core::chemical Namespace Reference

Namespaces
	carbohydrates
	element
	gasteiger
	mainchain_potential
	mmCIF
	NucleotideTools
	orbitals
	rings
	rna
	rotamers
	sdf

Classes
class	AcceptorAtomFilter
	The filter responsible for obtaining all acceptor atoms. More...
class	AddAtom
	add an atom to ResidueType More...
class	AddAtomAlias
	A patch operation for adding an atom alias to a ResidueType. More...
class	AddBond
	add a bond to ResidueType More...
class	AddBondType
	A patch operation for adding a specific type of bond to a ResidueType. More...
class	AddChi
	Add a chi angle to ResidueType. More...
class	AddChiRotamer
	Add a rotamer sample to a chi angle of the ResidueType. More...
class	AddConnect
class	AddConnectAndTrackingVirt
	add a connect and tracking virt to the atom More...
class	AddConnectDeleteChildProton
	add a connect to the atom, delete child proton More...
class	AddProperty
	add a property to ResidueType More...
class	AddProtonChi
class	Adduct
	Description of optional single-atom residue adducts. More...
class	APolarHydrogenFilter
	The filter responsible for all apolar hydrogens. More...
class	AppendMainchainAtom
	add a mainchain atom after the last mainchain atom More...
class	AromaticAtomFilter
	The filter responsible for all aromatic atoms. More...
class	Atom
class	AtomICoor
	A basic class containing info of internal coordinates needed for building an atom within a ResidueType. More...
class	AtomProperties
class	AtomPropertiesManager
class	AtomType
	basic atom type More...
class	AtomTypeDatabaseIO
class	AtomTypeSet
	a set of AtomTypes More...
class	AutomorphismIterator
	Enumerates the automorphisms of a residue, which are basically chemical symmetries that affect RMSD calculations. More...
class	Bond
	basic chemical Bond More...
class	CacheableResidueTypeSets
	A (Pose-cacheable) container for ResidueTypeSets. More...
class	ChangeAncestory
class	ChangeBondType
	A patch operation for changing the bond type of a given bond. More...
class	ChemicalManager
	a class managing different sets of atom_type_set and residue_type_set More...
class	ChiralFlipAtoms
	Execute chiral flip (primarily: at CA) More...
class	ChiralFlipNaming
	Execute chiral flip (primarily: at CA) More...
class	ClearChiRotamers
	A patch operation for clearing all rotamer bins from the chi of a ResidueType. More...
class	ConnectSulfurAndMakeVirtualProton
	Add a connection to the residue's sulfur and make a virtual proton to track the position of the connection atom. More...
class	CopyEdge
class	CopyVertex
class	DeleteActCoordAtom
	Delete an act coord atom Added by Andrew M. Watkins in April 2015. More...
class	DeleteAtom
	delete an atom More...
class	DeleteChildProton
	delete child proton More...
class	DeleteMetalbindingAtom
	Delete a metal binding atom Added by Andrew M. Watkins in April 2015. More...
class	DeleteProperty
	delete a property from ResidueType Added by Andy M. Chen in June 2009 This is needed for deleting properties, which occurs in certain PTM's (e.g. methylation) Rewritten by Vikram K. Mulligan on 25 Aug. 2016 to use enums wherever possible for speed. More...
class	DeleteTerminalChi
	Delete terminal chi angle Added by Andrew M. Watkins in April 2015. More...
class	DeleteVariantType
	A patch operation for deleting a VariantType from a ResidueType. More...
class	ElectronConfiguration
	describes the electron configuration of atoms More...
class	Element
	stores element properties More...
class	ElementSet
	A set of Bcl Elements. More...
class	GlobalResidueTypeSet
	A collection of ResidueType defined. More...
class	GraphvizPropertyWriter
	Callback class for write_graphviz - outputs properties for the nodes and edges. More...
class	HeavyAtomFilter
	The filter responsible for obtaining all heavy atoms. More...
class	HeavyAtomWithHydrogensFilter
	The filter responsible for finding heavy atoms with hydrogens. More...
class	HeavyAtomWithPolarHydrogensFilter
	The filter responsible for obtaining all heavy atoms with polar hydrogens attached to them. More...
class	HydrogenAtomFilter
	The filter responsible for all hydrogens. More...
class	ICoorAtomID
	Atom 's ID in internal coordinates in a ResidueType. More...
class	IdealBondLengthSet
	A set of Elements. More...
class	MergeBehaviorManager
class	Metapatch
	A class patching basic ResidueType to create variant types, containing multiple PatchCase. More...
class	MMAtomType
	Basic MM atom type. More...
class	MMAtomTypeSet
	A set of MMAtomTypes. More...
class	MutableChiRecord
	A class containing bundled info about chis. More...
class	MutableICoorRecord
	A basic class containing basic info of internal coordinates needed for building an atom within a ResidueType This is a simplified representation, used for MutableResidueType. It contains all the information, but is intended to be somewhat easier to update for added/deleted atoms than the standard AtomICoor. More...
class	MutableResidueConnection
	A simple class marking atoms at inter-residue connections. More...
class	MutableResidueType
	A class for defining a type of residue, modifiable version. More...
class	NCAARotLibBBTorsions
	Set the mainchain torsion indices that a noncanonical rotamer library depends upon. More...
class	NCAARotLibNumRotamerBins
	Set the number of rotamer bins per chi for an NCAA that is not in dunbrack. More...
class	NCAARotLibPath
	set the path to a rotamer library for an NCAA that is not in dunbrack More...
class	Orbital
	basic chemical atom More...
class	Patch
	A class patching basic ResidueType to create variant types, containing multiple PatchCase. More...
class	PatchCase
	A single case of a patch, eg proline Nterminus is a case of NtermProteinFull. More...
class	PatchOperation
	A single operation that needs to be applied in a residue patch. More...
class	PolarHydrogenFilter
	The filter responsible for all polar hydrogens. More...
class	PoseResidueTypeSet
	A ResidueTypeSet which can be cached in the Pose. More...
class	PrependMainchainAtom
	add a mainchain atom before the first mainchain atom More...
class	RamaPreproFilename
	Set the filenames for RamaPrePro scoring tables. More...
class	RamaPreproResname
	Set the residue name for RamaPrePro scoring tables. More...
class	RealFilter
	A filtered graph that doesn't contain fake/virtual atoms and fake/virtual bonds. More...
class	RedefineChi
	Redefine a chi angle Added by Andy M. Chen in June 2009 This is needed for certain PTMs. More...
class	RemoveRotamerSpecifications
	Remove existing rotamer specifications (of any type). More...
class	RenameAtom
	rename atom More...
class	ReplaceMainchainAtom
	replace a mainchain atom More...
class	ReplaceProtonWithBromine
	replace proton with bromine More...
class	ReplaceProtonWithChlorine
	replace proton with chlorine More...
class	ReplaceProtonWithEthyl
	replace proton with ethyl More...
class	ReplaceProtonWithFluorine
	replace proton with fluorine More...
class	ReplaceProtonWithHydroxyl
	replace proton with hydroxyl More...
class	ReplaceProtonWithIodine
	replace proton with iodine More...
class	ReplaceProtonWithMethoxy
	replace proton with methoxy More...
class	ReplaceProtonWithMethyl
	replace proton with methyl More...
class	ReplaceProtonWithTrifluoromethyl
	replace proton with trifluoromethyl More...
class	RerootEdgeSorter
	Edge sorting: Return true if we should prefer edge1 over edge2. More...
class	RerootRestypeVisitor
class	ResConnID
	The ResConnID could more properly be called the ResidueConnector. It stores the data necessary to describe how one ResidueConnection on a conformation::Residue is connected to the rest of the structure (Pose), by listing the other Residue's index and the ResidueConnection index. More...
class	ResetBondLength
	A patch operation for resetting the length of a bond within a ResidueType. More...
class	ResidueConnection
	A simple class marking atoms at inter-residue connections. More...
class	ResidueDatabaseIO
class	ResidueProperties
class	ResidueType
	A class for defining a type of residue. More...
class	ResidueTypeBase
	A base class for definiting types of residues. More...
class	ResidueTypeFinder
class	ResidueTypeKinWriter
class	ResidueTypeSelector
	A class picking out a subset of ResidueType by multiple criteria. More...
class	ResidueTypeSelectorSingle
	A base class for defining a ResidueTypeSelector by a single criterion. More...
class	ResidueTypeSet
	An abstract interface to a set of ResidueTypes. More...
class	ResidueTypeSetCache
struct	RestypeDestructionEvent
	special signal that the ResidueType is getting destroyed More...
class	RigidDistanceVisitor
	Utility visitor for find_nbr_dist Will only traverse those atoms in the "rigid" portion of graph around the starting atom. "Rigid" includes direct neighbors and atoms connected by non-rotatable bonds e.g. all rings, all double/triple bonds, methyl groups, single atoms, etc. More...
class	Selector_AA
	Does the residue belong to ANY of these AAs? More...
class	Selector_BASENAME
	Does the residue have to ANY of these basenames? More...
class	Selector_CMDFLAG
	Is a certain string in the command-line option -chemical:allow_patch present ? this selector does actually not depend on the residuetype it is queried for. More...
class	Selector_HAS_ATOMS
	Does the residue have ALL of the listed atoms?: More...
class	Selector_MATCH_VARIANTS
	Does the residue have ALL of the variant types and no more. More...
class	Selector_NAME1
	Does the residue belong to ANY of these one-letter codes? More...
class	Selector_NAME3
	Does the residue have ANY of these three-letter codes? More...
class	Selector_NO_VARIANTS
	Does the residue have NO variant types? More...
class	Selector_PROPERTY
	Does the residue have ANY of these properties? More...
class	Selector_UPPER_ATOM
	Does the main chain of this residue follow from the given position label? More...
class	Selector_VARIANT_TYPE
	Does the residue have ANY of variant types? More...
class	Set_AA
	set residue's aa More...
class	SetAllAtomsRepulsive
	set the residue neighbor radius More...
class	SetAtomicCharge
	set an atom's charge More...
class	SetAtomType
	set atom's chemical type More...
class	SetBackboneHeavyatom
	set an atom as backbone heavy atom More...
class	SetDisulfideAtomName
	set an atom as this residue's disulfide forming atom More...
class	SetFormalCharge
	A patch operation for setting the formal charge of a ResidueType's atom. More...
class	SetICoor
	set an atom's AtomICoord More...
class	SetInterchangeabilityGroup_String
	set the interchangeability_group string for a ResidueType More...
class	SetIO_String
	set residue's name1 and name3 More...
class	SetMMAtomType
	set atom's MM chemical type More...
class	SetNbrAtom
	set the residue neighbor atom More...
class	SetNbrRadius
	set the residue neighbor radius More...
class	SetNetFormalCharge
	A patch operation for setting the net formal charge of a whole ResidueType. More...
class	SetOrientAtom
	Set orient atom selection mode. More...
class	SetPolymerConnectAtom
	set an atom as polymer connection More...
class	SetVirtualShadow
	set virtual shadow atoms More...
class	VDDistanceMatrix
	Utility class for VD-indexed matrix. More...
class	VirtualizeAll
	virtualize all More...
class	VirtualizeSidechain
	virtualize sidechain More...

Typedefs
typedef utility::pointer::shared_ptr < Adduct >	AdductOP
typedef std::map< std::string, int >	AdductMap
typedef utility::pointer::shared_ptr < Atom >	AtomOP
typedef utility::pointer::shared_ptr < Atom const >	AtomCOP
typedef utility::pointer::weak_ptr < Atom >	AtomAP
typedef utility::vector1< AtomOP >	AtomOPs
typedef utility::vector1< AtomCOP >	AtomCOPs
typedef utility::vector1< AtomAP >	AtomAPs
using	AtomMemo = basic::datacache::DataMapObj< std::set< std::string > >
using	AtomMemoOP = utility::pointer::shared_ptr< AtomMemo >
typedef utility::pointer::shared_ptr < AtomProperties >	AtomPropertiesOP
typedef utility::pointer::shared_ptr < AtomProperties const >	AtomPropertiesCOP
typedef utility::pointer::shared_ptr < AtomTypeDatabaseIO > AtomTypeDatabaseIOOP typedef utility::pointer::shared_ptr < AtomTypeDatabaseIO const >	AtomTypeDatabaseIOCOP
typedef utility::pointer::weak_ptr < AtomTypeSet >	AtomTypeSetAP
typedef utility::pointer::weak_ptr < AtomTypeSet const >	AtomTypeSetCAP
typedef utility::pointer::shared_ptr < AtomTypeSet >	AtomTypeSetOP
typedef utility::pointer::shared_ptr < AtomTypeSet const >	AtomTypeSetCOP
typedef utility::pointer::shared_ptr < AutomorphismIterator >	AutomorphismIteratorOP
typedef utility::pointer::shared_ptr < AutomorphismIterator const >	AutomorphismIteratorCOP
typedef utility::pointer::shared_ptr < CacheableResidueTypeSets >	CacheableResidueTypeSetsOP
typedef utility::pointer::shared_ptr < CacheableResidueTypeSets const >	CacheableResidueTypeSetsCOP
typedef utility::pointer::shared_ptr < Element >	ElementOP
typedef utility::pointer::shared_ptr < Element const >	ElementCOP
typedef utility::pointer::weak_ptr < ElementSet >	ElementSetAP
typedef utility::pointer::weak_ptr < ElementSet const >	ElementSetCAP
typedef utility::pointer::shared_ptr < ElementSet >	ElementSetOP
typedef utility::pointer::shared_ptr < ElementSet const >	ElementSetCOP
typedef utility::pointer::shared_ptr < GlobalResidueTypeSet >	GlobalResidueTypeSetOP
typedef utility::pointer::shared_ptr < GlobalResidueTypeSet const >	GlobalResidueTypeSetCOP
typedef utility::pointer::weak_ptr < GlobalResidueTypeSet const >	GlobalResidueTypeSetCAP
typedef std::map < core::chemical::VD, core::kinematics::tree::AtomOP >	VdTreeatomMap
typedef utility::pointer::weak_ptr < IdealBondLengthSet >	IdealBondLengthSetAP
typedef utility::pointer::weak_ptr < IdealBondLengthSet const >	IdealBondLengthSetCAP
typedef utility::pointer::shared_ptr < IdealBondLengthSet >	IdealBondLengthSetOP
typedef utility::pointer::shared_ptr < IdealBondLengthSet const >	IdealBondLengthSetCOP
typedef int	AtomTypeIndex
typedef Real	BondLength
typedef utility::pointer::shared_ptr < MergeBehaviorManager >	MergeBehaviorManagerOP
typedef utility::pointer::shared_ptr < MergeBehaviorManager const >	MergeBehaviorManagerCOP
typedef utility::pointer::shared_ptr < Metapatch >	MetapatchOP
typedef utility::pointer::shared_ptr < Metapatch const >	MetapatchCOP
typedef utility::pointer::shared_ptr < MMAtomType >	MMAtomTypeOP
typedef utility::pointer::weak_ptr < MMAtomTypeSet >	MMAtomTypeSetAP
typedef utility::pointer::weak_ptr < MMAtomTypeSet const >	MMAtomTypeSetCAP
typedef utility::pointer::shared_ptr < MMAtomTypeSet >	MMAtomTypeSetOP
typedef utility::pointer::shared_ptr < MMAtomTypeSet const >	MMAtomTypeSetCOP
typedef utility::pointer::shared_ptr < MutableChiRecord >	MutableChiRecordOP
typedef utility::pointer::shared_ptr < MutableChiRecord const >	MutableChiRecordCOP
typedef utility::pointer::shared_ptr < MutableICoorRecord >	MutableICoorRecordOP
typedef utility::pointer::shared_ptr < MutableICoorRecord const >	MutableICoorRecordCOP
typedef utility::pointer::shared_ptr < MutableResidueType >	MutableResidueTypeOP
typedef utility::pointer::shared_ptr < MutableResidueType const >	MutableResidueTypeCOP
typedef utility::vector1 < MutableResidueTypeOP >	MutableResidueTypeOPs
typedef utility::vector1 < MutableResidueTypeCOP >	MutableResidueTypeCOPs
typedef utility::pointer::shared_ptr < Orbital >	OrbitalOP
typedef utility::pointer::shared_ptr < Orbital const >	OrbitalCOP
typedef utility::vector1 < OrbitalOP >	OrbitalOPs
typedef utility::vector1 < OrbitalCOP >	OrbitalCOPs
typedef utility::pointer::shared_ptr < PatchCase >	PatchCaseOP
typedef utility::pointer::shared_ptr < Patch >	PatchOP
typedef utility::pointer::shared_ptr < Patch const >	PatchCOP
typedef utility::pointer::shared_ptr < PatchOperation >	PatchOperationOP
typedef utility::pointer::shared_ptr < PoseResidueTypeSet >	PoseResidueTypeSetOP
typedef utility::pointer::shared_ptr < PoseResidueTypeSet const >	PoseResidueTypeSetCOP
typedef boost::undirected_graph< Atom, Bond >	ResidueGraph
typedef ResidueGraph::vertex_descriptor	VD
typedef ResidueGraph::edge_descriptor	ED
typedef utility::vector1< VD >	VDs
typedef boost::graph_traits < ResidueGraph > ::vertex_iterator	VIter
typedef std::pair< VIter, VIter >	VIterPair
typedef boost::graph_traits < ResidueGraph > ::edge_iterator	EIter
typedef std::pair< EIter, EIter >	EIterPair
typedef boost::graph_traits < ResidueGraph > ::out_edge_iterator	OutEdgeIter
typedef std::pair< OutEdgeIter, OutEdgeIter >	OutEdgeIterPair
typedef boost::graph_traits < ResidueGraph > ::adjacency_iterator	AdjacentIter
typedef std::pair < AdjacentIter, AdjacentIter >	AdjacentIterPair
typedef std::map< std::string, VD >	NameVDMap
typedef std::pair< std::string, VD >	NameVDPair
typedef std::pair < NameVDMap::iterator, bool >	NameVDInserted
typedef boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS, boost::property < boost::vertex_name_t, core::chemical::VD > , boost::property < boost::edge_name_t, core::chemical::ED > >	LightWeightResidueGraph
typedef boost::graph_traits < LightWeightResidueGraph > ::vertex_descriptor	lwrg_VD
typedef boost::graph_traits < LightWeightResidueGraph > ::edge_descriptor	lwrg_ED
typedef boost::graph_traits < LightWeightResidueGraph > ::vertex_iterator	lwrg_vd_iter
typedef std::pair < lwrg_vd_iter, lwrg_vd_iter >	lwrg_vd_pair_iter
typedef boost::graph_traits < LightWeightResidueGraph > ::edge_iterator	lwrg_edge_iter
typedef boost::graph_traits < LightWeightResidueGraph > ::out_edge_iterator	lwrg_out_edge_iter
typedef std::pair < lwrg_out_edge_iter, lwrg_out_edge_iter >	lwrg_out_edge_iter_pair
typedef utility::pointer::shared_ptr < ResidueProperties >	ResiduePropertiesOP
typedef utility::pointer::shared_ptr < ResidueProperties const >	ResiduePropertiesCOP
typedef boost::filtered_graph < ResidueGraph, RealFilter, RealFilter >	RealResidueGraph
typedef RealResidueGraph::vertex_descriptor	RealResidueVD
typedef RealResidueGraph::edge_descriptor	RealResidueED
typedef boost::graph_traits < RealResidueGraph > ::vertex_iterator	RealResidueVIter
typedef boost::graph_traits < RealResidueGraph > ::edge_iterator	RealResidueEIter
typedef boost::graph_traits < RealResidueGraph > ::out_edge_iterator	RealResidueOutEdgeIter
typedef std::pair < RealResidueOutEdgeIter, RealResidueOutEdgeIter >	RealResidueOutEdgeIterPair
typedef std::pair < RealResidueVIter, RealResidueVIter >	RealResidueVIterPair
typedef boost::graph_traits < RealResidueGraph > ::adjacency_iterator	RealResidueAdjacentIter
typedef std::pair < RealResidueAdjacentIter, RealResidueAdjacentIter >	RealResidueAdjacentIterPair
typedef boost::filtered_graph < ResidueGraph, boost::keep_all, HeavyAtomFilter >	HeavyAtomGraph
typedef HeavyAtomGraph::vertex_descriptor	HeavyAtomVD
typedef HeavyAtomGraph::edge_descriptor	HeavyAtomED
typedef boost::graph_traits < HeavyAtomGraph > ::vertex_iterator	HeavyAtomVIter
typedef boost::graph_traits < HeavyAtomGraph > ::edge_iterator	HeavyAtomEIter
typedef boost::graph_traits < HeavyAtomGraph > ::out_edge_iterator	HeavyAtomOutEdgeIter
typedef std::pair < HeavyAtomOutEdgeIter, HeavyAtomOutEdgeIter >	HeavyAtomOutEdgeIterPair
typedef std::pair < HeavyAtomVIter, HeavyAtomVIter >	HeavyAtomVIterPair
typedef boost::filtered_graph < ResidueGraph, boost::keep_all, AcceptorAtomFilter >	AcceptorAtomGraph
typedef boost::graph_traits < AcceptorAtomGraph > ::vertex_iterator	AcceptorAtomVIter
typedef boost::graph_traits < AcceptorAtomGraph > ::edge_iterator	AcceptorAtomEIter
typedef std::pair < AcceptorAtomVIter, AcceptorAtomVIter >	AcceptorAtomVIterPair
typedef boost::filtered_graph < ResidueGraph, boost::keep_all, HeavyAtomWithPolarHydrogensFilter >	HeavyAtomWithPolarHydrogensGraph
typedef boost::graph_traits < HeavyAtomWithPolarHydrogensGraph > ::vertex_iterator	HeavyAtomWithPolarHydrogensVIter
typedef boost::graph_traits < HeavyAtomWithPolarHydrogensGraph > ::edge_iterator	HeavyAtomWithPolarHydrogensEIter
typedef std::pair < HeavyAtomWithPolarHydrogensVIter, HeavyAtomWithPolarHydrogensVIter >	HeavyAtomWithPolarHydrogensVIterPair
typedef boost::filtered_graph < ResidueGraph, boost::keep_all, HeavyAtomWithHydrogensFilter >	HeavyAtomWithHydrogensGraph
typedef boost::graph_traits < HeavyAtomWithHydrogensGraph > ::vertex_iterator	HeavyAtomWithHydrogensVIter
typedef boost::graph_traits < HeavyAtomWithHydrogensGraph > ::edge_iterator	HeavyAtomWithHydrogensEIter
typedef std::pair < HeavyAtomWithHydrogensVIter, HeavyAtomWithHydrogensVIter >	HeavyAtomWithHydrogensVIterPair
typedef boost::filtered_graph < ResidueGraph, boost::keep_all, HydrogenAtomFilter >	HydrogenAtomGraph
typedef HydrogenAtomGraph::vertex_descriptor	HydrogenAtomVD
typedef HydrogenAtomGraph::edge_descriptor	HydrogenAtomED
typedef boost::graph_traits < HydrogenAtomGraph > ::vertex_iterator	HydrogenAtomVIter
typedef boost::graph_traits < HydrogenAtomGraph > ::edge_iterator	HHydrogenAtomEIter
typedef boost::graph_traits < HydrogenAtomGraph > ::out_edge_iterator	HydrogenAtomOutEdgeIter
typedef std::pair < HydrogenAtomOutEdgeIter, HydrogenAtomOutEdgeIter >	HydrogenAtomOutEdgeIterPair
typedef std::pair < HydrogenAtomVIter, HydrogenAtomVIter >	HydrogenAtomVIterPair
typedef boost::filtered_graph < ResidueGraph, boost::keep_all, AromaticAtomFilter >	AromaticAtomGraph
typedef boost::graph_traits < AromaticAtomGraph > ::vertex_iterator	AromaticAtomVIter
typedef boost::graph_traits < AromaticAtomGraph > ::edge_iterator	AromaticAtomEIter
typedef std::pair < AromaticAtomVIter, AromaticAtomVIter >	AromaticAtomVIterPair
typedef boost::filtered_graph < ResidueGraph, boost::keep_all, PolarHydrogenFilter >	PolarHydrogenGraph
typedef boost::graph_traits < PolarHydrogenGraph > ::vertex_iterator	PolarHydrogenVIter
typedef boost::graph_traits < PolarHydrogenGraph > ::edge_iterator	PolarHydrogenEIter
typedef std::pair < PolarHydrogenVIter, PolarHydrogenVIter >	PolarHydrogenVIterPair
typedef boost::filtered_graph < ResidueGraph, boost::keep_all, APolarHydrogenFilter >	APolarHydrogenGraph
typedef boost::graph_traits < APolarHydrogenGraph > ::vertex_iterator	APolarHydrogenVIter
typedef boost::graph_traits < APolarHydrogenGraph > ::edge_iterator	APolarHydrogenEIter
typedef std::pair < APolarHydrogenVIter, APolarHydrogenVIter >	APolarHydrogenVIterPair
typedef utility::pointer::weak_ptr < ResidueType >	ResidueTypeAP
typedef utility::pointer::weak_ptr < ResidueType const >	ResidueTypeCAP
typedef utility::pointer::shared_ptr < ResidueType >	ResidueTypeOP
typedef utility::pointer::shared_ptr < ResidueType const >	ResidueTypeCOP
typedef utility::vector1 < ResidueTypeOP >	ResidueTypeOPs
typedef utility::vector1 < ResidueTypeCAP >	ResidueTypeCAPs
typedef utility::vector1 < ResidueTypeCOP >	ResidueTypeCOPs
typedef utility::vector1< Size >	AtomIndices
typedef utility::vector1< Size >	OrbitalIndices
typedef utility::keys::Key2Tuple< Size, Size >	two_atom_set
typedef utility::keys::Key3Tuple< Size, Size, Size >	three_atom_set
typedef utility::keys::Key3Tuple< Size, Size, Size >	bondangle_atom_set
typedef utility::keys::Key4Tuple< Size, Size, Size, Size >	dihedral_atom_set
typedef utility::pointer::weak_ptr < ResidueTypeBase >	ResidueTypeBaseAP
typedef utility::pointer::weak_ptr < ResidueTypeBase const >	ResidueTypeBaseCAP
typedef utility::pointer::shared_ptr < ResidueTypeBase >	ResidueTypeBaseOP
typedef utility::pointer::shared_ptr < ResidueTypeBase const >	ResidueTypeBaseCOP
typedef utility::pointer::shared_ptr < ResidueTypeFinder >	ResidueTypeFinderOP
typedef utility::pointer::shared_ptr < ResidueTypeFinder const >	ResidueTypeFinderCOP
typedef utility::pointer::shared_ptr < ResidueTypeKinWriter >	ResidueTypeKinWriterOP
typedef utility::pointer::shared_ptr < ResidueTypeKinWriter const >	ResidueTypeKinWriterCOP
typedef utility::pointer::shared_ptr < ResidueTypeSelectorSingle >	ResidueTypeSelectorSingleOP
typedef utility::pointer::shared_ptr < ResidueTypeSelector >	ResidueTypeSelectorOP
typedef utility::pointer::shared_ptr < ResidueTypeSet >	ResidueTypeSetOP
typedef utility::pointer::shared_ptr < ResidueTypeSet const >	ResidueTypeSetCOP
typedef utility::pointer::weak_ptr < ResidueTypeSet const >	ResidueTypeSetCAP
typedef utility::pointer::shared_ptr < ResidueTypeSetCache >	ResidueTypeSetCacheOP
typedef utility::pointer::shared_ptr < ResidueTypeSetCache const >	ResidueTypeSetCacheCOP
typedef std::pair< AA, std::pair< utility::vector1 < std::string > , utility::vector1 < VariantType > > >	AA_VariantsExceptions
typedef std::tuple < ResidueTypeCOP, utility::vector1< VariantType > , utility::vector1 < std::string > , utility::vector1 < VariantType >, bool >	Restype_Variants_VariantStrings_Exceptions
	A type for key lookup. This consists of a BASE TYPE ResidueTypeCOP, a list of variants (by enum), a list of custom variants (by string), a list of variant exceptions (by enum), and a bool for whether to turn off metapatches. More...

