector selects residues in a given proximity of set focus residues |
| 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. Clears the Passed ResidueSubset |
| NotResidueSelector.cc | The NotResidueSelector negates the logic of its loaded ResidueSelector |
| NotResidueSelector.fwd.hh | Forward declaration of a class that negates ResidueSelector logic |
| 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 combines ResidueSelector logic |
| OrResidueSelector.hh | The OrResidueSelector combines logic from multiple ResidueSelectors |
| ResidueIndexSelector.cc | The ResidueIndexSelector selects residues using a string containing pose indices |
| 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 |
| 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 |
| 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 |
| ► 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 | 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 |
| 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 | Fwd header of classes for resfile options |
| ResfileReader.hh | Header of classes for resfile options |
| RotamerSampleOptions.cc | |
| RotamerSampleOptions.hh | Class to describe rotamer construction header |
| TaskFactory.cc | Task class to describe packer's behavior header |
| TaskFactory.fwd.hh | Task class to describe packer's behavior header |
| TaskFactory.hh | Factory class for the creation and initialization of PackerTask objects |
| make_symmetric_task.cc | Utility functions for handling of symmetric conformations |
| 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 |
| ► 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 | |
| util.cc | |
| util.hh | |
| ► datacache | |
| cacheable_observers.cc | Bunch of cacheable observers |
| 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.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 | A DataCache storing objects derived from basic::datacache::CacheableData |
| PositionConservedResiduesStore.cc | |
| PositionConservedResiduesStore.fwd.hh | |
| PositionConservedResiduesStore.hh | |
| ► full_model_info | |
| FullModelInfo.cc | Mapping from a working pose into a bigger pose, for swa monte carlo stuff |
| FullModelInfo.fwd.hh | Mapping from a working pose into a bigger pose, for swa monte carlo stuff |
| FullModelInfo.hh | Statistically derived rotamer pair potential class implementation |
| FullModelParameters.cc | |
| FullModelParameters.fwd.hh | |
| FullModelParameters.hh | |
| FullModelParameterType.cc | |
| FullModelParameterType.hh | |
| util.cc | Mapping from a working pose into a bigger pose, for swa monte carlo stuff |
| util.hh | Helper functions for SubToFull object, cached inside pose |
| ► metrics | |
| ► simple_calculators | |
| InterfaceDefinitionCalculatorBase.cc | InterfaceDefinitionCalculatorBase class |
| InterfaceDefinitionCalculatorBase.hh | |
| InterfaceDeltaEnergeticsCalculator.cc | InterfaceDeltaEnergeticsCalculator class |
| InterfaceDeltaEnergeticsCalculator.hh | |
| InterfaceNeighborDefinitionCalculator.cc | |
| InterfaceNeighborDefinitionCalculator.hh | |
| InterfaceSasaDefinitionCalculator.cc | SasaCalculatorLegacy class |
| InterfaceSasaDefinitionCalculator.hh | |
| SasaCalculator2.cc | SasaCalculator2 class |
| SasaCalculator2.hh | Calculator for SASA |
| SasaCalculatorLegacy.cc | SasaCalculatorLegacy class |
| SasaCalculatorLegacy.hh | |
| CalculatorFactory.cc | CalculatorFactory class |
| CalculatorFactory.hh | |
| PoseMetricCalculatorBase.fwd.hh | |
| PoseMetricCalculatorBase.hh | |
| PoseMetricContainer.cc | PoseMetricContainer class |
| PoseMetricContainer.fwd.hh | |
| PoseMetricContainer.hh | Container for managing PoseMetricCalculators |
| ► motif | |
| reference_frames.cc | Compute motif-related reference frames for residues, chemical groups, etc |
| 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 |
| ► rna | |
| RNA_BaseDoubletClasses.hh | |
| RNA_BasePairClassifier.cc | Implementation of Leontis/Westhof nucleic acid base-pair classification |
| RNA_BasePairClassifier.hh | |
| RNA_IdealCoord.cc | Apply ideal RNA geometry to a residue or a pose |
| RNA_IdealCoord.fwd.hh | Apply ideal RNA geometry to a residue or a pose |
| 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 | RNA suite assignment ported from suitename program |
| 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 | Utility functions for handling of symmetric conformations |
| util.hh | Utility functions for handling with symmetric conformations |
| annotated_sequence.cc | Utility functions for making poses from sequences |
| annotated_sequence.hh | Utility functions for making poses from sequences |
| CrystInfo.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 |
| Remarks.fwd.hh | |
| Remarks.hh | |
| selection.cc | Pose residue selections |
| selection.hh | Selcetion of pose residues |
| util.cc | Pose class utilities |
| util.hh | Pose utilities |
| util.tmpl.hh | Pose utilities |
| xyzStripeHashPose.cc | |
| xyzStripeHashPose.fwd.hh | |
| xyzStripeHashPose.hh | |
| ► scoring | |
| ► 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 |
| ► carbon_hbonds | |
| CarbonHBondEnergy.cc | Hydrogen bond energy method forward declaration |
| CarbonHBondEnergy.fwd.hh | Forward declaration of carbon-hydrogen-donor energy method class |
| CarbonHBondEnergy.hh | Hydrogen bond energy method class declaration |
| 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 | Base class for ConstraintCreators for the Constraint load-time factory registration scheme |
| BasicConstraintCreators.hh | Base class for ConstraintCreators for the Constraint load-time factory registration scheme |
| BigBinConstraint.cc | |
| BigBinConstraint.hh | |
| BoundConstraint.cc | |
| BoundConstraint.fwd.hh | Forward declaration |
| BoundConstraint.hh | |
| ConstantConstraint.cc | |
| ConstantConstraint.hh | |
| Constraint.cc | |
| Constraint.fwd.hh | |
| Constraint.hh | Base class definition for Constraint class hierarchy |
| ConstraintCreator.cc | Base class for ConstraintCreators for the Constraint load-time factory registration scheme |
| ConstraintCreator.fwd.hh | Base class for ConstraintCreators for the Constraint load-time factory registration scheme |
| ConstraintCreator.hh | Base class for ConstraintCreators for the Constraint load-time factory registration scheme |
| ConstraintEnergyContainer.cc | Constraints Energy Container class implementation |
| ConstraintEnergyContainer.fwd.hh | Constraints Energy Container class declaration |
| ConstraintEnergyContainer.hh | Constraints Energy Container class declaration |
| ConstraintFactory.cc | Factory for creating various types of constraints |
| ConstraintFactory.hh | Factory for creating various types of constraints |
| ConstraintGraph.cc | Constraints Energy Container class declaration |
| ConstraintGraph.fwd.hh | Constraints Energy Graph class forward declaration |
| ConstraintGraph.hh | Constraints Energy Container class declaration |
| ConstraintIO.cc | |
| ConstraintIO.hh | |
| Constraints.cc | |
| Constraints.fwd.hh | |
| Constraints.hh | |
| ConstraintsEnergy.cc | Constraints Energy Method declaration |
| 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.hh | A cacheable data wrapper for ConstraintsOPs for use in minimization |
| DihedralConstraint.cc | |
| DihedralConstraint.fwd.hh | |
| DihedralConstraint.hh | |
| DihedralPairConstraint.cc | Restrain a pair of residues to take the same torsion angles |
| DihedralPairConstraint.hh | Restrain a pair of residues to take the same torsion angles |
| DistancePairConstraint.cc | Restrain a pair of residues to take the same AtomPair constraint of another pair |
