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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  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  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  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< AtomOPAtomOPs
 
typedef utility::vector1< AtomCOPAtomCOPs
 
typedef utility::vector1< AtomAPAtomAPs
 
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
< AtomDatabaseIO > 
AtomDatabaseIOOP
 
typedef
utility::pointer::shared_ptr
< AtomDatabaseIO const > 
AtomDatabaseIOCOP
 
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
< 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< VDVDs
 
typedef boost::graph_traits
< ResidueGraph >
::vertex_iterator 
VIter
 
typedef std::pair< VIter, VIterVIterPair
 
typedef boost::graph_traits
< ResidueGraph >
::edge_iterator 
EIter
 
typedef std::pair< EIter, EIterEIterPair
 
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, VDNameVDMap
 
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 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::shared_ptr
< ResidueProperties
ResiduePropertiesOP
 
typedef
utility::pointer::shared_ptr
< ResidueProperties const > 
ResiduePropertiesCOP
 
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< SizeAtomIndices
 
typedef utility::vector1< SizeOrbitalIndices
 
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::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  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, 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, 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, SULFATED_SUGAR,
  SULFOAMINO_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,
  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_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_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, 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, AAsetup_name2aa ()
 setup the map that converts string name to AA enum More...
 
std::map< char, AAsetup_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...
 
ResidueTypeOP apply_adducts_to_residue (ResidueType const &rsd, utility::vector1< bool > &add_mask)
 Apply adducts to residue using a boolean mask. More...
 
ResidueTypeOPs 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")
 
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)
 
void pretty_print_atomicoor (std::ostream &out, AtomICoor const &start, ResidueType const &rsd_type, core::Size indent)
 
std::ostream & operator<< (std::ostream &output, AtomProperties const &object_to_output)
 
AtomPropertyoperator++ (AtomProperty &property)
 
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 (ResidueType &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 (ResidueType &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 (ResidueType &res)
 
void quick_ring_detection (ResidueType &res)
 
utility::vector1< VDget_connecting_atoms (ResidueType const &res, ED const &edge)
 
utility::vector1< VDget_connecting_atoms (ResidueGraph const &graph, ED const &edge)
 
ED get_bond (ResidueType const &res, VD const &source, VD const &target)
 
Real create_bond_length (gasteiger::GasteigerAtomTypeData const &atom1, gasteiger::GasteigerAtomTypeData const &atom2, BondName bond_type)
 
utility::vector1< VDsfind_chi_bonds (ResidueType 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, ResidueType 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")
 
void reroot_restype (core::chemical::ResidueType &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 (ICoorAtomID const &stub, std::set< VD > const &assigned, core::chemical::ResidueType 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::ResidueType &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")
 
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 (ResidueType 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, ResidueType const &rsd)
 
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")
 
id::AtomID atom_id_from_icoor_line (std::string const &name, ResidueType const &rsd)
 helper fxn More...
 
AtomIndices define_mainchain_atoms (ResidueTypeOP rsd)
 If polymer, determine a list of main chain atoms by shortest path from LOWER to UPPER. More...
 
ResidueTypeOP 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...
 
ResidueTypeOP 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...
 
ResidueTypeOP 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...
 
ResidueTypeOP 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...
 
ResidueTypeOP 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 set_up_mapfile_reassignments_from_commandline (ResidueTypeOP 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...
 
LightWeightResidueGraph convert_residuetype_to_light_graph (ResidueType const &res)
 
void rename_atoms (ResidueType &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 (ResidueType const &res, utility::vector1< utility::vector1< core::Real > > &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 (ResidueType 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 (ResidueType &res)
 Apply molfile_to_params style partial charges to the ResidueType. More...
 
ResidueTypeOP make_centroid (ResidueType const &res)
 Make a centroid version of the fullatom ResidueType passed in. 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)
 
ResiduePropertyoperator++ (ResidueProperty &property)
 
VariantTypeoperator++ (VariantType &variant)
 
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())
 
static basic::Tracer tr ("core.chemical.ResidueType")
 
std::string strip_whitespace (std::string const &name)
 
std::ostream & operator<< (std::ostream &output, ResidueType const &object_to_output)
 
std::string get_element_color (std::string const &element)
 
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...
 
void print_chis (std::ostream &out, ResidueType 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 (ResidueType const &res1, ResidueType 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< VariantTypepH_mode_exceptions ()
 check if user has set -pH_mode. More...
 