Enumerations
enum	AA {   aa_none = 0, aa_ala = 1, first_l_aa = aa_ala, aa_cys,   aa_asp, aa_glu, aa_phe, aa_gly,   aa_his, aa_ile, aa_lys, aa_leu,   aa_met, aa_asn, aa_pro, aa_gln,   aa_arg, aa_ser, aa_thr, aa_val,   aa_trp, aa_tyr, num_canonical_aas = aa_tyr, na_ade,   first_DNA_aa = na_ade, na_cyt, na_gua, na_thy,   last_DNA_aa = na_thy, na_rgu, na_rad, na_rcy,   na_ura, aa_dal, first_D_aa = aa_dal, aa_dcs,   aa_das, aa_dgu, aa_dph, aa_dhi,   aa_dil, aa_dly, aa_dle, aa_dme,   aa_dan, aa_dpr, aa_dgn, aa_dar,   aa_dse, aa_dth, aa_dva, aa_dtr,   aa_dty, last_D_aa = aa_dty, aa_b3a, first_beta3_aa = aa_b3a,   aa_b3c, aa_b3d, aa_b3e, aa_b3f,   aa_b3g, aa_b3h, aa_b3i, aa_b3k,   aa_b3l, aa_b3m, aa_b3n, aa_b3p,   aa_b3q, aa_b3r, aa_b3s, aa_b3t,   aa_b3v, aa_b3w, aa_b3y, aa_b3cisACPC,   aa_b3transACPC, aa_b3cisACHC, last_beta3_aa = aa_b3cisACHC, na_lra,   na_lrc, na_lrg, na_lur, ou3_ala,   first_oligourea = ou3_ala, ou3_cys, ou3_asp, ou3_glu,   ou3_phe, ou3_gly, ou3_his, ou3_ile,   ou3_lys, ou3_leu, ou3_met, ou3_asn,   ou3_pro, ou3_gln, ou3_arg, ou3_ser,   ou3_thr, ou3_val, ou3_trp, ou3_tyr,   ou3_aib, last_oligourea = ou3_aib, aa_h2o, aa_vrt,   aa_unp, aa_unk, num_aa_types = aa_unk }
	enumeration for amino acids and nucleotides types with the total number as num_aa_types More...
enum	ICoordAtomIDType { ICoordAtomIDType::INTERNAL = 1, ICoordAtomIDType::POLYMER_LOWER, ICoordAtomIDType::POLYMER_UPPER, ICoordAtomIDType::CONNECT }
	ICoordAtomIDType. More...
enum	AtomProperty {   NO_ATOM_PROPERTY = 0, FIRST_ATOM_PROPERTY = 1, H_DONOR, H_ACCEPTOR,   POLAR_HYDROGEN, AROMATIC_HYDROGEN, HAS_ORBITALS, VIRTUAL_ATOM,   REPULSIVE, AROMATIC_CARBON_WITH_FREE_VALENCE, N_ATOM_PROPERTIES = AROMATIC_CARBON_WITH_FREE_VALENCE }
	Enumerators for all the properties that can be assigned to a chemical::Atom. More...
enum	BondName {   UnknownBond =0, SingleBond =1, DoubleBond =2, TripleBond =3,   AromaticBond =4, OrbitalBond =5, PseudoBond =99 }
enum	BondOrder {   UnknownBondOrder =0, SingleBondOrder =1, DoubleBondOrder =2, TripleBondOrder =3,   OrbitalBondOrder, DeleteBondOrder, PseudoBondOrder =99 }
enum	BondConjugability { UnknownConjugability, NotConjugableBond, ConjugableBond }
	As with the BCL, bond conjugability is more about the atom types on either end of the bond than about the bond itself. A conjugatable bond is one where it is known that the atoms on both sides of the bond can participate in a conjugated system. Double, triple and aromatic bonds are always conjugatable, and single bonds are conjugatable if both atoms are in other triple, double, or aromatic systems. More...
enum	BondRingness { UnknownRingness, BondNotInRing, BondInRing }
enum	BondAromaticity { UnknownAromaticity, NonaromaticBond, IsAromaticBond }
	Proper aromaticity implies participation in a 4n+2 electron ring system. For simple single-double alternation, see conjugatable bond. More...
enum	BondIsometry { UnknownIsometry, NoBondIsometry, EIsometry, ZIsometry }
enum	TypeSetMode {   INVALID_t = 0, FULL_ATOM_t = 1, DEFAULT_t, CENTROID_t,   CENTROID_ROT_t, HYBRID_FA_STANDARD_CENTROID_t, COARSE_RNA_t, MIXED_t,   TYPE_SET_MODES_LENGTH = MIXED_t }
	A type set category is the "compatibility class" of a type set. That is, all e.g. ResidueTypes of a given TypeSetMode should be "compatible" with the scale of modeling resolution, indepenent of if they're in the same ResidueTypeSet. More...
enum	GreekDistance {   PRIMARY_ATOM = 0, ALPHA_ATOM, BETA_ATOM, GAMMA_ATOM,   DELTA_ATOM, EPSILON_ATOM, ZETA_ATOM, ETA_ATOM,   THETA_ATOM, IOTA_ATOM, KAPPA_ATOM, LAMBDA_ATOM,   MU_ATOM, NU_ATOM, XI_ATOM, OMICRON_ATOM,   PI_ATOM, SIGMA_ATOM, TAU_ATOM, UPSILON_ATOM,   PHI_ATOM, CHI_ATOM, PSI_ATOM, NA_GREEK_DISTANCE = 1023 }
	Enumerators for the Greek distance from the atom with the functional group of highest priority. More...
enum	merge_residue_behavior { mrb_do_not_merge, mrb_merge_w_prev, mrb_merge_w_next }
enum	Ancestor { anc_parent, anc_grandparent, anc_greatgrandparent }
	Change the parent, grandparent, or great-grandparent of an atom. More...
enum	ResidueProperty {   NO_PROPERTY = 0, FIRST_PROPERTY = 1, POLYMER = 1, LIGAND,   PROTEIN, CANONICAL_AA, CANONICAL_NUCLEIC, DNA,   RNA, TNA, PNA, PEPTOID,   OLIGOUREA, ARAMID, ORTHO_ARAMID, META_ARAMID,   PARA_ARAMID, PRE_METHYLENE_ORTHO_ARAMID, PRE_METHYLENE_META_ARAMID, PRE_METHYLENE_PARA_ARAMID,   POST_METHYLENE_ORTHO_ARAMID, POST_METHYLENE_META_ARAMID, POST_METHYLENE_PARA_ARAMID, PRE_METHYLENE_POST_METHYLENE_ORTHO_ARAMID,   PRE_METHYLENE_POST_METHYLENE_META_ARAMID, PRE_METHYLENE_POST_METHYLENE_PARA_ARAMID, CARBOHYDRATE, LIPID,   TERPENE, NUCLEOTIDE_DIPHOSPHATE, SRI, TRIAZOLE_LINKER,   METAL, SURFACE, WATER, TP3,   VIRTUALIZABLE_BY_PACKER, SOLVENT, VIRTUAL_RESIDUE, VRT1,   INVERTED_VIRTUAL_RESIDUE, LOWER_TERMINUS, UPPER_TERMINUS, BRANCH_POINT,   TERMINUS, LOWERTERM_TRUNC, UPPERTERM_TRUNC, COARSE,   ADDUCT, SC_ORBITALS, FRAGMENT, UPPERTERM_CAP,   LOWERTERM_CAP, POLAR, HYDROPHOBIC, CHARGED,   NEGATIVE_CHARGE, POSITIVE_CHARGE, AROMATIC, ALIPHATIC,   CYCLIC, METALBINDING, SIDECHAIN_THIOL, DISULFIDE_BONDED,   ELECTROPHILE, SIDECHAIN_AMINE, N_METHYLATED, MEMBRANE,   PHOSPHONATE, PHOSPHONATE_UPPER, ACETYLATED_NTERMINUS, METHYLATED_CTERMINUS,   DIMETHYLATED_CTERMINUS, ALPHA_AA, BETA_AA, GAMMA_AA,   L_AA, D_AA, ACHIRAL_BACKBONE, ACHIRAL_SIDECHAIN,   R_PEPTOID, S_PEPTOID, TAUTOMER, PURINE,   PYRIMIDINE, L_RNA, D_RNA, METHYLATED_NA,   TRIOSE, TETROSE, PENTOSE, HEXOSE,   HEPTOSE, OCTOSE, NONOSE, ALDOSE,   KETOSE, L_SUGAR, D_SUGAR, OXIROSE,   OXETOSE, FURANOSE, PYRANOSE, SEPTANOSE,   ALPHA_SUGAR, BETA_SUGAR, SIALIC_ACID, C1_MODIFIED,   C2_MODIFIED, C3_MODIFIED, C4_MODIFIED, C5_MODIFIED,   C6_MODIFIED, C7_MODIFIED, C8_MODIFIED, C9_MODIFIED,   GLYCOSIDE, ALDONIC_ACID, URONIC_ACID, DEOXY_SUGAR,   AMINO_SUGAR, ACETYLAMINO_SUGAR, ACETYL_SUGAR, R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR,   PHOSPHORYLATED_SUGAR, SULFATED_SUGAR, SULFOAMINO_SUGAR, THIO_SUGAR,   C_METHYLATED_SUGAR, PHOSPHATE, SPINLABEL, DIAMAGNETIC,   PARAMAGNETIC, N_PROPERTIES = PARAMAGNETIC }
	Enumerators for all the properties that can be assigned to a ResidueType. More...
enum	Hybridization {   SP2_HYBRID = 1, SP3_HYBRID, RING_HYBRID, UNKNOWN_HYBRID,   HYBRID_MAX = UNKNOWN_HYBRID }
enum	VariantType {   NO_VARIANT = 0, FIRST_VARIANT = 1, UPPER_TERMINUS_VARIANT = 1, LOWER_TERMINUS_VARIANT,   UPPERTERM_TRUNC_VARIANT, LOWERTERM_TRUNC_VARIANT, PHOSPHONATE_UPPER_VARIANT, CUTPOINT_LOWER,   CUTPOINT_UPPER, NTERM_CONNECT, CTERM_CONNECT, DISULFIDE,   SC_BRANCH_POINT, C1_BRANCH_POINT, C2_BRANCH_POINT, C3_BRANCH_POINT,   C4_BRANCH_POINT, C5_BRANCH_POINT, C6_BRANCH_POINT, C7_BRANCH_POINT,   C8_BRANCH_POINT, C9_BRANCH_POINT, SIDECHAIN_CONJUGATION, SG_CONNECT,   NE2_CONNECT, ZN_CONNECT, VIRTUAL_METAL_CONJUGATION, METHYLATED_NTERM_VARIANT,   ACETYLATED_NTERMINUS_VARIANT, METHYLATED_CTERMINUS_VARIANT, DIMETHYLATED_CTERMINUS_VARIANT, OOP_PRE,   OOP_POST, HBS_PRE, HBS_POST, A3B_HBS_PRE,   A3B_HBS_POST, CA_CONNECT, CA_CONNECT2, CA_CONNECT3,   CA_CONNECT4, CA_CONNECT5, CA_CONNECT6, CA_CONNECT7,   OE1_CONNECT, OE2_CONNECT, OD1_CONNECT, OD2_CONNECT,   O_CONNECT, OG_CONNECT, OG1_CONNECT, PROTONATED,   DEPROTONATED, ALTERNATIVE_PROTONATION, METHYLATION, DIMETHYLATION,   TRIMETHYLATION, ACETYLATION, PHOSPHORYLATION, SULFATION,   HYDROXYLATION, HYDROXYLATION1, HYDROXYLATION2, CARBOXYLATION,   DIIODINATION, N_METHYLATION, VIRTUAL_BB, VIRTUAL_SIDE_CHAIN,   VIRTUAL_RESIDUE_VARIANT, VIRTUAL_NTERM, VIRTUAL_PHOSPHATE, VIRTUAL_DNA_PHOSPHATE,   REPLS_BB, REPLONLY, REPL_PHOSPHATE, VIRTUAL_RIBOSE,   VIRTUAL_BACKBONE_EXCEPT_C1PRIME, VIRTUAL_BASE, VIRTUAL_BASE_HEAVY_ATOM, VIRTUAL_RNA_RESIDUE,   VIRTUAL_RNA_RESIDUE_EXCLUDE_PHOSPHATE, BULGE, VIRTUAL_O2PRIME_HYDROGEN, THREE_PRIME_END_OH,   THREE_PRIME_PHOSPHATE, THREE_PRIME_AZIDE, THREE_PRIME_DEOXY, FIVE_PRIME_END_OH,   FIVE_PRIME_THIOETHANOLAMINE_PHOSPHATE, FIVE_PRIME_END_PHOSPHATE, FIVE_PRIME_PHOSPHATE, FIVE_PRIME_RME_PHOSPHATE,   FIVEPRIME_CAP, THREE_PRIME_TWO_PRIME_CYCLIC_PHOSPHATE, DEOXY_O2PRIME, UPPER_CONNECTION_RNA,   THREE_PRIME_PACKABLE_PHOSPHATE, FIVE_PRIME_PACKABLE_PHOSPHATE, FIVE_PRIME_PACKABLE_TRIPHOSPHATE, PROTONATED_N1,   PROTONATED_N3, THREE_PRIME_FIVE_PRIME_METHYL_PHOSPHATE, BLOCK_STACK_ABOVE, BLOCK_STACK_BELOW,   N_ACETYLATION, N_FORMYLATION, C_METHYLAMIDATION, CTERM_AMIDATION,   C5_METHYLATED_NA, ALDONIC_ACID_VARIANT, C2_KETOALDONIC_ACID, C3_KETOALDONIC_ACID,   C4_KETOALDONIC_ACID, C5_KETOALDONIC_ACID, C6_KETOALDONIC_ACID, C7_KETOALDONIC_ACID,   C8_KETOALDONIC_ACID, URONIC_ACID_VARIANT, C1_DEOXY_SUGAR, C2_DEOXY_SUGAR,   C3_DEOXY_SUGAR, C4_DEOXY_SUGAR, C5_DEOXY_SUGAR, C6_DEOXY_SUGAR,   C7_DEOXY_SUGAR, C8_DEOXY_SUGAR, C9_DEOXY_SUGAR, C1_AMINO_SUGAR,   C2_AMINO_SUGAR, C3_AMINO_SUGAR, C4_AMINO_SUGAR, C5_AMINO_SUGAR,   C6_AMINO_SUGAR, C7_AMINO_SUGAR, C8_AMINO_SUGAR, C9_AMINO_SUGAR,   C1_ACETYLAMINO_SUGAR, C2_ACETYLAMINO_SUGAR, C3_ACETYLAMINO_SUGAR, C4_ACETYLAMINO_SUGAR,   C5_ACETYLAMINO_SUGAR, C6_ACETYLAMINO_SUGAR, C7_ACETYLAMINO_SUGAR, C8_ACETYLAMINO_SUGAR,   C9_ACETYLAMINO_SUGAR, C1_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C2_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C3_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR,   C4_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C5_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C6_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C7_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR,   C8_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C9_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C1_PHOSPHORYLATED_SUGAR, C2_PHOSPHORYLATED_SUGAR,   C3_PHOSPHORYLATED_SUGAR, C4_PHOSPHORYLATED_SUGAR, C5_PHOSPHORYLATED_SUGAR, C6_PHOSPHORYLATED_SUGAR,   C7_PHOSPHORYLATED_SUGAR, C8_PHOSPHORYLATED_SUGAR, C9_PHOSPHORYLATED_SUGAR, C1_SULFATED_SUGAR,   C2_SULFATED_SUGAR, C3_SULFATED_SUGAR, C4_SULFATED_SUGAR, C5_SULFATED_SUGAR,   C6_SULFATED_SUGAR, C7_SULFATED_SUGAR, C8_SULFATED_SUGAR, C9_SULFATED_SUGAR,   C1_SULFOAMINO_SUGAR, C2_SULFOAMINO_SUGAR, C3_SULFOAMINO_SUGAR, C4_SULFOAMINO_SUGAR,   C5_SULFOAMINO_SUGAR, C6_SULFOAMINO_SUGAR, C7_SULFOAMINO_SUGAR, C8_SULFOAMINO_SUGAR,   C9_SULFOAMINO_SUGAR, C1_THIO_SUGAR, C2_THIO_SUGAR, C3_THIO_SUGAR,   C4_THIO_SUGAR, C5_THIO_SUGAR, C6_THIO_SUGAR, C7_THIO_SUGAR,   C8_THIO_SUGAR, C9_THIO_SUGAR, C1_METHYLATED_SUGAR, C2_METHYLATED_SUGAR,   C3_METHYLATED_SUGAR, C4_METHYLATED_SUGAR, C5_METHYLATED_SUGAR, C6_METHYLATED_SUGAR,   C7_METHYLATED_SUGAR, C8_METHYLATED_SUGAR, C9_METHYLATED_SUGAR, C1_PHOSPHATE,   C2_PHOSPHATE, C3_PHOSPHATE, C4_PHOSPHATE, C5_PHOSPHATE,   C6_PHOSPHATE, C7_PHOSPHATE, C8_PHOSPHATE, C9_PHOSPHATE,   O1_ACETYL_SUGAR, O2_ACETYL_SUGAR, O3_ACETYL_SUGAR, O4_ACETYL_SUGAR,   O5_ACETYL_SUGAR, O6_ACETYL_SUGAR, O7_ACETYL_SUGAR, O8_ACETYL_SUGAR,   O9_ACETYL_SUGAR, METHYL_GLYCOSIDE, TRIAZOLAMERN, TRIAZOLAMERC,   CA2_COORDINATION, MG2_COORDINATION, CU2_COORDINATION, CO2_COORDINATION,   FE2_COORDINATION, FE3_COORDINATION, MN2_COORDINATION, LA3_COORDINATION,   LU3_COORDINATION, TB3_COORDINATION, TM3_COORDINATION, DY3_COORDINATION,   YB3_COORDINATION, ADDUCT_VARIANT, CENTROID_WITH_HA, SPECIAL_ROT,   SC_FRAGMENT, SHOVE_BB, N_VARIANTS = SHOVE_BB }
	Enumerators for all the ResidueType variants. More...

Functions
std::map< std::string, AA >	setup_name2aa ()
	setup the map that converts string name to AA enum More...
std::map< char, AA >	setup_oneletter2aa ()
	setup the map the converts one letter char to AA enum More...
std::map< std::string, AA > const &	name2aa ()
	map that converts string name to AA enum More...
std::map< char, AA > const &	oneletter2aa ()
	map that converts one letter char to AA enum More...
utility::vector1< std::string >	setup_aa2name ()
	setup the vector that maps AA enum to string name More...
utility::vector1< std::string > const &	aa2name ()
	vector that maps AA enum to string name More...
utility::vector1< char >	setup_aa2oneletter ()
	setup the vector that maps AA enum to one letter char More...
utility::vector1< char > const &	aa2oneletter ()
	vector that maps AA enum to one letter char More...
AA	aa_from_name (std::string const &name)
	Give an AA string 3-letter code, return its enum type. More...
AA	aa_from_one_or_three (std::string const &name)
bool	is_canonical_D_aa (AA const aa)
	Give an enum type, return true if and only if it is a D-amino acid that is the mirror image of a canonical alpha-L-amino acid. More...
bool	is_canonical_L_aa_or_gly (AA const aa)
	Given an enum type, return true if and only if it is a canonical L-amino acid. Rocco approves. More...
bool	is_canonical_beta3_aa (AA const aa)
	Given an enum type, return true if and only if it is a canonical beta-amino acid. More...
bool	is_aa_name_unknown (std::string const &name)
	Given aa three letter string, return true if it is an unknown aa. More...
AA	get_L_equivalent (AA const aa)
	Given an enum type for a D-amino acid with a canonical side-chain, return the enum type for the corresponding L-amino acid (or aa_unk if the corresponding L-amino acid cannot be determined). More...
AA	get_D_equivalent (AA const aa)
	Given an enum type for a L-amino acid with a canonical side-chain, return the enum type for the corresponding D-amino acid (or aa_unk if the corresponding D-amino acid cannot be determined). More...
std::istream &	operator>> (std::istream &is, AA &aa)
	input operator for AA enum type More...
std::ostream &	operator<< (std::ostream &os, AA const &aa)
	output operator for AA enum type More...
std::string	name_from_aa (AA aa)
	give a enum type and return the string name More...
char	oneletter_code_from_aa (AA aa)
	give a enum type and return the string name More...
AA	aa_from_oneletter_code (char onelettercode)
	give a 1 letter code and return the string name More...
bool	oneletter_code_specifies_aa (char onelettercode)
std::map< std::string, int >	parse_adduct_string (utility::options::StringVectorOption &add_vec)
	Convert input string to map of adducts->max usage. More...
void	error_check_requested_adducts (std::map< std::string, int > const &add_map, ResidueTypeCOPs const &rsd_types)
	Make sure any adducts requested actually exist. More...
MutableResidueTypeOP	apply_adducts_to_residue (ResidueType const &rsd, utility::vector1< bool > &add_mask)
	Apply adducts to residue using a boolean mask. More...
MutableResidueTypeOPs	create_adduct_combinations (ResidueType const &rsd, AdductMap ref_map, AdductMap count_map, utility::vector1< bool > add_mask, utility::vector1< Adduct >::const_iterator work_iter)
	Create correct combinations of adducts for a residue type. More...
void	error_check_requested_adducts (AdductMap const &add_map, ResidueTypeCOPs const &rsd_types)
	Make sure requested adducts exist in some residue. More...
static basic::Tracer	TR ("core.chemical.Atom")
std::ostream &	operator<< (std::ostream &out, Atom const &atom)
static basic::Tracer	TR ("core.chemical.AtomICoor")
ICoordAtomIDType	string_to_icoord_type (std::string const &)
	Convert a string designation into the corresponding ICoordAtomIDType enum. More...
Size	get_connection_number (std::string const &)
	Get the connection number from a string representing an CONNECT type (e.g. 4 from CONN4) More...
void	pretty_print_atomicoor (std::ostream &out, AtomICoor const &start, ResidueType const &rsd_type, core::Size indent, AtomMemoOP memo)
void	pretty_print_atomicoor (std::ostream &out, ResidueType const &rsd_type)
	print the icoord table starting at the root. More...
void	pretty_print_atomicoor (std::ostream &out, AtomICoor const &start, ResidueType const &rsd_type, core::Size indent=0)
	print the icoord table starting with the given icoord record More...
std::ostream &	operator<< (std::ostream &out, ICoordAtomIDType type)
std::ostream &	operator<< (std::ostream &output, AtomProperties const &object_to_output)
AtomProperty &	operator++ (AtomProperty &property)
AtomPropertiesOP	deep_copy (AtomProperties const &source)
std::ostream &	operator<< (std::ostream &out, const AtomType &atom_type)
bool	retype_is_aromatic (VD const &atom, ResidueGraph const &graph)
	An atom is aromatic if it has any aromatic bonds to a non-virtual atom. TODO: We need better aromatic ring detection. More...
void	rosetta_retype_fullatom (MutableResidueType &restype, bool preserve)
	Reassign Rosetta atom types based on the current fullatom heuristics. More...
static basic::Tracer	tr ("core.chemical.AtomTypeSet")
static basic::Tracer	TR ("core.chemical.Bond")
BondName	convert_to_BondName (std::string const &id)
std::ostream &	operator<< (std::ostream &out, Bond const &bond)
static basic::Tracer	TR ("core.chemical.bond_support")
gasteiger::GasteigerAtomTypeData::Properties	bond_order_to_property (const core::Size &BOND_ORDER_OR_AROMATIC)
	convert bond order or aromatic into the corresponding radius More...
void	find_bonds_in_rings (MutableResidueType &res, bool const complex_ring_detection=false)
	Determine which bonds are in rings, and set the BondRingness property of each. More...
void	complex_ring_detection (MutableResidueType &res)
void	quick_ring_detection (MutableResidueType &res)
utility::vector1< VD >	get_connecting_atoms (MutableResidueType const &res, ED const &edge)
utility::vector1< VD >	get_connecting_atoms (ResidueGraph const &graph, ED const &edge)
ED	get_bond (MutableResidueType const &res, VD const &source, VD const &target)
Real	create_bond_length (gasteiger::GasteigerAtomTypeData const &atom1, gasteiger::GasteigerAtomTypeData const &atom2, BondName bond_type)
	this will create a bond length based on gasteiger atom type definitions of bonds More...
utility::vector1< VDs >	find_chi_bonds (MutableResidueType const &restype)
	Find which bonds are rotatatable (chi) bonds Returns a list of four vds representing the chi. More...
bool	is_sp2_proton_chi (core::Size chi, MutableResidueType const &restype)
	Is the given chi a proton chi with the proton attached to an atom attached to an non-sp3 atom? More...
static basic::Tracer	TR ("core.chemical.ChemicalManager")
std::string const	FA_STANDARD ("fa_standard")
	tag name for querying fullatom chemical type set. More...
std::string const	CENTROID ("centroid")
	tag name for querying fullatom chemical type set. More...
std::string const	CENTROID_ROT ("centroid_rot")
	tag name for querying centroid_rot chemical type set. More...
std::string const	HYBRID_FA_STANDARD_CENTROID ("hybrid_fa_standard_centroid")
	tag name for querying hybrid fullatom+centroid chemical type set. More...
std::string const	COARSE_RNA ("coarse_rna")
	tag name for querying COARSE_RNA chemical type set. More...
TypeSetMode	type_set_mode_from_string (std::string const &mode, bool fail)
std::string	string_from_type_set_mode (TypeSetMode mode)
std::ostream &	operator<< (std::ostream &out, TypeSetMode mode)
std::ostream &	operator<< (std::ostream &out, ElectronConfiguration const &obj)
std::istream &	operator>> (std::istream &in, ElectronConfiguration &obj)
std::ostream &	operator<< (std::ostream &out, Element const &obj)
std::istream &	operator>> (std::istream &in, Element &obj)
static basic::Tracer	tr ("core.chemical.ElementSet")
static basic::Tracer	TR ("core.chemical.GlobalResidueTypeSet")
bool	sort_patchop_by_name (PatchOP p, PatchOP q)
static basic::Tracer	TR ("core.chemical.icoor_support")
VD	walk_back_to_find_usable_base (core::chemical::MutableResidueType const &restype, VD start, utility::vector1< VD > const &exclusions)
	Walk up the icoor tree to find alternate reference atoms Utility function for clean_up_dangling_connect() – we only go up the tree to make sure we don't get cycles. Won't choose atoms in exclusions (or the start) More...
void	clean_up_dangling_connect (core::chemical::MutableResidueType &restype, ICoordAtomIDType remove_type)
	Attempt to find new ICOOR definitions for entries in the ResidueType which rely on a now-deleted upper/lower connection (Connection type is specified by the passed type.) More...
void	reroot_restype (core::chemical::MutableResidueType &restype, core::chemical::ResidueGraph const &graph, core::chemical::VD root)
	Reroot the Icoord records of a ResidueType on the given atom We need direct access to the ResidueGraph, so this function can only be called by ResidueType itself. More...
bool	has_assigned_coords (std::string const &stub, std::set< VD > const &assigned, core::chemical::MutableResidueType const &restype)
	Utility function for fill_ideal_xyz_from_icoor() – does this ICoorAtomID have all the dependancies filled? More...
void	fill_ideal_xyz_from_icoor (core::chemical::MutableResidueType &restype, core::chemical::ResidueGraph const &graph)
static basic::Tracer	tr ("core.chemical")
static basic::Tracer	TR ("core.chemical.MergeBehaviorManager")
MergeBehaviorManager::AtomRenamingMap	mrb_map_from_correspondence (std::string const &correspondence)
merge_residue_behavior	mrb_from_name (std::string const &mrb)
static basic::Tracer	tr ("core.chemical")
static basic::Tracer	tr ("core.chemical")
static basic::Tracer	TR ("core.chemical.MutableChiRecord")
static basic::Tracer	TR ("core.chemical.MutableICoorRecord")
std::ostream &	operator<< (std::ostream &out, MutableICoorRecord const &icoor)
static basic::Tracer	TR ("core.chemical.MutableResidueType")
utility::vector1< VD >	remap_vect (utility::vector1< VD > const &vect, std::map< VD, VD > const &old_to_new)
std::string	correct_conn (std::string const &old, core::Size const conn_id_deleted)
	A short utility function for update_icoors_after_connection_deletion() More...
std::ostream &	operator<< (std::ostream &output, MutableResidueType const &object_to_output)
std::ostream &	operator<< (std::ostream &out, const Orbital &orbital)
static basic::Tracer	tr ("core.chemical.Patch")
std::string	tag_from_line (std::string const &line)
	handy function, return the first word from a line More...
std::string	residue_type_base_name (ResidueTypeBase const &rsd_type)
	helper function, returns the base residue name prior to any patching More...
std::string	residue_type_all_patches_name (ResidueType const &rsd_type)
	helper function, returns the name of all added patches More...
utility::vector1< std::string >	get_patch_names (ResidueType const &rsd_type)
void	setup_patch_atomic_charge_reassignments_from_commandline (std::string const &patch_name, TypeSetMode rsd_type_set_mode, ResidueTypeSelector const &rsd_selector, std::map< std::string, Real > &atomic_charge_reassignments)
	override patch partial charges with values from commandline More...
PatchCaseOP	case_from_lines (utility::vector1< std::string > const &lines, TypeSetMode res_type_set_mode, std::string const &patch_name)
	create a PatchCase from input lines More...
static basic::Tracer	tr ("core.chemical")
static basic::Tracer	TR_PatchOperations ("core.chemical.PatchOperations.hh")
std::string	expand_icoor_atom_name (std::string name, MutableResidueType const &rsd)
void	check_residue_has_atom (std::string const &atom_name, core::chemical::MutableResidueType const &rsd, std::string const &location)
PatchOperationOP	patch_operation_from_patch_file_line (std::string const &line, std::map< std::string, Real > const &atomic_charge_reassignments)
	Virtual constructor, returns 0 if no match. More...
bool	operator< (ResConnID const &lhs, ResConnID const &rhs)
bool	operator== (ResConnID const &lhs, ResConnID const &rhs)
bool	operator!= (ResConnID const &lhs, ResConnID const &rhs)
static basic::Tracer	tr ("core.chemical")
MutableResidueTypeOP	read_topology_file (std::string const &filename, chemical::ResidueTypeSetCOP rsd_type_set)
	function to convert params files into ResidueType objects (repackages string filename into istream, gets needed subsidiary type sets from rsd_type_set More...
MutableResidueTypeOP	read_topology_file (utility::io::izstream &istream, chemical::ResidueTypeSetCOP rsd_type_set)
	function to convert params files into ResidueType objects, gets needed subsidiary type sets from rsd_type_set More...
MutableResidueTypeOP	read_topology_file (std::istream &istream, std::string const &filename,chemical::ResidueTypeSetCOP rsd_type_set)
	function to convert params files into ResidueType objects, gets needed subsidiary type sets from rsd_type_set More...
MutableResidueTypeOP	read_topology_file (std::string const &filename, chemical::AtomTypeSetCAP atom_types, chemical::ElementSetCAP elements, chemical::MMAtomTypeSetCAP mm_atom_types, chemical::orbitals::OrbitalTypeSetCAP orbital_atom_types)
	function to convert params files into ResidueType objects (repackages string filename into istream) More...
MutableResidueTypeOP	read_topology_file (std::istream &data, std::string const &filename,chemical::AtomTypeSetCAP atom_types, chemical::ElementSetCAP elements, chemical::MMAtomTypeSetCAP mm_atom_types, chemical::orbitals::OrbitalTypeSetCAP orbital_atom_types)
	main function to convert params files into ResidueType objects More...
void	write_topology_file (ResidueType const &rsd, std::string filename="")
	writes a .params file from a given ResidueType object More...
void	write_graphviz (ResidueType const &rsd, std::ostream &out, bool header)
	Produces a graphviz dot representation of the ResidueType to the given output stream If header is true (the default) a line with an explanitory message will be printed first. More...
void	write_graphviz (MutableResidueType const &rsd, std::ostream &out, bool header)
void	set_up_mapfile_reassignments_from_commandline (ResidueTypeBaseOP rsd)
	Certain commandline flags override the default RamaPrePro maps used by the 20 canonical amino acids. This function applies those overrides. More...
void	setup_atom_type_reassignments_from_commandline (std::string const &rsd_type_name, TypeSetMode rsd_type_set_mode, std::map< std::string, std::string > &atom_type_reassignments)
void	setup_atomic_charge_reassignments_from_commandline (std::string const &rsd_type_name, TypeSetMode rsd_type_set_mode, std::map< std::string, Real > &atomic_charge_reassignments)
void	setup_icoor_reassignments_from_commandline (std::string const &rsd_type_name, TypeSetMode rsd_type_set_mode, std::map< std::string, utility::vector1< std::string > > &icoor_reassignments)
void	apply_symm_gly_corrections (std::string const &child_atom, core::Real &phi, core::Real &, core::Real &d, std::string &, std::string &, std::string &torsion_atom)
	Symmetrize the glycine params file (if the user has used the -symmetric_gly_tables option). More...
static basic::Tracer	TR ("core.chemical.residue_support")
ObjexxFCL::FArray2D_int	get_residue_path_distances (ResidueType const &res)
	relies on class Graph to find all pairs shortest path information More...
utility::vector1< VD >	mainchain_path (MutableResidueType const &res)
	Figure out the shortest path between the upper and lower connect atoms (inclusive) Will return an empty vector if one does not exist. More...
utility::vector1< VD >	shortest_path (MutableResidueType const &res, VD start, VD end)
	Figure out the shortest path between two atoms (inclusive) Will return an empty vector if one does not exist. More...
void	annotate_backbone (MutableResidueType &restype)
	Annotate "backbone" atoms. For the purpose of this function, backbone atoms are any atoms which are connected to another backbone atom by a non-rotatable, non-cut bond. Atoms connected to the upper and/or lower connect points are always backbone. Important - if Chis/cuts aren't properly annotated, all atoms will be backbone. More...
void	real_to_virtual (MutableResidueType &restype)
	Virtualize convert the MutableResidueType to a virtual type NOTE: This function does not rename the residue type. More...
LightWeightResidueGraph	convert_residuetype_to_light_graph (MutableResidueType const &res)
void	rename_atoms (MutableResidueType &res, bool preserve)
	Rename atoms in the residue type such that their names are unique. If preserve is true, only rename those which have no names or who have name conflicts. (Both of the conflicting atoms will be renamed.) More...
void	calculate_rigid_matrix (MutableResidueType const &res, VDDistanceMatrix &distances)
	Calculate the rigid matrix - assume that distances has been initialized to some really large value, and is square. More...
core::Real	find_nbr_dist (MutableResidueType const &res, VD &nbr_atom)
	Find the neighbor distance to the given neighbor atom. If nbr_atom is null_vertex, give the smallest neighbor distance, and set nbr_atom to the atom for that distance. More...
void	rosetta_recharge_fullatom (MutableResidueType &res)
	Apply molfile_to_params style partial charges to the ResidueType. More...
MutableResidueTypeOP	make_centroid (ResidueType const &res)
	Make a centroid version of the fullatom ResidueType passed in. More...
MutableResidueTypeOP	make_centroid (MutableResidueType const &res)
bool	residue_type_bases_identical (ResidueTypeBase const &r1, ResidueTypeBase const &r2)
bool	residue_types_identical (ResidueType const &res1, ResidueType const &res2)
	Are two ResidueTypes equivalent? This is here rather than as an operator on ResidueType because it's not the sort of thing one should be doing normally. This looks for exact equivalence, including atom order. More...
bool	compare_residue_connection (ResidueConnection const &rc1, ResidueConnection const &rc2, bool fuzzy=false)
	Are the two ResidueConnection objects equivalent Here instead of in operator== because of the fuzzy-real issue. More...
bool	compare_atom_icoor (AtomICoor const &aic1, AtomICoor const &aic2, bool fuzzy=false)
	Are the two ResidueConnection objects equivalent Here instead of in operator== because of the fuzzy-real issue. More...
bool	has (ResidueGraph const &graph, VD vd)
	Does a ResidueGraph have a given vertex descriptor? More...
bool	has (ResidueGraph const &graph, ED ed)
	Does a ResidueGraph have a given edge descriptor? More...
template<typename Graph >
void	regenerate_graph_vertex_index (Graph &graph)
	When adding and deleting nodes in a graph, sometimes the inner counting of nodes/edges gets outdated. Run this to fix the problem. More...
std::ostream &	operator<< (std::ostream &output, ResidueProperties const &object_to_output)
std::ostream &	operator<< (std::ostream &output, ResidueProperty const &object_to_output)
ResidueProperty &	operator++ (ResidueProperty &property)
VariantType &	operator++ (VariantType &variant)
ResiduePropertiesOP	deep_copy (ResidueProperties const &source)
std::map< std::string, ResidueProperty > const *	generate_string_to_property_map ()
static const std::map < std::string, ResidueProperty > *const	PROPERTY_MAP (generate_string_to_property_map())
utility::vector1< std::string > const *	generate_property_to_string_vector ()
static const utility::vector1 < std::string > *const	STRING_LIST (generate_property_to_string_vector())
template<class Graph >
core::Size	filtered_num_vertices (Graph const &graph)
	It's a frustrating truth, but num_vertices doesn't give the number of filtered vertices for filtered graphs, but instead gives the number of underlying vertices ... this gets the true number of filtered vertices. More...
RealResidueGraph	make_real_residue_graph (MutableResidueType const &restype)
	Convenience constructor. More...
HeavyAtomGraph	make_heavy_atom_graph (MutableResidueType const &restype)
	Convenience constructor. More...
AcceptorAtomGraph	make_acceptor_atom_graph (MutableResidueType const &restype)
	Convenience constructor. More...
HeavyAtomWithPolarHydrogensGraph	make_heavy_atom_with_polar_hydrogens_graph (MutableResidueType const &restype)
	Convenience constructor. More...
HeavyAtomWithHydrogensGraph	make_heavy_atom_with_hydrogens_graph (MutableResidueType const &restype)
	Convenience constructor. More...
HydrogenAtomGraph	make_hydrogen_atom_graph (MutableResidueType const &restype)
	Convenience constructor. More...
AromaticAtomGraph	make_aromatic_atom_graph (MutableResidueType const &restype)
	Convenience constructor. More...
PolarHydrogenGraph	make_polar_hydrogen_graph (MutableResidueType const &restype)
	Convenience constructor. More...
APolarHydrogenGraph	make_apolar_hydrogen_graph (MutableResidueType const &restype)
	Convenience constructor. More...
static basic::Tracer	TR ("core.chemical.ResidueType")
std::ostream &	operator<< (std::ostream &output, ResidueType const &object_to_output)
static basic::Tracer	TR ("core.chemical.ResidueTypeBase")
std::string	get_element_color (std::string const &element)
static basic::Tracer	TR ("core.chemical.ResidueTypeSelector")
ResidueTypeSelectorSingleOP	residue_selector_single_from_line (std::string const &line)
	create a singe ResidueTypeSelector from an input line. More...
static basic::Tracer	TR ("core.chemical.ResidueTypeSet")
static std::string const	chr_chains ("ABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890abcdefghijklmnopqrstuvwxyz")
static basic::Tracer	TR ("core.chemical.util")
core::chemical::ResidueTypeSetCAP	rsd_set_from_cmd_line ()
	Return a constant access pointer to the ResidueTypeSet specified by the command-line options. More...
void	add_atom_type_set_parameters_from_command_line (std::string const &atom_type_set_tag, AtomTypeSet &atom_type_set)
	Add additional parameter files not present in <atom-set-name>/extras.txt. More...
void	modify_atom_properties_from_command_line (std::string const &atom_type_set_tag, AtomTypeSet &atom_type_set)
	Modify atom_type properties from the command line. More...
std::string	formatted_icoord_tree (core::chemical::ResidueType const &restype)
	Return a string representing the internal coordinates tree of this ResidueType. More...
std::string	formatted_icoord_tree (core::chemical::MutableResidueType const &restype)
	Return a string representing the internal coordinates tree of this MutableResidueType (if any) More...
void	print_chis (std::ostream &out, ResidueType const &res)
	Utility to examine chi output. More...
void	print_chis (std::ostream &out, MutableResidueType const &res)
	Utility to examine chi output. More...
std::string	fixup_patches (std::string const &string_in)
	Replaces the deprecated "_p:" linker connecting ResidueType base names with their patch names with ":". More...
bool	variants_match_with_exceptions (ResidueTypeBase const &res1, ResidueTypeBase const &res2, utility::vector1< VariantType > list_of_variants_to_ignore)
	Are these two residues patched in exactly the same way, ignoring any VariantTypes in the list of exceptions? More...
utility::vector1< VariantType >	pH_mode_exceptions ()
	check if user has set -pH_mode. More...
bool	variants_match (ResidueTypeBase const &res1, ResidueTypeBase const &res2)
	Are these two residues patched in exactly the same way? More...
bool	nonadduct_variants_match (ResidueTypeBase const &res1, ResidueTypeBase const &res2)
	Similar to variants_match(), but allows different adduct-modified states. More...
utility::vector1< VariantType >	get_terminal_varianttypes ()
	Get a list of those VariantTypes that affect termini. More...
ResidueTypeCOP	find_best_match (ResidueTypeCOPs const &rsd_type_list, utility::vector1< std::string > const &atom_names, bool const ignore_atom_named_H)
	look for best match to atom_names More...
void	enlarge_h_lj_wdepth (utility::vector1< Real > &lj_wdepth, AtomTypeSet const &atom_type_set)
	Fang-Chieh Chou 8/10/2012. Use larger LJ_WDEPTH for protons to avoid clashes in RNA. More...
void	enlarge_h_lj_wdepth (AtomTypeSet &atom_type_set)
	Fang-Chieh Chou 8/10/2012. Use larger LJ_WDEPTH for protons to avoid clashes in RNA. More...
void	unset_acceptor_ether_oxygens (AtomTypeSet &atom_type_set)
	Rhiju. O3', O4', O5' in nucleic acids are ethers – turn them off as acceptors for H-bonds. More...
void	detect_ld_chirality_from_polymer_residue (core::chemical::MutableResidueType const &restype, bool &is_d_aa, bool &is_l_aa)
void	detect_ld_chirality_from_polymer_residue (std::map< std::string, Vector > const &xyz, std::string const &name3, bool &is_d_aa, bool &is_l_aa)
bool	heavy_atom_names_match (ResidueType const &first, ResidueType const &second)
	Return true if the two residues have the same number and name of heavy atoms. More...
bool	is_mainchain_torsion_also_ring_torsion (ResidueType const &res_type, uint torsion_index)
	Are these main-chain torsions also ring torsions? More...
std::map< std::string, VariantType > const *	generate_string_to_variant_map ()
static const std::map < std::string, VariantType > *const	VARIANT_MAP (generate_string_to_variant_map())
utility::vector1< std::string > const *	generate_variant_to_string_vector ()
static const utility::vector1 < std::string > *const	STRING_LIST (generate_variant_to_string_vector())

Variables
Real const	MAX_CHEMICAL_BOND_TO_HYDROGEN_LENGTH = { 1.35 }
	Maximum distance between a heavy atom and a hydrogen atom to which it is chemically bound Set in .cc file. More...
std::string const	FA_STANDARD
std::string const	CENTROID
std::string const	CENTROID_ROT
std::string const	HYBRID_FA_STANDARD_CENTROID
std::string const	COARSE_RNA
std::string const	PATCH_LINKER = ":"
	the string used to create new residue names after patching More...