| DistancePairConstraint.hh | Restrain a pair of residues to take the same torsion angles |
| 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 |
| 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 |
| NamedAtomPairConstraint.cc | |
| NamedAtomPairConstraint.fwd.hh | |
| NamedAtomPairConstraint.hh | |
| NonResidueTypeConstraint.cc | |
| NonResidueTypeConstraint.fwd.hh | |
| NonResidueTypeConstraint.hh | Implements favor_non_native_residue constraints, assigning an energy bonus to a residue if it matches the identity within the constraint object |
| ResidueTypeConstraint.cc | |
| ResidueTypeConstraint.fwd.hh | |
| ResidueTypeConstraint.hh | Implements favor_native_residue constraints, assigning an energy bonus to a residue if it matches the identity within the constraint object |
| ResidueTypeLinkingConstraint.cc | |
| ResidueTypeLinkingConstraint.fwd.hh | Constrainting two residues to be the same type, based on |
| ResidueTypeLinkingConstraint.hh | Implements favor_native_residue constraints, assigning an energy bonus to a residue if it matches the identity within the constraint object |
| 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 | Base class for ConstraintCreators for the Constraint load-time factory registration scheme |
| 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 | Scoring a structure against an electron density map |
| 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 | Custom atom pair distance energy |
| 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 | Constraints Energy Container class implementation |
| CentroidDisulfideEnergyContainer.fwd.hh | Constraints Energy Container class declaration |
| 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 | Centroid Disulfide Energy Databases |
| 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 | Constraints Energy Container class implementation |
| DisulfideMatchingEnergyContainer.fwd.hh | Constraints Energy Container class declaration |
| DisulfideMatchingEnergyContainer.hh | Disulfide Energy Container class declaration |
| DisulfideMatchingEnergyCreator.hh | Declaration for the class that connects DisulfideMatchingEnergy with the ScoringManager |
| DisulfideMatchingPotential.cc | Centroid Disulfide Energy Potentials |
| 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 | Disulfide Energy class forward declaration |
| FullatomDisulfideEnergyContainer.cc | Constraints Energy Container class implementation |
| FullatomDisulfideEnergyContainer.fwd.hh | Constraints Energy Container class declaration |
| 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 | 1st pass implementation of Kono + Sarai's protein-DNA interaction potential |
| DirectReadoutPotential.fwd.hh | |
| DirectReadoutPotential.hh | 1st pass implementation of Kono + Sarai's protein-DNA interaction potential |
| DNA_BasePotential.cc | |
| DNA_BasePotential.fwd.hh | |
| DNA_BasePotential.hh | |
| 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 | DNATorsion energy method class implementation |
| DNATorsionEnergy.fwd.hh | |
| DNATorsionEnergy.hh | Statistically derived rotamer pair potential class declaration |
| DNATorsionEnergyCreator.hh | Declaration for the class that connects DNATorsionEnergy with the ScoringManager |
| DNATorsionPotential.cc | DNATorsionPotential potential class implementation |
| DNATorsionPotential.fwd.hh | DNATorsionPotential potential class forward delcaration |
| 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 | Header file for ClassicAbinitio protocol |
| StrandPairing.cc | |
| StrandPairing.fwd.hh | Kinematics::ShortestPathInFoldTree forward declarations header |
| StrandPairing.hh | |
| util.cc | |
| util.hh | Read jump-definition file setups fold tree an chainbreak variants loop code didn't work because fold-tree to complicated ( overlapping loops ) |
| ► elec | |
| ElecAtom.cc | |
| ElecAtom.fwd.hh | |
| ElecAtom.hh | |
| FA_ElecEnergy.cc | Electrostatic energy with a distance-dependant dielectric |
| FA_ElecEnergy.fwd.hh | Electrostatic energy with a distance-dependant dielectric |
| FA_ElecEnergy.hh | Electrostatic energy with a distance-dependant dielectric |
| 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 | Electrostatics between aromatics and all surrounding atoms |
| 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 | Electrostatics for RNA |
| 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 | Electrostatic energy with a distance-dependant dielectric |
| FA_GrpElecEnergy.fwd.hh | Electrostatic energy with a distance-dependant dielectric |
| FA_GrpElecEnergy.hh | Electrostatic energy with a distance-dependant dielectric |
| FA_GrpElecEnergyCreator.hh | Declaration for the class that connects FA_ElecEnergy with the ScoringManager |
| GroupElec.cc | Electrostatic energy with a distance-dependant dielectric |
| GroupElec.hh | Electrostatic energy with a distance-dependant dielectric |
| 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 | Electrostatics for RNA |
| RNA_FA_ElecEnergyCreator.hh | Declaration for the class that connects RNA_FA_ElecEnergy with the ScoringManager |
| ► electron_density | |
| ElecDensAllAtomCenEnergy.cc | Scoring a structure's fit to electron density |
| ElecDensAllAtomCenEnergy.hh | Scoring a structure's fit to electron density |
| ElecDensAllAtomCenEnergyCreator.hh | Declaration for the class that connects ElecDensAllAtomCenEnergy with the ScoringManager |
| ElecDensCenEnergy.cc | Scoring a structure's fit to electron density |
| ElecDensCenEnergy.hh | Scoring a structure's fit to electron density |
| ElecDensCenEnergyCreator.hh | Declaration for the class that connects ElecDensCenEnergy with the ScoringManager |
| ElecDensEnergy.cc | Scoring a structure's fit to electron density |
| ElecDensEnergy.hh | Scoring a structure's fit to electron density |
| ElecDensEnergyCreator.hh | Declaration for the class that connects ElecDensEnergy with the ScoringManager |
| ElectronDensity.cc | Scoring a structure against an electron density map |
| ElectronDensity.fwd.hh | |
| ElectronDensity.hh | Scoring a structure against an electron density map |
| ElectronDensityLoader.cc | Options for constructing an electron density map |
| ElectronDensityLoader.fwd.hh | |
| ElectronDensityLoader.hh | Options for constructing an electron density map |
| ElectronDensityLoaderCreator.hh | Header for ElectronDensityLoader Creator for the load-time factory registration scheme |
| ElectronDensityOptions.cc | Options for constructing an electron density map |
| ElectronDensityOptions.fwd.hh | |
| ElectronDensityOptions.hh | Options for constructing an electron density map |
| ElectronDensityOptionsCreator.hh | Header for ElectronDensityOptions Creator for the load-time factory registration scheme |
| FastDensEnergy.cc | Scoring a structure's fit to electron density |
| FastDensEnergy.hh | Scoring a structure's fit to electron density |
| FastDensEnergyCreator.hh | Declaration for the class that connects FastDensEnergy with the ScoringManager |
| PattersonCorrEnergy.cc | Scoring a structure's fit to electron density |
| PattersonCorrEnergy.hh | Scoring a structure's fit to a patterson map |
| PattersonCorrEnergyCreator.hh | Declaration for the class that connects PattersonCorrEnergy with the ScoringManager |
| SplineInterp.cc | 3D spline interpolation methods. Based on implementation by Philippe Thevenaz, see comments below |
| SplineInterp.hh | 3D spline interpolation methods. Based on implementation by Philippe Thevenaz, see comments below |
| 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 | Declaration for the class that connects ElecDensAtomwiseEnergy with the ScoringManager |
