chemical Directory Reference

Directory dependency graph for chemical:

Directories
directory	carbohydrates
directory	gasteiger
directory	mainchain_potential
directory	mmCIF
directory	orbitals
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	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
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.