Typedef Documentation

typedef std::pair< AA, std::pair< utility::vector1< std::string >, utility::vector1< VariantType > > > core::chemical::AA_VariantsExceptions

typedef boost::graph_traits<AcceptorAtomGraph>::edge_iterator core::chemical::AcceptorAtomEIter

typedef boost::filtered_graph<ResidueGraph, boost::keep_all, AcceptorAtomFilter> core::chemical::AcceptorAtomGraph

typedef boost::graph_traits<AcceptorAtomGraph>::vertex_iterator core::chemical::AcceptorAtomVIter

typedef std::pair<AcceptorAtomVIter, AcceptorAtomVIter> core::chemical::AcceptorAtomVIterPair

typedef std::map< std::string, int > core::chemical::AdductMap

typedef utility::pointer::shared_ptr< Adduct > core::chemical::AdductOP

typedef boost::graph_traits<ResidueGraph>::adjacency_iterator core::chemical::AdjacentIter

typedef std::pair<AdjacentIter, AdjacentIter> core::chemical::AdjacentIterPair

typedef boost::graph_traits<APolarHydrogenGraph>::edge_iterator core::chemical::APolarHydrogenEIter

typedef boost::filtered_graph<ResidueGraph, boost::keep_all, APolarHydrogenFilter> core::chemical::APolarHydrogenGraph

typedef boost::graph_traits<APolarHydrogenGraph>::vertex_iterator core::chemical::APolarHydrogenVIter

typedef std::pair<APolarHydrogenVIter, APolarHydrogenVIter> core::chemical::APolarHydrogenVIterPair

typedef boost::graph_traits<AromaticAtomGraph>::edge_iterator core::chemical::AromaticAtomEIter

typedef boost::filtered_graph<ResidueGraph, boost::keep_all, AromaticAtomFilter> core::chemical::AromaticAtomGraph

typedef boost::graph_traits<AromaticAtomGraph>::vertex_iterator core::chemical::AromaticAtomVIter

typedef std::pair<AromaticAtomVIter, AromaticAtomVIter> core::chemical::AromaticAtomVIterPair

typedef utility::pointer::weak_ptr< Atom > core::chemical::AtomAP

typedef utility::vector1< AtomAP > core::chemical::AtomAPs

typedef utility::pointer::shared_ptr< Atom const > core::chemical::AtomCOP

typedef utility::vector1< AtomCOP > core::chemical::AtomCOPs

typedef utility::vector1< Size > core::chemical::AtomIndices

using core::chemical::AtomMemo = typedef basic::datacache::DataMapObj<std::set<std::string> >

using core::chemical::AtomMemoOP = typedef utility::pointer::shared_ptr<AtomMemo>

typedef utility::pointer::shared_ptr< Atom > core::chemical::AtomOP

typedef utility::vector1< AtomOP > core::chemical::AtomOPs

typedef utility::pointer::shared_ptr< AtomProperties const > core::chemical::AtomPropertiesCOP

typedef utility::pointer::shared_ptr< AtomProperties > core::chemical::AtomPropertiesOP

typedef utility::pointer::shared_ptr< AtomTypeDatabaseIO > AtomTypeDatabaseIOOP typedef utility::pointer::shared_ptr< AtomTypeDatabaseIO const > core::chemical::AtomTypeDatabaseIOCOP

typedef int core::chemical::AtomTypeIndex

typedef utility::pointer::weak_ptr< AtomTypeSet > core::chemical::AtomTypeSetAP

typedef utility::pointer::weak_ptr< AtomTypeSet const > core::chemical::AtomTypeSetCAP

typedef utility::pointer::shared_ptr< AtomTypeSet const > core::chemical::AtomTypeSetCOP

typedef utility::pointer::shared_ptr< AtomTypeSet > core::chemical::AtomTypeSetOP

typedef utility::pointer::shared_ptr< AutomorphismIterator const > core::chemical::AutomorphismIteratorCOP

typedef utility::pointer::shared_ptr< AutomorphismIterator > core::chemical::AutomorphismIteratorOP

typedef utility::keys::Key3Tuple< Size, Size, Size > core::chemical::bondangle_atom_set

typedef Real core::chemical::BondLength

typedef utility::pointer::shared_ptr< CacheableResidueTypeSets const > core::chemical::CacheableResidueTypeSetsCOP

typedef utility::pointer::shared_ptr< CacheableResidueTypeSets > core::chemical::CacheableResidueTypeSetsOP

typedef utility::keys::Key4Tuple< Size, Size, Size, Size > core::chemical::dihedral_atom_set

typedef ResidueGraph::edge_descriptor core::chemical::ED

typedef boost::graph_traits<ResidueGraph>::edge_iterator core::chemical::EIter

typedef std::pair<EIter, EIter> core::chemical::EIterPair

typedef utility::pointer::shared_ptr< Element const > core::chemical::ElementCOP

typedef utility::pointer::shared_ptr< Element > core::chemical::ElementOP

typedef utility::pointer::weak_ptr< ElementSet > core::chemical::ElementSetAP

typedef utility::pointer::weak_ptr< ElementSet const > core::chemical::ElementSetCAP

typedef utility::pointer::shared_ptr< ElementSet const > core::chemical::ElementSetCOP

typedef utility::pointer::shared_ptr< ElementSet > core::chemical::ElementSetOP

typedef utility::pointer::weak_ptr< GlobalResidueTypeSet const > core::chemical::GlobalResidueTypeSetCAP

typedef utility::pointer::shared_ptr< GlobalResidueTypeSet const > core::chemical::GlobalResidueTypeSetCOP

typedef utility::pointer::shared_ptr< GlobalResidueTypeSet > core::chemical::GlobalResidueTypeSetOP

typedef HeavyAtomGraph::edge_descriptor core::chemical::HeavyAtomED

typedef boost::graph_traits<HeavyAtomGraph>::edge_iterator core::chemical::HeavyAtomEIter

typedef boost::filtered_graph<ResidueGraph, boost::keep_all, HeavyAtomFilter> core::chemical::HeavyAtomGraph

typedef boost::graph_traits<HeavyAtomGraph>::out_edge_iterator core::chemical::HeavyAtomOutEdgeIter

typedef std::pair<HeavyAtomOutEdgeIter, HeavyAtomOutEdgeIter> core::chemical::HeavyAtomOutEdgeIterPair

typedef HeavyAtomGraph::vertex_descriptor core::chemical::HeavyAtomVD

typedef boost::graph_traits<HeavyAtomGraph>::vertex_iterator core::chemical::HeavyAtomVIter

typedef std::pair<HeavyAtomVIter, HeavyAtomVIter> core::chemical::HeavyAtomVIterPair

typedef boost::graph_traits<HeavyAtomWithHydrogensGraph>::edge_iterator core::chemical::HeavyAtomWithHydrogensEIter

typedef boost::filtered_graph<ResidueGraph, boost::keep_all, HeavyAtomWithHydrogensFilter> core::chemical::HeavyAtomWithHydrogensGraph

typedef boost::graph_traits<HeavyAtomWithHydrogensGraph>::vertex_iterator core::chemical::HeavyAtomWithHydrogensVIter

typedef std::pair<HeavyAtomWithHydrogensVIter, HeavyAtomWithHydrogensVIter> core::chemical::HeavyAtomWithHydrogensVIterPair

typedef boost::graph_traits<HeavyAtomWithPolarHydrogensGraph>::edge_iterator core::chemical::HeavyAtomWithPolarHydrogensEIter

typedef boost::filtered_graph<ResidueGraph, boost::keep_all, HeavyAtomWithPolarHydrogensFilter> core::chemical::HeavyAtomWithPolarHydrogensGraph

typedef boost::graph_traits<HeavyAtomWithPolarHydrogensGraph>::vertex_iterator core::chemical::HeavyAtomWithPolarHydrogensVIter

typedef std::pair<HeavyAtomWithPolarHydrogensVIter, HeavyAtomWithPolarHydrogensVIter> core::chemical::HeavyAtomWithPolarHydrogensVIterPair

typedef boost::graph_traits<HydrogenAtomGraph>::edge_iterator core::chemical::HHydrogenAtomEIter

typedef HydrogenAtomGraph::edge_descriptor core::chemical::HydrogenAtomED

typedef boost::filtered_graph<ResidueGraph, boost::keep_all, HydrogenAtomFilter> core::chemical::HydrogenAtomGraph

typedef boost::graph_traits<HydrogenAtomGraph>::out_edge_iterator core::chemical::HydrogenAtomOutEdgeIter

typedef std::pair<HydrogenAtomOutEdgeIter, HydrogenAtomOutEdgeIter> core::chemical::HydrogenAtomOutEdgeIterPair

typedef HydrogenAtomGraph::vertex_descriptor core::chemical::HydrogenAtomVD

typedef boost::graph_traits<HydrogenAtomGraph>::vertex_iterator core::chemical::HydrogenAtomVIter

typedef std::pair<HydrogenAtomVIter, HydrogenAtomVIter> core::chemical::HydrogenAtomVIterPair

typedef utility::pointer::weak_ptr< IdealBondLengthSet > core::chemical::IdealBondLengthSetAP

typedef utility::pointer::weak_ptr< IdealBondLengthSet const > core::chemical::IdealBondLengthSetCAP

typedef utility::pointer::shared_ptr< IdealBondLengthSet const > core::chemical::IdealBondLengthSetCOP

typedef utility::pointer::shared_ptr< IdealBondLengthSet > core::chemical::IdealBondLengthSetOP

typedef boost::adjacency_list< boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_name_t, core::chemical::VD>, boost::property<boost::edge_name_t, core::chemical::ED> > core::chemical::LightWeightResidueGraph

Light weight graph typedefs The light weight graph is a graph that holds a pointer to the edge descriptor and vertex descriptor or the ResidueGraph. We generate the light weight graph so that we can do rapid things like look for rings ina small molecule. Also

typedef boost::graph_traits<LightWeightResidueGraph>::edge_descriptor core::chemical::lwrg_ED

typedef boost::graph_traits<LightWeightResidueGraph>::edge_iterator core::chemical::lwrg_edge_iter

typedef boost::graph_traits<LightWeightResidueGraph>::out_edge_iterator core::chemical::lwrg_out_edge_iter

typedef std::pair<lwrg_out_edge_iter, lwrg_out_edge_iter> core::chemical::lwrg_out_edge_iter_pair

typedef boost::graph_traits<LightWeightResidueGraph>::vertex_descriptor core::chemical::lwrg_VD

typedef boost::graph_traits<LightWeightResidueGraph>::vertex_iterator core::chemical::lwrg_vd_iter

typedef std::pair<lwrg_vd_iter, lwrg_vd_iter> core::chemical::lwrg_vd_pair_iter

typedef utility::pointer::shared_ptr< MergeBehaviorManager const > core::chemical::MergeBehaviorManagerCOP

typedef utility::pointer::shared_ptr< MergeBehaviorManager > core::chemical::MergeBehaviorManagerOP

typedef utility::pointer::shared_ptr< Metapatch const > core::chemical::MetapatchCOP

typedef utility::pointer::shared_ptr< Metapatch > core::chemical::MetapatchOP

typedef utility::pointer::shared_ptr< MMAtomType > core::chemical::MMAtomTypeOP

typedef utility::pointer::weak_ptr< MMAtomTypeSet > core::chemical::MMAtomTypeSetAP

typedef utility::pointer::weak_ptr< MMAtomTypeSet const > core::chemical::MMAtomTypeSetCAP

typedef utility::pointer::shared_ptr< MMAtomTypeSet const > core::chemical::MMAtomTypeSetCOP

typedef utility::pointer::shared_ptr< MMAtomTypeSet > core::chemical::MMAtomTypeSetOP

typedef utility::pointer::shared_ptr< MutableChiRecord const > core::chemical::MutableChiRecordCOP

typedef utility::pointer::shared_ptr< MutableChiRecord > core::chemical::MutableChiRecordOP

typedef utility::pointer::shared_ptr< MutableICoorRecord const > core::chemical::MutableICoorRecordCOP

typedef utility::pointer::shared_ptr< MutableICoorRecord > core::chemical::MutableICoorRecordOP

typedef utility::pointer::shared_ptr< MutableResidueType const > core::chemical::MutableResidueTypeCOP

typedef utility::vector1< MutableResidueTypeCOP > core::chemical::MutableResidueTypeCOPs

typedef utility::pointer::shared_ptr< MutableResidueType > core::chemical::MutableResidueTypeOP

typedef utility::vector1< MutableResidueTypeOP > core::chemical::MutableResidueTypeOPs

typedef std::pair<NameVDMap::iterator, bool> core::chemical::NameVDInserted

typedef std::map< std::string, VD > core::chemical::NameVDMap

typedef std::pair<std::string, VD> core::chemical::NameVDPair

typedef utility::pointer::shared_ptr< Orbital const > core::chemical::OrbitalCOP

typedef utility::vector1< OrbitalCOP > core::chemical::OrbitalCOPs

typedef utility::vector1<Size> core::chemical::OrbitalIndices

typedef utility::pointer::shared_ptr< Orbital > core::chemical::OrbitalOP

typedef utility::vector1< OrbitalOP > core::chemical::OrbitalOPs

typedef boost::graph_traits<ResidueGraph>::out_edge_iterator core::chemical::OutEdgeIter

typedef std::pair<OutEdgeIter, OutEdgeIter> core::chemical::OutEdgeIterPair

typedef utility::pointer::shared_ptr< PatchCase > core::chemical::PatchCaseOP

typedef utility::pointer::shared_ptr< Patch const > core::chemical::PatchCOP

typedef utility::pointer::shared_ptr< Patch > core::chemical::PatchOP

typedef utility::pointer::shared_ptr< PatchOperation > core::chemical::PatchOperationOP

typedef boost::graph_traits<PolarHydrogenGraph>::edge_iterator core::chemical::PolarHydrogenEIter

typedef boost::filtered_graph<ResidueGraph, boost::keep_all, PolarHydrogenFilter> core::chemical::PolarHydrogenGraph

typedef boost::graph_traits<PolarHydrogenGraph>::vertex_iterator core::chemical::PolarHydrogenVIter

typedef std::pair<PolarHydrogenVIter, PolarHydrogenVIter> core::chemical::PolarHydrogenVIterPair

typedef utility::pointer::shared_ptr< PoseResidueTypeSet const > core::chemical::PoseResidueTypeSetCOP

typedef utility::pointer::shared_ptr< PoseResidueTypeSet > core::chemical::PoseResidueTypeSetOP

typedef boost::graph_traits<RealResidueGraph>::adjacency_iterator core::chemical::RealResidueAdjacentIter

typedef std::pair<RealResidueAdjacentIter, RealResidueAdjacentIter> core::chemical::RealResidueAdjacentIterPair

typedef RealResidueGraph::edge_descriptor core::chemical::RealResidueED

typedef boost::graph_traits<RealResidueGraph>::edge_iterator core::chemical::RealResidueEIter

typedef boost::filtered_graph<ResidueGraph, RealFilter, RealFilter> core::chemical::RealResidueGraph

typedef boost::graph_traits<RealResidueGraph>::out_edge_iterator core::chemical::RealResidueOutEdgeIter

typedef std::pair<RealResidueOutEdgeIter, RealResidueOutEdgeIter> core::chemical::RealResidueOutEdgeIterPair

typedef RealResidueGraph::vertex_descriptor core::chemical::RealResidueVD

typedef boost::graph_traits<RealResidueGraph>::vertex_iterator core::chemical::RealResidueVIter

typedef std::pair<RealResidueVIter, RealResidueVIter> core::chemical::RealResidueVIterPair

typedef boost::undirected_graph< Atom, Bond > core::chemical::ResidueGraph

typedef utility::pointer::shared_ptr< ResidueProperties const > core::chemical::ResiduePropertiesCOP

typedef utility::pointer::shared_ptr< ResidueProperties > core::chemical::ResiduePropertiesOP

typedef utility::pointer::weak_ptr< ResidueType > core::chemical::ResidueTypeAP

typedef utility::pointer::weak_ptr< ResidueTypeBase > core::chemical::ResidueTypeBaseAP

typedef utility::pointer::weak_ptr< ResidueTypeBase const > core::chemical::ResidueTypeBaseCAP

typedef utility::pointer::shared_ptr< ResidueTypeBase const > core::chemical::ResidueTypeBaseCOP

typedef utility::pointer::shared_ptr< ResidueTypeBase > core::chemical::ResidueTypeBaseOP

typedef utility::pointer::weak_ptr< ResidueType const > core::chemical::ResidueTypeCAP

typedef utility::vector1< ResidueTypeCAP > core::chemical::ResidueTypeCAPs

typedef utility::pointer::shared_ptr< ResidueType const > core::chemical::ResidueTypeCOP

typedef utility::vector1< ResidueTypeCOP > core::chemical::ResidueTypeCOPs

typedef utility::pointer::shared_ptr< ResidueTypeFinder const > core::chemical::ResidueTypeFinderCOP

typedef utility::pointer::shared_ptr< ResidueTypeFinder > core::chemical::ResidueTypeFinderOP

typedef utility::pointer::shared_ptr< ResidueTypeKinWriter const > core::chemical::ResidueTypeKinWriterCOP

typedef utility::pointer::shared_ptr< ResidueTypeKinWriter > core::chemical::ResidueTypeKinWriterOP

typedef utility::pointer::shared_ptr< ResidueType > core::chemical::ResidueTypeOP

typedef utility::vector1< ResidueTypeOP > core::chemical::ResidueTypeOPs

typedef utility::pointer::shared_ptr< ResidueTypeSelector > core::chemical::ResidueTypeSelectorOP

typedef utility::pointer::shared_ptr< ResidueTypeSelectorSingle > core::chemical::ResidueTypeSelectorSingleOP

typedef utility::pointer::shared_ptr< ResidueTypeSetCache const > core::chemical::ResidueTypeSetCacheCOP

typedef utility::pointer::shared_ptr< ResidueTypeSetCache > core::chemical::ResidueTypeSetCacheOP

typedef utility::pointer::weak_ptr< ResidueTypeSet const > core::chemical::ResidueTypeSetCAP

typedef utility::pointer::shared_ptr< ResidueTypeSet const > core::chemical::ResidueTypeSetCOP

typedef utility::pointer::shared_ptr< ResidueTypeSet > core::chemical::ResidueTypeSetOP

typedef std::tuple< ResidueTypeCOP, utility::vector1< VariantType >, utility::vector1< std::string >, utility::vector1< VariantType >, bool > core::chemical::Restype_Variants_VariantStrings_Exceptions

A type for key lookup. This consists of a BASE TYPE ResidueTypeCOP, a list of variants (by enum), a list of custom variants (by string), a list of variant exceptions (by enum), and a bool for whether to turn off metapatches.

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

typedef utility::keys::Key3Tuple< Size, Size, Size > core::chemical::three_atom_set

typedef utility::keys::Key2Tuple< Size, Size > core::chemical::two_atom_set

typedef ResidueGraph::vertex_descriptor core::chemical::VD

typedef utility::vector1< VD > core::chemical::VDs

typedef std::map< core::chemical::VD, core::kinematics::tree::AtomOP > core::chemical::VdTreeatomMap

typedef boost::graph_traits<ResidueGraph>::vertex_iterator core::chemical::VIter

typedef std::pair<VIter, VIter> core::chemical::VIterPair

Enumeration Type Documentation

enum core::chemical::AA

enumeration for amino acids and nucleotides types with the total number as num_aa_types

Enumerator
aa_none
aa_ala
first_l_aa
aa_cys
aa_asp
aa_glu
aa_phe
aa_gly
aa_his
aa_ile
aa_lys
aa_leu
aa_met
aa_asn
aa_pro
aa_gln
aa_arg
aa_ser
aa_thr
aa_val
aa_trp
aa_tyr
num_canonical_aas
na_ade
first_DNA_aa
na_cyt
na_gua
na_thy
last_DNA_aa
na_rgu
na_rad
na_rcy
na_ura
aa_dal
first_D_aa
aa_dcs
aa_das
aa_dgu
aa_dph
aa_dhi
aa_dil
aa_dly
aa_dle
aa_dme
aa_dan
aa_dpr
aa_dgn
aa_dar
aa_dse
aa_dth
aa_dva
aa_dtr
aa_dty
last_D_aa
aa_b3a
first_beta3_aa
aa_b3c
aa_b3d
aa_b3e
aa_b3f
aa_b3g
aa_b3h
aa_b3i
aa_b3k
aa_b3l
aa_b3m
aa_b3n
aa_b3p
aa_b3q
aa_b3r
aa_b3s
aa_b3t
aa_b3v
aa_b3w
aa_b3y
aa_b3cisACPC
aa_b3transACPC
aa_b3cisACHC
last_beta3_aa
na_lra
na_lrc
na_lrg
na_lur
ou3_ala
first_oligourea
ou3_cys
ou3_asp
ou3_glu
ou3_phe
ou3_gly
ou3_his
ou3_ile
ou3_lys
ou3_leu
ou3_met
ou3_asn
ou3_pro
ou3_gln
ou3_arg
ou3_ser
ou3_thr
ou3_val
ou3_trp
ou3_tyr
ou3_aib
last_oligourea
aa_h2o
aa_vrt
aa_unp
aa_unk
num_aa_types

enum core::chemical::Ancestor

Change the parent, grandparent, or great-grandparent of an atom.

Enumerator
anc_parent
anc_grandparent
anc_greatgrandparent

enum core::chemical::AtomProperty

Enumerators for all the properties that can be assigned to a chemical::Atom.

Enumerator
NO_ATOM_PROPERTY
FIRST_ATOM_PROPERTY
H_DONOR
H_ACCEPTOR
POLAR_HYDROGEN
AROMATIC_HYDROGEN
HAS_ORBITALS
VIRTUAL_ATOM
REPULSIVE
AROMATIC_CARBON_WITH_FREE_VALENCE
N_ATOM_PROPERTIES

enum core::chemical::BondAromaticity

Proper aromaticity implies participation in a 4n+2 electron ring system. For simple single-double alternation, see conjugatable bond.

Enumerator
UnknownAromaticity
NonaromaticBond
IsAromaticBond

enum core::chemical::BondConjugability

As with the BCL, bond conjugability is more about the atom types on either end of the bond than about the bond itself. A conjugatable bond is one where it is known that the atoms on both sides of the bond can participate in a conjugated system. Double, triple and aromatic bonds are always conjugatable, and single bonds are conjugatable if both atoms are in other triple, double, or aromatic systems.

Enumerator
UnknownConjugability
NotConjugableBond
ConjugableBond

enum core::chemical::BondIsometry

Enumerator
UnknownIsometry
NoBondIsometry
EIsometry
ZIsometry

enum core::chemical::BondName

Enumerator
UnknownBond
SingleBond
DoubleBond
TripleBond
AromaticBond
OrbitalBond
PseudoBond

enum core::chemical::BondOrder

Enumerator
UnknownBondOrder
SingleBondOrder
DoubleBondOrder
TripleBondOrder
OrbitalBondOrder
DeleteBondOrder
PseudoBondOrder

enum core::chemical::BondRingness

Enumerator
UnknownRingness
BondNotInRing
BondInRing

enum core::chemical::GreekDistance

Enumerators for the Greek distance from the atom with the functional group of highest priority.

Enumerator
PRIMARY_ATOM
ALPHA_ATOM
BETA_ATOM
GAMMA_ATOM
DELTA_ATOM
EPSILON_ATOM
ZETA_ATOM
ETA_ATOM
THETA_ATOM
IOTA_ATOM
KAPPA_ATOM
LAMBDA_ATOM
MU_ATOM
NU_ATOM
XI_ATOM
OMICRON_ATOM
PI_ATOM
SIGMA_ATOM
TAU_ATOM
UPSILON_ATOM
PHI_ATOM
CHI_ATOM
PSI_ATOM
NA_GREEK_DISTANCE

enum core::chemical::Hybridization

Enumerator
SP2_HYBRID
SP3_HYBRID
RING_HYBRID
UNKNOWN_HYBRID
HYBRID_MAX

enum core::chemical::ICoordAtomIDType

strong

ICoordAtomIDType.

• INTERNAL: atoms which inherently belong to this ResidueType
• POLYMER_LOWER: atom at the polymer lower connection, such as backbone C in the previous residue (N-term side)
• POLYMER_UPPER: atom at the polymer upper connection, such as backbone N in the next residue (C-term side)
• CONNECT: atoms from a non-adjacent residue which connect to this residue by non-polymer connection, such as disulfide

If you add anything to this enum, be sure to update the string_to_icoord_type() function.

Enumerator
INTERNAL
POLYMER_LOWER
POLYMER_UPPER
CONNECT

enum core::chemical::merge_residue_behavior

Enumerator
mrb_do_not_merge
mrb_merge_w_prev
mrb_merge_w_next

enum core::chemical::ResidueProperty

Enumerators for all the properties that can be assigned to a ResidueType.

Enumerator
NO_PROPERTY
FIRST_PROPERTY
POLYMER
LIGAND
PROTEIN
CANONICAL_AA
CANONICAL_NUCLEIC
DNA
RNA
TNA
PNA
PEPTOID
OLIGOUREA
ARAMID
ORTHO_ARAMID
META_ARAMID
PARA_ARAMID
PRE_METHYLENE_ORTHO_ARAMID
PRE_METHYLENE_META_ARAMID
PRE_METHYLENE_PARA_ARAMID
POST_METHYLENE_ORTHO_ARAMID
POST_METHYLENE_META_ARAMID
POST_METHYLENE_PARA_ARAMID
PRE_METHYLENE_POST_METHYLENE_ORTHO_ARAMID
PRE_METHYLENE_POST_METHYLENE_META_ARAMID
PRE_METHYLENE_POST_METHYLENE_PARA_ARAMID
CARBOHYDRATE
LIPID
TERPENE
NUCLEOTIDE_DIPHOSPHATE
SRI
TRIAZOLE_LINKER
METAL
SURFACE
WATER
TP3
VIRTUALIZABLE_BY_PACKER
SOLVENT
VIRTUAL_RESIDUE
VRT1
INVERTED_VIRTUAL_RESIDUE
LOWER_TERMINUS
UPPER_TERMINUS
BRANCH_POINT
TERMINUS
LOWERTERM_TRUNC
UPPERTERM_TRUNC
COARSE
ADDUCT
SC_ORBITALS
FRAGMENT
UPPERTERM_CAP
LOWERTERM_CAP
POLAR
HYDROPHOBIC
CHARGED
NEGATIVE_CHARGE
POSITIVE_CHARGE
AROMATIC
ALIPHATIC
CYCLIC
METALBINDING
SIDECHAIN_THIOL
DISULFIDE_BONDED
ELECTROPHILE
SIDECHAIN_AMINE
N_METHYLATED
MEMBRANE
PHOSPHONATE
PHOSPHONATE_UPPER
ACETYLATED_NTERMINUS
METHYLATED_CTERMINUS
DIMETHYLATED_CTERMINUS
ALPHA_AA
BETA_AA
GAMMA_AA
L_AA
D_AA
ACHIRAL_BACKBONE
ACHIRAL_SIDECHAIN
R_PEPTOID
S_PEPTOID
TAUTOMER
PURINE
PYRIMIDINE
L_RNA
D_RNA
METHYLATED_NA
TRIOSE
TETROSE
PENTOSE
HEXOSE
HEPTOSE
OCTOSE
NONOSE
ALDOSE
KETOSE
L_SUGAR
D_SUGAR
OXIROSE
OXETOSE
FURANOSE
PYRANOSE
SEPTANOSE
ALPHA_SUGAR
BETA_SUGAR
SIALIC_ACID
C1_MODIFIED
C2_MODIFIED
C3_MODIFIED
C4_MODIFIED
C5_MODIFIED
C6_MODIFIED
C7_MODIFIED
C8_MODIFIED
C9_MODIFIED
GLYCOSIDE
ALDONIC_ACID
URONIC_ACID
DEOXY_SUGAR
AMINO_SUGAR
ACETYLAMINO_SUGAR
ACETYL_SUGAR
R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR
PHOSPHORYLATED_SUGAR
SULFATED_SUGAR
SULFOAMINO_SUGAR
THIO_SUGAR
C_METHYLATED_SUGAR
PHOSPHATE
SPINLABEL
DIAMAGNETIC
PARAMAGNETIC
N_PROPERTIES

enum core::chemical::TypeSetMode

A type set category is the "compatibility class" of a type set. That is, all e.g. ResidueTypes of a given TypeSetMode should be "compatible" with the scale of modeling resolution, indepenent of if they're in the same ResidueTypeSet.

Enumerator
INVALID_t	Don't use this as a mode - it exists as an error signal only.
FULL_ATOM_t	Full atom modeling - all atoms are represented.
DEFAULT_t	For type sets where there really isn't a clear distinction between fullatom and centroid.
CENTROID_t	Standard Rosetta Centroid: amino acid sidechains are represented by a "superatom", and other atoms are represented by a unified-atom model. (No apolar hydrogens.)
CENTROID_ROT_t	A modification of the Centroid mode, where the amino acid sidechains have additional degrees of freedom.
HYBRID_FA_STANDARD_CENTROID_t	???
COARSE_RNA_t	???
MIXED_t	MIXED is not an actual mode, but is instead used for a a mixed TypeSetMode situation.
TYPE_SET_MODES_LENGTH

enum core::chemical::VariantType

Enumerators for all the ResidueType variants.

VariantTypes are primarily utilized by the patch system. All the type does is add an identifier that can be used later on in different protocols. It also helps the patch system keep track of which residues are patched with which patches.