| ElectronDensityAtomwise.cc | Elec_dens_atomwise scoring method implementation |
| ElectronDensityAtomwise.hh | Scoring a structure against an electron density map |
| ► etable | |
| ► coulomb | |
| Coulomb.cc | Evaluate Coulombic potential |
| 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 |
| 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 | Count pair for residue pairs connected with one bond, where the crossover from excluding to counting atom pair interactions is at 3 bonds |
| CountPairCrossover3.fwd.hh | Count pair for residue pairs where the crossover from excluding to counting atom pair interactions is at 3 bonds |
| 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 |
| 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 | Count pair for residue pairs connected with one bond, where the crossover from excluding to counting atom pair interactions is at 4 bonds |
| 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 | Count pair base class interface |
| ► 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 | Trie class for etable typedef |
| TrieCountPair1BC3.cc | |
| TrieCountPair1BC3.fwd.hh | |
| TrieCountPair1BC3.hh | |
| TrieCountPair1BC4.cc | |
| TrieCountPair1BC4.fwd.hh | |
| TrieCountPair1BC4.hh | |
| TrieCountPairAll.analytic_etable.cc | File which actually instantiates the templated trie-vs-trie and trie-vs-path algorithms for the analytic etable energy |
| TrieCountPairAll.cc | The functions that belong to TrieCountPairAll other than the templated trie-vs-trie and trie-vs-path templated function calls |
| 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.mm_inter.cc | File which actually instantiates the templated trie-vs-trie and trie-vs-path algorithms for the MM Lennard-Jones inter-residue energy |
| 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 | Implementation of count pair class to go along with the CountPairGeneric atom data |
| TrieCountPairGeneric.fwd.hh | |
| TrieCountPairGeneric.hh | |
| TrieCountPairNone.cc | |
| TrieCountPairNone.fwd.hh | |
| TrieCountPairNone.hh | |
| atom_pair_energy_inline.hh | |
| BaseEtableEnergy.hh | Etable energy method class declaration |
| BaseEtableEnergy.tmpl.hh | Atom pair energy functions |
| Etable.cc | |
| Etable.fwd.hh | |
| Etable.hh | |
| EtableEnergy.cc | Atom pair energy functions |
| EtableEnergy.fwd.hh | Score function class |
| EtableEnergy.hh | Score function class |
| 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 | Fiber diffraction data collector class |
| FiberDiffraction.fwd.hh | Fiber Diffraction forward declarations |
| FiberDiffraction.hh | Fiber diffraction data collector class |
| FiberDiffractionEnergy.cc | FiberDiffraction scoring and derivatives (all-atom) |
| FiberDiffractionEnergy.hh | FiberDiffraction scoring and derivatives (all-atom) |
| FiberDiffractionEnergyCreator.hh | Energy Creator for FiberDiffractionEnergy |
| FiberDiffractionEnergyDens.cc | FiberDiffractionDens scoring (low resolution, electron-density based) |
| FiberDiffractionEnergyDens.hh | FiberDiffractionDens scoring (low-resolution, electron density based) |
| FiberDiffractionEnergyDensCreator.hh | Energy Creator for FiberDiffractionEnergyDens |
| FiberDiffractionEnergyGpu.cc | FiberDiffraction scoring on GPU |
| FiberDiffractionEnergyGpu.hh | FiberDiffractionGpu soring and derivatives |
| FiberDiffractionEnergyGpuCreator.hh | Energy Creator for FiberDiffractionEnergy |
| 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 | Fast Hankel transform needed for low-resolution scoring of fiber diffraction data |
| hankel_kiss_fft.hh | Fast Hankel transform needed for low-resolution scoring of fiber diffraction data |
| util.cc | FiberDiffraction utility functions |
| util.hh | FiberDiffraction utility functions |
| util_ndft.cc | FiberDiffractionDens scoring |
| util_ndft.hh | FiberDiffractionDens utility scoring |
| 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 | Definition for functions used in definition of constraints |
| CircularPowerFunc.cc | Definition for functions used in definition of constraints |
| 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 | Definition for functions used in definition of constraints |
| 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 | Weighted constraint function that encapsulates other constraints |
| EtableFunc.cc | Definition for functions used in definition of constraints |
| EtableFunc.fwd.hh | Forward declaration for Etable functions |
| EtableFunc.hh | Definition for functions used in definition of constraints |
| FadeFunc.cc | Definition for functions used in definition of constraints |
| FadeFunc.fwd.hh | Forward declaration for Mixture functions |
| FadeFunc.hh | Definition for functions used in definition of constraints |
| FlatHarmonicFunc.cc | Definition for functions used in definition of constraints |
| 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 | Definition for functions used in loop closure terms |
| GaussianChainQuadrupleFunc.fwd.hh | Forward declaration for Mixture functions |
| GaussianChainQuadrupleFunc.hh | Definition for functions used in definition of loop closure energies |
| GaussianChainSingleFunc.cc | Definition for functions used in loop closure terms |
| GaussianChainSingleFunc.fwd.hh | Forward declaration for Mixture functions |
| GaussianChainSingleFunc.hh | Definition for functions used in definition of loop closure energies |
| GaussianChainTripleFunc.cc | Definition for functions used in loop closure terms |
| GaussianChainTripleFunc.fwd.hh | Forward declaration for Mixture functions |
| GaussianChainTripleFunc.hh | Definition for functions used in definition of loop closure energies |
| GaussianFunc.cc | Definition for functions used in definition of constraints |
| GaussianFunc.fwd.hh | Forward declaration for Gaussian functions |
| GaussianFunc.hh | Definition for functions used in definition of constraints |
| HarmonicFunc.cc | Definition for functions used in definition of constraints |
| HarmonicFunc.fwd.hh | Forward declaration for Mixture functions |
| HarmonicFunc.hh | Definition for functions used in definition of constraints |
| IdentityFunc.cc | Definition for functions used in definition of constraints |
| 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 | Forward declaration for CircularHarmonicFunc class |
| KarplusFunc.hh | Definition for functions used in definition of constraints |
| LinearPenaltyFunction.cc | |
| LinearPenaltyFunction.hh | Linear penalty for values outside a certain range |
| MinMultiHarmonicFunc.cc | Definition for functions used in definition of constraints |
| MinMultiHarmonicFunc.fwd.hh | Forward declaration for Mixture functions |
| MinMultiHarmonicFunc.hh | Definition for functions used in definition of constraints |
| 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 | Weighted constraint function that encapsulates other constraints |
| ScalarWeightedFunc.hh | Weighted constraint function that encapsulates other constraints |
| SigmoidFunc.cc | Definition for functions used in definition of constraints |
| SigmoidFunc.fwd.hh | Forward declaration for Mixture functions |
| SigmoidFunc.hh | Definition for functions used in definition of constraints |
| SkipViolFunc.cc | Weighted constraint function that reweights other constraints by a constant scalar value |
| SkipViolFunc.hh | Weighted constraint function that encapsulates other constraints |
| SoedingFunc.cc | Definition for functions used in definition of constraints |
| SoedingFunc.fwd.hh | Forward declaration for SoedingFunc class |
| SoedingFunc.hh | Definition for Johannes Soeding-style distance restraints |
