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chemical Directory Reference
Directory dependency graph for chemical:
src/core/chemical

Directories

directory  carbohydrates
 
directory  gasteiger
 
directory  mainchain_potential
 
directory  mmCIF
 
directory  orbitals
 
directory  rdkit
 
directory  residue_properties
 
directory  rings
 
directory  rna
 
directory  rotamers
 
directory  sdf
 

Files

file  AA.cc
 translation between amino acid enum and string name/one letter char codes
 
file  AA.hh
 
file  Adduct.cc
 definition of residue adduct class
 
file  Adduct.fwd.hh
 declaration of class for adducts on residues
 
file  Adduct.hh
 declaration of implementation class for residue adducts
 
file  adduct_util.cc
 
file  adduct_util.hh
 
file  Atom.cc
 
file  Atom.fwd.hh
 Class declaration for chemical::Atom.
 
file  Atom.hh
 Method definitions for chemical::Atom.
 
file  AtomICoor.cc
 declaration of implementation class for abstract class Residue
 
file  AtomICoor.fwd.hh
 declaration of implementation class for abstract class Residue
 
file  AtomICoor.hh
 declaration of implementation class for abstract class Residue
 
file  AtomProperties.cc
 Method definitions for AtomProperties.
 
file  AtomProperties.fwd.hh
 Forward declarations for AtomProperties.
 
file  AtomProperties.hh
 Declarations and simple accessor/mutator definitions for AtomProperties.
 
file  AtomPropertiesManager.cc
 Method definitions for AtomPropertiesManager.
 
file  AtomPropertiesManager.fwd.hh
 Forward declaration for AtomPropertiesManager.
 
file  AtomPropertiesManager.hh
 Method declarations for AtomPropertiesManager.
 
file  AtomProperty.hh
 Enumeration definitions for AtomProperties.
 
file  AtomProperty_mappings.cc
 
file  AtomRefMapping.hh
 A mapping of atom references (vds, indexes, names) to each other.
 
file  AtomType.cc
 A class for defining atom parameters, known as atom_types.
 
file  AtomType.fwd.hh
 
file  AtomType.hh
 A class for defining atom parameters, known as atom_types.
 
file  atomtype_support.cc
 
file  atomtype_support.hh
 
file  AtomTypeDatabaseIO.cc
 Write chemical information associated with atom types to a database.
 
file  AtomTypeDatabaseIO.fwd.hh
 
file  AtomTypeDatabaseIO.hh
 
file  AtomTypeSet.cc
 
file  AtomTypeSet.fwd.hh
 
file  AtomTypeSet.hh
 
file  automorphism.cc
 
file  automorphism.hh
 
file  Bond.cc
 
file  Bond.fwd.hh
 
file  Bond.hh
 
file  bond_support.cc
 
file  bond_support.hh
 support functions for class Bond; functions that should not be included as part of the class.
 
file  CacheableResidueTypeSets.cc
 A (Pose-cacheable) container for ResidueTypeSets.
 
file  CacheableResidueTypeSets.fwd.hh
 A (Pose-cacheable) container for ResidueTypeSets.
 
file  CacheableResidueTypeSets.hh
 A (Pose-cacheable) container for ResidueTypeSets.
 
file  ChemicalManager.cc
 
file  ChemicalManager.fwd.hh
 
file  ChemicalManager.hh
 Chemical manager class header.
 
file  ElectronConfiguration.cc
 
file  ElectronConfiguration.fwd.hh
 
file  ElectronConfiguration.hh
 
file  Element.cc
 The data for the element types.
 
file  Element.fwd.hh
 
file  Element.hh
 The data for the element types.
 
file  Elements.cc
 
file  Elements.hh
 All the elements known to mankind (me)...as of4/18/2014.
 
file  ElementSet.cc
 
file  ElementSet.fwd.hh
 
file  ElementSet.hh
 
file  GlobalResidueTypeSet.cc
 GlobalResidueTypeSet class.
 
file  GlobalResidueTypeSet.fwd.hh
 
file  GlobalResidueTypeSet.hh
 
file  GreekDistance.hh
 Enumeration definitions for GreekDistance.
 
file  icoor_support.cc
 external support for manipulating the ResidueType's icoor/ideal_xyz
 
file  icoor_support.hh
 
file  IdealBondLengthSet.cc
 
file  IdealBondLengthSet.fwd.hh
 
file  IdealBondLengthSet.hh
 
file  MergeBehaviorManager.cc
 
file  MergeBehaviorManager.fwd.hh
 
file  MergeBehaviorManager.hh
 
file  Metapatch.cc
 A structure for applying multiple Patches procedurally.
 
file  Metapatch.fwd.hh
 
file  Metapatch.hh
 
file  MMAtomType.cc
 Molecular mechanics atom type class.
 
file  MMAtomType.fwd.hh
 
file  MMAtomType.hh
 Molecular mechanics atom type class.
 
file  MMAtomTypeSet.cc
 
file  MMAtomTypeSet.fwd.hh
 
file  MMAtomTypeSet.hh
 
file  MutableChiRecord.cc
 A Chi record object for a MutableResidueType.
 
file  MutableChiRecord.fwd.hh
 A Chi record object for a MutableResidueType.
 
file  MutableChiRecord.hh
 A Chi record object for a MutableResidueType.
 
file  MutableICoorRecord.cc
 A ICoord record object for a MutableResidueType.
 
file  MutableICoorRecord.fwd.hh
 A ICoord record object for a MutableResidueType.
 
file  MutableICoorRecord.hh
 A ICoord record object for a MutableResidueType.
 