Enumerator
NO_VARIANT
FIRST_VARIANT
UPPER_TERMINUS_VARIANT
LOWER_TERMINUS_VARIANT
UPPERTERM_TRUNC_VARIANT
LOWERTERM_TRUNC_VARIANT
PHOSPHONATE_UPPER_VARIANT
CUTPOINT_LOWER
CUTPOINT_UPPER
NTERM_CONNECT
CTERM_CONNECT
DISULFIDE
SC_BRANCH_POINT
C1_BRANCH_POINT
C2_BRANCH_POINT
C3_BRANCH_POINT
C4_BRANCH_POINT
C5_BRANCH_POINT
C6_BRANCH_POINT
C7_BRANCH_POINT
C8_BRANCH_POINT
C9_BRANCH_POINT
SIDECHAIN_CONJUGATION
SG_CONNECT
NE2_CONNECT
ZN_CONNECT
VIRTUAL_METAL_CONJUGATION
METHYLATED_NTERM_VARIANT
ACETYLATED_NTERMINUS_VARIANT
METHYLATED_CTERMINUS_VARIANT
DIMETHYLATED_CTERMINUS_VARIANT
OOP_PRE
OOP_POST
HBS_PRE
HBS_POST
A3B_HBS_PRE
A3B_HBS_POST
CA_CONNECT
CA_CONNECT2
CA_CONNECT3
CA_CONNECT4
CA_CONNECT5
CA_CONNECT6
CA_CONNECT7
OE1_CONNECT
OE2_CONNECT
OD1_CONNECT
OD2_CONNECT
O_CONNECT
OG_CONNECT
OG1_CONNECT
PROTONATED
DEPROTONATED
ALTERNATIVE_PROTONATION
METHYLATION
DIMETHYLATION
TRIMETHYLATION
ACETYLATION
PHOSPHORYLATION
SULFATION
HYDROXYLATION
HYDROXYLATION1
HYDROXYLATION2
CARBOXYLATION
DIIODINATION
N_METHYLATION
VIRTUAL_BB
VIRTUAL_SIDE_CHAIN
VIRTUAL_RESIDUE_VARIANT
VIRTUAL_NTERM
VIRTUAL_PHOSPHATE
VIRTUAL_DNA_PHOSPHATE
REPLS_BB
REPLONLY
REPL_PHOSPHATE
VIRTUAL_RIBOSE
VIRTUAL_BACKBONE_EXCEPT_C1PRIME
VIRTUAL_BASE
VIRTUAL_BASE_HEAVY_ATOM
VIRTUAL_RNA_RESIDUE
VIRTUAL_RNA_RESIDUE_EXCLUDE_PHOSPHATE
BULGE
VIRTUAL_O2PRIME_HYDROGEN
THREE_PRIME_END_OH
THREE_PRIME_PHOSPHATE
THREE_PRIME_AZIDE
THREE_PRIME_DEOXY
FIVE_PRIME_END_OH
FIVE_PRIME_THIOETHANOLAMINE_PHOSPHATE
FIVE_PRIME_END_PHOSPHATE
FIVE_PRIME_PHOSPHATE
FIVE_PRIME_RME_PHOSPHATE
FIVEPRIME_CAP
THREE_PRIME_TWO_PRIME_CYCLIC_PHOSPHATE
DEOXY_O2PRIME
UPPER_CONNECTION_RNA
THREE_PRIME_PACKABLE_PHOSPHATE
FIVE_PRIME_PACKABLE_PHOSPHATE
FIVE_PRIME_PACKABLE_TRIPHOSPHATE
PROTONATED_N1
PROTONATED_N3
THREE_PRIME_FIVE_PRIME_METHYL_PHOSPHATE
BLOCK_STACK_ABOVE
BLOCK_STACK_BELOW
N_ACETYLATION
N_FORMYLATION
C_METHYLAMIDATION
CTERM_AMIDATION
C5_METHYLATED_NA
ALDONIC_ACID_VARIANT
C2_KETOALDONIC_ACID
C3_KETOALDONIC_ACID
C4_KETOALDONIC_ACID
C5_KETOALDONIC_ACID
C6_KETOALDONIC_ACID
C7_KETOALDONIC_ACID
C8_KETOALDONIC_ACID
URONIC_ACID_VARIANT
C1_DEOXY_SUGAR
C2_DEOXY_SUGAR
C3_DEOXY_SUGAR
C4_DEOXY_SUGAR
C5_DEOXY_SUGAR
C6_DEOXY_SUGAR
C7_DEOXY_SUGAR
C8_DEOXY_SUGAR
C9_DEOXY_SUGAR
C1_AMINO_SUGAR
C2_AMINO_SUGAR
C3_AMINO_SUGAR
C4_AMINO_SUGAR
C5_AMINO_SUGAR
C6_AMINO_SUGAR
C7_AMINO_SUGAR
C8_AMINO_SUGAR
C9_AMINO_SUGAR
C1_ACETYLAMINO_SUGAR
C2_ACETYLAMINO_SUGAR
C3_ACETYLAMINO_SUGAR
C4_ACETYLAMINO_SUGAR
C5_ACETYLAMINO_SUGAR
C6_ACETYLAMINO_SUGAR
C7_ACETYLAMINO_SUGAR
C8_ACETYLAMINO_SUGAR
C9_ACETYLAMINO_SUGAR
C1_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR
C2_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR
C3_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR
C4_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR
C5_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR
C6_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR
C7_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR
C8_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR
C9_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR
C1_PHOSPHORYLATED_SUGAR
C2_PHOSPHORYLATED_SUGAR
C3_PHOSPHORYLATED_SUGAR
C4_PHOSPHORYLATED_SUGAR
C5_PHOSPHORYLATED_SUGAR
C6_PHOSPHORYLATED_SUGAR
C7_PHOSPHORYLATED_SUGAR
C8_PHOSPHORYLATED_SUGAR
C9_PHOSPHORYLATED_SUGAR
C1_SULFATED_SUGAR
C2_SULFATED_SUGAR
C3_SULFATED_SUGAR
C4_SULFATED_SUGAR
C5_SULFATED_SUGAR
C6_SULFATED_SUGAR
C7_SULFATED_SUGAR
C8_SULFATED_SUGAR
C9_SULFATED_SUGAR
C1_SULFOAMINO_SUGAR
C2_SULFOAMINO_SUGAR
C3_SULFOAMINO_SUGAR
C4_SULFOAMINO_SUGAR
C5_SULFOAMINO_SUGAR
C6_SULFOAMINO_SUGAR
C7_SULFOAMINO_SUGAR
C8_SULFOAMINO_SUGAR
C9_SULFOAMINO_SUGAR
C1_THIO_SUGAR
C2_THIO_SUGAR
C3_THIO_SUGAR
C4_THIO_SUGAR
C5_THIO_SUGAR
C6_THIO_SUGAR
C7_THIO_SUGAR
C8_THIO_SUGAR
C9_THIO_SUGAR
C1_METHYLATED_SUGAR
C2_METHYLATED_SUGAR
C3_METHYLATED_SUGAR
C4_METHYLATED_SUGAR
C5_METHYLATED_SUGAR
C6_METHYLATED_SUGAR
C7_METHYLATED_SUGAR
C8_METHYLATED_SUGAR
C9_METHYLATED_SUGAR
C1_PHOSPHATE
C2_PHOSPHATE
C3_PHOSPHATE
C4_PHOSPHATE
C5_PHOSPHATE
C6_PHOSPHATE
C7_PHOSPHATE
C8_PHOSPHATE
C9_PHOSPHATE
O1_ACETYL_SUGAR
O2_ACETYL_SUGAR
O3_ACETYL_SUGAR
O4_ACETYL_SUGAR
O5_ACETYL_SUGAR
O6_ACETYL_SUGAR
O7_ACETYL_SUGAR
O8_ACETYL_SUGAR
O9_ACETYL_SUGAR
METHYL_GLYCOSIDE
TRIAZOLAMERN
TRIAZOLAMERC
CA2_COORDINATION
MG2_COORDINATION
CU2_COORDINATION
CO2_COORDINATION
FE2_COORDINATION
FE3_COORDINATION
MN2_COORDINATION
LA3_COORDINATION
LU3_COORDINATION
TB3_COORDINATION
TM3_COORDINATION
DY3_COORDINATION
YB3_COORDINATION
ADDUCT_VARIANT
CENTROID_WITH_HA
SPECIAL_ROT
SC_FRAGMENT
SHOVE_BB
N_VARIANTS

Function Documentation

utility::vector1< std::string > const& core::chemical::aa2name ( )

inline

vector that maps AA enum to string name

References setup_aa2name().

Referenced by name_from_aa().

utility::vector1< char > const& core::chemical::aa2oneletter ( )

inline

vector that maps AA enum to one letter char

References setup_aa2oneletter().

Referenced by oneletter_code_from_aa().

AA core::chemical::aa_from_name

(

std::string const &

name

)

Give an AA string 3-letter code, return its enum type.

References core::sequence::end, and name2aa().

Referenced by core::chemical::ResidueTypeBase::aa(), aa_from_one_or_three(), protocols::protein_interface_design::movers::BuildAlaPose::apply(), protocols::hbnet::ConstrainHBondNetwork::apply(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::splice::Splice::apply(), protocols::flxbb::InterlockAroma::apply(), protocols::flxbb::FilterStructs_TotalCharge::apply(), core::pack::task::operation::RestrictYSDesign::apply(), core::chemical::ResidueTypeBase::backbone_aa(), core::chemical::ResidueTypeBase::base_analogue(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), protocols::motifs::Motif::build_rotamers(), core::chemical::rotamers::CenrotRotamerLibrarySpecification::CenrotRotamerLibrarySpecification(), core::pack::dunbrack::cenrot::CenrotLibrary::create_centroid_rotamer_libraries_from_ASCII(), protocols::hotspot_hashing::HotspotStubSet::create_hotspot_after_pose(), core::chemical::rotamers::DunbrackRotamerLibrarySpecification::DunbrackRotamerLibrarySpecification(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::get_oneletter_codes(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::frag_picker::SidechainContactDistCutoff::initialize(), protocols::match::Matcher::initialize_from_file(), core::io::mmtf::make_current_group(), protocols::motifs::make_dna_mutations(), protocols::motifs::MotifDnaPacker::motif_expansion_inner_loop(), core::chemical::ResidueTypeBase::na_analogue(), protocols::protein_interface_design::movers::BuildAlaPose::parse_my_tag(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::parse_my_tag(), protocols::simple_filters::NeighborTypeFilter::parse_my_tag(), protocols::stepwise::modeler::rna::phosphate::position_five_prime_phosphate_SLOW(), core::pack::interaction_graph::SurfacePotential::read_average_res_hASA_database_file(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::read_from_file(), protocols::optimize_weights::PNatAAOptEPositionData::read_from_file(), protocols::noesy_assign::ResonanceList::read_from_stream(), core::scoring::P_AA::read_P_AA(), core::scoring::P_AA::read_P_AA_n(), core::scoring::P_AA::read_P_AA_pp(), core::scoring::P_AA_ss::read_P_AA_ss(), core::scoring::Ramachandran::read_rama_map_file_shapovalov(), protocols::fldsgn::potentials::SetAACompositionPotential::set_parameters(), and setup_patch_atomic_charge_reassignments_from_commandline().

AA core::chemical::aa_from_one_or_three

(

std::string const &

name

)

References aa_from_name(), and aa_from_oneletter_code().

Referenced by protocols::antibody::design::AntibodySeqDesignTFCreator::disable_disallowed_aa(), protocols::task_operations::ResidueProbDesignOperation::set_aa_probabilities_from_file(), and protocols::antibody::design::CDRSeqDesignOptionsParser::set_disallow_amino_acids().

AA core::chemical::aa_from_oneletter_code

(

char

onelettercode

)

give a 1 letter code and return the string name

References aa_unk, core::sequence::end, and oneletter2aa().

Referenced by core::sequence::AnnotatedSequence::aa(), aa_from_one_or_three(), protocols::noesy_assign::ResonanceList::aa_from_resid(), core::pack::task::operation::RestrictAbsentCanonicalAASRLT::aas_to_keep(), core::pack::task::operation::RestrictAbsentCanonicalAASExceptNativeRLT::aas_to_keep(), core::scoring::abego3aa_to_index(), protocols::simple_moves::RepeatPropagationMover::add_cap_seq(), core::scoring::methods::NMerSVMEnergy::add_pssm_features(), protocols::forge::components::BDR::allowed_surface_aa(), protocols::forge::remodel::RemodelMover::allowed_surface_aa(), core::conformation::Residue::annotated_name(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::matdes::SchemePlaceMotifsMover::apply(), protocols::task_operations::ConservativeDesignOperation::apply(), protocols::task_operations::ThreadSequenceOperation::apply(), protocols::evolution::NucleotideMutation::apply(), protocols::task_operations::JointSequenceOperation::apply(), protocols::simple_moves::SimpleThreadingMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), protocols::pose_creation::MergePDBatOverlapMover::assign_seq(), protocols::pose_creation::MakeJunctionsMover::assign_seq(), protocols::splice::SpliceOutTail::build_ideal_segment(), protocols::splice::SpliceInTail::build_ideal_segment(), protocols::splice::SpliceIn::build_ideal_segment(), protocols::splice::SpliceOut::build_ideal_segment(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_binding_data(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), core::scoring::ScoringManager::create_nmer_pssm(), protocols::stepwise::monte_carlo::mover::AddMover::create_residue_to_add(), protocols::parser::ScoreFunctionLoader::create_scorefxn_from_tag(), core::scoring::dna::DirectReadoutPotential::DirectReadoutPotential(), core::pack::task::operation::DisallowIfNonnativeRLT::disallow_aas(), core::pack::task::operation::DisallowIfNonnative::disallow_aas(), protocols::frag_picker::scores::ProfileScoreSubMatrix::do_caching(), protocols::pose_length_moves::InsertResMover::extendRegion(), protocols::pose_length_moves::PossibleLoop::extendRegion(), protocols::pose_length_moves::NearNativeLoopCloser::extendRegion(), core::scoring::motif::ResPairMotif::fill_pose_with_motif(), core::scoring::methods::FreeDOF_Energy::finalize_total_energy(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), core::enzymes::get_AA_3_letter_codes_or_punctuation_from_1_letter_code_at_position(), protocols::recon_design::get_candidate_AAs(), protocols::motif_grafting::movers::MotifGraftMover::get_fragments_by_CA_distances_and_NCpoints_restrains(), core::conformation::get_residue_from_name1(), protocols::simple_filters::ResidueDepthFilter::get_residue_similarity(), protocols::task_operations::DsspDesignOperation::get_restrictions(), protocols::flxbb::LayerDesignOperation::get_restrictions(), protocols::forge::remodel::RemodelData::getLoopsToBuildFromBlueprint(), protocols::sasa_scores::help_load_data(), core::pack::task::PIKAA::initialize_from_tokens(), core::pack::task::NOTAA::initialize_from_tokens(), core::sequence::ProfSimScoringScheme::initialize_parameters(), core::import_pose::libraries::ChunkSet::insert_protein_chunk_into_pose(), core::pack::task::operation::RestrictAbsentCanonicalAAS::keep_aas(), protocols::antibody::AntibodyDatabaseManager::load_cdr_design_data_for_cdrs(), protocols::antibody::design::MutateFrameworkForCluster::load_data(), protocols::task_operations::ConservativeDesignOperation::load_data_from_db(), protocols::noesy_assign::MethylNameLibrary::load_database_table(), protocols::protein_interface_design::ReportPSSMDifferences::load_pssm_data(), protocols::optimize_weights::IterativeOptEDriver::load_pssm_data(), core::scoring::dna::DNA_EnvPairPotential::load_score_tables(), protocols::protein_interface_design::movers::PlaceOnLoop::loop_length(), protocols::denovo_design::task_operations::make_aa_bitmap_from_allowed_aas(), protocols::denovo_design::task_operations::make_aa_bitmap_from_forbidden_aas(), protocols::pmut_scan::PointMutScanDriver::make_mutant_structure(), protocols::membrane::MPMutateRelaxMover::make_mutations(), core::fragment::make_pose_from_sequence_(), protocols::tcr::match_template_and_target_sequence(), protocols::analysis::InterfaceAnalyzerMover::mut_to_gly(), core::scoring::nv::NVlookup::NVlookup(), core::fragment::picking_old::vall::VallResidue::order_vector(), protocols::frag_picker::VallResidue::order_vector(), protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::ParallelBetaPairingPreferenceFilter(), protocols::mean_field::AAMatrix::parse_aa_line(), core::pack::task::operation::DesignRestrictions::parse_tag(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::partition(), protocols::loop_modeler::perturbers::LoopHashPerturber::perturb_subset(), core::scoring::motif::Xfres::place_sidechain_in_pose(), protocols::multistate_design::PosType::PosType(), protocols::ligand_docking::ProtLigEnsemble::prepare_single_ligand_pose(), protocols::pack_daemon::EntityFunc::process_AA_SET_line(), protocols::forge::components::BDR::process_continuous_design_string(), protocols::forge::remodel::RemodelMover::process_continuous_design_string(), protocols::forge::components::BDR::process_insert_design_string(), protocols::forge::remodel::RemodelMover::process_insert_design_string(), protocols::pack_daemon::EntityFunc::process_SET_CONDITION_line(), protocols::dna::DnaInterfacePacker::protein_scan(), core::sequence::MatrixScoringScheme::read_data(), core::io::PositionDdGInfo::read_ddg_predictions_file(), core::sequence::SequenceProfile::read_from_binary_chk(), core::sequence::SequenceProfile::read_from_checkpoint(), core::sequence::SequenceProfile::read_from_file(), protocols::noesy_assign::ResonanceList::read_from_stream(), protocols::read_in_mutations(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::read_params(), core::pack::task::TARGET::residue_action(), core::pose::residue_types_from_sequence(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::ROT2res(), core::sequence::MatrixScoringScheme::score(), protocols::frag_picker::scores::HydrophobicityProfileSimilarity::score(), protocols::indexed_structure_store::SegmentSequenceProfile::segment_profile(), protocols::task_operations::RestrictConservedLowDdgOperation::seqprof_wt_aa(), protocols::forge::remodel::RemodelLoopMover::set_starting_sequence(), protocols::hydrate::set_task_and_movemap(), protocols::noesy_assign::FragsToAtomDist::swap_atoms(), protocols::simple_moves::ResTypeFragmentMover::swap_residue_types(), protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::to_sequence_profile(), protocols::antibody::design::transform_sequence_to_mutation_set(), and core::sequence::MatrixScoringScheme::values_for_aa().

void core::chemical::add_atom_type_set_parameters_from_command_line	(	std::string const &	atom_type_set_tag,
		AtomTypeSet &	atom_type_set
	)

Add additional parameter files not present in <atom-set-name>/extras.txt.

Called by ChemicalManager at time of AtomTypeSet creation.

References core::chemical::AtomTypeSet::add_parameters_from_file(), protocols::abinitio::filename(), and TR().

Referenced by core::chemical::ChemicalManager::create_atom_type_set().

void core::chemical::annotate_backbone

(

MutableResidueType &

restype

)

Annotate "backbone" atoms. For the purpose of this function, backbone atoms are any atoms which are connected to another backbone atom by a non-rotatable, non-cut bond. Atoms connected to the upper and/or lower connect points are always backbone. Important - if Chis/cuts aren't properly annotated, all atoms will be backbone.

References core::chemical::MutableResidueType::all_atoms(), core::chemical::MutableResidueType::atom(), core::chemical::MutableResidueType::bond(), core::chemical::MutableResidueType::bonded_neighbors(), core::chemical::MutableResidueType::chi_atom_vds(), protocols::sparta::contains(), core::chemical::Bond::cut_bond(), core::chemical::Atom::is_backbone(), core::chemical::MutableResidueType::lower_connect_atom(), core::chemical::MutableResidueType::lower_connect_id(), protocols::sic_dock::scores::nbr, core::chemical::MutableResidueType::nchi(), core::chemical::MutableResidueType::upper_connect_atom(), and core::chemical::MutableResidueType::upper_connect_id().

Referenced by core::chemical::MutableResidueType::autodetermine_chi_bonds().

MutableResidueTypeOP core::chemical::apply_adducts_to_residue	(	ResidueType const &	rsd,
		utility::vector1< bool > &	add_mask
	)

Apply adducts to residue using a boolean mask.

References core::chemical::PatchCase::add_operation(), ADDUCT_VARIANT, core::chemical::PatchCase::apply(), core::chemical::ResidueTypeBase::defined_adducts(), core::chemical::ResidueTypeBase::name(), and TR().

Referenced by create_adduct_combinations().

void core::chemical::apply_symm_gly_corrections	(	std::string const &	child_atom,
		core::Real &	phi,
		core::Real &	,
		core::Real &	d,
		std::string &	,
		std::string &	,
		std::string &	torsion_atom
	)

Symmetrize the glycine params file (if the user has used the -symmetric_gly_tables option).

Ugh. Special-case logic.

Author

Vikram K. Mulligan, Baker laboratory (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by read_topology_file().

gasteiger::GasteigerAtomTypeData::Properties core::chemical::bond_order_to_property

(

const core::Size &

BOND_ORDER_OR_AROMATIC

)

convert bond order or aromatic into the corresponding radius

Parameters

BOND_ORDER_OR_AROMATIC

bond type in notation: 1=single, 2=double, 3=triple, 4=aromatic

References core::chemical::gasteiger::GasteigerAtomTypeData::CovalentRadiusAromaticBond, core::chemical::gasteiger::GasteigerAtomTypeData::CovalentRadiusDoubleBond, core::chemical::gasteiger::GasteigerAtomTypeData::CovalentRadiusSingleBond, core::chemical::gasteiger::GasteigerAtomTypeData::CovalentRadiusTripleBond, update_ResidueType_enum_files::properties, and core::chemical::gasteiger::GasteigerAtomTypeData::VdWaalsRadiusCSD.

Referenced by create_bond_length().

void core::chemical::calculate_rigid_matrix	(	MutableResidueType const &	res,
		VDDistanceMatrix &	distances
	)

Calculate the rigid matrix - assume that distances has been initialized to some really large value, and is square.

Calculate the rigid matrix - assume that distances has been initialized to some really large value, and is square Helper for find_nbr_dist.

References core::chemical::MutableResidueType::all_atoms(), core::chemical::MutableResidueType::atom_iterators(), core::chemical::MutableResidueType::atom_name(), core::chemical::MutableResidueType::graph(), core::chemical::ResidueTypeBase::name(), and TR().

Referenced by find_nbr_dist().

PatchCaseOP core::chemical::case_from_lines	(	utility::vector1< std::string > const &	lines,
		TypeSetMode	res_type_set_mode,
		std::string const &	patch_name
	)

create a PatchCase from input lines

add selector_ from lines enclosed by "BEGIN_SELECTOR" and "END_SELECTOR".
add operations_ from each input line containing a single operation

References patch_operation_from_patch_file_line(), setup_patch_atomic_charge_reassignments_from_commandline(), and tag_from_line().

Referenced by core::chemical::Metapatch::get_one_patch(), core::chemical::Metapatch::read_file(), and core::chemical::Patch::read_file().

std::string const core::chemical::CENTROID

(

"centroid"

)

tag name for querying fullatom chemical type set.

std::string const core::chemical::CENTROID_ROT

(

"centroid_rot"

)

tag name for querying centroid_rot chemical type set.

void core::chemical::check_residue_has_atom	(	std::string const &	atom_name,
		core::chemical::MutableResidueType const &	rsd,
		std::string const &	location
	)

References core::chemical::MutableResidueType::has(), INTERNAL, core::chemical::ResidueTypeBase::name(), and string_to_icoord_type().

Referenced by core::chemical::SetICoor::apply().

static std::string const core::chemical::chr_chains ( "ABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890abcdefghijklmnopqrstuvwxyz"  )

static

Referenced by core::pose::full_model_info::figure_out_conventional_chains_from_full_model_info(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_new_chainIDs(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_residue_information(), and core::pack::task::ResfileContents::parse_resid().

void core::chemical::clean_up_dangling_connect	(	core::chemical::MutableResidueType &	restype,
		ICoordAtomIDType	remove_type
	)

Attempt to find new ICOOR definitions for entries in the ResidueType which rely on a now-deleted upper/lower connection (Connection type is specified by the passed type.)

Assumes that all of the xyz coordinates are updated.

References core::chemical::MutableResidueType::atom(), core::chemical::MutableResidueType::atom_iterators(), core::chemical::MutableResidueType::atom_name(), core::chemical::MutableResidueType::atom_vertex(), core::chemical::MutableICoorRecord::d(), core::chemical::MutableResidueType::icoor(), core::chemical::Atom::ideal_xyz(), INTERNAL, core::chemical::MutableResidueType::lower_connect_id(), core::chemical::ResidueTypeBase::name(), POLYMER_LOWER, POLYMER_UPPER, core::chemical::MutableResidueType::set_icoor(), core::chemical::MutableICoorRecord::stub_atom1(), core::chemical::MutableICoorRecord::stub_atom2(), core::chemical::MutableICoorRecord::stub_type1(), core::chemical::MutableICoorRecord::stub_type2(), core::chemical::MutableICoorRecord::stub_type3(), core::chemical::MutableICoorRecord::theta(), TR(), core::chemical::MutableResidueType::upper_connect_id(), walk_back_to_find_usable_base(), and core::chemical::MutableICoorRecord::xyz().

Referenced by core::chemical::SetPolymerConnectAtom::apply().

std::string const core::chemical::COARSE_RNA

(

"coarse_rna"

)

tag name for querying COARSE_RNA chemical type set.

bool core::chemical::compare_atom_icoor	(	AtomICoor const &	aic1,
		AtomICoor const &	aic2,
		bool	fuzzy
	)

Are the two ResidueConnection objects equivalent Here instead of in operator== because of the fuzzy-real issue.

References core::chemical::AtomICoor::built_atom(), core::chemical::AtomICoor::d(), core::chemical::AtomICoor::phi(), core::chemical::AtomICoor::stub_atom1(), core::chemical::AtomICoor::stub_atom2(), core::chemical::AtomICoor::stub_atom3(), and core::chemical::AtomICoor::theta().

Referenced by compare_residue_connection(), and residue_types_identical().

bool core::chemical::compare_residue_connection	(	ResidueConnection const &	rc1,
		ResidueConnection const &	rc2,
		bool	fuzzy
	)

Are the two ResidueConnection objects equivalent Here instead of in operator== because of the fuzzy-real issue.

References core::chemical::ResidueConnection::atomno(), compare_atom_icoor(), core::chemical::ResidueConnection::icoor(), and core::chemical::ResidueConnection::index().

Referenced by residue_types_identical().

void core::chemical::complex_ring_detection

(

MutableResidueType &

res

)

References core::chemical::MutableResidueType::atom_name(), core::chemical::MutableResidueType::bond(), BondInRing, convert_residuetype_to_light_graph(), core::chemical::MutableResidueType::graph(), and core::chemical::Bond::ringness().

Referenced by find_bonds_in_rings().

LightWeightResidueGraph core::chemical::convert_residuetype_to_light_graph

(

MutableResidueType const &

res

)

References protocols::forge::methods::add_vertex(), and core::chemical::MutableResidueType::graph().

Referenced by complex_ring_detection().

BondName core::chemical::convert_to_BondName

(

std::string const &

id

)

References AromaticBond, DoubleBond, OrbitalBond, PseudoBond, SingleBond, TripleBond, and UnknownBond.

Referenced by core::chemical::AddBondType::apply(), core::chemical::ChangeBondType::apply(), and read_topology_file().

std::string core::chemical::correct_conn	(	std::string const &	old,
		core::Size const	conn_id_deleted
	)

A short utility function for update_icoors_after_connection_deletion()

References CONNECT, get_connection_number(), string_to_icoord_type(), and core::id::to_string().

Referenced by core::chemical::MutableResidueType::update_icoors_after_connection_deletion().

MutableResidueTypeOPs core::chemical::create_adduct_combinations	(	ResidueType const &	rsd,
		AdductMap	ref_map,
		AdductMap	count_map,
		utility::vector1< bool >	add_mask,
		utility::vector1< Adduct >::const_iterator	work_iter
	)

Create correct combinations of adducts for a residue type.

References apply_adducts_to_residue(), and core::chemical::ResidueTypeBase::defined_adducts().

Referenced by core::chemical::GlobalResidueTypeSet::place_adducts().

Real core::chemical::create_bond_length	(	gasteiger::GasteigerAtomTypeData const &	atom1,
		gasteiger::GasteigerAtomTypeData const &	atom2,
		BondName	bond_type
	)

this will create a bond length based on gasteiger atom type definitions of bonds

References bond_order_to_property(), and core::chemical::gasteiger::GasteigerAtomTypeData::get_atom_type_property().

AtomPropertiesOP core::chemical::deep_copy

(

AtomProperties const &

source

)

ResiduePropertiesOP core::chemical::deep_copy

(

ResidueProperties const &

source

)

void core::chemical::detect_ld_chirality_from_polymer_residue	(	core::chemical::MutableResidueType const &	restype,
		bool &	is_d_aa,
		bool &	is_l_aa
	)

References core::chemical::MutableResidueType::all_atoms(), core::chemical::MutableResidueType::atom(), core::chemical::MutableResidueType::atom_name(), core::chemical::Atom::ideal_xyz(), core::chemical::ResidueTypeBase::name(), and protocols::kinmatch::xyz().

Referenced by core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_resolve_residue_types(), and read_topology_file().

void core::chemical::detect_ld_chirality_from_polymer_residue	(	std::map< std::string, Vector > const &	xyz,
		std::string const &	name3,
		bool &	is_d_aa,
		bool &	is_l_aa
	)

void core::chemical::enlarge_h_lj_wdepth	(	utility::vector1< Real > &	lj_wdepth,
		AtomTypeSet const &	atom_type_set
	)

Fang-Chieh Chou 8/10/2012. Use larger LJ_WDEPTH for protons to avoid clashes in RNA.

References core::chemical::AtomTypeSet::atom_type_index(), and core::chemical::AtomTypeSet::n_atomtypes().

Referenced by enlarge_h_lj_wdepth(), core::scoring::etable::Etable::initialize_from_input_atomset(), and core::chemical::AtomTypeSet::legacy_command_line_post_processing().

void core::chemical::enlarge_h_lj_wdepth

(

AtomTypeSet &

atom_type_set

)

Fang-Chieh Chou 8/10/2012. Use larger LJ_WDEPTH for protons to avoid clashes in RNA.

References enlarge_h_lj_wdepth(), and core::chemical::AtomTypeSet::n_atomtypes().

void core::chemical::error_check_requested_adducts	(	std::map< std::string, int > const &	add_map,
		ResidueTypeCOPs const &	rsd_types
	)

Make sure requested adducts exist in some residue.

Make sure requested adducts exist in some residue.

References core::chemical::ResidueTypeBase::defined_adducts().

Referenced by core::chemical::GlobalResidueTypeSet::place_adducts().

void core::chemical::error_check_requested_adducts	(	std::map< std::string, int > const &	add_map,
		ResidueTypeCOPs const &	rsd_types
	)

Make sure any adducts requested actually exist.

Make sure requested adducts exist in some residue.

References core::chemical::ResidueTypeBase::defined_adducts().

Referenced by core::chemical::GlobalResidueTypeSet::place_adducts().

std::string core::chemical::expand_icoor_atom_name	(	std::string	name,
		MutableResidueType const &	rsd
	)

References core::chemical::MutableResidueType::n_possible_residue_connections().

Referenced by core::chemical::SetICoor::apply().

std::string const core::chemical::FA_STANDARD

(

"fa_standard"

)

tag name for querying fullatom chemical type set.

void core::chemical::fill_ideal_xyz_from_icoor	(	core::chemical::MutableResidueType &	restype,
		core::chemical::ResidueGraph const &	graph
	)

Contains logic originally from read_topology_file()

References core::pose::motif::a(), core::chemical::MutableResidueType::atom_name(), core::chemical::MutableResidueType::atom_vertex(), core::chemical::MutableICoorRecord::build_xyz(), core::kinematics::Stub::create_orthogonal(), core::chemical::MutableResidueType::has(), has_assigned_coords(), core::chemical::MutableResidueType::icoor(), core::chemical::ResidueTypeBase::name(), core::chemical::MutableResidueType::natoms(), core::chemical::MutableResidueType::set_ideal_xyz(), protocols::fldsgn::potentials::sspot::spherical(), and TR().

Referenced by core::chemical::MutableResidueType::fill_ideal_xyz_from_icoor(), and core::chemical::ResidueDatabaseIO::read_residue_type_icoor().

template<class Graph >

core::Size core::chemical::filtered_num_vertices

(

Graph const &

graph

)

It's a frustrating truth, but num_vertices doesn't give the number of filtered vertices for filtered graphs, but instead gives the number of underlying vertices ... this gets the true number of filtered vertices.

ResidueTypeCOP core::chemical::find_best_match	(	ResidueTypeCOPs const &	rsd_type_list,
		utility::vector1< std::string > const &	atom_names,
		bool const	ignore_atom_named_H
	)

look for best match to atom_names

taken out of build_pose_as_is1 rsd_type should have all the atoms present in xyz try to minimize atoms missing from xyz

References core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::has(), and core::chemical::ResidueType::natoms().

Referenced by core::chemical::ResidueTypeFinder::get_best_match_residue_type_for_atom_names().

void core::chemical::find_bonds_in_rings	(	MutableResidueType &	res,
		bool const	complex_ring
	)

Determine which bonds are in rings, and set the BondRingness property of each.

References core::chemical::MutableResidueType::bond(), BondNotInRing, complex_ring_detection(), core::chemical::MutableResidueType::graph(), quick_ring_detection(), and core::chemical::Bond::ringness().

Referenced by core::chemical::ReplaceProtonWithTrifluoromethyl::apply(), core::chemical::ReplaceProtonWithMethyl::apply(), core::chemical::ReplaceProtonWithMethoxy::apply(), core::chemical::ReplaceProtonWithEthyl::apply(), core::chemical::ReplaceProtonWithChlorine::apply(), core::chemical::ReplaceProtonWithFluorine::apply(), core::chemical::ReplaceProtonWithBromine::apply(), core::chemical::ReplaceProtonWithIodine::apply(), core::chemical::ReplaceProtonWithHydroxyl::apply(), core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType(), and reroot_restype().

utility::vector1< VDs > core::chemical::find_chi_bonds

(

MutableResidueType const &

restype

)

Find which bonds are rotatatable (chi) bonds Returns a list of four vds representing the chi.

Assumes:

• Complete Atom/bond graph
• All element types have been set
• All bond_names have been set.
• Ringness has been set for all bonds
• The Icoor graph has been set.

References core::pose::motif::a(), core::chemical::MutableResidueType::atom(), core::chemical::MutableResidueType::atom_base(), core::chemical::MutableResidueType::atom_name(), protocols::match::upstream::b, core::chemical::MutableResidueType::bond(), core::chemical::MutableResidueType::bond_iterators(), BondInRing, core::chemical::element::C, core::pack::dunbrack::c, core::chemical::Atom::element_type(), core::chemical::MutableResidueType::graph(), core::chemical::element::H, core::chemical::Bond::order(), core::chemical::MutableResidueType::root_atom(), SingleBond, core::id::swap(), TR(), TripleBondOrder, and UnknownRingness.

Referenced by core::chemical::MutableResidueType::autodetermine_chi_bonds().

core::Real core::chemical::find_nbr_dist	(	MutableResidueType const &	res,
		VD &	nbr_atom
	)

Find the neighbor distance to the given neighbor atom. If nbr_atom is null_vertex, give the smallest neighbor distance, and set nbr_atom to the atom for that distance.

The neighbor distance here is adjusted for rotatable bonds - It should be at least as large as the maximum neighbor distance in any torsional rotamer If the neighbor atom is not provided, the atom chosen will be a multiply-bonded heavy atom.

Assumes:

• All atoms and bond are present
• All ideal_xyz coordinates have been set
• All elements have been set

All ring bonds have been annotated

References core::chemical::MutableResidueType::all_atoms(), core::chemical::MutableResidueType::atom(), core::chemical::MutableResidueType::atom_iterators(), core::chemical::MutableResidueType::atom_name(), core::chemical::MutableResidueType::bonded_neighbor_iterators(), calculate_rigid_matrix(), core::chemical::Atom::element_type(), core::chemical::VDDistanceMatrix::find_max_over(), core::chemical::element::H, core::chemical::ResidueTypeBase::name(), core::chemical::MutableResidueType::natoms(), core::chemical::MutableResidueType::null_vertex, and TR().

Referenced by core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType().

std::string core::chemical::fixup_patches

(

std::string const &

string_in

)

Replaces the deprecated "_p:" linker connecting ResidueType base names with their patch names with ":".

Note

This is here for backwards compatibility.

References PATCH_LINKER.

Referenced by core::chemical::ResidueTypeSet::has_name(), core::chemical::ResidueTypeSet::name_mapOP(), core::chemical::ResidueTypeSet::name_mapOP_write_locked(), and core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff().

std::string core::chemical::formatted_icoord_tree

(

core::chemical::ResidueType const &

restype

)

Return a string representing the internal coordinates tree of this ResidueType.

Note

Mainly intended for debugging purposes.

References core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::icoor(), and core::chemical::ResidueType::natoms().

Referenced by print_chis().

std::string core::chemical::formatted_icoord_tree

(

core::chemical::MutableResidueType const &

restype

)

Return a string representing the internal coordinates tree of this MutableResidueType (if any)

Note

Mainly intended for debugging purposes. MutableResidueTypes don't necessarily have an icoor tree.