| SOGFunc.cc | Definition for functions used in definition of constraints |
| 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 | Definition for functions used in definition of constraints |
| SquareWell2Func.fwd.hh | Forward declaration for Mixture functions |
| SquareWell2Func.hh | Definition for functions used in definition of constraints |
| SquareWellFunc.cc | Definition for functions used in definition of constraints |
| 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 | Implementation of phenix "top-out" function Similar to Geman-McClure: harmonic near 'x0_', flat past 'limit_' |
| 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 | Geometric solvation energy, with environment dependence allowed. Note ContextIndependent version is faster |
| ContextDependentGeometricSolEnergy.fwd.hh | Hydrogen bond energy method forward declaration |
| ContextDependentGeometricSolEnergy.hh | Geometric solvation energy (context dependent) |
| ContextDependentGeometricSolEnergyCreator.hh | Declaration for the class that connects GeometricSolEnergy with the ScoringManager |
| ContextIndependentGeometricSolEnergy.cc | Similar to the standard version of GeometricSolEnergy.cc BUT without the CONTEXT_DEPENDENT stuff |
| ContextIndependentGeometricSolEnergy.fwd.hh | Hydrogen bond energy method forward declaration |
| ContextIndependentGeometricSolEnergy.hh | Geometric solvation energy |
| ContextIndependentGeometricSolEnergyCreator.hh | Declaration for the class that connects GeometricSolEnergy with the ScoringManager |
| 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.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 | Solvation model based on penalizing potential for Hbonding to solvent |
| 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 | Electrostatics energy method for aromatic side chain (stand-in for pi/pi interactions) |
| HackAroEnergy.fwd.hh | Electrostatics for RNA class forward declaration |
| HackAroEnergy.hh | Electrostatics for RNA |
| HackAroEnergyCreator.hh | Declaration for the class that connects HackAroEnergy with the ScoringManager |
| ► hbonds | |
| ► hbtrie | |
| HBAtom.cc | |
| HBAtom.fwd.hh | |
| HBAtom.hh | |
| HBCountPairFunction.cc | |
| HBCountPairFunction.fwd.hh | |
| HBCountPairFunction.hh | |
| HBCPData.cc | CountPair Data for a residue with one connection point |
| HBCPData.fwd.hh | |
| HBCPData.hh | This class enforces the sc/bb hbond exclusion rule for use in the trie |
| HBondTrie.fwd.hh | Trie class for etable typedef |
| constants.hh | Core::scoring package type declarations |
| FadeInterval.cc | FadeInterval class, used a simplified cross term for the hbond score term |
| FadeInterval.fwd.hh | FadeInterval class, used a simplified cross term for the hbond score term |
| FadeInterval.hh | FadeInterval class, used a simplified cross term for the hbond score term |
| HBEvalTuple.cc | Tuple describing data about the donor and acceptor in a single hbond |
| 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 | Database containing params for HBondEnergy |
| HBondEnergy.cc | Hydrogen bond energy method forward declaration |
| HBondEnergy.fwd.hh | Hydrogen bond energy method forward declaration |
| HBondEnergy.hh | Hydrogen bond energy method class declaration |
| 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 | |
| hbonds_geom.cc | |
| hbonds_geom.hh | |
| HBondSet.cc | Hydrogen bond set class implementation |
| HBondSet.fwd.hh | Hydrogen bond set for a pose forward declaration |
| HBondSet.hh | Hydrogen bond set class declaration |
| HBondTypeManager.cc | HBond enumeration type manager |
| 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 | |
| ► loop_graph | |
| Loop.cc | |
| Loop.fwd.hh | |
| Loop.hh | |
| LoopCloseEnergy.cc | Cost of bringing two chains together |
| LoopCloseEnergy.hh | Loop closure energy, currently defined for RNA |
| 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 | |
| ► memb_etable | |
| MembEtable.cc | Generate the table for fa_atr/rep and fa_sol with membrane additions |
| MembEtable.fwd.hh | |
| MembEtable.hh | Generate the table for fa_atr/rep and fa_sol with membrane additions |
| ► membrane | |
| FaMPEnvEnergy.cc | LK-Type Membrane Environment Energy |
| FaMPEnvEnergy.fwd.hh | LK-Type Membrane Environment Energy |
| FaMPEnvEnergy.hh | LK-Type Membrane Environment Energy |
| FaMPEnvEnergyCreator.hh | Membrane Environment Energy |
| FaMPEnvSmoothEnergy.cc | Fullatom Smoothed Membrane Environment Energy |
| 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 | LK-Type Membrane Solvation Energy |
| 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 | Membrane Environemnt CBeta Energy |
| MPCBetaEnergy.fwd.hh | Membrane Environemnt CBeta Energy |
| MPCBetaEnergy.hh | Membrane Environemnt CBeta Energy |
| MPCBetaEnergyCreator.hh | Membrane Environemnt CBeta Energy |
| 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 | Membrane Lipophibicity Term |
| 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 | |
| ► dfire | |
| DFIRE_Energy.cc | |
| DFIRE_Energy.fwd.hh | Ramachandran energy method class forward declaration |
| DFIRE_Energy.hh | |
| DFIRE_EnergyCreator.hh | |
| DFIRE_Potential.cc | |
| DFIRE_Potential.fwd.hh | PoissonBoltzmann potential class forward delcaration |
| 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 | Smooth, differentiable version of centroid hbond term |
| 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 | |
| CenRotEnvEnergy.cc | CenRot version of centroid env |
| CenRotEnvEnergy.hh | CenRot version of centroid env |
| CenRotEnvEnergyCreator.hh | CenRot version of centroid env |
| CenRotPairEnergy.cc | CenRot version of cen pair |
| CenRotPairEnergy.hh | CenRot version of cen pair |
| CenRotPairEnergyCreator.hh | CenRot version of cen pair |
| 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 | Etable energy method class declaration |
| 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 | Context-Dependent, Long-Range, Two-Body Energy class declaration |
| 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 | Score function class |
| 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-Independent, Long-Range, Two-Body Energy class declaration |
| ContextIndependentOneBodyEnergy.cc | |
| ContextIndependentOneBodyEnergy.fwd.hh | |
| ContextIndependentOneBodyEnergy.hh | Score function class |
| ContextIndependentTwoBodyEnergy.cc | Short-ranged, context-independent, two-body energy class implementation |
| 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 | Statistically derived DNA contact potential class declaration |
| DirectReadoutEnergy.hh | Statistically derived DNA contact potential class declaration |
| DirectReadoutEnergyCreator.hh | Declaration for the class that connects DirectReadoutEnergy with the ScoringManager |
| DistanceChainbreakEnergy.cc | Atom pair energy functions |
| DistanceChainbreakEnergy.fwd.hh | Etable energy method class declaration |
| DistanceChainbreakEnergy.hh | Etable energy method class declaration |
| DistanceChainbreakEnergyCreator.hh | Declaration for the class that connects DistanceChainbreakEnergy with the ScoringManager |
| DNA_BaseEnergy.cc | |
| DNA_BaseEnergy.fwd.hh | Statistically derived rotamer pair potential class declaration |
| DNA_BaseEnergy.hh | Statistically derived rotamer pair potential class declaration |
| DNA_BaseEnergyCreator.hh | Declaration for the class that connects DNA_BaseEnergy with the ScoringManager |
| EnergyMethod.cc | Base class for energy classes |
| EnergyMethod.fwd.hh | Energy Method class forward declaration and EnergyMethodType enum definition |