bool variants_match (ResidueType const &res1, ResidueType const &res2)
 Are these two residues patched in exactly the same way? More...
 
bool nonadduct_variants_match (ResidueType const &res1, ResidueType const &res2)
 Similar to variants_match(), but allows different adduct-modified states. More...
 
utility::vector1< VariantTypeget_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 (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::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 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 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 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::pointer::shared_ptr< AtomDatabaseIO const > core::chemical::AtomDatabaseIOCOP
typedef utility::pointer::shared_ptr< AtomDatabaseIO > core::chemical::AtomDatabaseIOOP
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::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 utility::pointer::shared_ptr< CacheableResidueTypeSets const > core::chemical::CacheableResidueTypeSetsCOP
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 HeavyAtomGraph::vertex_descriptor core::chemical::HeavyAtomVD
typedef boost::graph_traits<HeavyAtomGraph>::vertex_iterator core::chemical::HeavyAtomVIter
typedef boost::graph_traits<HeavyAtomWithHydrogensGraph>::edge_iterator core::chemical::HeavyAtomWithHydrogensEIter
typedef boost::graph_traits<HeavyAtomWithHydrogensGraph>::vertex_iterator core::chemical::HeavyAtomWithHydrogensVIter
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 HydrogenAtomGraph::vertex_descriptor core::chemical::HydrogenAtomVD
typedef boost::graph_traits<HydrogenAtomGraph>::vertex_iterator core::chemical::HydrogenAtomVIter
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 boost::graph_traits<LightWeightResidueGraph>::vertex_descriptor core::chemical::lwrg_VD
typedef boost::graph_traits<LightWeightResidueGraph>::vertex_iterator core::chemical::lwrg_vd_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 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 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 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 RealResidueGraph::edge_descriptor core::chemical::RealResidueED
typedef boost::graph_traits<RealResidueGraph>::edge_iterator core::chemical::RealResidueEIter
typedef boost::graph_traits<RealResidueGraph>::out_edge_iterator core::chemical::RealResidueOutEdgeIter
typedef RealResidueGraph::vertex_descriptor core::chemical::RealResidueVD
typedef boost::graph_traits<RealResidueGraph>::vertex_iterator core::chemical::RealResidueVIter
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< 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< 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 boost::graph_traits<ResidueGraph>::vertex_iterator core::chemical::VIter
typedef std::pair<VIter, VIter> core::chemical::VIterPair

Enumeration Type Documentation

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 

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

Enumerator
anc_parent 
anc_grandparent 
anc_greatgrandparent 

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 

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

Enumerator
UnknownAromaticity 
NonaromaticBond 
IsAromaticBond 

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 
Enumerator
UnknownIsometry 
NoBondIsometry 
EIsometry 
ZIsometry 
Enumerator
UnknownBond 
SingleBond 
DoubleBond 
TripleBond 
AromaticBond 
OrbitalBond 
PseudoBond 
Enumerator
UnknownBondOrder 
SingleBondOrder 
DoubleBondOrder 
TripleBondOrder 
OrbitalBondOrder 
PseudoBondOrder 
Enumerator
UnknownRingness 
BondNotInRing 
BondInRing 

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 
Enumerator
SP2_HYBRID 
SP3_HYBRID 
RING_HYBRID 
UNKNOWN_HYBRID 
HYBRID_MAX 
Enumerator
mrb_do_not_merge 
mrb_merge_w_prev 
mrb_merge_w_next 

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 
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 
SULFATED_SUGAR 
SULFOAMINO_SUGAR 
C_METHYLATED_SUGAR 
PHOSPHATE 
SPINLABEL 
DIAMAGNETIC 
PARAMAGNETIC 
N_PROPERTIES 

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 

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 
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_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_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 
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::ResidueType::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::ResidueType::backbone_aa(), core::chemical::ResidueType::base_analogue(), protocols::simple_moves::WaterBoxMover::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::ResidueType::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(), core::chemical::ResidueType::rotamer_aa(), 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)
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::evolution::NucleotideMutation::apply(), protocols::task_operations::ThreadSequenceOperation::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(), 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(), core::scoring::methods::NMerPSSMEnergy::read_nmer_pssm(), 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().