References core::chemical::MutableResidueType::all_atoms(), core::chemical::MutableResidueType::atom_name(), core::chemical::MutableResidueType::atom_vertex(), core::chemical::MutableResidueType::has(), core::chemical::MutableResidueType::icoor(), core::chemical::MutableResidueType::null_vertex, and core::chemical::MutableResidueType::root_atom().

utility::vector1< std::string > const* core::chemical::generate_property_to_string_vector

(

)

References ACETYL_SUGAR, ACETYLAMINO_SUGAR, ACETYLATED_NTERMINUS, ACHIRAL_BACKBONE, ACHIRAL_SIDECHAIN, ADDUCT, ALDONIC_ACID, ALDOSE, ALIPHATIC, ALPHA_AA, ALPHA_SUGAR, AMINO_SUGAR, ARAMID, AROMATIC, BETA_AA, BETA_SUGAR, BRANCH_POINT, C1_MODIFIED, C2_MODIFIED, C3_MODIFIED, C4_MODIFIED, C5_MODIFIED, C6_MODIFIED, C7_MODIFIED, C8_MODIFIED, C9_MODIFIED, C_METHYLATED_SUGAR, CANONICAL_AA, CANONICAL_NUCLEIC, CARBOHYDRATE, CHARGED, COARSE, CYCLIC, D_AA, D_RNA, D_SUGAR, DEOXY_SUGAR, DIAMAGNETIC, DIMETHYLATED_CTERMINUS, DISULFIDE_BONDED, DNA, ELECTROPHILE, FRAGMENT, FURANOSE, GAMMA_AA, GLYCOSIDE, HEPTOSE, HEXOSE, HYDROPHOBIC, INVERTED_VIRTUAL_RESIDUE, KETOSE, L_AA, L_RNA, L_SUGAR, LIGAND, LIPID, LOWER_TERMINUS, LOWERTERM_CAP, LOWERTERM_TRUNC, MEMBRANE, META_ARAMID, METAL, METALBINDING, METHYLATED_CTERMINUS, METHYLATED_NA, N_METHYLATED, N_PROPERTIES, NEGATIVE_CHARGE, NONOSE, NUCLEOTIDE_DIPHOSPHATE, OCTOSE, OLIGOUREA, ORTHO_ARAMID, OXETOSE, OXIROSE, PARA_ARAMID, PARAMAGNETIC, PENTOSE, PEPTOID, PHOSPHATE, PHOSPHONATE, PHOSPHONATE_UPPER, PHOSPHORYLATED_SUGAR, PNA, POLAR, POLYMER, POSITIVE_CHARGE, POST_METHYLENE_META_ARAMID, POST_METHYLENE_ORTHO_ARAMID, POST_METHYLENE_PARA_ARAMID, PRE_METHYLENE_META_ARAMID, PRE_METHYLENE_ORTHO_ARAMID, PRE_METHYLENE_PARA_ARAMID, PRE_METHYLENE_POST_METHYLENE_META_ARAMID, PRE_METHYLENE_POST_METHYLENE_ORTHO_ARAMID, PRE_METHYLENE_POST_METHYLENE_PARA_ARAMID, PROTEIN, PURINE, PYRANOSE, PYRIMIDINE, R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, R_PEPTOID, RNA, S_PEPTOID, SC_ORBITALS, SEPTANOSE, SIALIC_ACID, SIDECHAIN_AMINE, SIDECHAIN_THIOL, SOLVENT, SPINLABEL, SRI, SULFATED_SUGAR, SULFOAMINO_SUGAR, SURFACE, TAUTOMER, TERMINUS, TERPENE, TETROSE, THIO_SUGAR, TNA, TP3, TRIAZOLE_LINKER, TRIOSE, UPPER_TERMINUS, UPPERTERM_CAP, UPPERTERM_TRUNC, URONIC_ACID, VIRTUAL_RESIDUE, VIRTUALIZABLE_BY_PACKER, VRT1, and WATER.

std::map< std::string, ResidueProperty > const* core::chemical::generate_string_to_property_map

(

)

References ACETYL_SUGAR, ACETYLAMINO_SUGAR, ACETYLATED_NTERMINUS, ACHIRAL_BACKBONE, ACHIRAL_SIDECHAIN, ADDUCT, ALDONIC_ACID, ALDOSE, ALIPHATIC, ALPHA_AA, ALPHA_SUGAR, AMINO_SUGAR, ARAMID, AROMATIC, BETA_AA, BETA_SUGAR, BRANCH_POINT, C1_MODIFIED, C2_MODIFIED, C3_MODIFIED, C4_MODIFIED, C5_MODIFIED, C6_MODIFIED, C7_MODIFIED, C8_MODIFIED, C9_MODIFIED, C_METHYLATED_SUGAR, CANONICAL_AA, CANONICAL_NUCLEIC, CARBOHYDRATE, CHARGED, COARSE, CYCLIC, D_AA, D_RNA, D_SUGAR, DEOXY_SUGAR, DIAMAGNETIC, DIMETHYLATED_CTERMINUS, DISULFIDE_BONDED, DNA, ELECTROPHILE, FRAGMENT, FURANOSE, GAMMA_AA, GLYCOSIDE, HEPTOSE, HEXOSE, HYDROPHOBIC, INVERTED_VIRTUAL_RESIDUE, KETOSE, L_AA, L_RNA, L_SUGAR, LIGAND, LIPID, LOWER_TERMINUS, LOWERTERM_CAP, LOWERTERM_TRUNC, MEMBRANE, META_ARAMID, METAL, METALBINDING, METHYLATED_CTERMINUS, METHYLATED_NA, N_METHYLATED, NEGATIVE_CHARGE, NO_PROPERTY, NONOSE, NUCLEOTIDE_DIPHOSPHATE, OCTOSE, OLIGOUREA, ORTHO_ARAMID, OXETOSE, OXIROSE, PARA_ARAMID, PARAMAGNETIC, PENTOSE, PEPTOID, PHOSPHATE, PHOSPHONATE, PHOSPHONATE_UPPER, PHOSPHORYLATED_SUGAR, PNA, POLAR, POLYMER, POSITIVE_CHARGE, POST_METHYLENE_META_ARAMID, POST_METHYLENE_ORTHO_ARAMID, POST_METHYLENE_PARA_ARAMID, PRE_METHYLENE_META_ARAMID, PRE_METHYLENE_ORTHO_ARAMID, PRE_METHYLENE_PARA_ARAMID, PRE_METHYLENE_POST_METHYLENE_META_ARAMID, PRE_METHYLENE_POST_METHYLENE_ORTHO_ARAMID, PRE_METHYLENE_POST_METHYLENE_PARA_ARAMID, PROTEIN, PURINE, PYRANOSE, PYRIMIDINE, R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, R_PEPTOID, RNA, S_PEPTOID, SC_ORBITALS, SEPTANOSE, SIALIC_ACID, SIDECHAIN_AMINE, SIDECHAIN_THIOL, SOLVENT, SPINLABEL, SRI, SULFATED_SUGAR, SULFOAMINO_SUGAR, SURFACE, TAUTOMER, TERMINUS, TERPENE, TETROSE, THIO_SUGAR, TNA, TP3, TRIAZOLE_LINKER, TRIOSE, UPPER_TERMINUS, UPPERTERM_CAP, UPPERTERM_TRUNC, URONIC_ACID, VIRTUAL_RESIDUE, VIRTUALIZABLE_BY_PACKER, VRT1, and WATER.

std::map< std::string, VariantType > const* core::chemical::generate_string_to_variant_map

(

)

References A3B_HBS_POST, A3B_HBS_PRE, ACETYLATED_NTERMINUS_VARIANT, ACETYLATION, ADDUCT_VARIANT, ALDONIC_ACID_VARIANT, ALTERNATIVE_PROTONATION, BLOCK_STACK_ABOVE, BLOCK_STACK_BELOW, BULGE, C1_ACETYLAMINO_SUGAR, C1_AMINO_SUGAR, C1_BRANCH_POINT, C1_DEOXY_SUGAR, C1_METHYLATED_SUGAR, C1_PHOSPHATE, C1_PHOSPHORYLATED_SUGAR, C1_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C1_SULFATED_SUGAR, C1_SULFOAMINO_SUGAR, C1_THIO_SUGAR, C2_ACETYLAMINO_SUGAR, C2_AMINO_SUGAR, C2_BRANCH_POINT, C2_DEOXY_SUGAR, C2_KETOALDONIC_ACID, C2_METHYLATED_SUGAR, C2_PHOSPHATE, C2_PHOSPHORYLATED_SUGAR, C2_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C2_SULFATED_SUGAR, C2_SULFOAMINO_SUGAR, C2_THIO_SUGAR, C3_ACETYLAMINO_SUGAR, C3_AMINO_SUGAR, C3_BRANCH_POINT, C3_DEOXY_SUGAR, C3_KETOALDONIC_ACID, C3_METHYLATED_SUGAR, C3_PHOSPHATE, C3_PHOSPHORYLATED_SUGAR, C3_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C3_SULFATED_SUGAR, C3_SULFOAMINO_SUGAR, C3_THIO_SUGAR, C4_ACETYLAMINO_SUGAR, C4_AMINO_SUGAR, C4_BRANCH_POINT, C4_DEOXY_SUGAR, C4_KETOALDONIC_ACID, C4_METHYLATED_SUGAR, C4_PHOSPHATE, C4_PHOSPHORYLATED_SUGAR, C4_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C4_SULFATED_SUGAR, C4_SULFOAMINO_SUGAR, C4_THIO_SUGAR, C5_ACETYLAMINO_SUGAR, C5_AMINO_SUGAR, C5_BRANCH_POINT, C5_DEOXY_SUGAR, C5_KETOALDONIC_ACID, C5_METHYLATED_NA, C5_METHYLATED_SUGAR, C5_PHOSPHATE, C5_PHOSPHORYLATED_SUGAR, C5_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C5_SULFATED_SUGAR, C5_SULFOAMINO_SUGAR, C5_THIO_SUGAR, C6_ACETYLAMINO_SUGAR, C6_AMINO_SUGAR, C6_BRANCH_POINT, C6_DEOXY_SUGAR, C6_KETOALDONIC_ACID, C6_METHYLATED_SUGAR, C6_PHOSPHATE, C6_PHOSPHORYLATED_SUGAR, C6_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C6_SULFATED_SUGAR, C6_SULFOAMINO_SUGAR, C6_THIO_SUGAR, C7_ACETYLAMINO_SUGAR, C7_AMINO_SUGAR, C7_BRANCH_POINT, C7_DEOXY_SUGAR, C7_KETOALDONIC_ACID, C7_METHYLATED_SUGAR, C7_PHOSPHATE, C7_PHOSPHORYLATED_SUGAR, C7_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C7_SULFATED_SUGAR, C7_SULFOAMINO_SUGAR, C7_THIO_SUGAR, C8_ACETYLAMINO_SUGAR, C8_AMINO_SUGAR, C8_BRANCH_POINT, C8_DEOXY_SUGAR, C8_KETOALDONIC_ACID, C8_METHYLATED_SUGAR, C8_PHOSPHATE, C8_PHOSPHORYLATED_SUGAR, C8_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C8_SULFATED_SUGAR, C8_SULFOAMINO_SUGAR, C8_THIO_SUGAR, C9_ACETYLAMINO_SUGAR, C9_AMINO_SUGAR, C9_BRANCH_POINT, C9_DEOXY_SUGAR, C9_METHYLATED_SUGAR, C9_PHOSPHATE, C9_PHOSPHORYLATED_SUGAR, C9_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C9_SULFATED_SUGAR, C9_SULFOAMINO_SUGAR, C9_THIO_SUGAR, C_METHYLAMIDATION, CA2_COORDINATION, CA_CONNECT, CA_CONNECT2, CA_CONNECT3, CA_CONNECT4, CA_CONNECT5, CA_CONNECT6, CA_CONNECT7, CARBOXYLATION, CENTROID_WITH_HA, CO2_COORDINATION, CTERM_AMIDATION, CTERM_CONNECT, CU2_COORDINATION, CUTPOINT_LOWER, CUTPOINT_UPPER, DEOXY_O2PRIME, DEPROTONATED, DIIODINATION, DIMETHYLATED_CTERMINUS_VARIANT, DIMETHYLATION, DISULFIDE, DY3_COORDINATION, FE2_COORDINATION, FE3_COORDINATION, FIVE_PRIME_END_OH, FIVE_PRIME_END_PHOSPHATE, FIVE_PRIME_PACKABLE_PHOSPHATE, FIVE_PRIME_PACKABLE_TRIPHOSPHATE, FIVE_PRIME_PHOSPHATE, FIVE_PRIME_RME_PHOSPHATE, FIVE_PRIME_THIOETHANOLAMINE_PHOSPHATE, FIVEPRIME_CAP, HBS_POST, HBS_PRE, HYDROXYLATION, HYDROXYLATION1, HYDROXYLATION2, LA3_COORDINATION, LOWER_TERMINUS_VARIANT, LOWERTERM_TRUNC_VARIANT, LU3_COORDINATION, METHYL_GLYCOSIDE, METHYLATED_CTERMINUS_VARIANT, METHYLATED_NTERM_VARIANT, METHYLATION, MG2_COORDINATION, MN2_COORDINATION, N_ACETYLATION, N_FORMYLATION, N_METHYLATION, NE2_CONNECT, NO_VARIANT, NTERM_CONNECT, O1_ACETYL_SUGAR, O2_ACETYL_SUGAR, O3_ACETYL_SUGAR, O4_ACETYL_SUGAR, O5_ACETYL_SUGAR, O6_ACETYL_SUGAR, O7_ACETYL_SUGAR, O8_ACETYL_SUGAR, O9_ACETYL_SUGAR, O_CONNECT, OD1_CONNECT, OD2_CONNECT, OE1_CONNECT, OE2_CONNECT, OG1_CONNECT, OG_CONNECT, OOP_POST, OOP_PRE, PHOSPHONATE_UPPER_VARIANT, PHOSPHORYLATION, PROTONATED, PROTONATED_N1, PROTONATED_N3, REPL_PHOSPHATE, REPLONLY, REPLS_BB, SC_BRANCH_POINT, SC_FRAGMENT, SG_CONNECT, SHOVE_BB, SIDECHAIN_CONJUGATION, SPECIAL_ROT, SULFATION, TB3_COORDINATION, THREE_PRIME_AZIDE, THREE_PRIME_DEOXY, THREE_PRIME_END_OH, THREE_PRIME_FIVE_PRIME_METHYL_PHOSPHATE, THREE_PRIME_PACKABLE_PHOSPHATE, THREE_PRIME_PHOSPHATE, THREE_PRIME_TWO_PRIME_CYCLIC_PHOSPHATE, TM3_COORDINATION, TRIAZOLAMERC, TRIAZOLAMERN, TRIMETHYLATION, UPPER_CONNECTION_RNA, UPPER_TERMINUS_VARIANT, UPPERTERM_TRUNC_VARIANT, URONIC_ACID_VARIANT, VIRTUAL_BACKBONE_EXCEPT_C1PRIME, VIRTUAL_BASE, VIRTUAL_BASE_HEAVY_ATOM, VIRTUAL_BB, VIRTUAL_DNA_PHOSPHATE, VIRTUAL_METAL_CONJUGATION, VIRTUAL_NTERM, VIRTUAL_O2PRIME_HYDROGEN, VIRTUAL_PHOSPHATE, VIRTUAL_RESIDUE_VARIANT, VIRTUAL_RIBOSE, VIRTUAL_RNA_RESIDUE, VIRTUAL_RNA_RESIDUE_EXCLUDE_PHOSPHATE, VIRTUAL_SIDE_CHAIN, YB3_COORDINATION, and ZN_CONNECT.

utility::vector1< std::string > const* core::chemical::generate_variant_to_string_vector

(

)

References A3B_HBS_POST, A3B_HBS_PRE, ACETYLATED_NTERMINUS_VARIANT, ACETYLATION, ADDUCT_VARIANT, ALDONIC_ACID_VARIANT, ALTERNATIVE_PROTONATION, BLOCK_STACK_ABOVE, BLOCK_STACK_BELOW, BULGE, C1_ACETYLAMINO_SUGAR, C1_AMINO_SUGAR, C1_BRANCH_POINT, C1_DEOXY_SUGAR, C1_METHYLATED_SUGAR, C1_PHOSPHATE, C1_PHOSPHORYLATED_SUGAR, C1_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C1_SULFATED_SUGAR, C1_SULFOAMINO_SUGAR, C1_THIO_SUGAR, C2_ACETYLAMINO_SUGAR, C2_AMINO_SUGAR, C2_BRANCH_POINT, C2_DEOXY_SUGAR, C2_KETOALDONIC_ACID, C2_METHYLATED_SUGAR, C2_PHOSPHATE, C2_PHOSPHORYLATED_SUGAR, C2_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C2_SULFATED_SUGAR, C2_SULFOAMINO_SUGAR, C2_THIO_SUGAR, C3_ACETYLAMINO_SUGAR, C3_AMINO_SUGAR, C3_BRANCH_POINT, C3_DEOXY_SUGAR, C3_KETOALDONIC_ACID, C3_METHYLATED_SUGAR, C3_PHOSPHATE, C3_PHOSPHORYLATED_SUGAR, C3_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C3_SULFATED_SUGAR, C3_SULFOAMINO_SUGAR, C3_THIO_SUGAR, C4_ACETYLAMINO_SUGAR, C4_AMINO_SUGAR, C4_BRANCH_POINT, C4_DEOXY_SUGAR, C4_KETOALDONIC_ACID, C4_METHYLATED_SUGAR, C4_PHOSPHATE, C4_PHOSPHORYLATED_SUGAR, C4_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C4_SULFATED_SUGAR, C4_SULFOAMINO_SUGAR, C4_THIO_SUGAR, C5_ACETYLAMINO_SUGAR, C5_AMINO_SUGAR, C5_BRANCH_POINT, C5_DEOXY_SUGAR, C5_KETOALDONIC_ACID, C5_METHYLATED_NA, C5_METHYLATED_SUGAR, C5_PHOSPHATE, C5_PHOSPHORYLATED_SUGAR, C5_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C5_SULFATED_SUGAR, C5_SULFOAMINO_SUGAR, C5_THIO_SUGAR, C6_ACETYLAMINO_SUGAR, C6_AMINO_SUGAR, C6_BRANCH_POINT, C6_DEOXY_SUGAR, C6_KETOALDONIC_ACID, C6_METHYLATED_SUGAR, C6_PHOSPHATE, C6_PHOSPHORYLATED_SUGAR, C6_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C6_SULFATED_SUGAR, C6_SULFOAMINO_SUGAR, C6_THIO_SUGAR, C7_ACETYLAMINO_SUGAR, C7_AMINO_SUGAR, C7_BRANCH_POINT, C7_DEOXY_SUGAR, C7_KETOALDONIC_ACID, C7_METHYLATED_SUGAR, C7_PHOSPHATE, C7_PHOSPHORYLATED_SUGAR, C7_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C7_SULFATED_SUGAR, C7_SULFOAMINO_SUGAR, C7_THIO_SUGAR, C8_ACETYLAMINO_SUGAR, C8_AMINO_SUGAR, C8_BRANCH_POINT, C8_DEOXY_SUGAR, C8_KETOALDONIC_ACID, C8_METHYLATED_SUGAR, C8_PHOSPHATE, C8_PHOSPHORYLATED_SUGAR, C8_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C8_SULFATED_SUGAR, C8_SULFOAMINO_SUGAR, C8_THIO_SUGAR, C9_ACETYLAMINO_SUGAR, C9_AMINO_SUGAR, C9_BRANCH_POINT, C9_DEOXY_SUGAR, C9_METHYLATED_SUGAR, C9_PHOSPHATE, C9_PHOSPHORYLATED_SUGAR, C9_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C9_SULFATED_SUGAR, C9_SULFOAMINO_SUGAR, C9_THIO_SUGAR, C_METHYLAMIDATION, CA2_COORDINATION, CA_CONNECT, CA_CONNECT2, CA_CONNECT3, CA_CONNECT4, CA_CONNECT5, CA_CONNECT6, CA_CONNECT7, CARBOXYLATION, CENTROID_WITH_HA, CO2_COORDINATION, CTERM_AMIDATION, CTERM_CONNECT, CU2_COORDINATION, CUTPOINT_LOWER, CUTPOINT_UPPER, DEOXY_O2PRIME, DEPROTONATED, DIIODINATION, DIMETHYLATED_CTERMINUS_VARIANT, DIMETHYLATION, DISULFIDE, DY3_COORDINATION, FE2_COORDINATION, FE3_COORDINATION, FIVE_PRIME_END_OH, FIVE_PRIME_END_PHOSPHATE, FIVE_PRIME_PACKABLE_PHOSPHATE, FIVE_PRIME_PACKABLE_TRIPHOSPHATE, FIVE_PRIME_PHOSPHATE, FIVE_PRIME_RME_PHOSPHATE, FIVE_PRIME_THIOETHANOLAMINE_PHOSPHATE, FIVEPRIME_CAP, HBS_POST, HBS_PRE, HYDROXYLATION, HYDROXYLATION1, HYDROXYLATION2, LA3_COORDINATION, LOWER_TERMINUS_VARIANT, LOWERTERM_TRUNC_VARIANT, LU3_COORDINATION, METHYL_GLYCOSIDE, METHYLATED_CTERMINUS_VARIANT, METHYLATED_NTERM_VARIANT, METHYLATION, MG2_COORDINATION, MN2_COORDINATION, N_ACETYLATION, N_FORMYLATION, N_METHYLATION, N_VARIANTS, NE2_CONNECT, NTERM_CONNECT, O1_ACETYL_SUGAR, O2_ACETYL_SUGAR, O3_ACETYL_SUGAR, O4_ACETYL_SUGAR, O5_ACETYL_SUGAR, O6_ACETYL_SUGAR, O7_ACETYL_SUGAR, O8_ACETYL_SUGAR, O9_ACETYL_SUGAR, O_CONNECT, OD1_CONNECT, OD2_CONNECT, OE1_CONNECT, OE2_CONNECT, OG1_CONNECT, OG_CONNECT, OOP_POST, OOP_PRE, PHOSPHONATE_UPPER_VARIANT, PHOSPHORYLATION, PROTONATED, PROTONATED_N1, PROTONATED_N3, REPL_PHOSPHATE, REPLONLY, REPLS_BB, SC_BRANCH_POINT, SC_FRAGMENT, SG_CONNECT, SHOVE_BB, SIDECHAIN_CONJUGATION, SPECIAL_ROT, SULFATION, TB3_COORDINATION, THREE_PRIME_AZIDE, THREE_PRIME_DEOXY, THREE_PRIME_END_OH, THREE_PRIME_FIVE_PRIME_METHYL_PHOSPHATE, THREE_PRIME_PACKABLE_PHOSPHATE, THREE_PRIME_PHOSPHATE, THREE_PRIME_TWO_PRIME_CYCLIC_PHOSPHATE, TM3_COORDINATION, TRIAZOLAMERC, TRIAZOLAMERN, TRIMETHYLATION, UPPER_CONNECTION_RNA, UPPER_TERMINUS_VARIANT, UPPERTERM_TRUNC_VARIANT, URONIC_ACID_VARIANT, VIRTUAL_BACKBONE_EXCEPT_C1PRIME, VIRTUAL_BASE, VIRTUAL_BASE_HEAVY_ATOM, VIRTUAL_BB, VIRTUAL_DNA_PHOSPHATE, VIRTUAL_METAL_CONJUGATION, VIRTUAL_NTERM, VIRTUAL_O2PRIME_HYDROGEN, VIRTUAL_PHOSPHATE, VIRTUAL_RESIDUE_VARIANT, VIRTUAL_RIBOSE, VIRTUAL_RNA_RESIDUE, VIRTUAL_RNA_RESIDUE_EXCLUDE_PHOSPHATE, VIRTUAL_SIDE_CHAIN, YB3_COORDINATION, and ZN_CONNECT.

ED core::chemical::get_bond	(	MutableResidueType const &	res,
		VD const &	source,
		VD const &	target
	)

References core::chemical::MutableResidueType::graph().

utility::vector1< VD > core::chemical::get_connecting_atoms	(	MutableResidueType const &	res,
		ED const &	edge
	)

References core::chemical::MutableResidueType::graph().

utility::vector1< VD > core::chemical::get_connecting_atoms	(	ResidueGraph const &	graph,
		ED const &	edge
	)

Size core::chemical::get_connection_number

(

std::string const &

name

)

Get the connection number from a string representing an CONNECT type (e.g. 4 from CONN4)

Referenced by core::chemical::MutableICoorRecord::build_xyz(), core::chemical::MutableICoorRecord::buildable(), correct_conn(), has_assigned_coords(), core::chemical::ICoorAtomID::ICoorAtomID(), core::chemical::MutableResidueType::set_icoor(), core::chemical::MutableResidueType::update_icoors_after_connection_deletion(), and core::chemical::MutableICoorRecord::xyz().

AA core::chemical::get_D_equivalent

(

AA const

aa

)

Given an enum type for a L-amino acid with a canonical side-chain, return the enum type for the corresponding D-amino acid (or aa_unk if the corresponding D-amino acid cannot be determined).

References aa_ala, aa_arg, aa_asn, aa_asp, aa_cys, aa_dal, aa_dan, aa_dar, aa_das, aa_dcs, aa_dgn, aa_dgu, aa_dhi, aa_dil, aa_dle, aa_dly, aa_dme, aa_dph, aa_dpr, aa_dse, aa_dth, aa_dtr, aa_dty, aa_dva, aa_gln, aa_glu, aa_his, aa_ile, aa_leu, aa_lys, aa_met, aa_phe, aa_pro, aa_ser, aa_thr, aa_trp, aa_tyr, aa_unk, aa_val, na_lra, na_lrc, na_lrg, na_lur, na_rad, na_rcy, na_rgu, and na_ura.

Referenced by core::chemical::ChiralFlipNaming::apply(), and core::conformation::get_residue_from_name1().

std::string core::chemical::get_element_color

(

std::string const &

element

)

Referenced by core::chemical::ResidueTypeKinWriter::write_restype().

AA core::chemical::get_L_equivalent

(

AA const

aa

)

Given an enum type for a D-amino acid with a canonical side-chain, return the enum type for the corresponding L-amino acid (or aa_unk if the corresponding L-amino acid cannot be determined).

References aa_ala, aa_arg, aa_asn, aa_asp, aa_cys, aa_dal, aa_dan, aa_dar, aa_das, aa_dcs, aa_dgn, aa_dgu, aa_dhi, aa_dil, aa_dle, aa_dly, aa_dme, aa_dph, aa_dpr, aa_dse, aa_dth, aa_dtr, aa_dty, aa_dva, aa_gln, aa_glu, aa_his, aa_ile, aa_leu, aa_lys, aa_met, aa_phe, aa_pro, aa_ser, aa_thr, aa_trp, aa_tyr, aa_unk, aa_val, na_lra, na_lrc, na_lrg, na_lur, na_rad, na_rcy, na_rgu, and na_ura.

Referenced by core::pack::dunbrack::SingleResidueDunbrackLibraryCreator::create(), core::scoring::ResidueExclParams::create_excl_info(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::RamaPrePro::eval_rpp_rama_score(), core::scoring::P_AA::get_l_equivalent(), core::scoring::Ramachandran::get_l_equivalent(), core::scoring::HydroxylTorsionPotential::get_restag(), core::scoring::methods::get_restag(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_from_chi_static(), core::scoring::RamaPrePro::random_mainchain_torsions(), and setup_patch_atomic_charge_reassignments_from_commandline().

utility::vector1< std::string > core::chemical::get_patch_names

(

ResidueType const &

rsd_type

)

References residue_type_all_patches_name().

Referenced by core::chemical::Metapatch::atoms(), and protocols::residue_optimization::MetapatchEnumeration::generate_derived_types().

ObjexxFCL::FArray2D_int core::chemical::get_residue_path_distances

(

ResidueType const &

res

)

relies on class Graph to find all pairs shortest path information

References core::chemical::ResidueType::natoms(), and core::chemical::ResidueType::nbrs().

Referenced by core::chemical::ResidueType::define_mainchain_atoms(), and core::chemical::ResidueType::initialize_derived_data().

utility::vector1< VariantType > core::chemical::get_terminal_varianttypes

(

)

Get a list of those VariantTypes that affect termini.

Author

Vikram K. Mulligan.

References A3B_HBS_POST, A3B_HBS_PRE, ACETYLATED_NTERMINUS_VARIANT, C_METHYLAMIDATION, CTERM_CONNECT, CUTPOINT_LOWER, CUTPOINT_UPPER, FIVE_PRIME_END_OH, FIVE_PRIME_END_PHOSPHATE, FIVE_PRIME_PACKABLE_PHOSPHATE, FIVE_PRIME_PHOSPHATE, HBS_POST, HBS_PRE, LOWER_TERMINUS_VARIANT, LOWERTERM_TRUNC_VARIANT, METHYLATED_CTERMINUS_VARIANT, METHYLATED_NTERM_VARIANT, N_ACETYLATION, NTERM_CONNECT, OOP_POST, OOP_PRE, PHOSPHONATE_UPPER_VARIANT, THREE_PRIME_END_OH, THREE_PRIME_FIVE_PRIME_METHYL_PHOSPHATE, THREE_PRIME_PACKABLE_PHOSPHATE, THREE_PRIME_PHOSPHATE, TRIAZOLAMERC, TRIAZOLAMERN, UPPER_TERMINUS_VARIANT, UPPERTERM_TRUNC_VARIANT, VIRTUAL_NTERM, and VIRTUAL_PHOSPHATE.

bool core::chemical::has ( ResidueGraph const &  graph, VD  vd  )

inline

Does a ResidueGraph have a given vertex descriptor?

Referenced by protocols::multistage_rosetta_scripts::NoFailDataMap::add(), protocols::abinitio::StructureStore::add(), protocols::rna::movers::RNAIdealizeMover::add_bond_angle_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_angle_constraint(), protocols::rna::movers::RNAIdealizeMover::add_bond_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_dihedral_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_length_constraint(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::add_cyclic_constraints(), protocols::match::downstream::ClassicMatchAlgorithm::add_external_geom_sampler(), core::pose::datacache::ObserverCache::attach(), core::pose::datacache::ObserverCache::detach(), core::chemical::MutableResidueType::has(), protocols::mean_field::jagged_array< AAProb >::has_value(), protocols::match::upstream::ProteinUpstreamBuilder::initialize_rescoords(), core::pose::datacache::ObserverCache::is_attached(), core::conformation::Conformation::jump_atom_id(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::reindex_AtomIDs(), protocols::denovo_design::remove_missing_jump_atoms(), protocols::denovo_design::components::Segment::set_template_pose(), shortest_path(), and protocols::sewing::data_storage::SmartAssembly::to_pose().

bool core::chemical::has ( ResidueGraph const &  graph, ED  ed  )

inline

Does a ResidueGraph have a given edge descriptor?

bool core::chemical::has_assigned_coords	(	std::string const &	stub,
		std::set< VD > const &	assigned,
		core::chemical::MutableResidueType const &	restype
	)

Utility function for fill_ideal_xyz_from_icoor() – does this ICoorAtomID have all the dependancies filled?

References core::chemical::MutableResidueType::atom_vertex(), CONNECT, get_connection_number(), core::chemical::MutableResidueType::has(), core::chemical::MutableResidueConnection::icoor(), INTERNAL, core::chemical::MutableResidueType::lower_connect(), core::chemical::ResidueTypeBase::name(), POLYMER_LOWER, POLYMER_UPPER, core::chemical::MutableResidueType::residue_connection(), string_to_icoord_type(), and core::chemical::MutableResidueType::upper_connect().

Referenced by fill_ideal_xyz_from_icoor().

bool core::chemical::heavy_atom_names_match	(	ResidueType const &	first,
		ResidueType const &	second
	)

Return true if the two residues have the same number and name of heavy atoms.

References core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::nheavyatoms(), core::chemical::orbitals::strip_whitespace(), and TR().

std::string const core::chemical::HYBRID_FA_STANDARD_CENTROID

(

"hybrid_fa_standard_centroid"

)

tag name for querying hybrid fullatom+centroid chemical type set.

bool core::chemical::is_aa_name_unknown

(

std::string const &

name

)

Given aa three letter string, return true if it is an unknown aa.

Author

Steven Cobms (steve.nosp@m.n.co.nosp@m.mbs1@.nosp@m.gmai.nosp@m.l.com)

References core::sequence::end, and name2aa().

Referenced by core::io::mmtf::make_current_group().

bool core::chemical::is_canonical_beta3_aa

(

AA const

aa

)

Given an enum type, return true if and only if it is a canonical beta-amino acid.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References first_beta3_aa, and last_beta3_aa.

bool core::chemical::is_canonical_D_aa

(

AA const

aa

)

Give an enum type, return true if and only if it is a D-amino acid that is the mirror image of a canonical alpha-L-amino acid.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References first_D_aa, and last_D_aa.

Referenced by core::chemical::rotamers::DunbrackRotamerLibrarySpecification::aa(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), core::pack::dunbrack::SingleResidueDunbrackLibraryCreator::create(), core::scoring::ResidueExclParams::create_excl_info(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_derivs_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_length_derivs(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_improper_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::methods::CartesianBondedEnergy::eval_residue_pair_derivatives_sorted(), core::scoring::RamaPrePro::eval_rpp_rama_derivatives(), core::scoring::RamaPrePro::eval_rpp_rama_score(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), protocols::simple_filters::TMsAACompFilter::find_aa_composition(), core::scoring::HydroxylTorsionPotential::get_restag(), core::scoring::methods::get_restag(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_from_chi_static(), core::scoring::P_AA::is_canonical_d_aminoacid(), core::scoring::Ramachandran::is_canonical_d_aminoacid(), protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber::perturb_chain(), core::scoring::RamaPrePro::random_mainchain_torsions(), core::scoring::methods::RamachandranEnergy::residue_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), and setup_patch_atomic_charge_reassignments_from_commandline().

bool core::chemical::is_canonical_L_aa_or_gly

(

AA const

aa

)

Given an enum type, return true if and only if it is a canonical L-amino acid. Rocco approves.

Given an enum type, return true if and only if it is a canonical L-amino acid.

Author

Steven Cobms (steve.nosp@m.n.co.nosp@m.mbs1@.nosp@m.gmai.nosp@m.l.com)

Note

Also returns true if this is a glycine.

Author

Steven Cobms (steve.nosp@m.n.co.nosp@m.mbs1@.nosp@m.gmai.nosp@m.l.com)

References first_l_aa, and num_canonical_aas.

Referenced by protocols::nmr::pre::PREMover::apply(), core::scoring::OmegaTether::eval_omega_score_residue(), core::scoring::RamaPrePro::eval_rpp_rama_derivatives(), core::scoring::RamaPrePro::eval_rpp_rama_score(), protocols::simple_filters::TMsAACompFilter::find_aa_composition(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_from_chi_static(), core::import_pose::libraries::ChunkSet::insert_protein_chunk_into_pose(), core::io::mmtf::make_current_group(), core::pack::task::operation::DesignRestrictions::parse_tag(), core::scoring::RamaPrePro::random_mainchain_torsions(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::read_file(), set_up_mapfile_reassignments_from_commandline(), and setup_patch_atomic_charge_reassignments_from_commandline().

bool core::chemical::is_mainchain_torsion_also_ring_torsion	(	ResidueType const &	res_type,
		uint	torsion_index
	)

Are these main-chain torsions also ring torsions?