| EnergyMethod.hh | Base class for energy classes |
| 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 | Score function class |
| EnergyMethodOptions.fwd.hh | Score function class |
| EnergyMethodOptions.hh | Score function class |
| EnergyMethodRegistrator.hh | Declaration of the base class for EnergyMethod factory registration and creation |
| EnvEnergy.cc | Statistically derived rotamer pair potential class implementation |
| 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 | Statistically derived rotamer pair potential class declaration |
| EnvSmoothEnergy.hh | Statistically derived fullatom environment 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 | LK Solvation using hemisphere culling class forward declaration |
| Fa_MbsolvEnergy.hh | LK-type Membrane Solvation |
| 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 | Statistically derived rotamer pair potential class declaration |
| 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 | C++ implementaion of GOAP(Generalized Orientation-dependent, All-atom statistical Potential) by Zhou H & Skolnick J, Biophys J 2011, 101(8):2043-52 |
| GoapEnergy.hh | C++ implementaion of GOAP(Generalized Orientation-dependent, All-atom statistical Potential) by Zhou H & Skolnick J, Biophys J 2011, 101(8):2043-52 |
| GoapEnergyCreator.hh | |
| HybridVDW_Energy.cc | Statistically derived rotamer pair potential class implementation |
| HybridVDW_Energy.fwd.hh | Statistically derived rotamer pair potential class declaration |
| 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 | Atom pair energy functions |
| LinearChainbreakEnergy.fwd.hh | Etable energy method class declaration |
| LinearChainbreakEnergy.hh | Etable energy method class declaration |
| LinearChainbreakEnergyCreator.cc | LinearChainbreakEnergyCreator implementation |
| LinearChainbreakEnergyCreator.hh | Declaration for the class that connects LinearChainbreakEnergy with the ScoringManager |
| LK_BallEnergy.cc | Orientation dependent variant of the LK Solvation using |
| LK_BallEnergy.fwd.hh | LK Solvation using hemisphere culling class declaration |
| LK_BallEnergy.hh | Orientation dependent variant of the LK Solvation using |
| LK_BallEnergyCreator.hh | Declaration for the class that connects LK_BallEnergy with the ScoringManager |
| LK_BallInfo.cc | Orientation dependent variant of the LK Solvation using |
| LK_BallInfo.hh | Orientation dependent variant of the LK Solvation using |
| LK_hack.cc | LK Solvation using hemisphere culling class declaration |
| LK_hack.fwd.hh | LK Solvation using hemisphere culling class forward declaration |
| 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 Solvation using hemisphere culling class forward declaration |
| LK_PolarNonPolarEnergy.hh | LK Solvation using hemisphere culling class 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 | Statistically derived rotamer pair potential class implementation |
| MembraneCbetaEnergy.fwd.hh | Statistically derived rotamer pair potential class declaration |
| 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 | Statistically derived rotamer pair potential class declaration |
| MembraneCenPairEnergy.hh | Membrane Pair Term |
| MembraneCenPairEnergyCreator.hh | Declaration for the class that connects MembraneCenPairEnergy with the ScoringManager |
| MembraneEnvEnergy.cc | Statistically derived rotamer pair potential class implementation |
| MembraneEnvEnergy.fwd.hh | Statistically derived rotamer pair potential class declaration |
| MembraneEnvEnergy.hh | Membrane Environment Cbeta Energy |
| MembraneEnvEnergyCreator.hh | Declaration for the class that connects MembraneEnvEnergy with the ScoringManager |
| MembraneEnvPenalties.cc | RMS Energy function. Used to optimize the RMSD between two structures |
| MembraneEnvPenalties.fwd.hh | Statistically derived rotamer pair potential class declaration |
| 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 | Statistically derived smooth membrane environment potential class declaration |
| MembraneEnvSmoothEnergy.hh | Statistically derived smooth membrane environment potential class declaration |
| MembraneEnvSmoothEnergyCreator.hh | Declaration for the class that connects MembraneEnvSmoothEnergy with the ScoringManager |
| MembraneLipo.cc | RMS Energy function. Used to optimize the RMSD between two structures |
| MembraneLipo.fwd.hh | Statistically derived rotamer pair potential class declaration |
| 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 | Molecular mechanics torsion energy |
| 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 | Molecular mechanics bond length score class |
| 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 | Molecular mechanics lj energy |
| 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 | Molecular mechanics lj energy |
| 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 | Molecular mechanics torsion energy |
| 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 |
| NMerPSSMEnergy.cc | PSSMerence energy method implementation |
| NMerPSSMEnergy.fwd.hh | PSSMerence energy method forward declaration |
| NMerPSSMEnergy.hh | PSSM energy method declaration |
| NMerPSSMEnergyCreator.hh | Declaration for the class that connects NMerPSSMEnergy with the ScoringManager |
| NMerRefEnergy.cc | Reference energy method implementation |
| NMerRefEnergy.fwd.hh | Reference energy method forward declaration |
| NMerRefEnergy.hh | Reference energy method declaration |
| NMerRefEnergyCreator.hh | Declaration for the class that connects NMerRefEnergy with the ScoringManager |
| NMerSVMEnergy.cc | SVMerence energy method implementation |
| NMerSVMEnergy.fwd.hh | SVMerence energy method forward declaration |
| NMerSVMEnergy.hh | SVM energy method declaration |
| NMerSVMEnergyCreator.hh | Declaration for the class that connects NMerSVMEnergy with the ScoringManager |
| 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 | Probability of observing an amino acid, given its phi/psi energy method forward declaration |
| P_AA_pp_Energy.hh | Probability of observing an amino acid, given its phi/psi energy method declaration |
| P_AA_pp_EnergyCreator.hh | Declaration for the class that connects P_AA_pp_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 | Etable energy method class declaration |
| 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 | Declaration for the class that connects PB_elec energy with the ScoringManager |
| 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 |
| Rama2BOffsetEnergy.cc | |
| Rama2BOffsetEnergy.fwd.hh | |
| Rama2BOffsetEnergy.hh | |
| Rama2BOffsetEnergyCreator.hh | Declaration for the class that connects Rama2BOffsetEnergy with the ScoringManager |
| 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 | Ramachandran energy method class implementation |
| RamachandranEnergy2B.fwd.hh | Ramachandran energy method class forward declaration |
| 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 |
| ReferenceEnergy.cc | Reference energy method implementation |
| ReferenceEnergy.fwd.hh | Reference energy method forward declaration |
| ReferenceEnergy.hh | Reference energy method declaration |
| 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 | RDC energy - comparing experimental RDC values to calculated values |
| 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 | Declaration for the class that connects RG_Energy_Fast 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 | Declaration for the class that connects SA_Energy with the ScoringManager |
| SecondaryStructureEnergy.cc | Statistically derived rotamer pair potential class implementation |