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

id::AtomID core::chemical::atom_id_from_icoor_line ( std::string const &  name,
ResidueType const &  rsd 
)

helper fxn

References core::id::GLOBAL_BOGUS_ATOM_ID.

gasteiger::GasteigerAtomTypeData::Properties core::chemical::bond_order_to_property ( const core::Size BOND_ORDER_OR_AROMATIC)
void core::chemical::calculate_rigid_matrix ( ResidueType const &  res,
utility::vector1< utility::vector1< core::Real > > &  distances 
)

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

Calculate the rigid matrix for neighbor atom finding Assume that distances has been initialized to some really large value, and is square.

References core::chemical::ResidueType::atom_iterators(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::graph(), core::chemical::ResidueType::name(), core::chemical::ResidueType::natoms(), 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.

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

tag name for querying COARSE_RNA chemical type set.

void core::chemical::complex_ring_detection ( ResidueType res)
LightWeightResidueGraph core::chemical::convert_residuetype_to_light_graph ( ResidueType const &  res)
BondName core::chemical::convert_to_BondName ( std::string const &  id)
ResidueTypeOPs 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::ResidueType::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 
)
AtomIndices core::chemical::define_mainchain_atoms ( ResidueTypeOP  rsd)

If polymer, determine a list of main chain atoms by shortest path from LOWER to UPPER.

References core::id::D, get_residue_path_distances(), protocols::sic_dock::scores::nbr, and tr().

Referenced by core::chemical::sdf::MolFileIOMolecule::convert_to_ResidueType(), 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 
)
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::ResidueType::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::ResidueType::defined_adducts().

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

std::string core::chemical::expand_icoor_atom_name ( std::string  name,
ResidueType const &  rsd 
)
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::ResidueType restype,
core::chemical::ResidueGraph const &  graph 
)
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 ( ResidueType res,
bool const  complex_ring 
)
utility::vector1< VDs > core::chemical::find_chi_bonds ( ResidueType const &  restype)
core::Real core::chemical::find_nbr_dist ( ResidueType 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::ResidueType::atom(), core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::atom_vertex(), core::chemical::ResidueType::bonded_neighbor_iterators(), calculate_rigid_matrix(), core::chemical::Atom::element_type(), core::sequence::end, core::chemical::element::H, core::chemical::ResidueType::name(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::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().

