chemical Directory Reference

Directory dependency graph for chemical:

Directories
directory	carbohydrates
directory	gasteiger
directory	mmCIF
directory	orbitals
directory	residue_properties
directory	rings
directory	rna
directory	rotamers
directory	sdf

Files
file	AA.cc [code]
	translation between amino acid enum and string name/one letter char codes
file	AA.hh [code]
file	Adduct.cc [code]
	definition of residue adduct class
file	Adduct.fwd.hh [code]
	declaration of class for adducts on residues
file	Adduct.hh [code]
	declaration of implementation class for residue adducts
file	adduct_util.cc [code]
file	adduct_util.hh [code]
file	Atom.cc [code]
file	Atom.fwd.hh [code]
	Class declaration for chemical::Atom.
file	Atom.hh [code]
	Method definitions for chemical::Atom.
file	AtomICoor.cc [code]
	declaration of implementation class for abstract class Residue
file	AtomICoor.fwd.hh [code]
	declaration of implementation class for abstract class Residue
file	AtomICoor.hh [code]
	declaration of implementation class for abstract class Residue
file	AtomProperties.cc [code]
	Method definitions for AtomProperties.
file	AtomProperties.fwd.hh [code]
	Forward declarations for AtomProperties.
file	AtomProperties.hh [code]
	Declarations and simple accessor/mutator definitions for AtomProperties.
file	AtomPropertiesManager.cc [code]
	Method definitions for AtomPropertiesManager.
file	AtomPropertiesManager.fwd.hh [code]
	Forward declaration for AtomPropertiesManager.
file	AtomPropertiesManager.hh [code]
	Method declarations for AtomPropertiesManager.
file	AtomProperty.hh [code]
	Enumeration definitions for AtomProperties.
file	AtomProperty_mappings.cc [code]
file	AtomType.cc [code]
	A class for defining atom parameters, known as atom_types.
file	AtomType.fwd.hh [code]
file	AtomType.hh [code]
	A class for defining atom parameters, known as atom_types.
file	atomtype_support.cc [code]
file	atomtype_support.hh [code]
file	AtomTypeDatabaseIO.cc [code]
	Write chemical information associated with atom types to a database.
file	AtomTypeDatabaseIO.fwd.hh [code]
file	AtomTypeDatabaseIO.hh [code]
file	AtomTypeSet.cc [code]
file	AtomTypeSet.fwd.hh [code]
file	AtomTypeSet.hh [code]
file	automorphism.cc [code]
file	automorphism.hh [code]
file	Bond.cc [code]
file	Bond.fwd.hh [code]
file	Bond.hh [code]
file	bond_support.cc [code]
file	bond_support.hh [code]
	support functions for class Bond; functions that should not be included as part of the class.
file	ChemicalManager.cc [code]
file	ChemicalManager.fwd.hh [code]
file	ChemicalManager.hh [code]
	Chemical manager class header.
file	ElectronConfiguration.cc [code]
file	ElectronConfiguration.fwd.hh [code]
file	ElectronConfiguration.hh [code]
file	Element.cc [code]
	The data for the element types.
file	Element.fwd.hh [code]
file	Element.hh [code]
	The data for the element types.
file	Elements.cc [code]
file	Elements.hh [code]
	All the elements known to mankind (me)...as of4/18/2014.
file	ElementSet.cc [code]
file	ElementSet.fwd.hh [code]
file	ElementSet.hh [code]
file	GreekDistance.hh [code]
	Enumeration definitions for GreekDistance.
file	icoor_support.cc [code]
	external support for manipulating the ResidueType's icoor/ideal_xyz
file	icoor_support.hh [code]
file	IdealBondLengthSet.cc [code]
file	IdealBondLengthSet.fwd.hh [code]
file	IdealBondLengthSet.hh [code]
file	MergeBehaviorManager.cc [code]
file	MergeBehaviorManager.fwd.hh [code]
file	MergeBehaviorManager.hh [code]
file	Metapatch.cc [code]
	A structure for applying multiple Patches procedurally.
file	Metapatch.fwd.hh [code]
file	Metapatch.hh [code]
file	MMAtomType.cc [code]
	Molecular mechanics atom type class.
file	MMAtomType.fwd.hh [code]
file	MMAtomType.hh [code]
	Molecular mechanics atom type class.
file	MMAtomTypeSet.cc [code]
file	MMAtomTypeSet.fwd.hh [code]
file	MMAtomTypeSet.hh [code]
file	Orbital.cc [code]
file	Orbital.fwd.hh [code]
file	Orbital.hh [code]
file	Patch.cc [code]
	Implementation class for abstract class Residue.