| SecondaryStructureEnergy.fwd.hh | Statistically derived rotamer pair potential class declaration |
| SecondaryStructureEnergy.hh | Statistically derived rotamer pair potential class declaration |
| SecondaryStructureEnergyCreator.hh | Declaration for the class that connects SecondaryStructureEnergy with the ScoringManager |
| SequenceDependentRefEnergy.cc | Reference energy method implementation |
| SequenceDependentRefEnergy.fwd.hh | Reference energy method forward declaration |
| SequenceDependentRefEnergy.hh | Reference energy method declaration |
| 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 | Smooth, differentiable, version of cenpair |
| SmoothCenPairEnergyCreator.hh | Smooth, differentiable, version of cenpair |
| SmoothEnvEnergy.cc | Smooth, differentiable, version of centroid env |
| SmoothEnvEnergy.hh | Smooth, differentiable, version of centroid env |
| SmoothEnvEnergyCreator.hh | Smooth, differentiable, version of centroid env |
| 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 | Declaration for the class that connects SymmetricLigandEnergy with the ScoringManager |
| 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 |
| WaterAdductHBondEnergy.cc | |
| WaterAdductHBondEnergy.fwd.hh | Energy potential for water mediated hydrogen bonds involving adduct-placed water molecules |
| 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 | Energetic offset/cost for placing a water adduct on an amino or nucleic acid |
| WaterAdductIntraEnergy.fwd.hh | Energetic offset/cost for placing a water adduct on an amino or nucleic acid |
| 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 | Term for chi3 on tyrosine residues to prefer the hydrogen lie in the plane of the ring |
| YHHPlanarityEnergy.fwd.hh | Probability of observing an amino acid, given its phi/psi energy method forward declaration |
| YHHPlanarityEnergy.hh | Probability of observing an amino acid, given its phi/psi energy method declaration |
| YHHPlanarityEnergyCreator.hh | Declaration for the class that connects P_AA_pp_Energy with the ScoringManager |
| ► 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 | Molecular mechanics bond angle library |
| 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 | Class to store bond angle parameters for a set of ResidueTypes |
| 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 | Molecular mechanics bond length score class |
| 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 | Molecular mechanics lj library |
| 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 | Molecular mechanics torsion library |
| 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 | Typedefs and forward declarations for class NVlookup |
| NVlookup.hh | Neighbor Vector algorithm lookup table processing class declaration |
| NVscore.cc | |
| NVscore.fwd.hh | Typedefs and forward declarations for class NVscore |
| NVscore.hh | Neighbor Vector algorithm for solvation approximation class declaration |
| NVscoreCreator.hh | Declaration for the class that connects NVscore with the ScoringManager |
| ► 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 | Packing Score |
| HolesEnergy.hh | Packing Score |
| HolesEnergyCreator.hh | Declaration for the class that connects HolesEnergy with the ScoringManager |
| HolesEnergyRes.cc | Packing Score |
| HolesEnergyRes.hh | Packing Score |
| HolesParams.hh | Packing Score Params |
| HolesParamsRes.hh | Packing Score Params |
| PoseBalls.cc | |
| PoseBalls.hh | |
| PoseBallsLite.cc | |
| PoseBallsLite.hh | |
| surf_vol.cc | Packing Score |
| surf_vol.hh | Packing Score |
| 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 | Declaration for the class that connects RNA_ChemicalMappingEnergy with the ScoringManager |
| RNA_DataBackboneEnergy.cc | Statistically derived rotamer pair potential class implementation |
| RNA_DataBackboneEnergy.fwd.hh | Statistically derived rotamer pair potential class declaration |
| 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 | Statistically derived rotamer pair potential class implementation |
| RNA_DataInfo.fwd.hh | Statistically derived rotamer pair potential class implementation |
| RNA_DataInfo.hh | Statistically derived rotamer pair potential class implementation |
| 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 | Radius of gyration energy function definition |
| RG_Energy_RNA.hh | Radius of gyration score for RNA, to match Rosetta++ |
| RG_Energy_RNACreator.hh | Declaration for the class that connects RG_Energy_RNA with the ScoringManager |
| RNA_AtomVDW.cc | |
| RNA_AtomVDW.fwd.hh | Statistically derived rotamer pair potential class declaration |
| RNA_AtomVDW.hh | Information on which atoms to use for computing clashes |
| RNA_BulgeEnergy.cc | RNA_Bulge energy method implementation |
| RNA_BulgeEnergy.fwd.hh | RNA_Bulge energy method forward declaration |
| RNA_BulgeEnergy.hh | Score function class |
| RNA_BulgeEnergyCreator.hh | Declaration for the class that connects RNA_BulgeEnergy with the ScoringManager |
| RNA_CentroidInfo.cc | Statistically derived rotamer pair potential class implementation |
| RNA_CentroidInfo.fwd.hh | Statistically derived rotamer pair potential class implementation |
| RNA_CentroidInfo.hh | Statistically derived rotamer pair potential class implementation |
| RNA_EnergyMethodOptions.cc | |
| RNA_EnergyMethodOptions.fwd.hh | |
| RNA_EnergyMethodOptions.hh | |
| RNA_FilteredBaseBaseInfo.cc | Statistically derived RNA potential |
| RNA_FilteredBaseBaseInfo.fwd.hh | Statistically derived rotamer pair potential class implementation |
| RNA_FilteredBaseBaseInfo.hh | Statistically derived RNA potential |
| RNA_FullAtomStackingEnergy.cc | Statistically derived rotamer pair potential class implementation |
| RNA_FullAtomStackingEnergy.fwd.hh | Statistically derived rotamer pair potential class declaration |
| RNA_FullAtomStackingEnergy.hh | Statistically derived rotamer pair potential class declaration |
| RNA_FullAtomStackingEnergyCreator.hh | Declaration for the class that connects RNA_FullAtomStackingEnergy with the ScoringManager |
| RNA_FullAtomVDW_BasePhosphate.cc | RNA_FullAtomVDW_BasePhosphate energy method class implementation |
| 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 | Declaration for the class that connects RNA_FullAtomVDW_BasePhosphate with the ScoringManager |
| RNA_JR_SuiteEnergy.cc | Jane Richardson style RNA Suite Energy |
| RNA_JR_SuiteEnergy.fwd.hh | Jane Richardson style RNA Suite Energy |
| RNA_JR_SuiteEnergy.hh | Jane Richardson style RNA Suite Energy |
| RNA_JR_SuiteEnergyCreator.hh | Declaration for the class that connects RNA_JR_SuiteEnergy with the ScoringManager |
| RNA_LJ_BaseEnergy.cc | |
| RNA_LJ_BaseEnergy.fwd.hh | LJ Aromatic Energy |
| 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 | Statistically derived rotamer pair potential class implementation |
| RNA_LowResolutionPotential.fwd.hh | Statistically derived rotamer pair potential class implementation |
| RNA_LowResolutionPotential.hh | Statistically derived rotamer pair potential class implementation |
| RNA_Mg_Energy.cc | Statistically derived Mg(2+) binding potential for RNA |
| RNA_Mg_Energy.hh | Statistically derived Mg(2+) binding potential for RNA |
| RNA_Mg_EnergyCreator.hh | Declaration for the class that connects RNA_Mg_Energy with the ScoringManager |
| RNA_Mg_KnowledgeBasedPotential.cc | |
| RNA_Mg_KnowledgeBasedPotential.fwd.hh | Statistically derived rotamer pair potential class declaration |
| RNA_Mg_KnowledgeBasedPotential.hh | Information on which atoms to use for computing clashes |
| RNA_PairwiseLowResolutionEnergy.cc | Statistically derived rotamer pair potential class implementation |