References core::chemical::ResidueType::is_cyclic(), core::chemical::ResidueType::mainchain_atoms(), core::chemical::ResidueType::n_nus(), and core::chemical::ResidueType::nu_atoms().

Referenced by protocols::loops::loop_closure::ccd::CCDLoopClosureMover::adjust_residue_to_minimize_deviation(), and core::pose::setup_dof_mask_from_move_map().

bool core::chemical::is_sp2_proton_chi	(	core::Size	chi,
		MutableResidueType const &	restype
	)

Is the given chi a proton chi with the proton attached to an atom attached to an non-sp3 atom?

The use case is to see if the proton chi should flat or staggered with rotamers

References AromaticBond, core::chemical::MutableResidueType::bond(), core::chemical::MutableResidueType::bond_iterators(), core::chemical::Bond::bond_name(), core::chemical::MutableResidueType::chi_atom_vds(), DoubleBond, and SingleBond.

Referenced by core::chemical::MutableResidueType::autodetermine_chi_bonds().

utility::vector1< VD > core::chemical::mainchain_path

(

MutableResidueType const &

res

)

Figure out the shortest path between the upper and lower connect atoms (inclusive) Will return an empty vector if one does not exist.

References core::chemical::MutableResidueType::lower_connect_atom(), core::chemical::MutableResidueType::lower_connect_id(), shortest_path(), core::chemical::MutableResidueType::upper_connect_atom(), and core::chemical::MutableResidueType::upper_connect_id().

Referenced by core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType().

AcceptorAtomGraph core::chemical::make_acceptor_atom_graph ( MutableResidueType const &  restype )

inline

Convenience constructor.

References core::chemical::ResidueTypeBase::atom_type_set_ptr(), and core::chemical::MutableResidueType::graph().

APolarHydrogenGraph core::chemical::make_apolar_hydrogen_graph ( MutableResidueType const &  restype )

inline

Convenience constructor.

References core::chemical::ResidueTypeBase::atom_type_set_ptr(), and core::chemical::MutableResidueType::graph().

AromaticAtomGraph core::chemical::make_aromatic_atom_graph ( MutableResidueType const &  restype )

inline

Convenience constructor.

References core::chemical::ResidueTypeBase::atom_type_set_ptr(), and core::chemical::MutableResidueType::graph().

MutableResidueTypeOP core::chemical::make_centroid

(

ResidueType const &

res

)

Make a centroid version of the fullatom ResidueType passed in.

May return a nullptr if the conversion is not possible

This uses the same crude heuristics as in molfile_to_params That is, all heavy atoms and polar hydrogens are transfered over 1:1, and non-polar hydrogens are deleted.

Of particular note is that it makes no attempt to transfer things over into "Superatoms"

Current limitation: it cannot convert a ResidueType which has connections, if any of the ICOORs depend on deleted hydrogens.

Assumes:

• Input ResidueType is complete and finalized

Referenced by core::chemical::GlobalResidueTypeSet::attempt_readin(), core::util::generate_replacement_restype(), and core::chemical::GlobalResidueTypeSet::init_restypes_from_commandline().

MutableResidueTypeOP core::chemical::make_centroid

(

MutableResidueType const &

res

)

References core::chemical::MutableResidueType::all_atoms(), core::chemical::MutableResidueType::atom(), core::chemical::ResidueTypeBase::atom_type_set(), CENTROID, CENTROID_t, FULL_ATOM_t, core::chemical::AtomTypeSet::has_atom(), INTERNAL, core::chemical::MutableResidueType::n_possible_residue_connections(), core::chemical::ResidueTypeBase::name(), and TR().

HeavyAtomGraph core::chemical::make_heavy_atom_graph ( MutableResidueType const &  restype )

inline

Convenience constructor.

References core::chemical::ResidueTypeBase::atom_type_set_ptr(), and core::chemical::MutableResidueType::graph().

HeavyAtomWithHydrogensGraph core::chemical::make_heavy_atom_with_hydrogens_graph ( MutableResidueType const &  restype )

inline

Convenience constructor.

References core::chemical::ResidueTypeBase::atom_type_set_ptr(), and core::chemical::MutableResidueType::graph().

HeavyAtomWithPolarHydrogensGraph core::chemical::make_heavy_atom_with_polar_hydrogens_graph ( MutableResidueType const &  restype )

inline

Convenience constructor.

References core::chemical::ResidueTypeBase::atom_type_set_ptr(), and core::chemical::MutableResidueType::graph().

HydrogenAtomGraph core::chemical::make_hydrogen_atom_graph ( MutableResidueType const &  restype )

inline

Convenience constructor.

References core::chemical::ResidueTypeBase::atom_type_set_ptr(), and core::chemical::MutableResidueType::graph().

PolarHydrogenGraph core::chemical::make_polar_hydrogen_graph ( MutableResidueType const &  restype )

inline

Convenience constructor.

References core::chemical::ResidueTypeBase::atom_type_set_ptr(), and core::chemical::MutableResidueType::graph().

RealResidueGraph core::chemical::make_real_residue_graph ( MutableResidueType const &  restype )

inline

Convenience constructor.

References core::chemical::MutableResidueType::graph().

void core::chemical::modify_atom_properties_from_command_line	(	std::string const &	atom_type_set_tag,
		AtomTypeSet &	atom_type_set
	)

Modify atom_type properties from the command line.

Called by ChemicalManager at time of AtomTypeSet creation.

References core::chemical::AtomTypeSet::atom_type_index(), core::chemical::AtomTypeSet::has_atom(), and TR().

Referenced by core::chemical::ChemicalManager::create_atom_type_set().

merge_residue_behavior core::chemical::mrb_from_name

(

std::string const &

mrb

)

References mrb_do_not_merge, mrb_merge_w_next, and mrb_merge_w_prev.

Referenced by core::chemical::MergeBehaviorManager::read_merge_behaviors_from_database_file().

MergeBehaviorManager::AtomRenamingMap core::chemical::mrb_map_from_correspondence

(

std::string const &

correspondence

)

Referenced by core::chemical::MergeBehaviorManager::read_merge_behaviors_from_database_file().

std::map< std::string, AA > const& core::chemical::name2aa ( )

inline

map that converts string name to AA enum

References setup_name2aa().

Referenced by aa_from_name(), is_aa_name_unknown(), operator>>(), and setup_aa2name().

std::string core::chemical::name_from_aa

(

AA

aa

)

give a enum type and return the string name

References protocols::cluster::calibur::aa, aa2name(), and num_aa_types.

Referenced by protocols::noesy_assign::MethylNames::aa_name(), core::conformation::Residue::annotated_name(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), protocols::stepwise::modeler::rna::base_atoms_square_deviation(), protocols::splice::SpliceOutTail::build_ideal_segment(), protocols::splice::SpliceInTail::build_ideal_segment(), protocols::splice::SpliceIn::build_ideal_segment(), protocols::splice::SpliceOut::build_ideal_segment(), protocols::matdes::ClashCheckFilter::compute(), protocols::fldsgn::filters::CoreDunbrackFilter::compute(), core::scoring::ResidueExclParams::create_excl_info(), core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_10_from_ASCII(), protocols::stepwise::monte_carlo::mover::AddMover::create_residue_to_add(), core::chemical::rotamers::DunbrackRotamerLibrarySpecification::describe(), core::chemical::rotamers::CenrotRotamerLibrarySpecification::describe(), protocols::antibody::design::AntibodySeqDesignTFCreator::disable_disallowed_aa(), protocols::dna::dna_base_partner(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), protocols::pose_length_moves::InsertResMover::extendRegion(), protocols::pose_length_moves::PossibleLoop::extendRegion(), protocols::pose_length_moves::NearNativeLoopCloser::extendRegion(), core::scoring::motif::ResPairMotif::fill_pose_with_motif(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), core::enzymes::get_AA_3_letter_codes_or_punctuation_from_1_letter_code_at_position(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_larmord(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_calc_chem_shift_value_nuchemics(), protocols::recon_design::get_candidate_AAs(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), protocols::stepwise::modeler::rna::rigid_body::get_max_centroid_to_atom_distance(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), core::scoring::HydroxylTorsionPotential::get_restag(), core::scoring::methods::get_restag(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::import_exp_chemical_shift_data(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), core::pack::task::PIKAA::initialize_from_tokens(), core::pack::task::NOTAA::initialize_from_tokens(), protocols::stepwise::modeler::rna::is_virtual_base(), protocols::noesy_assign::CrossPeakInfo::label_atom_name(), protocols::noesy_assign::label_atom_name(), protocols::protein_interface_design::movers::PlaceOnLoop::loop_length(), protocols::simple_filters::ResidueDepthFilter::make_context(), protocols::membrane::MPMutateRelaxMover::make_mutations(), protocols::tcr::match_template_and_target_sequence(), protocols::pose_metric_calculators::SequenceComparison::measure_sequence_recovery(), operator<<(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::operator==(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::operator==(), core::pack::dunbrack::SingleResidueDunbrackLibrary::operator==(), protocols::noesy_assign::MethylNameLibrary::operator[](), protocols::optimize_weights::IterativeOptEDriver::output_weighted_unfolded_energies(), protocols::loop_modeler::perturbers::LoopHashPerturber::perturb_subset(), protocols::stepwise::modeler::rna::phosphate_square_deviation(), core::scoring::motif::Xfres::place_sidechain_in_pose(), core::scoring::rna::chemical_shift::print_chemical_shift_data(), core::pack::interaction_graph::SurfacePotential::read_average_res_hASA_database_file(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::read_file(), core::pack::dunbrack::RotamerLibrary::read_from_binary(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::read_from_file(), protocols::noesy_assign::ResonanceList::read_from_stream(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::read_params(), core::scoring::PointWaterPotential::read_pointwater_tables(), core::chemical::ResidueDatabaseIO::read_residue_type(), read_topology_file(), core::scoring::methods::MembraneEnvSmoothEnergy::representative_atom_name(), core::scoring::methods::EnvSmoothEnergy::representative_atom_name(), core::scoring::membrane::FaMPEnvSmoothEnergy::representative_atom_name(), core::pack::task::ResidueLevelTask_::restrict_absent_nas(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::ROT2res(), protocols::simple_moves::MutateResidue::set_res_name(), core::scoring::fiber_diffraction::setup_centroid_scatter(), protocols::mean_field::RotProb::show(), protocols::mean_field::AAProb::show(), core::pose::rna::update_edge_hbond_numbers(), core::pack::dunbrack::RotamerLibrary::validate_dunbrack_binary(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::verify_protonated_H1_adenosine_variants(), and protocols::noesy_assign::Resonance::write_to_stream().

bool core::chemical::nonadduct_variants_match	(	ResidueTypeBase const &	res1,
		ResidueTypeBase const &	res2
	)

Similar to variants_match(), but allows different adduct-modified states.

References ADDUCT_VARIANT, and variants_match_with_exceptions().

std::map< char, AA > const& core::chemical::oneletter2aa ( )

inline

map that converts one letter char to AA enum

References setup_oneletter2aa().

Referenced by aa_from_oneletter_code(), oneletter_code_specifies_aa(), and setup_aa2oneletter().

char core::chemical::oneletter_code_from_aa

(

AA

aa

)

give a enum type and return the string name

References protocols::cluster::calibur::aa, aa2oneletter(), and num_canonical_aas.

Referenced by protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::calc_taskop_filters::ConservedPosMutationFilter::apply(), protocols::splice::Splice::apply(), core::scoring::membrane::MPResidueLipophilicityEnergy::calc_energy(), core::scoring::membrane::MPSpanInsertionEnergy::calc_span_score(), protocols::optimize_weights::IterativeOptEDriver::collect_sequence_recovery_data_from_slave_cpus(), protocols::simple_filters::MembAccesResidueLipophilicityFilter::compute(), protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::compute(), protocols::mean_field::AAMatrix::dump_transfac(), protocols::pmut_scan::PointMutScanDriver::fill_mutations_list(), protocols::simple_filters::TMsAACompFilter::find_aa_composition(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), protocols::antibody::design::NativeAntibodySeq::get_native_sequence_matching_current_length(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::get_oneletter_codes(), protocols::simple_filters::ResidueDepthFilter::get_residue_similarity(), protocols::constel::FilterBySASA::has_low_per_atom_sasa(), protocols::frag_picker::SidechainContactDistCutoff::initialize(), protocols::design_opt::insert_point_mut_filter_vals(), protocols::matdes::insert_point_mut_filter_vals(), core::io::mmtf::make_current_group(), protocols::ddg::ddGMover::mutation_label(), protocols::constel::pair_constel_set(), protocols::constel::pair_constel_set_idx2(), core::scoring::methods::ProQ_Energy::profile_index_to_aa(), core::sequence::SequenceProfile::read_from_checkpoint(), core::sequence::SequenceProfile::read_from_file(), protocols::noesy_assign::ResonanceList::read_from_stream(), core::scoring::membrane::MPHelicalityEnergy::residue_energy(), protocols::indexed_structure_store::SegmentSequenceProfile::segment_profile(), protocols::loops::set_secstruct_from_dssp(), setup_patch_atomic_charge_reassignments_from_commandline(), core::fragment::SingleResidueFragData::steal(), protocols::constel::SingResCnlCrea::strip_atoms(), protocols::constel::target_constel(), protocols::multistate_design::PosType::to_string(), protocols::constel::triple_constel_set(), protocols::constel::triple_constel_set_idx3(), protocols::noesy_assign::PeakFileFormat_Sparky::write_assignment(), protocols::noesy_assign::PeakFileFormat_xpk::write_assignment(), protocols::optimize_weights::IterativeOptEDriver::write_new_scorefile(), protocols::noesy_assign::ResonanceList::write_talos_format(), protocols::noesy_assign::Resonance::write_to_stream(), and protocols::constel::SingResCnlCrea::zero_occ_for_deleted_atoms().

bool core::chemical::oneletter_code_specifies_aa

(

char

onelettercode

)

References oneletter2aa().

Referenced by core::pack::task::operation::RestrictAbsentCanonicalAASRLT::aas_to_keep(), core::pack::task::operation::RestrictAbsentCanonicalAASExceptNativeRLT::aas_to_keep(), core::conformation::Residue::annotated_name(), protocols::task_operations::JointSequenceOperation::apply(), protocols::simple_moves::SimpleThreadingMover::apply(), core::pack::task::operation::DisallowIfNonnativeRLT::disallow_aas(), core::pack::task::operation::DisallowIfNonnative::disallow_aas(), core::scoring::methods::FreeDOF_Energy::finalize_total_energy(), core::pack::task::PIKAA::initialize_from_tokens(), core::pack::task::NOTAA::initialize_from_tokens(), core::pack::task::operation::RestrictAbsentCanonicalAAS::keep_aas(), protocols::protein_interface_design::movers::LoopLengthChange::parse_my_tag(), core::pack::task::operation::DesignRestrictions::parse_tag(), protocols::pack_daemon::EntityFunc::process_AA_SET_line(), protocols::pack_daemon::EntityFunc::process_SET_CONDITION_line(), core::sequence::MatrixScoringScheme::read_data(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::read_params(), core::pack::task::TARGET::residue_action(), protocols::task_operations::ConservativeDesignOperation::skip_resid(), and core::sequence::MatrixScoringScheme::values_for_aa().

bool core::chemical::operator!=	(	ResConnID const &	lhs,
		ResConnID const &	rhs
	)

AtomProperty & core::chemical::operator++

(

AtomProperty &

property

)

ResidueProperty & core::chemical::operator++

(

ResidueProperty &

property

)

VariantType & core::chemical::operator++

(

VariantType &

variant

)

bool core::chemical::operator<	(	ResConnID const &	lhs,
		ResConnID const &	rhs
	)

References core::chemical::ResConnID::conn_id_, and core::chemical::ResConnID::res_id_.

std::ostream& core::chemical::operator<<	(	std::ostream &	out,
		const Orbital &	orbital
	)

References core::conformation::membrane::out, and core::chemical::Orbital::print().

std::ostream& core::chemical::operator<<	(	std::ostream &	out,
		const AtomType &	atom_type
	)

References core::conformation::membrane::out, and core::chemical::AtomType::print().

std::ostream & core::chemical::operator<<	(	std::ostream &	output,
		AtomProperties const &	object_to_output
	)

References core::chemical::AtomProperties::show().

std::ostream& core::chemical::operator<<	(	std::ostream &	out,
		Bond const &	bond
	)

References core::conformation::membrane::out, and core::chemical::Bond::print().

std::ostream& core::chemical::operator<< ( std::ostream &  out, MutableICoorRecord const &  icoor  )

inline

References core::conformation::membrane::out, and core::chemical::MutableICoorRecord::show().

std::ostream & core::chemical::operator<<	(	std::ostream &	out,
		Atom const &	atom
	)

References core::conformation::membrane::out, and core::chemical::Atom::show().

std::ostream& core::chemical::operator<< ( std::ostream &  out, Element const &  obj  )

inline

References core::chemical::Element::write().

std::ostream& core::chemical::operator<< ( std::ostream &  out, ElectronConfiguration const &  obj  )

inline

References core::chemical::ElectronConfiguration::write().

std::ostream & core::chemical::operator<<	(	std::ostream &	output,
		ResidueProperties const &	object_to_output
	)

References core::chemical::ResidueProperties::show().

std::ostream & core::chemical::operator<<	(	std::ostream &	output,
		ResidueProperty const &	object_to_output
	)

References core::chemical::ResidueProperties::get_string_from_property().

std::ostream & core::chemical::operator<<	(	std::ostream &	out,
		TypeSetMode	mode
	)

References core::conformation::membrane::out, and string_from_type_set_mode().

std::ostream & core::chemical::operator<<	(	std::ostream &	os,
		AA const &	aa
	)

output operator for AA enum type

example usage: std::cout << aa_gly << std::endl;

References name_from_aa().

std::ostream & core::chemical::operator<<	(	std::ostream &	out,
		ICoordAtomIDType	type
	)

References CONNECT, INTERNAL, core::conformation::membrane::out, POLYMER_LOWER, and POLYMER_UPPER.

std::ostream & core::chemical::operator<<	(	std::ostream &	output,
		ResidueType const &	object_to_output
	)

References core::chemical::ResidueType::show().

std::ostream & core::chemical::operator<<	(	std::ostream &	output,
		MutableResidueType const &	object_to_output
	)

References core::chemical::MutableResidueType::show().

bool core::chemical::operator==	(	ResConnID const &	lhs,
		ResConnID const &	rhs
	)

References core::chemical::ResConnID::conn_id_, and core::chemical::ResConnID::res_id_.

Referenced by core::pack::annealer::SequenceSymmetricAnnealer::create_corresponding_mress_for_mres(), and protocols::constraints_additional::SequenceCoupling1BDConstraint::operator==().

std::istream& core::chemical::operator>> ( std::istream &  in, Element &  obj  )

inline

References core::chemical::Element::read().

std::istream& core::chemical::operator>> ( std::istream &  in, ElectronConfiguration &  obj  )

inline

References core::chemical::ElectronConfiguration::read().

std::istream & core::chemical::operator>>	(	std::istream &	is,
		AA &	aa
	)

input operator for AA enum type

read in a string name from a file or std::cin and directly convert it to an AA enum type, for example, std::cin >> AA. This will first check if the lookup map has been set up already. If the string name cannot be converted properly, it will flag the input stream as failure (e.g., istream.fail() is true) and set AA enum type to aa_unk.

References aa_unk, core::sequence::end, and name2aa().

AdductMap core::chemical::parse_adduct_string

(

utility::options::StringVectorOption &

add_vec

)

Convert input string to map of adducts->max usage.

Referenced by core::chemical::GlobalResidueTypeSet::place_adducts().

PatchOperationOP core::chemical::patch_operation_from_patch_file_line	(	std::string const &	line,
		std::map< std::string, Real > const &	atomic_charge_reassignments
	)

Virtual constructor, returns 0 if no match.

References protocols::cluster::calibur::aa, anc_grandparent, anc_greatgrandparent, anc_parent, core::simple_metrics::metrics::mean, protocols::hybridization::path, and tr().

Referenced by case_from_lines().

utility::vector1< VariantType > core::chemical::pH_mode_exceptions

(

)

check if user has set -pH_mode.

used to determine exceptions to PROTONATION/DEPROTONAT in variants_match.

References DEPROTONATED, and PROTONATED.

Referenced by core::pack::palette::PackerPalette::decide_what_to_do_with_base_type(), core::pack::palette::PackerPalette::decide_what_to_do_with_existing_type(), and variants_match().

void core::chemical::pretty_print_atomicoor	(	std::ostream &	out,
		AtomICoor const &	start,
		ResidueType const &	rsd_type,
		core::Size	indent,
		AtomMemoOP	memo
	)

References core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_name(), core::chemical::ICoorAtomID::atomno(), core::chemical::AtomICoor::built_atom(), CONNECT, core::chemical::AtomICoor::d(), core::chemical::ResidueType::has(), core::chemical::ResidueType::icoor(), INTERNAL, core::chemical::ResidueTypeBase::name(), core::chemical::ResidueType::natoms(), core::chemical::AtomICoor::phi(), POLYMER_LOWER, POLYMER_UPPER, core::chemical::AtomICoor::stub_atom(), core::chemical::AtomICoor::stub_atom1(), and core::chemical::AtomICoor::theta().

Referenced by core::chemical::ResidueType::debug_dump_icoor(), core::conformation::Residue::fill_missing_atoms(), and pretty_print_atomicoor().

void core::chemical::pretty_print_atomicoor	(	std::ostream &	out,
		ResidueType const &	rsd_type
	)

print the icoord table starting at the root.

References core::chemical::ResidueType::icoor(), pretty_print_atomicoor(), and core::chemical::ResidueType::root_atom().

void core::chemical::pretty_print_atomicoor	(	std::ostream &	out,
		AtomICoor const &	start,
		ResidueType const &	rsd_type,
		core::Size	indent
	)

print the icoord table starting with the given icoord record

References pretty_print_atomicoor().

void core::chemical::print_chis	(	std::ostream &	out,
		ResidueType const &	res
	)

Utility to examine chi output.

References core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::chi_atoms(), formatted_icoord_tree(), core::chemical::ResidueType::is_proton_chi(), core::chemical::ResidueTypeBase::name(), and core::chemical::ResidueType::nchi().

void core::chemical::print_chis	(	std::ostream &	out,
		MutableResidueType const &	res
	)

Utility to examine chi output.

References core::chemical::MutableResidueType::atom_name(), core::chemical::MutableResidueType::chi_atom_vds(), formatted_icoord_tree(), core::chemical::MutableResidueType::is_proton_chi(), core::chemical::ResidueTypeBase::name(), and core::chemical::MutableResidueType::nchi().

static const std::map< std::string, ResidueProperty >* const core::chemical::PROPERTY_MAP ( generate_string_to_property_map()  )

static

void core::chemical::quick_ring_detection

(

MutableResidueType &

res

)

References core::chemical::MutableResidueType::atom_name(), core::chemical::MutableResidueType::bond(), BondInRing, core::chemical::MutableResidueType::graph(), and core::chemical::Bond::ringness().

Referenced by find_bonds_in_rings().

MutableResidueTypeOP core::chemical::read_topology_file	(	std::string const &	filename,
		chemical::ResidueTypeSetCOP	rsd_type_set
	)

function to convert params files into ResidueType objects (repackages string filename into istream, gets needed subsidiary type sets from rsd_type_set

Referenced by core::chemical::ResidueTypeSet::add_base_residue_type(), core::chemical::ResidueTypeSet::add_unpatchable_residue_type(), core::chemical::GlobalResidueTypeSet::init_restypes_from_commandline(), core::chemical::GlobalResidueTypeSet::init_restypes_from_database(), core::scoring::FACTSRsdTypeInfo::initialize_parameters(), and read_topology_file().

MutableResidueTypeOP core::chemical::read_topology_file	(	utility::io::izstream &	istream,
		chemical::ResidueTypeSetCOP	rsd_type_set
	)

function to convert params files into ResidueType objects, gets needed subsidiary type sets from rsd_type_set

References read_topology_file().

MutableResidueTypeOP core::chemical::read_topology_file	(	std::istream &	istream,
		std::string const &	filename,
		chemical::ResidueTypeSetCOP	rsd_type_set
	)

function to convert params files into ResidueType objects, gets needed subsidiary type sets from rsd_type_set

References read_topology_file().

MutableResidueTypeOP core::chemical::read_topology_file	(	std::string const &	filename,
		chemical::AtomTypeSetCAP	atom_types,
		chemical::ElementSetCAP	elements,
		chemical::MMAtomTypeSetCAP	mm_atom_types,
		chemical::orbitals::OrbitalTypeSetCAP	orbital_atom_types
	)

function to convert params files into ResidueType objects (repackages string filename into istream)

References protocols::abinitio::filename(), and read_topology_file().

MutableResidueTypeOP core::chemical::read_topology_file	(	std::istream &	data,
		std::string const &	filename,
		chemical::AtomTypeSetCAP	atom_types,
		chemical::ElementSetCAP	elements,
		chemical::MMAtomTypeSetCAP	mm_atom_types,
		chemical::orbitals::OrbitalTypeSetCAP	orbital_atom_types
	)

main function to convert params files into ResidueType objects

Construct a ResidueType from a file. Example files are currently in main/database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/ directory These files contain information about each basic ResidueType which can be patched to created various variant types.

The topology file (.params file) is formatted as follows:

The file may contain any number of lines. Blank lines and lines beginning with "#" are ignored. Each non-ignored line must begin with a string, a "tag", which describes a piece of data for the ResidueType. The tags may be given in any order, though they will be processed so that ATOM tag lines are read first.

Valid tags are: AA: Gives the element of the AA enumeration (src/core/chemical/AA.hh) that is appropriate for this residue type. This information is used by the knowledge-based potentials which already encode information specifically for proteins or nucleic acids, and is also used by the RotamerLibrary to retrieve the appropriate rotamer library. Provide "aa_unk" here for "unknown" if not dealing with a canonical amino or nucleic acid. E.g., "AA SER" from SER.params

ACT_COORD_ATOMS: Lists the atoms that define the "action coordinate" which is used by the fa_pair potential followed by the "END" token. E.g., "ACT_COORD_ATOMS OG END" from SER.params.

ADD_RING: Declares a ring within the residue, its index, its saturation type (optional) and the atoms that define it. E.g., " ADD_RING 1 AROMATIC CG CD1 CE1 CZ CE2 CD2" from TYR.params.

ADDUCT: Defines an adduct as part of this residue type giving: a) the name, b) the adduct atom name, c) the adduct atom type, d) the adduct mm type, e) the adduct partial charge, and the f) the distance, g) improper bond angle, and h) dihedral that describe how to build the adduct from the i) parent, i) grandparent, and j) great grandparent atoms. E.g., "ADDUCT DNA_MAJOR_GROOVE_WATER WN6 HOH H 0.0 -6.000000 44.000000 2.990000 N6 C6 C5" from ADE.params.

ATOM: Declare a new atom by name and list several of its properties. This line is column formatted. The atom's name must be in columns 6-9 so that "ATOM CA ..." declares a different atom from "ATOM CA ...". This is for PDB formatting. All atom names must be distinct, and all atom names must be distinct when ignoring whitespace ("CA " and " CA " could not coexist). After the atom name is read, the rest of the line is simply whitespace delimited. Next, the (Rosetta) atom type name is given (which must have been defined in the input AtomTypeSet), and then the mm atom type name is given (which must have been defined in the input MMAtomTypeSet). Finally, the charge for this atom is given, either as the next input or (ignoring the next input) the one after, if the "parse_charge" flag is on (whatever that is). E.g., "ATOM CB CH3 CT3 -0.27 0.000" from ALA.params.

ATOM_ALIAS: Add alternative name(s) for a given atom, for example to be used when loading a PDB file. This line is column formatted. The canonical Rosetta atom name should be in columns 12-15, with the alternative names coming in columns 17-20, 22-25, etc: "ATOM_ALIAS RRRR 1111 2222 3333 ..." As with the ATOM line, whitespace matters. and aliases must be unique with respect to each other and with canonical names, even when whitespace is ignored

BACKBONE_AA: Sets the "backbone_aa" for a particular residue, which can be used to template the backbone scoring (rama and p_aa_pp terms). For example, "BACKBONE_AA ILE" in the non-canonical 4,5-dihydroxyisoleucine params file tells Rosetta to use isoleucine's ramachandran map and p_aa_pp scoring for this noncanonical.

BASE_ANALOGUE: Sets the "base_analogue" for a particular residue, which can be used for sidechain/base specific features. For example, peptide nucleic acid versions of RGU have a sidechain that works JUST LIKE RGU's.

NA_ANALOGUE: Sets the "na_analogue" for a particular residue, which can be used in fragment assembly. For example, it is a REALLY good first approximation that 5-methyl-uridine (i.e., thymine-but-on-ribose) can work with fragments identified by na_ura.

BOND: Declares a bond between two atoms giving their names. This line is whitespace delimited. E.g., "BOND N CA" from ALA.params.

BOND_TYPE: Declares a bond between two atoms, giving their names, and also describing the chemical nature of the bond. (The BOND_TYPE line takes the place of a BOND line - do not specify both.) Standard SDF-style numeric descriptors are accepted. (1, 2, 3 for single, double, triple), along with text version SINGLE, DOUBLE, TRIPLE, UNK (unknown), PSEUDO (pseudo bond), ORBITAL, ARO, AMIDE, CARBOXY (for delocalized carboxylate) and DELOCALIZED. Currently UNK/PSEUDO are treated identically, as are ARO/AMIDE/CARBOXY/DELOCALIZED. See convert_to_BondName() in src/core/chemical/Bond.cc for details on parsing.

CHARGE: Declares a charge for a particular atom. Format CHARGE atom type value Currently valid types are FORMAL. (Partial charges are handled above.) E.g. "CHARGE OG2 FORMAL -1"

CHI: A misnomer for non-amino acids, declares a side-chain dihedral, its index, and the four atoms that define it. E.g., "CHI 2 CA CB CG CD1" from PHE.params.

CHI_ROTAMERS: Lists the chi mean/standard-deviation pairs that define how to build rotamer samples. This is useful for residue types which do not come with their own rotamer libraries. E.g., "CHI_ROTAMERS 2 180 15" from carbohydrates/to5-beta-D-Psip.params.

CONNECT: Declares that an inter-residue chemical bond exists from a given atom. E.g. "CONNECT SG" from CYD.params. NOTE: Connection order is assumed to be preserved between residue types: connection #2 on one residue type is assumed to be "the same" as connection #2 on another residue type, if the two residue types are going to be exchanged in the packer (as ALA might be swapped out for ARG). CONNECT tags are processed in the order they are listed in the input file. For polymeric residue types (e.g., proteins, DNA, RNA, saccharides) "LOWER_CONNECT" and "UPPER_CONNECT" should be listed before any additional CONNECT records. CONNECTs are assigned an index beginning after the LOWER_CONNECT and UPPER_CONNECT, if present. That is, if a topology file lists both a LOWER_CONNECT and an UPPER_CONNECT, the 1st CONNECT will we given the index 3.

CUT_BOND: Declares a previously-declared bond to be off-limits to the basic atom-tree construction logic (user-defined atom trees can be created which defy this declaration, if desired). This is useful in cases where the chemical graph contains cycles. E.g. "CUT_BOND O4' C1'" from URA.params.

FIRST_SIDECHAIN_ATOM: Gives the name of the first side-chain atom. All heavy atoms that were declared before the first side-chain atom in the topology file are considered backbone atoms (but not necessarily main-chain atoms). All heavy atoms after the first side-chain atom are considered side-chain atoms. Hydrogen atoms are either side-chain or backbone depending on the heavy atom to which they are bound. E.g., "FIRST_SIDECHAIN_ATOM CB" from SER.params.

IO_STRING: Gives the three-letter and one-letter codes that are used to read and write this residue type from and to PDB files, and to FASTA files. This tag is column formatted. Columns 11-13 are for the three-letter code. Column 15 is for the 1-letter code. E.g., "IO_STRING Glc Z".

INTERCHANGEABILITY_GROUP: Gives the name for the group of ResidueType objects that are functionally Interchangeable (but which may have different variant types). This information is used by the packer to discern what ResidueType to put at a particular position. If this tag is not given in the topology file, the three-letter code given by the IO_STRING tag is used instead.

ICOOR_INTERNAL: Describes the geometry of the residue type from internal coordinates giving a) the atom, b) the torsion, phi, in degrees c) the improper bond angle that is (180-bond angle) in degrees, theta, d) the bond length, d, in Angstroms e) the parent atom, f) the grand-parent, and g) the great-grandparent. The first three atoms in the file have a peculiar structure where: 1) at1 lists itself as its own parent, at2 as its grand parent, and at3 as its great-grandparent, 2) at2 lists at1 as its parent, itself as its grand parent, and at3 as its great-grandparent, and 3) at3 list at2 as its parent, at1 as its grand parent, and itself as its great-grandparent. The atoms "LOWER" and "UPPER" are given for polymeric residues to describe the ideal coordinate of the previous and next residues. For non-polymeric inter-residue connections, atoms "CONN#" should be given (e.g., CONN3 for the disulfide connection in CYD). The number for an inter-residue connection comes from the order in which the connection is declared in the file, and includes the LOWER_CONNECT and UPPER_CONNECT connections in this count (e.g., for CYD, there is a LOWER_CONNECT, and UPPER_CONNECT, and only a single CONNECT declaration, so the disulfide connection is the third connection). The order in which internal coordinate data for atoms are given, excepting the first three, must define a "tree" in that atom geometry must only be specified in terms of atoms whose geometry has already been specified. Improper dihedrals may be specified, where the great grandparent is not the parent atom of the grandparent but in these cases, the great grandparent does need to be a child of the grandparent. E.g., "ICOOR_INTERNAL CB -122.000000 69.862976 1.516263 CA N C" from SER.params.

LOWER_CONNECT: For a polymer residue, declares which atom forms the "lower" inter-residue connection (chemical bond), i.e., the bond to residue i-1. E.g., "LOWER_CONNECT N" from SER.params.

LOWEST_RING_CONFORMER: For a cyclic residue, declares which ideal ring conformation is most stable by IUPAC name. There is no check in place for valid IUPAC conformer names; if the name is not found in the database, no lowest conformer will be set. E.g., "LOWEST_RING_CONFORMER 4C1" from to3-alpha-D-Glcp.params.