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, N_METHYLATED, N_PROPERTIES, NEGATIVE_CHARGE, NONOSE, NUCLEOTIDE_DIPHOSPHATE, OCTOSE, OLIGOUREA, ORTHO_ARAMID, OXETOSE, OXIROSE, PARA_ARAMID, PARAMAGNETIC, PENTOSE, PEPTOID, PHOSPHATE, PHOSPHONATE, PHOSPHONATE_UPPER, 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, 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, N_METHYLATED, NEGATIVE_CHARGE, NO_PROPERTY, NONOSE, NUCLEOTIDE_DIPHOSPHATE, OCTOSE, OLIGOUREA, ORTHO_ARAMID, OXETOSE, OXIROSE, PARA_ARAMID, PARAMAGNETIC, PENTOSE, PEPTOID, PHOSPHATE, PHOSPHONATE, PHOSPHONATE_UPPER, 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, 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_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C1_SULFATED_SUGAR, C1_SULFOAMINO_SUGAR, C2_ACETYLAMINO_SUGAR, C2_AMINO_SUGAR, C2_BRANCH_POINT, C2_DEOXY_SUGAR, C2_KETOALDONIC_ACID, C2_METHYLATED_SUGAR, C2_PHOSPHATE, C2_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C2_SULFATED_SUGAR, C2_SULFOAMINO_SUGAR, C3_ACETYLAMINO_SUGAR, C3_AMINO_SUGAR, C3_BRANCH_POINT, C3_DEOXY_SUGAR, C3_KETOALDONIC_ACID, C3_METHYLATED_SUGAR, C3_PHOSPHATE, C3_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C3_SULFATED_SUGAR, C3_SULFOAMINO_SUGAR, C4_ACETYLAMINO_SUGAR, C4_AMINO_SUGAR, C4_BRANCH_POINT, C4_DEOXY_SUGAR, C4_KETOALDONIC_ACID, C4_METHYLATED_SUGAR, C4_PHOSPHATE, C4_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C4_SULFATED_SUGAR, C4_SULFOAMINO_SUGAR, C5_ACETYLAMINO_SUGAR, C5_AMINO_SUGAR, C5_BRANCH_POINT, C5_DEOXY_SUGAR, C5_KETOALDONIC_ACID, C5_METHYLATED_SUGAR, C5_PHOSPHATE, C5_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C5_SULFATED_SUGAR, C5_SULFOAMINO_SUGAR, C6_ACETYLAMINO_SUGAR, C6_AMINO_SUGAR, C6_BRANCH_POINT, C6_DEOXY_SUGAR, C6_KETOALDONIC_ACID, C6_METHYLATED_SUGAR, C6_PHOSPHATE, C6_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C6_SULFATED_SUGAR, C6_SULFOAMINO_SUGAR, C7_ACETYLAMINO_SUGAR, C7_AMINO_SUGAR, C7_BRANCH_POINT, C7_DEOXY_SUGAR, C7_KETOALDONIC_ACID, C7_METHYLATED_SUGAR, C7_PHOSPHATE, C7_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C7_SULFATED_SUGAR, C7_SULFOAMINO_SUGAR, C8_ACETYLAMINO_SUGAR, C8_AMINO_SUGAR, C8_BRANCH_POINT, C8_DEOXY_SUGAR, C8_KETOALDONIC_ACID, C8_METHYLATED_SUGAR, C8_PHOSPHATE, C8_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C8_SULFATED_SUGAR, C8_SULFOAMINO_SUGAR, C9_ACETYLAMINO_SUGAR, C9_AMINO_SUGAR, C9_BRANCH_POINT, C9_DEOXY_SUGAR, C9_METHYLATED_SUGAR, C9_PHOSPHATE, C9_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C9_SULFATED_SUGAR, C9_SULFOAMINO_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, 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_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C1_SULFATED_SUGAR, C1_SULFOAMINO_SUGAR, C2_ACETYLAMINO_SUGAR, C2_AMINO_SUGAR, C2_BRANCH_POINT, C2_DEOXY_SUGAR, C2_KETOALDONIC_ACID, C2_METHYLATED_SUGAR, C2_PHOSPHATE, C2_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C2_SULFATED_SUGAR, C2_SULFOAMINO_SUGAR, C3_ACETYLAMINO_SUGAR, C3_AMINO_SUGAR, C3_BRANCH_POINT, C3_DEOXY_SUGAR, C3_KETOALDONIC_ACID, C3_METHYLATED_SUGAR, C3_PHOSPHATE, C3_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C3_SULFATED_SUGAR, C3_SULFOAMINO_SUGAR, C4_ACETYLAMINO_SUGAR, C4_AMINO_SUGAR, C4_BRANCH_POINT, C4_DEOXY_SUGAR, C4_KETOALDONIC_ACID, C4_METHYLATED_SUGAR, C4_PHOSPHATE, C4_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C4_SULFATED_SUGAR, C4_SULFOAMINO_SUGAR, C5_ACETYLAMINO_SUGAR, C5_AMINO_SUGAR, C5_BRANCH_POINT, C5_DEOXY_SUGAR, C5_KETOALDONIC_ACID, C5_METHYLATED_SUGAR, C5_PHOSPHATE, C5_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C5_SULFATED_SUGAR, C5_SULFOAMINO_SUGAR, C6_ACETYLAMINO_SUGAR, C6_AMINO_SUGAR, C6_BRANCH_POINT, C6_DEOXY_SUGAR, C6_KETOALDONIC_ACID, C6_METHYLATED_SUGAR, C6_PHOSPHATE, C6_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C6_SULFATED_SUGAR, C6_SULFOAMINO_SUGAR, C7_ACETYLAMINO_SUGAR, C7_AMINO_SUGAR, C7_BRANCH_POINT, C7_DEOXY_SUGAR, C7_KETOALDONIC_ACID, C7_METHYLATED_SUGAR, C7_PHOSPHATE, C7_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C7_SULFATED_SUGAR, C7_SULFOAMINO_SUGAR, C8_ACETYLAMINO_SUGAR, C8_AMINO_SUGAR, C8_BRANCH_POINT, C8_DEOXY_SUGAR, C8_KETOALDONIC_ACID, C8_METHYLATED_SUGAR, C8_PHOSPHATE, C8_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C8_SULFATED_SUGAR, C8_SULFOAMINO_SUGAR, C9_ACETYLAMINO_SUGAR, C9_AMINO_SUGAR, C9_BRANCH_POINT, C9_DEOXY_SUGAR, C9_METHYLATED_SUGAR, C9_PHOSPHATE, C9_R3PRIMEHYDROXYBUTYRYLAMINO_SUGAR, C9_SULFATED_SUGAR, C9_SULFOAMINO_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, 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 ( ResidueType const &  res,
VD const &  source,
VD const &  target 
)
utility::vector1< VD > core::chemical::get_connecting_atoms ( ResidueType const &  res,
ED const &  edge 
)
utility::vector1< VD > core::chemical::get_connecting_atoms ( ResidueGraph const &  graph,
ED const &  edge 
)
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)
AA core::chemical::get_L_equivalent ( AA const  aa)
utility::vector1< std::string > core::chemical::get_patch_names ( ResidueType const &  rsd_type)
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 define_mainchain_atoms(), and core::chemical::ResidueType::update_derived_data().