| RNA_PairwiseLowResolutionEnergy.fwd.hh | Statistically derived rotamer pair potential class declaration |
| 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 | Statistically derived rotamer pair potential class implementation |
| RNA_RawBaseBaseInfo.fwd.hh | Statistically derived rotamer pair potential class implementation |
| RNA_RawBaseBaseInfo.hh | Statistically derived rotamer pair potential class implementation |
| RNA_ScoringInfo.cc | Statistically derived rotamer pair potential class implementation |
| RNA_ScoringInfo.fwd.hh | Statistically derived rotamer pair potential class implementation |
| RNA_ScoringInfo.hh | Statistically derived rotamer pair potential class implementation |
| RNA_ScoringUtil.cc | |
| RNA_ScoringUtil.hh | |
| RNA_SugarCloseEnergy.cc | RNA_SugarClose energy method class implementation |
| RNA_SugarCloseEnergy.fwd.hh | OmegaTether energy method class forward declaration |
| RNA_SugarCloseEnergy.hh | Statistically derived rotamer pair potential class declaration |
| RNA_SugarCloseEnergyCreator.hh | Declaration for the class that connects RNA_SugarCloseEnergy with the ScoringManager |
| RNA_SuiteEnergy.cc | RNA Suite Energy |
| RNA_SuiteEnergy.fwd.hh | RNA Suite Energy |
| RNA_SuiteEnergy.hh | RNA Suite Energy |
| RNA_SuiteEnergyCreator.hh | Declaration for the class that connects RNA_SuiteEnergy with the ScoringManager |
| RNA_SuitePotential.cc | RNA_SuitePotential potential class implementation |
| RNA_SuitePotential.fwd.hh | RNA_SuitePotential potential class forward delcaration |
| RNA_SuitePotential.hh | RNA_SuitePotential potential class delcaration |
| RNA_TorsionEnergy.cc | RNA_Torsion energy method class implementation |
| RNA_TorsionEnergy.fwd.hh | OmegaTether energy method class forward declaration |
| 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 potential class implementation |
| RNA_TorsionPotential.fwd.hh | RNA_TorsionPotential potential class forward delcaration |
| RNA_TorsionPotential.hh | RNA_TorsionPotential potential class delcaration |
| RNA_VDW_Energy.cc | Statistically derived clash check for RNA |
| RNA_VDW_Energy.fwd.hh | Statistically derived rotamer pair potential class declaration |
| 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 | Statistically derived rotamer pair potential class declaration |
| StackElecEnergy.hh | FA_Elec, but just 'perpendicular' to bases... trying to separate from H-bonds & geom_sol |
| 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 | Collects histogram of distances between atoms of given SAXS-types, e.g. distances between ARG-CEN and TRP-CEN |
| FastSAXSEnergy.cc | FastSAX scoring of Stovgaard et al (BMC Bioinf. 2010) |
| FastSAXSEnergy.hh | FastSAX scoring of Stovgaard et al (BMC Bioinf. 2010) |
| 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 | Represents an atomic scattering form factor |
| 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 | "Energy" based on a similarity of theoretical SAXS spectrum computed for a pose and the experimental data |
| SAXSEnergy.hh | "Energy" based on a similarity of theoretical SAXS spectrum computed for a pose and the experimental data |
| SAXSEnergyCEN.hh | "Energy" based on a similarity of theoretical SAXS spectrum computed for a pose and the experimental data |
| SAXSEnergyCreator.hh | Declaration for the class that connects SAXSEnergyCreator with the ScoringManager |
| SAXSEnergyCreatorCEN.cc | "Energy" based on a similarity of theoretical SAXS spectrum computed for a pose and the experimental data |
| SAXSEnergyCreatorCEN.hh | Declaration for the class that connects SAXSEnergyCreatorCEN with the ScoringManager |
| SAXSEnergyCreatorFA.cc | "Energy" based on a similarity of theoretical SAXS spectrum computed for a pose and the experimental data |
| SAXSEnergyCreatorFA.hh | Declaration for the class that connects SAXSEnergyCreatorFA with the ScoringManager |
| SAXSEnergyFA.hh | "Energy" based on a similarity of theoretical SAXS spectrum computed for a pose and the experimental data |
| SinXOverX.cc | |
| SinXOverX.hh | Declaration for the class that connects SAXSEnergyCreator with the ScoringManager |
| ► sc | |
| MolecularSurfaceCalculator.cc | Implementation of molecular surface calculation for shape complementarity |
| MolecularSurfaceCalculator.fwd.hh | Forward header for the Molecular Surface Calculator |
| MolecularSurfaceCalculator.hh | Headers for the Molecular Surface Calculator |
| ShapeComplementarityCalculator.cc | Headers for the Shape Complementarity Calculator |
| ShapeComplementarityCalculator.fwd.hh | Headers for the Shape Complementarity Calculator |
| ShapeComplementarityCalculator.hh | Headers for the Shape Complementarity Calculator |
| ShapeComplementarityCalculator_Private.hh | Private headers for the Shape Complementarity Calculator |
| ► 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 | Implementation of symmetric design bonus class |
| symE.fwd.hh | Typedefs and forward declarations for class symE |
| symE.hh | Header declarations for class symE |
| symECreator.hh | Declaration for the class that connects symE with the ScoringManager |
| ► symmetry | |
| SymmetricEnergies.cc | Symmetrical Energies class to store cached energies and track the residue neighbor relationships |
| 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 | ScoreFunction class definition |
| 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 | |
| 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 | 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 |
| TrieCountPairBase.fwd.hh | |
| TrieCountPairBase.hh | |
| ► vdwaals | |
| VDW_Energy.cc | Low resolution (centroid) repulsive energy |
| VDW_Energy.fwd.hh | Low resolution (centroid) repulsive energy |
| 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 class definition |
| APBSWrapper.fwd.hh | APBSWrapper forward delcaration |
| APBSWrapper.hh | APBSWrapper class declaration |
| AtomVDW.cc | |
| AtomVDW.fwd.hh | Statistically derived rotamer pair potential class declaration |
| AtomVDW.hh | Statistically derived rotamer pair potential class declaration |
| CenHBPotential.cc | Smooth, differentiable version of centroid hbond term |
| CenHBPotential.fwd.hh | Smooth, differentiable version of centroid hbond term |
| CenHBPotential.hh | Smooth, differentiable version of centroid hbond term |
| CenRotEnvPairPotential.cc | CenRot version of cen pair/env |
| CenRotEnvPairPotential.fwd.hh | CenRot version of cen pair |
| CenRotEnvPairPotential.hh | CenRot version of cen pair |
| 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 | Context graph type enumeration |
| DenseEnergyContainer.cc | A container for storing all-against-all energies as the upper triangle of a matrix |
| DenseEnergyContainer.fwd.hh | A container interface for storing and scoring long range energies |
| DenseEnergyContainer.hh | A container for storing all-against-all energies as the upper triangle of a matrix |
| DerivVectorPair.fwd.hh | Class for storing a pair of derivative vectors, f1 and f2, used in our internal-geometry minimization algorithm |
| DerivVectorPair.hh | Class for storing a pair of derivative vectors, f1 and f2, used in our internal-geometry minimization algorithm |
| 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 | ScoreFunction class definition |
| DockingScoreFunction.fwd.hh | Core::scoring::DockingScoreFunction forward declarations |
| DockingScoreFunction.hh | Symmetric Score function class |
| 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 | Statistically derived rotamer pair potential class implementation |
| EnvPairPotential.fwd.hh | Statistically derived rotamer pair potential class implementation |