LOW_RING_CONFORMERS: For a cyclic residue, declares which ideal ring conformations are local minima/stable by IUPAC name. (If present, the LOWEST_RING_CONFORMER will automatically included to this subset within RingConformerSet.) There is no check in place for valid IUPAC conformer names; if the name is not found in the database, that conform- er will not be added to the subset. E.g., "LOW_RING_CONFORMERS O3B B14 3S1 5S1 2SO BO3 1S3 14B 1S5 B25 OS2 1C4" from to3-alpha-D-Glcp.params.

MAINCHAIN_ATOMS: This is a list of atom names that define the main chain. The main chain describes the linear connection of atoms from the lower-terminus to the upper-terminus in a residue. This is NOT synonymous with "backbone atoms". (Backbone atoms are any atoms NOT included in a side chain, as defined by FIRST_SIDECHAIN_ATOM. See above.) All main-chain atoms will necessarily be backbone atoms, but not all backbone atoms are main-chain atoms because some residues include rings and/or non-rotatable functional groups. For example, the carbonyl oxygen of an amino acid residue is a backbone atom but NOT a part of the main chain. If a topology file does not include a MAINCHAIN_ATOMS record, Rosetta will determine the main chain by finding the shortest path from lower terminus to upper terminus, which may be through any CUT_BONDs you have defined! Use of this tag is required for those residue types that ONLY come in LOWER_TERMINUS or UPPER_TERMINUS varieties, such as any residue type that serves exclusively as a "cap" for a larger polymer. E.g., "MAINCHAIN_ATOMS C1 C2 C3 C4 O4" from an aldohexopyranose topology file.

METAL_BINDING_ATOMS: For polymer residue types that can bind metals (METALBINDING property), this is a list of the atoms that can form a direct bond to the metal. For example, in ASP.params, it would read: "METAL_BINDING_ATOMS OD1 OD2" DISULFIDE_ATOM_NAME: For polymer residue types that can form disulfide bonds (SIDECHAIN_THIOL property), this is the atom it does so with. For example, in CYS.params, it would read: "DISULFIDE_ATOM_NAME SG"

NAME: Gives the name for this ResidueType. The name for each ResidueType must be unique within a ResidueTypeSet. It is not limited to three letters. E.g., "NAME SER" from SER.params.

NBR_ATOM: Declares the name of the atom which will be used to define the center of the residue for neighbor calculations. The coordinate of this atom is used along side the radius given in in the NBR_RADIUS tag. This atom should be chosen to not move during packing so that neighbor relationships can be discerned for an entire set of rotamers from the backbone coordinates from the existing residue. E.g., "NBR_ATOM CB" from SER.params.

NBR_RADIUS: Declares a radius that defines a sphere which, when centered on the NBR_ATOM, is guaranteed to contain all heavy atoms under all possible dihedral angle assignments (but where bond angles and lengths are considered ideal). This is used to determine which residues are close enough that they might interact. Only the interactions of those such residues are ever evaluated by the scoring machinery. E.g., "NBR_RADIUS 3.4473" from SER.params.

NCAA_ROTLIB_PATH: Gives the path to the rotamer library file to use for a non-canonical amino acid. E.g., "NCAA_ROTLIB_PATH E35.rotlib" from d-ncaa/d-5-fluoro-tryptophan.params See the ROTAMERS tag for a more general way of specifying how to build rotamers.

NCAA_ROTLIB_NUM_ROTAMER_BINS: Lists the number of rotamers and the number of bins for each rotamer. E.g., "NCAA_ROTLIB_NUM_ROTAMER_BINS 2 3 2" from d-ncaa/d-5-fluoro-tryptophan.params See the ROTAMERS tag for a more general way of specifying how to build rotamers.

NCAA_SEMIROTAMERIC: Indicates if a NCAA is semirotameric (this is hard coded for canonicals)

NCAA_ROTLIB_BB_TORSIONS: This is followed by a series of integers indicating which of the mainchain torsions are used for backbone-dependent rotamers in sampling and scoring. For example, in oliogureas, the line is "NCAA_ROTLIB_BB_TORSIONS 1 2 3", indicating that mainchain torsions 1, 2, and 3 (but not mainchain torsion 4 or the inter-residue torsion) are used for backbone-dependent rotamers. If not specified, all mainchain torsions except the final, inter-residue torsion are used. (For example, for alpha-amino acids, phi and psi, but not omega, are used, so "NCAA_ROTLIB_BB_TORSIONS 1 2" is implied and needs not be written out explicitly).

NET_FORMAL_CHARGE: The overall charge on this residue. This must be an integer, though it can be positive or negative.

NRCHI_START_ANGLE: The lower bound for non rotameric chi sampling (sometimes you don't want 0 or 180 to be minimum so you get both sides of these critical values; take this from the input file you used with MakeRotLib

NRCHI_SYMMETRIC: Indicates if the nonrotameric chi is symmetric (PHE); if absent it is assumed not (ASN)

NU: Declares an internal ring dihedral, its index, and the four atoms that define it. E.g., "NU 2 C1 C2 C3 C4 ".

NUMERIC_PROPERTY: Stores an arbitrary float value that goes along with an arbitrary string key in a ResidueType. No examples can be currently found in the database (10/13). E.g., "NUMERIC_PROPERTY twelve 12.0" would be a way to store the number "12.0" with the key "twelve".

ORIENT_ATOM: Describes how to orient rotamers onto an existing residue either by orienting onto the NBR_ATOM atom, or by using the more complicated (default) logic in ResidueType::select_orient_atoms. There are two options here: "ORIENT_ATOM NBR" (orient onto NBR_ATOM) and "ORIENT_ATOM DEFAULT". If this tag is not given in the topology file, then the default behavior is used. E.g., "SET_ORIENT_ATOM NBR" from SC_Fragment.txt

PDB_ROTAMERS: Gives the file name that describes entire-residue rotamers which can be used in the packer to consider alternate conformations for a residue. This is commonly used for small molecules. See the ROTAMERS tag for a more general way of specifying how to build rotamers.

PROPERTIES: Adds a given set of property strings to a residue type. E.g., "PROPERTIES PROTEIN AROMATIC SC_ORBITALS" from TYR.params.

PROTON_CHI: Declares a previously-declared chi angle to be a "proton chi" and describe how this dihedral should be sampled by code that takes discrete sampling of side-chain conformations. The structure of these samples is as follows: First the word "SAMPLES" is given. Next the number of samples should be given. Next a list of dihedral angles, in degrees, should be given. Next, the word "EXTRA" is given. Next the number of extra samples is given. Finally, a list of perturbations angles, in degrees, is given. In cases where extra rotamers are requested (e.g., with the -ex2 flag), then the listed samples are are perturbed +/- the listed perturbations. E.g., "PROTON_CHI 2 SAMPLES 18 0 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 EXTRA 0" from SER.params.

RAMA_PREPRO_FILENAME: Specify mainchain torsion potential to be used for this ResidueType when scoring with the rama_prepro score term. Two strings follow. The first is the filename for general scoring, and the second is the filename for scoring in the special case of this residue occurring before a proline residue.

RAMA_PREPRO_RESNAME: The name of the amino acid as listed in the rama_prepro scoring table file in the database. If not specified, the amino acid name is used.

REMAP_PDB_ATOM_NAMES: When reading in a PDB, attempt to match the input atoms for this residue based on elements and estimated connectivity, rather than atom names. (Connectivity by CONECT lines is ignored.) This only applies to input poses, and not to individually loaded residues, e.g. from the PDB_ROTAMERS line.

ROTAMER_AA: Sets the "rotamer_aa" for a particular residue, which can be used to describe to the RotamerLibrary what amino acid to mimic for the sake of building rotamers. E.g., "ROTAMER_AA SER" See the ROTAMERS tag for a more general way of specifying how to build rotamers.

ROTAMERS: Sets the rotamer generation to a given type. The line should be formatted as "ROTAMERS <TAG> <optional data>", where <TAG> specifies what sort of rotamer library to build for this residue, and <optional data>=""> is type-specific data describing how to build. E.g. "ROTAMERS DUNBRACK SER" will cause Serine-like Dunbrack rotamers to be used for this residue type, and "ROTAMERS PDB /path/to/ligand.conf.pdb" will cause the rotamer library to be read from the PDB file "/path/to/ligand.conf.pdb" Currently the following types are known (more may be added):

• BASIC - simple rotamer library with no parameters (Just the input residue)
• DUNBRACK - Dunbrack rotamer library for the given aa (e.g. "SER")
• CENROT - Centroid rotamers for the given aa (e.g. "SER")
• NCAA - Non-canonical amino acid libraries (<filename> <bins for="" each="" rotamer>="">)
• PDB - Rotamer library loaded from PDB (<filename>) - Note that unlike PDB_ROTAMERS, the filename is not relative to the params file location.

STRING_PROPERTY: Stores an arbitrary string value with a given string key. No example can be currently found in the database (10/13). A valid case would be "STRING_PROPERTY count twelve" which could store the string "twelve" for the key "count".

TYPE: States whether this is a polymeric or ligand residue type. E.g., "TYPE POLYMER" or "TYPE LIGAND" which adds either "POLYMER" or "LIGAND" properties to this residue type.

UPPER_CONNECT: For a polymer residue, declares which atom forms the "upper" inter-residue connection (chemical bond), i.e., the bond to residue i+1. E.g., "UPPER_CONNECT C" from SER.params.

VARIANT: Declares this residue type to have a particular variant type. Variant types are used by the packer to determine which ResidueTypes are compatible with a given starting residue. Variants are similar to properties, except that the packer does not restrict itself to residue types that have the same set of properties. Variant information is also used by the residue-type-patching system to avoid applying patches to certain residue types. E.g., "VARIANT DISULFIDE". from CYD.params.

VARIANT_OF: Used with VARIANT, this declares the "base name" of the ResidueType for which this is a VARIANT_TYPE. E.g., "VARIANT_OF CYT".

VIRTUAL_SHADOW: Declares the first atom as a shadower of the second atom, implying that the atoms ought to be restrained to lie directly on top of each other. E.g. "VIRTUAL_SHADOW NV N" from PRO.params. Currently, the cart_bonded and ring_close energy terms are the only energy terms that enforce this.

References aa_gly, aa_ser, aa_thr, core::chemical::rings::ALIPHATIC, apply_symm_gly_corrections(), core::chemical::rings::AROMATIC, BondInRing, convert_to_BondName(), CYCLIC, detect_ld_chirality_from_polymer_residue(), FULL_ATOM_t, core::simple_metrics::metrics::mean, name_from_aa(), protocols::hybridization::path, core::chemical::Bond::ringness(), rot(), protocols::cluster::calibur::rotate(), set_up_mapfile_reassignments_from_commandline(), setup_atom_type_reassignments_from_commandline(), setup_atomic_charge_reassignments_from_commandline(), setup_icoor_reassignments_from_commandline(), tr(), and protocols::hybridization::val.

void core::chemical::real_to_virtual

(

MutableResidueType &

restype

)

Virtualize convert the MutableResidueType to a virtual type NOTE: This function does not rename the residue type.

Make all atoms virtual

Author

Sebastian Rämisch raemi.nosp@m.sch@.nosp@m.scrip.nosp@m.ps.e.nosp@m.du

References core::chemical::ResidueTypeBase::add_property(), core::chemical::MutableResidueType::all_atoms(), core::chemical::MutableResidueType::atom(), core::chemical::Atom::charge(), core::chemical::Atom::is_virtual(), and core::chemical::MutableResidueType::set_atom_type().

Referenced by core::pose::Pose::real_to_virtual().

template<typename Graph >

void core::chemical::regenerate_graph_vertex_index

(

Graph &

graph

)

When adding and deleting nodes in a graph, sometimes the inner counting of nodes/edges gets outdated. Run this to fix the problem.

References core::sequence::end.

Referenced by core::chemical::MutableResidueType::add_atom(), and core::chemical::gasteiger::assign_gasteiger_atom_types().

utility::vector1<VD> core::chemical::remap_vect	(	utility::vector1< VD > const &	vect,
		std::map< VD, VD > const &	old_to_new
	)

Referenced by core::chemical::MutableResidueType::operator=().

void core::chemical::rename_atoms	(	MutableResidueType &	res,
		bool	preserve
	)

Rename atoms in the residue type such that their names are unique. If preserve is true, only rename those which have no names or who have name conflicts. (Both of the conflicting atoms will be renamed.)

References core::chemical::MutableResidueType::atom(), core::chemical::Atom::element_type(), core::chemical::MutableResidueType::graph(), core::chemical::Atom::name(), core::chemical::ResidueTypeBase::remap_pdb_atom_names(), core::chemical::MutableResidueType::rename_atom(), core::id::to_string(), and TR().

Referenced by core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType().

void core::chemical::reroot_restype	(	core::chemical::MutableResidueType &	restype,
		core::chemical::ResidueGraph const &	graph,
		core::chemical::VD	root
	)

Reroot the Icoord records of a ResidueType on the given atom We need direct access to the ResidueGraph, so this function can only be called by ResidueType itself.

Doing a depth first search here because that's what molfile_to_params.py does: "Protein residues appear to go depth first, so that all chi angles ride on each other." RM: Doing a breadth first search would likely result in a shallower tree, but with possibly different behavior on how ring atom trees are built.

Note that updating the ICOOR records will also update the atom_base values. ... Which has the knock-on effect of possibly invalidating the chi values. The validity of the chis will be checked, and if the new icoord tree has invalidated them, they will be re-assigned.

Assumes:

• All bonds and atoms exist in the graph,
• The graph is completely connected.
• All ideal xyz coordinates are updated.

References core::chemical::MutableResidueType::atom_base(), core::chemical::MutableResidueType::atom_name(), core::chemical::MutableResidueType::autodetermine_chi_bonds(), core::chemical::MutableResidueType::chi_atom_vds(), core::chemical::MutableResidueType::chi_valid(), core::chemical::MutableResidueType::clear_icoor(), core::id::D, find_bonds_in_rings(), core::chemical::MutableResidueType::has(), core::chemical::MutableResidueType::natoms(), core::chemical::MutableResidueType::nchi(), core::id::PHI, core::chemical::MutableResidueType::set_icoor(), core::id::THETA, and TR().

Referenced by core::chemical::MutableResidueType::assign_internal_coordinates().

ResidueTypeSelectorSingleOP core::chemical::residue_selector_single_from_line

(

std::string const &

line

)

create a singe ResidueTypeSelector from an input line.

References protocols::cluster::calibur::aa, update_ResidueType_enum_files::properties, and TR().

Referenced by core::chemical::ResidueTypeSelector::add_line().

std::string core::chemical::residue_type_all_patches_name

(

ResidueType const &

rsd_type

)

helper function, returns the name of all added patches

References core::chemical::ResidueTypeBase::name(), and PATCH_LINKER.

Referenced by core::util::add_covalent_linkage_helper(), core::chemical::ResidueTypeFinder::filter_all_patch_names(), get_patch_names(), and protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper().

std::string core::chemical::residue_type_base_name

(

ResidueTypeBase const &

rsd_type

)

helper function, returns the base residue name prior to any patching

References protocols::vip::base_name(), core::chemical::ResidueTypeBase::name(), and PATCH_LINKER.

Referenced by core::util::add_covalent_linkage_helper(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), core::chemical::ResidueTypeFinder::filter_by_residue_type_base_name(), core::chemical::ResidueTypeFinder::fixes_interchangeability_group(), core::chemical::ResidueTypeFinder::fixes_name3(), protocols::residue_optimization::MetapatchEnumeration::generate_derived_types(), protocols::simple_moves::chiral::get_chiral_residue_type(), core::chemical::ResidueTypeFinder::get_possible_base_unpatchable_residue_types(), core::chemical::ResidueTypeSet::get_residue_type_with_custom_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::chemical::ResidueTypeFinder::initialize_relevant_pdb_components(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), and core::pose::Pose::virtual_to_real().

bool core::chemical::residue_type_bases_identical	(	ResidueTypeBase const &	r1,
		ResidueTypeBase const &	r2
	)

References core::chemical::ResidueTypeBase::aa(), core::chemical::ResidueTypeBase::atom_aliases(), core::chemical::ResidueTypeBase::atom_type_set_ptr(), core::chemical::ResidueTypeBase::backbone_aa(), core::chemical::ResidueTypeBase::base_analogue(), core::chemical::ResidueTypeBase::base_name(), core::chemical::ResidueTypeBase::canonical_atom_aliases(), core::chemical::ResidueTypeBase::defined_adducts(), core::chemical::ResidueTypeBase::element_set_ptr(), core::chemical::ResidueTypeBase::force_nbr_atom_orient(), core::chemical::ResidueTypeBase::gasteiger_atom_typeset(), core::chemical::ResidueTypeBase::get_disulfide_atom_name(), core::chemical::ResidueTypeBase::get_metal_binding_atoms(), core::chemical::ResidueTypeBase::get_rama_prepro_mainchain_torsion_potential_name(), core::chemical::ResidueTypeBase::get_rama_prepro_map_file_name(), core::chemical::ResidueTypeBase::interchangeability_group(), core::chemical::ResidueTypeBase::is_metapatched(), core::chemical::ResidueTypeBase::mm_atom_types_ptr(), core::chemical::ResidueTypeBase::mode(), core::chemical::ResidueTypeBase::n_orbitals(), core::chemical::ResidueTypeBase::na_analogue(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueTypeBase::name1(), core::chemical::ResidueTypeBase::name3(), core::chemical::ResidueTypeBase::net_formal_charge(), core::chemical::ResidueTypeBase::orbital_types_ptr(), core::chemical::ResidueTypeBase::properties(), and core::chemical::ResidueTypeBase::remap_pdb_atom_names().

Referenced by residue_types_identical().

bool core::chemical::residue_types_identical	(	ResidueType const &	r1,
		ResidueType const &	r2
	)

Are two ResidueTypes equivalent? This is here rather than as an operator on ResidueType because it's not the sort of thing one should be doing normally. This looks for exact equivalence, including atom order.

References core::chemical::ResidueType::abase2(), core::chemical::ResidueType::accpt_pos(), core::chemical::ResidueType::accpt_pos_sc(), core::chemical::ResidueType::actcoord_atoms(), core::chemical::ResidueType::all_bb_atoms(), core::chemical::ResidueType::all_sc_atoms(), core::chemical::ResidueType::atom_base(), core::chemical::ResidueType::atom_being_shadowed(), core::chemical::ResidueType::atom_charge(), core::chemical::ResidueType::atom_depends_on_connection(), core::chemical::ResidueType::atom_depends_on_lower_polymeric_connection(), core::chemical::ResidueType::atom_depends_on_upper_polymeric_connection(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::atom_properties(), core::chemical::ResidueType::atom_type_index(), core::chemical::ResidueType::atoms_last_controlled_by_chi(), core::chemical::ResidueType::atoms_with_orb_index(), core::chemical::ResidueType::attached_H_begin(), core::chemical::ResidueType::attached_H_end(), core::chemical::ResidueType::bondangle(), core::chemical::ResidueType::bondangles_for_atom(), core::chemical::ResidueType::bonded_neighbor(), core::chemical::ResidueType::bonded_neighbor_ringnesses(), core::chemical::ResidueType::bonded_neighbor_types(), core::chemical::ResidueType::bonded_orbitals(), core::chemical::ResidueType::chi_2_proton_chi(), core::chemical::ResidueType::chi_atoms(), core::chemical::ResidueType::chi_rotamers(), compare_atom_icoor(), compare_residue_connection(), core::chemical::ResidueType::cut_bond_neighbor(), core::chemical::ResidueType::dihedral(), core::chemical::ResidueType::dihedrals_for_atom(), core::chemical::ResidueType::element(), core::chemical::ResidueType::first_sidechain_hydrogen(), core::chemical::ResidueType::formal_charge(), core::chemical::ResidueType::gasteiger_atom_type(), core::chemical::ResidueType::get_base_type_cop(), core::chemical::ResidueType::Haro_index(), core::chemical::ResidueType::has_polymer_dependent_groups(), core::chemical::ResidueType::heavyatom_has_polar_hydrogens(), core::chemical::ResidueType::Hpol_index(), core::chemical::ResidueType::Hpos_apolar(), core::chemical::ResidueType::Hpos_polar(), core::chemical::ResidueType::Hpos_polar_sc(), core::chemical::ResidueType::icoor(), core::chemical::ResidueType::ideal_xyz(), core::chemical::ResidueType::is_proton_chi(), core::chemical::ResidueType::last_backbone_atom(), core::chemical::ResidueType::last_controlling_chi(), core::chemical::ResidueType::low_ring_conformers(), core::chemical::ResidueType::lower_connect_id(), core::chemical::ResidueType::lowest_ring_conformers(), core::chemical::ResidueType::mainchain_atoms(), core::chemical::ResidueType::mass(), core::chemical::ResidueType::mm_atom_type_index(), core::chemical::ResidueType::n_hbond_acceptors(), core::chemical::ResidueType::n_hbond_donors(), core::chemical::ResidueType::n_non_polymeric_residue_connections(), core::chemical::ResidueType::n_polymeric_residue_connections(), core::chemical::ResidueType::n_possible_residue_connections(), core::chemical::ResidueType::n_proton_chi(), core::chemical::ResidueType::n_ring_conformer_sets(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nbonds(), core::chemical::ResidueType::nbr_atom(), core::chemical::ResidueType::nbr_radius(), core::chemical::ResidueType::nchi(), core::chemical::ResidueType::ndihe(), core::chemical::ResidueType::nheavyatoms(), core::chemical::ResidueType::nu_atoms(), core::chemical::ResidueType::num_bondangles(), core::chemical::ResidueType::path_distances(), core::chemical::ResidueType::proton_chi_2_chi(), core::chemical::ResidueType::proton_chi_extra_samples(), core::chemical::ResidueType::proton_chi_samples(), protocols::hybridization::r1, protocols::hybridization::r2, core::chemical::ResidueType::residue_connection(), residue_type_bases_identical(), core::chemical::ResidueType::ring_atoms(), core::chemical::ResidueType::ring_conformer_set(), core::chemical::ResidueType::root_atom(), and core::chemical::ResidueType::upper_connect_id().

bool core::chemical::retype_is_aromatic	(	VD const &	atom,
		ResidueGraph const &	graph
	)

An atom is aromatic if it has any aromatic bonds to a non-virtual atom. TODO: We need better aromatic ring detection.

References AromaticBond, core::chemical::Atom::element_type(), and protocols::hybridization::t.

Referenced by rosetta_retype_fullatom().

void core::chemical::rosetta_recharge_fullatom

(

MutableResidueType &

res

)

Apply molfile_to_params style partial charges to the ResidueType.

These partial charges are based off of the Rosetta atom type, adjusted such that the net partial charge is equal to the net formal charge.

These charges are almost certainly dodgy. If you have any other source of partial charges that are at all reasonable, you probably want to consider those instead.

Assumes:

• All atoms and bond are present.
• All atom types have been set.
• Formal charges (if any) have been set.

References core::chemical::MutableResidueType::atom(), core::chemical::ResidueTypeBase::atom_type_set(), core::chemical::Atom::charge(), core::chemical::Atom::formal_charge(), core::chemical::MutableResidueType::graph(), core::chemical::ResidueTypeBase::name(), and TR().

Referenced by core::chemical::ReplaceProtonWithTrifluoromethyl::apply(), core::chemical::ReplaceProtonWithMethyl::apply(), core::chemical::ReplaceProtonWithMethoxy::apply(), core::chemical::ReplaceProtonWithEthyl::apply(), core::chemical::ReplaceProtonWithChlorine::apply(), core::chemical::ReplaceProtonWithFluorine::apply(), core::chemical::ReplaceProtonWithBromine::apply(), core::chemical::ReplaceProtonWithIodine::apply(), core::chemical::ReplaceProtonWithHydroxyl::apply(), and core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType().

void core::chemical::rosetta_retype_fullatom	(	MutableResidueType &	restype,
		bool	preserve
	)

Reassign Rosetta atom types based on the current fullatom heuristics.

If preserve is true, only retype those atoms which have an atom_type_index of zero.

The logic here comes from molfile_to_params.py Which is itself based on Rosetta++ ligand_ns.cc set_rosetta_atom_types(), and has been validated against the Meiler and Baker 2006 cross docking test set assignments.

I'm not saying the logic is good, but it's the logic we're using.

This function assumes that:

• All bonds and atoms exist.
• Bond types (bond_name) are correctly set
• The appropriate element objects have been set in Atoms.

If preserve is true, only retype those atoms which have an atom_type_index of zero.

References core::pose::motif::a(), AromaticBond, core::chemical::Atom::atom_type_index(), core::chemical::ResidueTypeBase::atom_type_set(), core::chemical::element::B, core::chemical::element::Br, core::chemical::element::C, core::chemical::element::Ca, core::chemical::element::Cl, core::chemical::element::Co, core::chemical::element::Cu, DoubleBond, core::chemical::Atom::element_type(), core::chemical::element::F, core::chemical::element::Fe, core::chemical::MutableResidueType::graph(), core::chemical::element::H, core::chemical::AtomTypeSet::has_atom(), core::chemical::element::I, core::chemical::element::K, core::chemical::element::Mg, core::chemical::element::N, core::chemical::element::Na, core::chemical::element::name_from_elements(), core::chemical::element::O, core::chemical::element::P, retype_is_aromatic(), core::chemical::element::S, core::chemical::MutableResidueType::set_atom_type(), SingleBond, protocols::hybridization::t, TripleBond, and core::chemical::element::Zn.

Referenced by core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType().

core::chemical::ResidueTypeSetCAP core::chemical::rsd_set_from_cmd_line

(

)

Return a constant access pointer to the ResidueTypeSet specified by the command-line options.

Referenced by protocols::simple_filters::StructureSimilarityEvaluatorCreator::add_evaluators(), protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), protocols::boinc::boincOutputFilter(), protocols::denovo_design::construct_dummy_pose(), protocols::jd2::PoseInputStreamJobInputter::fill_jobs(), protocols::hotspot_hashing::StubGenerator::getStubByName(), protocols::comparative_modeling::AlignmentClustering::poses_from_cmd_line(), and protocols::comparative_modeling::poses_from_cmd_line().

void core::chemical::set_up_mapfile_reassignments_from_commandline

(

ResidueTypeBaseOP

rsd

)

Certain commandline flags override the default RamaPrePro maps used by the 20 canonical amino acids. This function applies those overrides.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References is_canonical_L_aa_or_gly().

Referenced by read_topology_file().

utility::vector1< std::string > core::chemical::setup_aa2name

(

)

setup the vector that maps AA enum to string name

References name2aa(), and num_aa_types.

Referenced by aa2name().

utility::vector1< char > core::chemical::setup_aa2oneletter

(

)

setup the vector that maps AA enum to one letter char

References num_aa_types, and oneletter2aa().

Referenced by aa2oneletter().

void core::chemical::setup_atom_type_reassignments_from_commandline	(	std::string const &	rsd_type_name,
		TypeSetMode	rsd_type_set_mode,
		std::map< std::string, std::string > &	atom_type_reassignments
	)

References tr(), and type_set_mode_from_string().

Referenced by read_topology_file().

void core::chemical::setup_atomic_charge_reassignments_from_commandline	(	std::string const &	rsd_type_name,
		TypeSetMode	rsd_type_set_mode,
		std::map< std::string, Real > &	atomic_charge_reassignments
	)

References tr(), and type_set_mode_from_string().

Referenced by read_topology_file().

void core::chemical::setup_icoor_reassignments_from_commandline	(	std::string const &	rsd_type_name,
		TypeSetMode	rsd_type_set_mode,
		std::map< std::string, utility::vector1< std::string > > &	icoor_reassignments
	)

References tr(), and type_set_mode_from_string().

Referenced by read_topology_file().

std::map< std::string, AA > core::chemical::setup_name2aa

(

)

setup the map that converts string name to AA enum

References aa_ala, aa_arg, aa_asn, aa_asp, aa_b3a, aa_b3c, aa_b3cisACHC, aa_b3cisACPC, aa_b3d, aa_b3e, aa_b3f, aa_b3g, aa_b3h, aa_b3i, aa_b3k, aa_b3l, aa_b3m, aa_b3n, aa_b3p, aa_b3q, aa_b3r, aa_b3s, aa_b3t, aa_b3transACPC, aa_b3v, aa_b3w, aa_b3y, aa_cys, aa_dal, aa_dan, aa_dar, aa_das, aa_dcs, aa_dgn, aa_dgu, aa_dhi, aa_dil, aa_dle, aa_dly, aa_dme, aa_dph, aa_dpr, aa_dse, aa_dth, aa_dtr, aa_dty, aa_dva, aa_gln, aa_glu, aa_gly, aa_h2o, aa_his, aa_ile, aa_leu, aa_lys, aa_met, aa_phe, aa_pro, aa_ser, aa_thr, aa_trp, aa_tyr, aa_unk, aa_unp, aa_val, aa_vrt, na_ade, na_cyt, na_gua, na_rad, na_rcy, na_rgu, na_thy, na_ura, ou3_aib, ou3_ala, ou3_arg, ou3_asn, ou3_asp, ou3_cys, ou3_gln, ou3_glu, ou3_gly, ou3_his, ou3_ile, ou3_leu, ou3_lys, ou3_met, ou3_phe, ou3_pro, ou3_ser, ou3_thr, ou3_trp, ou3_tyr, and ou3_val.

Referenced by name2aa().

std::map< char, AA > core::chemical::setup_oneletter2aa

(

)

setup the map the converts one letter char to AA enum

References aa_ala, aa_arg, aa_asn, aa_asp, aa_cys, aa_gln, aa_glu, aa_gly, aa_h2o, aa_his, aa_ile, aa_leu, aa_lys, aa_met, aa_phe, aa_pro, aa_ser, aa_thr, aa_trp, aa_tyr, aa_unk, aa_unp, aa_val, aa_vrt, na_ade, na_cyt, na_gua, na_rad, na_rcy, na_rgu, na_thy, and na_ura.

Referenced by oneletter2aa().

void core::chemical::setup_patch_atomic_charge_reassignments_from_commandline	(	std::string const &	patch_name,
		TypeSetMode	rsd_type_set_mode,
		ResidueTypeSelector const &	rsd_selector,
		std::map< std::string, Real > &	atomic_charge_reassignments
	)

override patch partial charges with values from commandline

References core::chemical::ResidueTypeBase::aa(), aa_from_name(), core::chemical::ResidueTypeBase::add_property(), get_L_equivalent(), is_canonical_D_aa(), is_canonical_L_aa_or_gly(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueTypeBase::name1(), core::chemical::ResidueTypeBase::name3(), oneletter_code_from_aa(), tr(), and type_set_mode_from_string().

Referenced by case_from_lines().

utility::vector1< VD > core::chemical::shortest_path	(	MutableResidueType const &	res,
		VD	start,
		VD	end
	)

Figure out the shortest path between two atoms (inclusive) Will return an empty vector if one does not exist.

References core::sequence::end, core::chemical::MutableResidueType::graph(), has(), protocols::hybridization::path, and protocols::loops::start.

Referenced by protocols::toolbox::ResidueNetwork::average_shortest_path_length(), protocols::toolbox::ResidueNetwork::connectivity_index(), mainchain_path(), protocols::abinitio::KinematicAbinitio::set_max_seq_sep(), protocols::loop_grower::DensSkeleton::shortest_path(), and protocols::loop_grower::DensSkeleton::shortest_path_bfs().

bool core::chemical::sort_patchop_by_name	(	PatchOP	p,
		PatchOP	q
	)

std::string core::chemical::string_from_type_set_mode

(

TypeSetMode

mode

)

References CENTROID, CENTROID_ROT, CENTROID_ROT_t, CENTROID_t, COARSE_RNA, COARSE_RNA_t, DEFAULT_t, FA_STANDARD, FULL_ATOM_t, HYBRID_FA_STANDARD_CENTROID, HYBRID_FA_STANDARD_CENTROID_t, INVALID_t, and TR().

Referenced by core::chemical::ChemicalManager::atom_type_set(), operator<<(), protocols::features::ResidueTypesFeatures::report_features(), core::chemical::ChemicalManager::residue_type_set(), core::util::switch_to_centroid_rot_set(), protocols::sewing::data_storage::SmartAssembly::to_pose(), and core::io::serialization::write_binary().

static const utility::vector1< std::string >* const core::chemical::STRING_LIST ( generate_property_to_string_vector()  )

static

Referenced by core::chemical::ResidueProperties::get_string_from_property(), and core::chemical::ResidueProperties::get_string_from_variant().

static const utility::vector1< std::string >* const core::chemical::STRING_LIST ( generate_variant_to_string_vector()  )

static

ICoordAtomIDType core::chemical::string_to_icoord_type

(

std::string const &

name

)

Convert a string designation into the corresponding ICoordAtomIDType enum.

References CONNECT, INTERNAL, POLYMER_LOWER, and POLYMER_UPPER.