utility::vector1< VariantType > core::chemical::get_terminal_varianttypes ( )
bool core::chemical::has ( ResidueGraph const &  graph,
VD  vd 
)
inline
bool core::chemical::has ( ResidueGraph const &  graph,
ED  ed 
)
inline

Does a ResidueGraph have a given edge descriptor?

bool core::chemical::has_assigned_coords ( ICoorAtomID const &  stub,
std::set< VD > const &  assigned,
core::chemical::ResidueType const &  restype 
)
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::methods::GenericBondedEnergy::defines_score_for_residue_pair(), 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::GenericBondedEnergy::eval_intrares_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::methods::GenericBondedEnergy::eval_intrares_energy(), 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)
bool core::chemical::is_mainchain_torsion_also_ring_torsion ( ResidueType const &  res_type,
uint  torsion_index 
)
bool core::chemical::is_sp2_proton_chi ( core::Size  chi,
ResidueType 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::ResidueType::bond(), core::chemical::ResidueType::bond_iterators(), core::chemical::Bond::bond_name(), core::chemical::ResidueType::chi_atom_vds(), DoubleBond, and SingleBond.

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

ResidueTypeOP 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:

References core::chemical::ResidueType::atom(), core::chemical::ResidueType::atom_name(), core::chemical::Atom::atom_type_index(), core::chemical::ResidueType::atom_type_set(), CENTROID, CENTROID_t, core::chemical::ResidueType::clone(), FULL_ATOM_t, core::chemical::AtomTypeSet::has_atom(), core::chemical::ICoorAtomID::INTERNAL, core::chemical::ResidueType::n_possible_residue_connections(), core::chemical::ResidueType::name(), and TR().

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

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)
MergeBehaviorManager::AtomRenamingMap core::chemical::mrb_map_from_correspondence ( std::string const &  correspondence)
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::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_10_from_ASCII(), protocols::stepwise::monte_carlo::mover::AddMover::create_residue_to_add(), 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::membrane::FaMPEnvSmoothEnergy::representative_atom_name(), core::scoring::methods::EnvSmoothEnergy::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 ( ResidueType const &  res1,
ResidueType 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::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(), 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::multistate_design::PosType::to_string(), 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(), and protocols::noesy_assign::Resonance::write_to_stream().

bool core::chemical::oneletter_code_specifies_aa ( char  onelettercode)
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 
)
std::ostream& core::chemical::operator<< ( std::ostream &  out,
const Orbital &  orbital 
)
std::ostream& core::chemical::operator<< ( std::ostream &  out,
const AtomType &  atom_type 
)
std::ostream & core::chemical::operator<< ( std::ostream &  output,
AtomProperties const &  object_to_output 
)
std::ostream& core::chemical::operator<< ( std::ostream &  out,
Bond const &  bond 
)
std::ostream& core::chemical::operator<< ( std::ostream &  out,
Element const &  obj 
)
inline
std::ostream & core::chemical::operator<< ( std::ostream &  out,
Atom const &  atom 
)
std::ostream& core::chemical::operator<< ( std::ostream &  out,
ElectronConfiguration const &  obj 
)
inline
std::ostream & core::chemical::operator<< ( std::ostream &  output,
ResidueProperties const &  object_to_output 
)
std::ostream & core::chemical::operator<< ( std::ostream &  output,
ResidueProperty const &  object_to_output 
)
std::ostream & core::chemical::operator<< ( std::ostream &  out,
TypeSetMode  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 &  output,
ResidueType const &  object_to_output 
)
bool core::chemical::operator== ( ResConnID const &  lhs,
ResConnID const &  rhs 
)
std::istream& core::chemical::operator>> ( std::istream &  in,
Element &  obj 
)
inline
std::istream& core::chemical::operator>> ( std::istream &  in,
ElectronConfiguration &  obj 
)
inline
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 
)
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 
)
void core::chemical::pretty_print_atomicoor ( std::ostream &  out,
ResidueType const &  rsd_type 
)
void core::chemical::pretty_print_atomicoor ( std::ostream &  out,
AtomICoor const &  start,
ResidueType const &  rsd_type,
core::Size  indent 
)
void core::chemical::print_chis ( std::ostream &  out,
ResidueType const &  res 
)
static const std::map< std::string, ResidueProperty >* const core::chemical::PROPERTY_MAP ( generate_string_to_property_map()  )
static
void core::chemical::quick_ring_detection ( ResidueType res)
ResidueTypeOP core::chemical::read_topology_file ( std::string const &  filename,
chemical::ResidueTypeSetCOP  rsd_type_set 
)
ResidueTypeOP 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().