| EnvPairPotential.hh | Statistically derived rotamer pair potential class implementation |
| GenBornPotential.cc | |
| GenBornPotential.fwd.hh | |
| GenBornPotential.hh | |
| interpolation_util.hh | Useful function for interpolation.. |
| LREnergyContainer.cc | A container interface for storing and scoring long range energies |
| LREnergyContainer.fwd.hh | A container for storing and scoring long range energies forward declaration |
| LREnergyContainer.hh | A container interface for storing and scoring long range energies |
| Membrane_FAPotential.cc | Membrane FA Potential - Class for Fullatom Membrane Scoring Methods |
| Membrane_FAPotential.fwd.hh | Membrane FA Potential - Class for Fullatom Membrane Scoring Methods |
| Membrane_FAPotential.hh | Membrane FA Potential - Class for Fullatom Membrane Scoring Methods |
| 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 |
| MembraneTopology.fwd.hh | Membrane Topology |
| MembraneTopology.hh | MembraneTopology |
| 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 | ScoreFunction class definition. A easy way to deal with the low-res score function problem in replica docking |
| MinScoreScoreFunction.fwd.hh | Core::scoring::MinScoreScoreFunction forward declarations |
| MinScoreScoreFunction.hh | Symmetric Score function class |
| 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 | A container interface for storing and scoring long range energies |
| 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 | Amino acid probability arrays and functions |
| P_AA.hh | Amino acid probability arrays and functions |
| PairEPotential.cc | PairE knowledge-based potential class |
| PairEPotential.fwd.hh | PairE knowledge-based potential class forward delcaration |
| PairEPotential.hh | PairE knowledge-based potential class delcaration |
| PeptideBondedEnergyContainer.cc | A container interface long range energies for n->n+1 interactions only |
| PeptideBondedEnergyContainer.fwd.hh | A container interface long range energies for n->n+1 interactions only |
| PeptideBondedEnergyContainer.hh | A container interface long range energies for n->n+1 interactions only |
| PoissonBoltzmannPotential.cc | PoissonBoltzmann potential class implementation |
| PoissonBoltzmannPotential.fwd.hh | PoissonBoltzmann potential class forward delcaration |
| PoissonBoltzmannPotential.hh | Poisson Boltzmann potential class delcaration |
| ProQPotential.cc | Membrane Potential |
| ProQPotential.fwd.hh | Membrane Potential |
| ProQPotential.hh | ProQembrane Potential |
| ProteinTorsion.hh | Ramachandran potential class delcaration |
| Rama2BOffset.cc | |
| Rama2BOffset.fwd.hh | |
| Rama2BOffset.hh | Rama2BOffset potential class delcaration |
| Ramachandran.cc | Ramachandran potential class implementation |
| Ramachandran.fwd.hh | Ramachandran potential class forward delcaration |
| Ramachandran.hh | Ramachandran potential class delcaration |
| Ramachandran2B.cc | Neighbor-dependent Ramachandran potential class implementation |
| Ramachandran2B.fwd.hh | Ramachandran potential class forward delcaration |
| Ramachandran2B.hh | Neighbor-dependent Ramachandran 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 | Uses NMR RDC for scoring |
| ResidueNeighborList.cc | A container class for use by the Etable and FA_Elec classes for storing lists of atom neighbors |
| 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 stuff from rosetta++ |
| rms_util.tmpl.hh | RMS stuff from rosetta++ that requires templates |
| 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 | Score function class |
| ScoreFunctionInfo.hh | Score function class |
| ScoreType.cc | |
| ScoreType.hh | Score type enumeration |
| ScoreTypeManager.cc | |
| ScoreTypeManager.hh | Score type enumeration |
| ScoringManager.cc | Scoring manager class |
| ScoringManager.fwd.hh | Scoring manager class header |
| ScoringManager.hh | Scoring manager class header |
| SecondaryStructurePotential.cc | Scoring manager class header |
| SecondaryStructurePotential.fwd.hh | Scoring manager class header |
| SecondaryStructurePotential.hh | Scoring manager class header |
| SecondaryStructureWeights.cc | Scoring manager class header |
| SecondaryStructureWeights.hh | Scoring manager class header |
| SmoothEnvPairPotential.cc | Smooth, differentiable version of centroid env and pair terms |
| SmoothEnvPairPotential.fwd.hh | Smooth, differentiable version of centroid env and pair terms |
| SmoothEnvPairPotential.hh | Smooth, differentiable version of centroid env and pair terms |
| SS_Info.cc | Scoring manager class header |
| SS_Info.fwd.hh | Data cache forward declarations for the secondary-structure based scores |
| SS_Info.hh | Scoring manager class header |
| SS_Killhairpins_Info.cc | Scoring manager class header |
| SS_Killhairpins_Info.fwd.hh | Scoring manager class header |
| 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 | Reimplementation of TMscore sequence-based structure superposition |
| 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 |
| WaterAdductHBondPotential.cc | |
| WaterAdductHBondPotential.fwd.hh | |
| WaterAdductHBondPotential.hh | |
| ► sequence | |
| 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 | Base class for SequenceCreators for the Sequence load-time factory registration scheme |
| BasicSequenceCreators.hh | Base class for BasicSequenceCreators for the BasicSequence load-time factory registration scheme |
| 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 | Class for holding information on a dynamic programming matrix |
| 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 | Class definition for a given scoring scheme for an alignment |
| 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 | Factory for creating various types of constraints |
| Sequence.cc | Method definitions for Sequence class |
| Sequence.fwd.hh | Forward declaration for Sequence class |
| Sequence.hh | Class definition for a sequence |
| SequenceAlignment.cc | Class definition for a multiple sequence alignment |
| SequenceAlignment.fwd.hh | Forward declaration for SequenceAlignment class |
| SequenceAlignment.hh | Class definition for a multiple sequence alignment |
| SequenceCoupling.cc | Class definition for a sequence coupling profile that |
| SequenceCoupling.fwd.hh | Forward declaration for class SequenceCoupling |
| SequenceCoupling.hh | Class definition for a sequence coupling profile that |
| SequenceCreator.cc | Base class for SequenceCreators for the Sequence load-time factory registration scheme |
| SequenceCreator.fwd.hh | Base class for SequenceCreators for the Sequence load-time factory registration scheme |
| 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 | Silent input file reader for mini |
| 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 | Class definition for a class that aligns two Sequence objects using a ScoringScheme object and the Smith-Waterman alignment algorithm |
| SWAligner.fwd.hh | Forward declaration for SWAligner class |
| SWAligner.hh | Class definition for a class that aligns two Sequence objects using ScoringScheme and the Smith-Waterman alignment algorithm |
| util.cc | Small bundle of utilities for dealing with sequences |
| util.hh | Small bundle of utilities for dealing with sequences |
| ► util | |
| ABEGOManager.cc | Class for ABEGO |
| ABEGOManager.fwd.hh | Foward header file for class of ABEGO |
| ABEGOManager.hh | Header file for class of ABEGO plus |
| 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 | Utilities for working with metalloproteins |
| 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 |
1.8.7