file  MutableResidueConnection.cc
 A class representing a connection point to another residue for a MutableResidueType.
 
file  MutableResidueConnection.fwd.hh
 A version of ResidueConnection used with MutableResidueType.
 
file  MutableResidueConnection.hh
 Inter-residue chemical bond connection point class declaration.
 
file  MutableResidueType.cc
 Method definitions for MutableResidueType.
 
file  MutableResidueType.fwd.hh
 declaration of MutableResidueType class
 
file  MutableResidueType.hh
 Method declarations and simple accessors/getters for MutableResidueType.
 
file  NucleotideTools.cc
 
file  NucleotideTools.hh
 
file  Orbital.cc
 
file  Orbital.fwd.hh
 
file  Orbital.hh
 
file  Patch.cc
 Implementation class for abstract class Residue.
 
file  Patch.fwd.hh
 
file  Patch.hh
 
file  PatchOperation.cc
 Polymorphic classes representing the contents of a residue-type patch file.
 
file  PatchOperation.fwd.hh
 
file  PatchOperation.hh
 Polymorphic classes representing the contents of a residue-type patch file.
 
file  PoseResidueTypeSet.cc
 A ResidueTypeSet which can be cached in the Pose.
 
file  PoseResidueTypeSet.fwd.hh
 A ResidueTypeSet which can be cached in the Pose.
 
file  PoseResidueTypeSet.hh
 A ResidueTypeSet which can be cached in the Pose.
 
file  ResConnID.cc
 
file  ResConnID.fwd.hh
 
file  ResConnID.hh
 
file  residue_io.cc
 helper methods for ResidueType input/output
 
file  residue_io.hh
 
file  residue_support.cc
 
file  residue_support.hh
 support functions for class residue; functions that should not be included as part of the class.
 
file  ResidueConnection.cc
 Auto-generated serialization template functions.
 
file  ResidueConnection.fwd.hh
 declaration of implementation class for abstract class Residue
 
file  ResidueConnection.hh
 Inter-residue chemical bond connection point class declaration.
 
file  ResidueDatabaseIO.cc
 
file  ResidueDatabaseIO.fwd.hh
 
file  ResidueDatabaseIO.hh
 
file  ResidueGraphTypes.hh
 Graph structure for ResidueType.
 
file  ResidueGraphTypes.srlz.hh
 Helper functions for serializing objects in ResidueGraphTypes.hh and associated.
 
file  ResidueProperties.cc
 Method definitions for ResidueProperties.
 
file  ResidueProperties.fwd.hh
 Forward declarations for ResidueProperties.
 
file  ResidueProperties.hh
 Declarations and simple accessor/mutator definitions for ResidueProperties.
 
file  ResidueProperty.hh
 Enumeration definition for ResidueProperty.
 
file  ResidueProperty_mappings.cc
 Method definitions for private singleton methods declared in AtomPropertiesManager.hh.
 
file  ResidueSubGraphTypes.cc
 
file  ResidueSubGraphTypes.hh
 Filtered subgraphs.
 
file  ResidueType.cc
 Method definitions for ResidueType.
 
file  ResidueType.fwd.hh
 declaration of implementation class for abstract class Residue
 
file  ResidueType.hh
 Method declarations and simple accessors/getters for ResidueType.
 
file  ResidueType.srlz.cc
 Serialization and deserialization routines for when working with globally-accessible ResidueTypes.
 
file  ResidueType.srlz.hh
 Serialization and deserialization routines for when working with globally-accessible ResidueTypes.
 
file  ResidueTypeBase.cc
 Method definitions for ResidueTypeBase.
 
file  ResidueTypeBase.fwd.hh
 declaration of implementation class for abstract class Residue
 
file  ResidueTypeBase.hh
 Method declarations and simple accessors/getters for ResidueTypeBase.
 
file  ResidueTypeFinder.cc
 
file  ResidueTypeFinder.fwd.hh
 
file  ResidueTypeFinder.hh
 Functions to find residue_type(s) from ResidueTypeSet without requiring instantiation of all rsd_types.
 
file  ResidueTypeKinWriter.cc
 Class to write kinemage-formatted output for Residue and chemical.
 
file  ResidueTypeKinWriter.fwd.hh
 
file  ResidueTypeKinWriter.hh
 Class to write kinemage-formatted output for ResidueType.
 
file  ResidueTypeSelector.cc
 
file  ResidueTypeSelector.fwd.hh
 
file  ResidueTypeSelector.hh
 
file  ResidueTypeSet.cc
 ResidueTypeSet class.
 
file  ResidueTypeSet.fwd.hh
 
file  ResidueTypeSet.hh
 
file  ResidueTypeSet.srlz.cc
 Serialization and deserialization routines for when working with ResidueTypeSets.
 
file  ResidueTypeSet.srlz.hh
 Serialization and deserialization routines for when working with ResidueTypeSets.
 
file  ResidueTypeSetCache.cc
 
file  ResidueTypeSetCache.fwd.hh
 
file  ResidueTypeSetCache.hh
 
file  RestypeDestructionEvent.fwd.hh
 forward declaration for core::chemical::RestypeDestructionEvent
 
file  RestypeDestructionEvent.hh
 
file  types.hh
 rosetta project type declarations
 
file  util.cc
 Utilities for modifying and utilizing ResidueTypes and other core::chemical classes.
 
file  util.hh
 Utilities for modifying and utilizing Residues and other core::chemical classes.
 
file  VariantType.hh
 Enumeration definition for VariantType.
 
file  VariantType_mappings.cc
 Method definitions for private static methods declared in ResidueProperties.hh.