file	Patch.fwd.hh [code]
file	Patch.hh [code]
file	PatchOperation.cc [code]
	Polymorphic classes representing the contents of a residue-type patch file.
file	PatchOperation.fwd.hh [code]
file	PatchOperation.hh [code]
	Polymorphic classes representing the contents of a residue-type patch file.
file	ResConnID.cc [code]
file	ResConnID.fwd.hh [code]
file	ResConnID.hh [code]
file	residue_io.cc [code]
	helper methods for ResidueType input/output
file	residue_io.hh [code]
file	residue_support.cc [code]
file	residue_support.hh [code]
	support functions for class residue; functions that should not be included as part of the class.
file	ResidueConnection.fwd.hh [code]
	declaration of implementation class for abstract class Residue
file	ResidueConnection.hh [code]
	Inter-residue chemical bond connection point class declaration.
file	ResidueDatabaseIO.cc [code]
file	ResidueDatabaseIO.fwd.hh [code]
file	ResidueDatabaseIO.hh [code]
file	ResidueGraphTypes.cc [code]
file	ResidueGraphTypes.hh [code]
	Graph structure for ResidueType.
file	ResidueLoader.cc [code]
file	ResidueLoader.fwd.hh [code]
	implementation of the Residue Loader
file	ResidueLoader.hh [code]
file	ResidueLoaderCreator.hh [code]
file	ResidueLoaderOptions.cc [code]
	forward headers for the Residue Loader Options
file	ResidueLoaderOptions.fwd.hh [code]
	forward headers for the Residue Loader Options
file	ResidueLoaderOptions.hh [code]
	forward headers for the Residue Loader Options
file	ResidueLoaderOptionsCreator.hh [code]
file	ResidueProperties.cc [code]
	Method definitions for ResidueProperties.
file	ResidueProperties.fwd.hh [code]
	Forward declarations for ResidueProperties.
file	ResidueProperties.hh [code]
	Declarations and simple accessor/mutator definitions for ResidueProperties.
file	ResidueProperty.hh [code]
	Enumeration definition for ResidueProperty.
file	ResidueProperty_mappings.cc [code]
	Method definitions for private singleton methods declared in AtomPropertiesManager.hh.
file	ResidueType.cc [code]
	Method definitions for ResidueType.
file	ResidueType.fwd.hh [code]
	declaration of implementation class for abstract class Residue
file	ResidueType.hh [code]
	Method declarations and simple accessors/getters for ResidueType.
file	ResidueType.srlz.cc [code]
	Serialization and deserialization routines for when working with globally-accessible ResidueTypes.
file	ResidueType.srlz.hh [code]
	Serialization and deserialization routines for when working with globally-accessible ResidueTypes.
file	ResidueTypeFinder.cc [code]
file	ResidueTypeFinder.fwd.hh [code]
file	ResidueTypeFinder.hh [code]
	Functions to find residue_type(s) from ResidueTypeSet without requiring instantiation of all rsd_types.
file	ResidueTypeKinWriter.cc [code]
	Class to write kinemage-formatted output for Residue and chemical.
file	ResidueTypeKinWriter.fwd.hh [code]
file	ResidueTypeKinWriter.hh [code]
	Class to write kinemage-formatted output for ResidueType.
file	ResidueTypeSelector.cc [code]
file	ResidueTypeSelector.fwd.hh [code]
file	ResidueTypeSelector.hh [code]
file	ResidueTypeSet.cc [code]
	ResidueTypeSet class.
file	ResidueTypeSet.fwd.hh [code]
file	ResidueTypeSet.hh [code]
file	ResidueTypeSet.srlz.cc [code]
	Serialization and deserialization routines for when working with globally-accessible ResidueTypeSets.
file	ResidueTypeSet.srlz.hh [code]
	Serialization and deserialization routines for when working with globally-accessible ResidueTypeSets.
file	ResidueTypeSetCache.cc [code]
file	ResidueTypeSetCache.fwd.hh [code]
file	ResidueTypeSetCache.hh [code]
file	types.hh [code]
file	util.cc [code]
	Utilities for modifying and utilizing Residues and other core::chemical classes.
file	util.hh [code]
	Utilities for modifying and utilizing Residues and other core::chemical classes.
file	VariantType.hh [code]
	Enumeration definition for VariantType.
file	VariantType_mappings.cc [code]
	Method definitions for private static methods declared in ResidueProperties.hh.