Referenced by core::chemical::MutableICoorRecord::build_xyz(), check_residue_has_atom(), correct_conn(), has_assigned_coords(), core::chemical::ICoorAtomID::ICoorAtomID(), and core::chemical::MutableResidueType::set_icoor().

std::string core::chemical::tag_from_line

(

std::string const &

line

)

handy function, return the first word from a line

Referenced by case_from_lines(), core::chemical::Metapatch::read_file(), and core::chemical::Patch::read_file().

static basic::Tracer core::chemical::tr ( "core.chemical"  )

static

static basic::Tracer core::chemical::TR ( "core.chemical.bond_support"  )

static

static basic::Tracer core::chemical::TR ( "core.chemical.Bond"  )

static

static basic::Tracer core::chemical::tr ( "core.chemical"  )

static

static basic::Tracer core::chemical::TR ( "core.chemical.MutableChiRecord"  )

static

static basic::Tracer core::chemical::tr ( "core.chemical.ElementSet"  )

static

static basic::Tracer core::chemical::TR ( "core.chemical.ResidueTypeSelector"  )

static

static basic::Tracer core::chemical::TR ( "core.chemical.AtomICoor"  )

static

static basic::Tracer core::chemical::TR ( "core.chemical.MutableICoorRecord"  )

static

static basic::Tracer core::chemical::TR ( "core.chemical.util"  )

static

static basic::Tracer core::chemical::TR ( "core.chemical.icoor_support"  )

static

static basic::Tracer core::chemical::TR ( "core.chemical.Atom"  )

static

Referenced by core::chemical::MutableResidueType::add_actcoord_atom(), add_atom_type_set_parameters_from_command_line(), core::chemical::ResidueTypeSet::add_base_residue_type(), core::chemical::MutableResidueType::add_chi(), core::chemical::ResidueTypeSelector::add_line(), core::chemical::ResidueTypeSetCache::add_residue_type(), core::chemical::ResidueTypeSet::add_unpatchable_residue_type(), apply_adducts_to_residue(), core::chemical::ResidueTypeFinder::apply_basic_filters(), core::chemical::ResidueTypeFinder::apply_filters_after_patches(), core::chemical::ResidueTypeFinder::apply_preferences_and_discouragements(), core::chemical::MutableResidueType::assign_internal_coordinates(), core::chemical::ICoorAtomID::atom_id(), core::chemical::ResidueTypeSet::atom_type_set(), core::chemical::PoseResidueTypeSet::atom_type_set(), core::chemical::MutableResidueType::atom_vertex(), core::chemical::GlobalResidueTypeSet::attempt_readin(), core::chemical::MutableResidueType::autodetermine_chi_bonds(), core::chemical::MutableICoorRecord::buildable(), calculate_rigid_matrix(), clean_up_dangling_connect(), core::chemical::ResidueType::copy_atom_info(), core::chemical::ChemicalManager::create_residue_type_set(), core::chemical::ResidueType::debug_dump_icoor(), core::chemical::ResidueType::define_mainchain_atoms(), core::chemical::MutableResidueType::delete_atom(), core::chemical::MutableResidueType::delete_chi(), core::chemical::MutableResidueType::delete_child_proton(), core::chemical::MutableResidueType::delete_nu(), core::chemical::MutableResidueType::delete_ring(), core::chemical::MutableResidueType::dump_vd_info(), core::chemical::PoseResidueTypeSet::element_set(), core::chemical::GlobalResidueTypeSet::extra_nonparam_restypes_from_commandline(), fill_ideal_xyz_from_icoor(), core::chemical::ResidueTypeFinder::filter_all_patch_names(), core::chemical::ResidueTypeFinder::filter_all_properties(), core::chemical::ResidueTypeFinder::filter_all_variants_matched(), core::chemical::ResidueTypeFinder::filter_by_aa(), core::chemical::ResidueTypeFinder::filter_by_base_property(), core::chemical::ResidueTypeFinder::filter_by_interchangeability_group(), core::chemical::ResidueTypeFinder::filter_by_name1(), core::chemical::ResidueTypeFinder::filter_by_name3(), core::chemical::ResidueTypeFinder::filter_by_residue_type_base_name(), core::chemical::ResidueTypeFinder::filter_disallow_properties(), core::chemical::ResidueTypeFinder::filter_disallow_variants(), core::chemical::ResidueTypeFinder::filter_special_cases(), find_chi_bonds(), find_nbr_dist(), core::chemical::ResidueTypeSet::force_add_base_residue_type_already_write_locked(), core::chemical::ResidueTypeFinder::get_all_possible_residue_types(), core::chemical::ResidueTypeFinder::get_best_match_residue_type_for_atom_names(), core::chemical::rings::RingConformerSet::get_ideal_conformer_by_CP_parameters(), core::chemical::rings::RingConformerSet::get_ideal_conformer_from_nus(), core::chemical::Bond::GetMaximumElectrons(), core::chemical::Bond::GetMinimumElectrons(), core::chemical::Bond::GetNumberOfElectrons(), core::chemical::Bond::GetSDAltFileID(), core::chemical::Bond::GetSDFileID(), core::chemical::GlobalResidueTypeSet::GlobalResidueTypeSet(), core::chemical::ResidueProperties::has_property(), heavy_atom_names_match(), core::chemical::ICoorAtomID::ICoorAtomID(), core::chemical::GlobalResidueTypeSet::init_patches_from_database(), core::chemical::GlobalResidueTypeSet::init_restypes_from_commandline(), core::chemical::GlobalResidueTypeSet::init_restypes_from_database(), core::chemical::ResidueType::initialize_derived_data(), core::chemical::rings::is_atom_axial_or_equatorial_to_ring(), core::chemical::Atom::is_fake(), core::chemical::ResidueProperties::is_variant_type(), core::chemical::GlobalResidueTypeSet::lazy_load_base_type_already_write_locked(), core::chemical::GlobalResidueTypeSet::load_exclude_pdb_component_ids(), core::chemical::GlobalResidueTypeSet::load_pdb_component(), core::chemical::GlobalResidueTypeSet::load_residue_types_from_sql_database(), make_centroid(), core::chemical::PoseResidueTypeSet::mm_atom_type_set(), modify_atom_properties_from_command_line(), core::chemical::PoseResidueTypeSet::orbital_type_set(), core::chemical::GlobalResidueTypeSet::params_files_from_commandline(), protocols::recces::pose_setup_from_file(), core::chemical::ResidueType::print_bondangles(), core::chemical::ResidueType::print_pretty_path_distances(), core::chemical::carbohydrates::read_codes_and_roots_from_database_file(), core::chemical::rings::read_conformers_from_database_file_for_ring_size(), core::chemical::carbohydrates::read_linkage_conformers_from_database_file(), core::chemical::MergeBehaviorManager::read_merge_behaviors_from_database_file(), core::chemical::carbohydrates::read_nomenclature_table_from_database_file(), core::chemical::carbohydrates::read_ring_sizes_and_morphemes_from_database_file(), core::chemical::carbohydrates::read_short_names_to_iupac_format_string(), protocols::recces::recces_pose_setup(), rename_atoms(), core::chemical::ResidueTypeBase::report_adducts(), reroot_restype(), residue_selector_single_from_line(), rosetta_recharge_fullatom(), core::chemical::MutableResidueType::set_atom_type(), core::chemical::MutableResidueType::set_icoor(), core::chemical::MutableResidueType::set_lower_connect_atom(), core::chemical::MutableResidueType::set_upper_connect_atom(), core::chemical::ResidueProperties::set_variant_type(), core::chemical::Bond::SetSDFType(), core::chemical::RerootRestypeVisitor::start_vertex(), string_from_type_set_mode(), and core::chemical::MutableResidueType::validate_residue_type().

static basic::Tracer core::chemical::TR ( "core.chemical.MergeBehaviorManager"  )

static

static basic::Tracer core::chemical::TR ( "core.chemical.residue_support"  )

static

static basic::Tracer core::chemical::tr ( "core.chemical"  )

static

static basic::Tracer core::chemical::tr ( "core.chemical.AtomTypeSet"  )

static

Referenced by core::chemical::AtomTypeSet::add_parameters_from_file(), core::chemical::PatchCase::apply(), core::chemical::Patch::apply(), core::chemical::NCAARotLibPath::apply(), core::chemical::NCAARotLibBBTorsions::apply(), core::chemical::ConnectSulfurAndMakeVirtualProton::apply(), core::chemical::ChiralFlipAtoms::apply(), core::chemical::AddConnectAndTrackingVirt::apply(), core::chemical::AtomTypeSet::clone_atom_types_from_commandline(), protocols::cutoutdomain::CutOutDomain::find_nearest_res(), patch_operation_from_patch_file_line(), core::chemical::Metapatch::read_file(), core::chemical::ElementSet::read_file(), core::chemical::MMAtomTypeSet::read_file(), core::chemical::AtomTypeSet::read_file(), core::chemical::Patch::read_file(), read_topology_file(), setup_atom_type_reassignments_from_commandline(), setup_atomic_charge_reassignments_from_commandline(), setup_icoor_reassignments_from_commandline(), setup_patch_atomic_charge_reassignments_from_commandline(), protocols::vip::VIP_Mover::VIP_Mover(), and write_topology_file().

static basic::Tracer core::chemical::tr ( "core.chemical"  )

static

static basic::Tracer core::chemical::TR ( "core.chemical.ChemicalManager"  )

static

static basic::Tracer core::chemical::tr ( "core.chemical"  )

static

static basic::Tracer core::chemical::TR ( "core.chemical.ResidueTypeSet"  )

static

static basic::Tracer core::chemical::TR ( "core.chemical.ResidueTypeBase"  )

static

static basic::Tracer core::chemical::TR ( "core.chemical.GlobalResidueTypeSet"  )

static

static basic::Tracer core::chemical::TR ( "core.chemical.ResidueType"  )

static

static basic::Tracer core::chemical::TR ( "core.chemical.MutableResidueType"  )

static

static basic::Tracer core::chemical::tr ( "core.chemical.Patch"  )

static

static basic::Tracer core::chemical::TR_PatchOperations ( "core.chemical.PatchOperations.hh"  )

static

Referenced by core::chemical::DeleteAtom::apply(), core::chemical::SetBackboneHeavyatom::apply(), core::chemical::SetPolymerConnectAtom::apply(), core::chemical::AddProperty::apply(), core::chemical::DeleteProperty::apply(), core::chemical::AddChi::apply(), core::chemical::RedefineChi::apply(), core::chemical::DeleteTerminalChi::apply(), core::chemical::AddChiRotamer::apply(), core::chemical::ClearChiRotamers::apply(), core::chemical::AddAtom::apply(), core::chemical::AddBond::apply(), core::chemical::SetAtomicCharge::apply(), core::chemical::SetFormalCharge::apply(), core::chemical::SetAtomType::apply(), core::chemical::SetMMAtomType::apply(), core::chemical::SetICoor::apply(), core::chemical::ResetBondLength::apply(), core::chemical::PrependMainchainAtom::apply(), core::chemical::AppendMainchainAtom::apply(), core::chemical::ReplaceMainchainAtom::apply(), core::chemical::SetNbrAtom::apply(), core::chemical::SetVirtualShadow::apply(), and core::chemical::SetDisulfideAtomName::apply().

TypeSetMode core::chemical::type_set_mode_from_string	(	std::string const &	mode,
		bool	fail = true
	)

If fail is true, utility_exit if the mode cannot be converted, if not, return the invalid type.

References CENTROID, CENTROID_ROT, CENTROID_ROT_t, CENTROID_t, COARSE_RNA, COARSE_RNA_t, DEFAULT_t, FA_STANDARD, FULL_ATOM_t, HYBRID_FA_STANDARD_CENTROID, HYBRID_FA_STANDARD_CENTROID_t, and INVALID_t.

Referenced by protocols::simple_moves::SwitchResidueTypeSetMover::apply(), core::import_pose::ImportPoseOptions::init_from_options(), core::chemical::GlobalResidueTypeSet::init_restypes_from_database(), core::import_pose::ImportPoseOptions::parse_my_tag(), core::chemical::AtomTypeSet::read_meta_file(), setup_atom_type_reassignments_from_commandline(), setup_atomic_charge_reassignments_from_commandline(), setup_icoor_reassignments_from_commandline(), and setup_patch_atomic_charge_reassignments_from_commandline().

void core::chemical::unset_acceptor_ether_oxygens

(

AtomTypeSet &

atom_type_set

)

Rhiju. O3', O4', O5' in nucleic acids are ethers – turn them off as acceptors for H-bonds.

References core::chemical::AtomTypeSet::atom_type_index().

Referenced by core::chemical::AtomTypeSet::legacy_command_line_post_processing().

static const std::map< std::string, VariantType >* const core::chemical::VARIANT_MAP ( generate_string_to_variant_map()  )

static

bool core::chemical::variants_match	(	ResidueTypeBase const &	res1,
		ResidueTypeBase const &	res2
	)

Are these two residues patched in exactly the same way?

If pH mode is being used, this function returns true, even if the two residues compared have different protonation states.

References pH_mode_exceptions(), and variants_match_with_exceptions().

Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(), and protocols::enzdes::EnzdesBaseProtocol::cst_minimize().

bool core::chemical::variants_match_with_exceptions	(	ResidueTypeBase const &	res1,
		ResidueTypeBase const &	res2,
		utility::vector1< VariantType >	list_of_variants_to_ignore
	)

Are these two residues patched in exactly the same way, ignoring any VariantTypes in the list of exceptions?

Author

Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References FIRST_VARIANT, core::chemical::ResidueProperties::get_list_of_custom_variants(), core::chemical::ResidueProperties::has_custom_variant_types(), core::chemical::ResidueProperties::is_variant_type(), N_VARIANTS, and core::chemical::ResidueTypeBase::properties().

Referenced by protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), nonadduct_variants_match(), and variants_match().

VD core::chemical::walk_back_to_find_usable_base	(	core::chemical::MutableResidueType const &	restype,
		VD	start,
		utility::vector1< VD > const &	exclusions
	)

Walk up the icoor tree to find alternate reference atoms Utility function for clean_up_dangling_connect() – we only go up the tree to make sure we don't get cycles. Won't choose atoms in exclusions (or the start)

References core::chemical::MutableResidueType::atom_base(), core::chemical::MutableResidueType::atom_name(), core::chemical::MutableResidueType::bonded_neighbor_iterators(), core::chemical::MutableResidueType::root_atom(), and protocols::loops::start.

Referenced by clean_up_dangling_connect().

void core::chemical::write_graphviz	(	ResidueType const &	rsd,
		std::ostream &	out,
		bool	header
	)

Produces a graphviz dot representation of the ResidueType to the given output stream If header is true (the default) a line with an explanitory message will be printed first.

Produces a graphviz dot representation of the ResidueType to the given output stream If header is true (the default) a line with an explanatory message will be printed first.

Referenced by core::io::pose_from_sfr::remap_names_on_geometry().

void core::chemical::write_graphviz	(	MutableResidueType const &	rsd,
		std::ostream &	out,
		bool	header
	)

References core::chemical::MutableResidueType::graph(), and core::chemical::ResidueTypeBase::name().

void core::chemical::write_topology_file	(	ResidueType const &	rsd,
		std::string	filename
	)

writes a .params file from a given ResidueType object

function to write out a topology file given a residue type, can be used to debug on the fly generated residue types. Note: not perfect yet, the enums for the connection types are given in numbers instead of names

References core::chemical::ResidueTypeBase::aa(), core::chemical::ResidueType::actcoord_atoms(), core::chemical::rings::AROMATIC, AromaticBond, core::chemical::ResidueTypeBase::atom_aliases(), core::chemical::ResidueType::atom_being_shadowed(), core::chemical::ResidueType::atom_charge(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::atom_type(), core::chemical::ResidueConnection::atomno(), core::chemical::ResidueTypeBase::backbone_aa(), core::chemical::ResidueTypeBase::base_analogue(), protocols::vip::base_name(), core::chemical::ResidueTypeBase::base_name(), core::chemical::ResidueType::bond_type(), core::chemical::ResidueType::chi_atoms(), core::chemical::ResidueType::chi_rotamers(), core::chemical::ResidueType::cut_bond_neighbor(), core::chemical::AtomICoor::d(), core::chemical::ResidueTypeBase::defined_adducts(), DoubleBond, core::chemical::ResidueType::first_sidechain_atom(), core::chemical::ResidueTypeBase::force_nbr_atom_orient(), core::chemical::ResidueType::formal_charge(), core::chemical::ResidueTypeBase::get_disulfide_atom_name(), core::chemical::ResidueProperties::get_list_of_properties(), core::chemical::ResidueType::get_metal_binding_atoms(), core::chemical::ResidueTypeBase::get_rama_prepro_mainchain_torsion_potential_name(), core::chemical::ResidueTypeBase::get_rama_prepro_map_file_name(), core::chemical::ResidueType::has_shadow_atoms(), core::chemical::ResidueType::icoor(), core::chemical::ResidueTypeBase::interchangeability_group(), core::chemical::ResidueType::is_ligand(), core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueType::is_proton_chi(), core::chemical::ResidueType::low_ring_conformers(), core::chemical::ResidueType::lower_connect(), core::chemical::ResidueType::lower_connect_id(), core::chemical::ResidueType::lowest_ring_conformers(), core::chemical::ResidueType::mainchain_atoms(), core::chemical::ResidueType::mm_atom_type(), core::chemical::ResidueType::n_nus(), core::chemical::ResidueType::n_possible_residue_connections(), core::chemical::ResidueType::n_rings(), core::chemical::ResidueTypeBase::na_analogue(), core::chemical::MMAtomType::name(), core::chemical::ICoorAtomID::name(), core::chemical::AtomType::name(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueTypeBase::name1(), core::chemical::ResidueTypeBase::name3(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nbr_atom(), core::chemical::ResidueType::nbr_radius(), core::chemical::ResidueType::nbrs(), core::chemical::ResidueType::nchi(), core::chemical::ResidueTypeBase::net_formal_charge(), core::chemical::ResidueType::nu_atoms(), core::chemical::ResidueProperties::numeric_properties(), OrbitalBond, core::conformation::membrane::out, core::chemical::AtomICoor::phi(), core::chemical::ResidueTypeBase::properties(), update_ResidueType_enum_files::properties, core::chemical::ResidueType::proton_chi_extra_samples(), core::chemical::ResidueType::proton_chi_samples(), PseudoBond, core::chemical::ResidueTypeBase::remap_pdb_atom_names(), core::chemical::ResidueType::residue_connection(), core::chemical::ResidueType::ring_atoms(), core::chemical::ResidueType::ring_saturation_type(), core::chemical::ResidueTypeBase::rotamer_library_specification(), SingleBond, core::chemical::ResidueProperties::string_properties(), core::chemical::AtomICoor::stub_atom1(), core::chemical::AtomICoor::stub_atom2(), core::chemical::AtomICoor::stub_atom3(), core::chemical::AtomICoor::theta(), tr(), TripleBond, core::chemical::ResidueType::upper_connect(), core::chemical::ResidueType::upper_connect_id(), core::chemical::ResidueTypeBase::variant_types(), and update_ResidueType_enum_files::variants.

Variable Documentation

std::string const core::chemical::CENTROID

Referenced by protocols::topology_broker::add_cmdline_claims(), protocols::mpi_refinement::MultiObjective::add_objective_function_info(), protocols::loop_grower::LoopPartialSolution::add_sheets(), protocols::flexpep_docking::FlexPepDockingProtocol::addLowResStatistics(), protocols::simple_moves::CombinePoseMover::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply(), protocols::rbsegment_relax::IdealizeHelicesMover::apply(), protocols::ub_e2c::ubi_e2c_modeler::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply(), protocols::antibody::AntibodyModelerProtocol::apply(), protocols::rna::denovo::RNA_FragmentMonteCarlo::apply(), protocols::docking::DockingEnsemblePrepackProtocol::apply(), protocols::normalmode::NormalModeRelaxMover::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::parser::FragmentReader::apply(), protocols::antibody_legacy::GraftMover::apply(), protocols::grafting::CCDEndsGraftMover::apply(), protocols::antibody_legacy::CDRH3Modeler::apply(), protocols::grafting::AnchoredGraftMover::apply(), protocols::loop_grower::SheetSampler::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::antibody_legacy::CloseOneMover::apply(), protocols::anchored_design::AnchoredPerturbMover::apply(), core::scoring::AtomVDW::AtomVDW(), protocols::simple_moves::StructProfileMover::calc_cenlist(), protocols::simple_moves::GunnCost::compute_gunn(), protocols::membrane::visualize::VisualizeEmbeddingMover::create_embedding_virtual(), core::scoring::saxs::SAXSEnergyCreator::create_energy_method(), protocols::membrane::visualize::VisualizeMembraneMover::create_membrane_virtual(), protocols::pose_length_moves::NearNativeLoopCloser::create_potential_loops(), core::chemical::ChemicalManager::create_residue_type_set(), core::scoring::disulfides::CentroidDisulfidePotential::disulfide_params(), protocols::abinitio::AbrelaxApplication::do_rerun(), protocols::ub_e2c::ubi_e2c_modeler::evaluate_native(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), protocols::star::generate_extended_pose(), protocols::abinitio::AbrelaxApplication::generate_extended_pose(), protocols::pose_creation::MergePDBMover::generate_overlaps(), protocols::legacy_sewing::LegacyAssemblyMover::get_centroid_pose(), protocols::simple_filters::ResidueDepthFilter::get_SDE_score(), protocols::tcr::ind_remodel_tcr_cdr_loops(), protocols::ub_e2c::ubi_e2c_modeler::init_d77_perturbation(), protocols::jd2::archive::ArchiveBase::init_from_decoy_set(), protocols::ub_e2c::ubi_e2c_modeler::init_k48r_perturbation(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::initialize_ghost_pose(), protocols::topology_broker::TopologyBroker::initialize_sequence(), protocols::docking::DockingEnsemble::load_ensemble(), protocols::features::PoseConformationFeatures::load_sequence(), protocols::floppy_tail::FloppyTailMover::low_res(), make_centroid(), protocols::helical_bundle_predict::HelicalBundlePredictApplication::make_pose_from_fasta_contents(), core::fragment::make_pose_from_frags(), protocols::ub_e2c::ubi_e2c_modeler::monoub_apply(), protocols::ub_e2c::ubi_e2c_modeler::monoub_first_perturbation(), protocols::legacy_sewing::Assembly::native_positions(), protocols::checkpoint::pose_from_binary_silent_file(), protocols::jd2::LargeNstructJobInputter::pose_from_job(), core::import_pose::poseOPs_from_files(), protocols::topology_broker::CoordConstraintClaimer::read_cst_pose(), protocols::topology_broker::StartStructClaimer::read_tag(), protocols::pose_metric_calculators::ClashCountCalculator::recompute(), protocols::checkpoint::CheckPointer::recover_checkpoint(), protocols::fold_from_loops::NubInitioMover::refold_pose(), protocols::legacy_sewing::Assembly::reorder(), protocols::ub_e2c::ubi_e2c_modeler::restore_cter(), core::fragment::FragmentRmsd::rmsd(), protocols::mpi_refinement::WorkUnit_bbGauss::run(), protocols::mpi_refinement::WorkUnit_MD::run(), protocols::mpi_refinement::WorkUnit_NormalMode::run(), protocols::mpi_refinement::WorkUnit_RamaPerturber::run(), protocols::mpi_refinement::WorkUnit_PartialAbinitio::run(), protocols::abinitio::run_boinc_debug(), protocols::legacy_sewing::scoring::LegacyClashScorer::score(), protocols::symmetric_docking::SymDockProtocol::score_only(), protocols::forge::components::VarLengthBuild::set_starting_non_canonical(), protocols::abinitio::AbrelaxApplication::setup_fold(), protocols::docking::TemperedDocking::setup_objects(), protocols::docking::DockingProtocol::setup_objects(), string_from_type_set_mode(), protocols::topology_broker::SymmetryClaimer::symmetry_duplicate(), protocols::flexpep_docking::FlexPepDockingLowRes::to_centroid(), protocols::flexpep_docking::FlexPepDockingAbInitio::to_centroid(), and type_set_mode_from_string().

std::string const core::chemical::CENTROID_ROT

Referenced by protocols::loop_grower::LoopPartialSolution::add_sheets(), protocols::hybridization::CartesianHybridize::apply(), protocols::loop_grower::SheetSampler::apply(), protocols::abinitio::ClassicAbinitio::do_stage4_cycles(), string_from_type_set_mode(), and type_set_mode_from_string().

std::string const core::chemical::COARSE_RNA

Referenced by core::import_pose::make_coarse_pose(), core::import_pose::make_extended_coarse_pose(), string_from_type_set_mode(), and type_set_mode_from_string().

std::string const core::chemical::FA_STANDARD

Referenced by core::chemical::IdealBondLengthSet::add_bond_length(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_symmetric(), protocols::loop_grower::LoopPartialSolution::add_sheets(), protocols::denovo_design::components::add_to_pose(), protocols::rna::AlignmentEnergy::AlignmentEnergy(), core::fragment::rna::analyze_for_homology(), protocols::hydrate::append_single_far_away_water(), protocols::protein_interface_design::movers::DockAndRetrieveSidechains::apply(), protocols::ub_e2c::ubi_e2c_modeler::apply(), protocols::stepwise::monte_carlo::mover::FromScratchMover::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply(), protocols::antibody::AntibodyModelerProtocol::apply(), protocols::membrane::HelixFromSequence::apply(), protocols::rna::denovo::RNA_FragmentMonteCarlo::apply(), protocols::docking::DockingEnsemblePrepackProtocol::apply(), protocols::rna::movers::RNAIdealizeMover::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::loop_grower::FragmentExtension::apply(), protocols::antibody_legacy::GraftMover::apply(), protocols::antibody_legacy::CDRH3Modeler::apply(), protocols::loop_grower::SheetSampler::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::antibody_legacy::CloseOneMover::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), protocols::fold_from_loops::utils::attach_n_and_c_unfolded_poses_to_pose(), core::pack::rotamer_set::build_rotated_water_rotamers(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), protocols::docking::DockingEnsemble::calculate_highres_ref_energy(), core::scoring::fiber_diffraction::centroid_scatter(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), protocols::noesy_assign::FragsToAtomDist::compute_average_distances(), core::scoring::geometric_solvation::compute_exact_geosol(), protocols::toolbox::pose_manipulation::construct_poly_ala_pose(), protocols::toolbox::pose_manipulation::construct_poly_beta_ala_pose(), protocols::toolbox::pose_manipulation::construct_poly_d_ala_pose(), protocols::toolbox::pose_manipulation::construct_poly_d_beta_ala_pose(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(), core::chemical::IdealBondLengthSet::contains_bond_length(), protocols::membrane::visualize::VisualizeEmbeddingMover::create_embedding_virtual(), protocols::pack_daemon::create_entity_resfile_contents(), core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_02_from_ASCII(), core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_10_from_ASCII(), core::scoring::ScoringManager::create_memb_etable_instance(), protocols::membrane::visualize::VisualizeMembraneMover::create_membrane_virtual(), core::scoring::ScoringManager::create_mm_bondangle_library_instance(), core::scoring::ScoringManager::create_mm_bondlength_library_instance(), core::scoring::ScoringManager::create_mm_lj_library_instance(), core::scoring::ScoringManager::create_mm_torsion_library_instance(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::create_new_submotif(), protocols::simple_moves::ConstrainToIdealMover::create_pose_reference(), core::chemical::ChemicalManager::create_residue_type_set(), core::scoring::geometric_solvation::DatabaseOccSolEne::DatabaseOccSolEne(), protocols::electron_density::DockIntoDensityMover::do_refinement(), protocols::abinitio::AbrelaxApplication::do_rerun(), protocols::legacy_sewing::scoring::LegacyMotifScorer::dump_motif(), protocols::enzdes::EnzdesBaseProtocol::EnzdesBaseProtocol(), core::scoring::ScoringManager::etable(), protocols::ub_e2c::ubi_e2c_modeler::evaluate_native(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::ExactOccludedHbondSolEnergy(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), protocols::jd3::full_model_inputters::PDBFullModelInputter::full_model_from_input_source(), protocols::jd3::full_model_inputters::SilentFileFullModelInputter::full_model_from_input_source(), protocols::legacy_sewing::LegacyRepeatAssemblyMover::generate_assembly(), protocols::stepwise::sampler::protein::generate_beta_database_test(), protocols::residue_optimization::MetapatchEnumeration::generate_derived_types(), protocols::legacy_sewing::Assembly::generate_native_rotamers_map(), protocols::mainchain_potential::GenerateMainchainPotential::generate_pose(), protocols::ligand_docking::generate_unique_name(), protocols::pose_creation::MakeJunctionsMover::get_and_cache_pdb(), protocols::stepwise::modeler::rna::get_binary_rna_silent_struct_safe(), core::chemical::IdealBondLengthSet::get_bond_length(), protocols::enzdes::AddOrRemoveMatchCsts::get_EnzConstraintIO_for_cstfile(), protocols::pose_length_moves::PossibleLoop::get_finalPoseOP(), protocols::legacy_sewing::LegacyAssemblyMover::get_fullatom_pose(), protocols::magnesium::get_mg_rsd(), protocols::motif_grafting::movers::MotifGraftMover::get_mono_aa_pose_copy(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::get_nc_name_codes(), core::import_pose::get_pdb_and_cleanup(), protocols::hydrate::get_ready_for_sew_packing(), protocols::simple_moves::AddCavitiesMover::get_suck_res(), protocols::cyclic_peptide::PeptideCyclizeMover::get_values(), protocols::metal_interface::MatchGrafter::graft(), protocols::hydrate::hydrate_cavities(), protocols::hydrate::hydrate_hyfile(), protocols::stepwise::legacy::modeler::rna::import_pose_from_silent_file(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::tcr::ind_remodel_tcr_cdr_loops(), core::pose::rna::RNA_IdealCoord::init(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::initialize(), core::scoring::rna::RNA_LowResolutionPotential::initialize_atom_numbers_for_backbone_score_calculations(), core::scoring::rna::data::RNA_DataBackboneEnergy::initialize_atom_numbers_sugar(), protocols::match::initialize_atomtype_2_probe_radius_map(), protocols::match::MatcherTask::initialize_enzdes_input_data_from_command_line(), protocols::match::MatcherTask::initialize_enzdes_input_data_with_mcfi_list(), core::import_pose::RNA_DeNovoSetup::initialize_from_command_line(), core::import_pose::RNA_DeNovoSetup::initialize_from_options(), protocols::rna::denovo::RNA_FragmentMonteCarlo::initialize_parameters(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::initialize_parameters_and_input(), protocols::ncbb::SecStructFinder::initialize_pose(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), protocols::vardist_solaccess::VarSolDistSasaCalculator::initialize_sasa_arrays(), protocols::ligand_docking::LigandDockMain::LigandDockMain(), protocols::features::PoseConformationFeatures::load_sequence(), protocols::ncbb::ResidueReplacementRebuildMover::make_new_pose(), core::scoring::ScoringManager::make_partially_soft_etable(), protocols::simple_moves::PeriodicBoxMover::make_vrt(), protocols::cryst::MakeLayerMover::make_vrt(), protocols::cryst::MakeLatticeMover::make_vrt(), protocols::make_rot_lib::MakeRotLibOptionsData::MakeRotLibOptionsData(), protocols::ub_e2c::ubi_e2c_modeler::monoub_apply(), protocols::motifs::Motif::Motif(), protocols::legacy_sewing::Assembly::native_positions(), protocols::rna::movers::RNAThreadAndMinimizeMover::obtain_rtypes_for_target_sequence(), core::conformation::orient_residue_for_ideal_bond(), protocols::legacy_sewing::LegacyAssemblyMover::output_stats(), protocols::rna::denovo::RNA_DeNovoProtocol::output_to_silent_file(), protocols::abinitio::abscript::RigidChunkCM::parse_my_tag(), protocols::match::MatcherMover::parse_my_tag(), protocols::fldsgn::BluePrintBDR::parse_my_tag(), protocols::enzdes::ResidueConformerFilter::parse_my_tag(), protocols::mainchain_potential::GenerateMainchainPotential::patches_can_apply(), protocols::hydrate::place_de_novo_wat_at_anchor(), protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_asymmetric(), protocols::cyclic_peptide::crosslinker::TMA_Helper::place_tma_symmetric(), protocols::checkpoint::pose_from_binary_silent_file(), core::import_pose::pose_from_file(), protocols::make_rot_lib::MakeRotLibJobInputter::pose_from_job(), protocols::comparative_modeling::ThreadingJobInputter::pose_from_job(), core::io::pose_from_pose(), protocols::recces::pose_setup_from_file(), core::import_pose::poseOPs_from_files(), core::import_pose::poses_from_files(), protocols::fold_from_loops::NubInitioMover::post_process(), protocols::legacy_sewing::Assembly::prepare_for_packing(), core::import_pose::process_input_file(), protocols::motifs::MotifSearch::protein_dna_motif(), protocols::motifs::LigandMotifSearch::protein_dna_motif(), protocols::sic_dock::read_biounit(), core::scoring::RamaPrePro::read_canonical_rpp_tables(), protocols::jumping::ResiduePairJumpSetup::read_file(), core::pack::dunbrack::RotamerLibrary::read_from_binary(), protocols::scoring::VDW_CachedRepScreenInfo::read_in_VDW_rep_screen_pose(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::read_in_VDW_rep_screen_pose(), protocols::legacy_sewing::read_native_residue_file(), protocols::topology_broker::FibrilModelingClaimer::read_tag(), protocols::topology_broker::RigidChunkClaimer::read_tag(), protocols::topology_broker::MetalloClaimer::read_tag(), protocols::abinitio::IterativeBase::reassign_noesy_data(), protocols::checkpoint::CheckPointer::recover_checkpoint(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::resample_full_model(), core::pack::interaction_graph::RotamerDotsRadiusData::RotamerDotsRadiusData(), protocols::mpi_refinement::WorkUnit_bbGauss::run(), protocols::mpi_refinement::WorkUnit_MD::run(), protocols::mpi_refinement::WorkUnit_FragInsert::run(), protocols::mpi_refinement::WorkUnit_NormalMode::run(), protocols::mpi_refinement::WorkUnit_KicCloser::run(), protocols::mpi_refinement::WorkUnit_RamaPerturber::run(), protocols::mpi_refinement::WorkUnit_PartialAbinitio::run(), core::select::util::select_coord_for_residue(), protocols::vardist_solaccess::VarSolDistSasaCalculator::set_atom_type_radii(), protocols::forge::constraints::InvrotTreeRCG::set_cstfile(), protocols::hydrate::set_dew_waters_not_to_be_included(), protocols::vardist_solaccess::VarSolDistSasaCalculator::set_element_radii(), protocols::ligand_docking::LigandDesign::set_fragments(), protocols::ligand_docking::GrowLigand::set_fragments(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_mainchain_torsions(), protocols::abinitio::AbrelaxApplication::setup_fold(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_fold_tree(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), protocols::docking::DockingProtocol::setup_objects(), protocols::stepwise::legacy::modeler::rna::setup_pose_setup_class(), core::scoring::rna::RNA_LowResolutionPotential::setup_precise_zeta_cutoffs(), protocols::stepwise::legacy::modeler::rna::setup_simple_full_length_rna_working_parameters(), protocols::motifs::single_residue_from_stream(), string_from_type_set_mode(), protocols::flexpep_docking::FlexPepDockingLowRes::to_allatom(), type_set_mode_from_string(), protocols::jobdist::universal_main(), and core::import_pose::RNA_HelixAssembler::use_phenix_geo().

std::string const core::chemical::HYBRID_FA_STANDARD_CENTROID

Referenced by string_from_type_set_mode(), and type_set_mode_from_string().

Real const core::chemical::MAX_CHEMICAL_BOND_TO_HYDROGEN_LENGTH = { 1.35 }

Maximum distance between a heavy atom and a hydrogen atom to which it is chemically bound Set in .cc file.

S-H bond length in CYS.

Referenced by core::scoring::rna::RNA_FullAtomStackingEnergy::atomic_interaction_cutoff(), core::scoring::elec::FA_GrpElecEnergy::atomic_interaction_cutoff(), core::scoring::etable::BaseEtableEnergy< Derived >::atomic_interaction_cutoff(), core::scoring::etable::Etable::calculate_hydrogen_atom_reach(), and core::scoring::elec::FA_ElecEnergy::hydrogen_interaction_cutoff().

std::string const core::chemical::PATCH_LINKER = ":"

the string used to create new residue names after patching

Referenced by core::chemical::ResidueTypeSet::figure_out_last_patch_from_name(), fixup_patches(), core::scoring::methods::get_restag(), core::chemical::Patch::patched_name(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), residue_type_all_patches_name(), and residue_type_base_name().