ResidueTypeOP 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().

ResidueTypeOP 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().

ResidueTypeOP 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.

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.

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, apply_symm_gly_corrections(), BondInRing, convert_to_BondName(), define_mainchain_atoms(), 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(), core::kinematics::Stub::spherical(), core::chemical::orbitals::strip_whitespace(), tr(), and protocols::hybridization::val.

Referenced by read_topology_file().

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::gasteiger::assign_gasteiger_atom_types(), and core::chemical::ResidueType::finalize().

void core::chemical::rename_atoms ( ResidueType &  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::ResidueType::atom(), core::chemical::Atom::element_type(), core::chemical::ResidueType::graph(), core::chemical::Atom::name(), core::chemical::ResidueType::remap_pdb_atom_names(), core::id::to_string(), and TR().

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

void core::chemical::reroot_restype ( core::chemical::ResidueType 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::ResidueType::atom_base(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::autodetermine_chi_bonds(), core::chemical::ResidueType::chi_atom_vds(), core::id::D, core::chemical::ResidueType::has(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nchi(), core::id::PHI, core::chemical::ResidueType::set_icoor(), core::id::THETA, and TR().

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

ResidueTypeSelectorSingleOP core::chemical::residue_selector_single_from_line ( std::string const &  line)
std::string core::chemical::residue_type_all_patches_name ( ResidueType const &  rsd_type)
std::string core::chemical::residue_type_base_name ( ResidueType const &  rsd_type)
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 ( ResidueType &  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::ResidueType::atom(), core::chemical::ResidueType::atom_type_set(), core::chemical::Atom::charge(), core::chemical::Atom::formal_charge(), core::chemical::ResidueType::graph(), core::chemical::ResidueType::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 ( ResidueType 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::ResidueType::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::ResidueType::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::ResidueType::set_atom_type(), SingleBond, core::chemical::ResidueType::smallest_ring_size(), 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 ( )
void core::chemical::set_up_mapfile_reassignments_from_commandline ( ResidueTypeOP  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 ( )
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 
)
bool core::chemical::sort_patchop_by_name ( PatchOP  p,
PatchOP  q 
)
std::string core::chemical::string_from_type_set_mode ( TypeSetMode  mode)
static const utility::vector1< std::string >* const core::chemical::STRING_LIST ( generate_property_to_string_vector()  )
static
static const utility::vector1< std::string >* const core::chemical::STRING_LIST ( generate_variant_to_string_vector()  )
static
std::string core::chemical::strip_whitespace ( std::string const &  name)
inline
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.ElementSet"  )
static
static basic::Tracer core::chemical::TR ( "core.chemical.icoor_support"  )
static
static basic::Tracer core::chemical::TR ( "core.chemical.util"  )
static
static basic::Tracer core::chemical::TR ( "core.chemical.residue_support"  )
static
static basic::Tracer core::chemical::TR ( "core.chemical.Atom"  )
static

Referenced by add_atom_type_set_parameters_from_command_line(), core::chemical::ResidueTypeSet::add_base_residue_type(), 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::ICoorAtomID::atom_id(), core::chemical::ResidueTypeSet::atom_type_set(), core::chemical::PoseResidueTypeSet::atom_type_set(), core::chemical::GlobalResidueTypeSet::attempt_readin(), calculate_rigid_matrix(), core::chemical::ChemicalManager::create_residue_type_set(), 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(),