Rosetta Core  2014.35
Namespaces | Classes | Typedefs | Enumerations | Functions | Variables
core::chemical Namespace Reference

Namespaces

 carbohydrates
 
 element
 
 gasteiger
 
 orbitals
 
 rna
 
 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  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  AppendInterchangeabilityGroup_String
 Append a string to the existing interchangeability_group string for a ResidueType. 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  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  ChemicalManager
 a class managing different sets of atom_type_set and residue_type_set More...
 
class  CopyEdge
 
class  CopyVertex
 
class  DeleteAtom
 delete an atom 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) 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  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  MMAtomType
 Basic MM atom type. More...
 
class  MMAtomTypeSet
 A set of MMAtomTypes. 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  PrependMainchainAtom
 add a mainchain atom before the first mainchain atom 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  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  ResidueConnection
 A simple class marking atoms at inter-residue connections. More...
 
class  ResidueDatabaseIO
 
class  ResidueLoader
 
class  ResidueLoaderCreator
 
class  ResidueLoaderOptions
 
class  ResidueLoaderOptionsCreator
 
class  ResidueProperties
 
class  ResidueSelector
 A class picking out a subset of ResidueType by multiple criteria. More...
 
class  ResidueSelectorSingle
 A base class for defining a ResidueSelector by a single criterion. More...
 
class  ResidueType
 A class for defining a type of residue. More...
 
class  ResidueTypeKinWriter
 
class  ResidueTypeSet
 A collection of ResidueType defined. 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...
 
struct  RingConformer
 
class  RingConformerSet
 
class  Selector_AA
 Does the residue belong to ANY of these AAs? 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_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 to 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_POSITION
 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  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  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 atom's chemical type 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  SetOrientAtom
 Set orient atom selection mode. More...
 
class  SetPolymerConnectAtom
 set an atom as polymer connection More...
 

Typedefs

typedef
utility::pointer::owning_ptr
< Adduct
AdductOP
 
typedef std::map< std::string,
int
AdductMap
 
typedef
utility::pointer::owning_ptr
< Atom
AtomOP
 
typedef
utility::pointer::owning_ptr
< Atom const > 
AtomCOP
 
typedef
utility::pointer::access_ptr
< Atom
AtomAP
 
typedef utility::vector1< AtomOPAtomOPs
 
typedef utility::vector1< AtomCOPAtomCOPs
 
typedef utility::vector1< AtomAPAtomAPs
 
typedef
basic::datacache::DataMapObj
< std::set< std::string > > 
AtomMemo
 
typedef
utility::pointer::owning_ptr
< AtomMemo
AtomMemoOP
 
typedef
utility::pointer::owning_ptr
< AtomTypeDatabaseIO >
AtomTypeDatabaseIOOP typedef
utility::pointer::owning_ptr
< AtomTypeDatabaseIO const > 
AtomTypeDatabaseIOCOP
 
typedef
utility::pointer::access_ptr
< AtomTypeSet
AtomTypeSetAP
 
typedef
utility::pointer::access_ptr
< AtomTypeSet const > 
AtomTypeSetCAP
 
typedef
utility::pointer::owning_ptr
< AtomTypeSet
AtomTypeSetOP
 
typedef
utility::pointer::owning_ptr
< AutomorphismIterator
AutomorphismIteratorOP
 
typedef
utility::pointer::owning_ptr
< AutomorphismIterator const > 
AutomorphismIteratorCOP
 
typedef
utility::pointer::owning_ptr
< Element
ElementOP
 
typedef
utility::pointer::owning_ptr
< Element const > 
ElementCOP
 
typedef
utility::pointer::access_ptr
< ElementSet
ElementSetAP
 
typedef
utility::pointer::access_ptr
< ElementSet const > 
ElementSetCAP
 
typedef
utility::pointer::owning_ptr
< ElementSet
ElementSetOP
 
typedef
utility::pointer::owning_ptr
< ElementSet const > 
ElementSetCOP
 
typedef std::map
< core::chemical::VD,
core::kinematics::tree::AtomOP
VdTreeatomMap
 
typedef
utility::pointer::access_ptr
< IdealBondLengthSet
IdealBondLengthSetAP
 
typedef
utility::pointer::access_ptr
< IdealBondLengthSet const > 
IdealBondLengthSetCAP
 
typedef
utility::pointer::owning_ptr
< IdealBondLengthSet
IdealBondLengthSetOP
 
typedef int AtomTypeIndex
 
typedef Real BondLength
 
typedef
utility::pointer::access_ptr
< MMAtomTypeSet
MMAtomTypeSetAP
 
typedef
utility::pointer::access_ptr
< MMAtomTypeSet const > 
MMAtomTypeSetCAP
 
typedef
utility::pointer::owning_ptr
< MMAtomTypeSet
MMAtomTypeSetOP
 
typedef
utility::pointer::owning_ptr
< Orbital
OrbitalOP
 
typedef
utility::pointer::owning_ptr
< Orbital const > 
OrbitalCOP
 
typedef utility::vector1
< OrbitalOP
OrbitalOPs
 
typedef utility::vector1
< OrbitalCOP
OrbitalCOPs
 
typedef
utility::pointer::owning_ptr
< PatchCase
PatchCaseOP
 
typedef
utility::pointer::owning_ptr
< Patch
PatchOP
 
typedef
utility::pointer::owning_ptr
< PatchOperation
PatchOperationOP
 
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::owning_ptr
< ResidueProperties
ResiduePropertiesOP
 
typedef
utility::pointer::owning_ptr
< ResidueProperties const > 
ResiduePropertiesCOP
 
typedef
utility::pointer::owning_ptr
< ResidueSelectorSingle
ResidueSelectorSingleOP
 
typedef
utility::pointer::owning_ptr
< ResidueSelector
ResidueSelectorOP
 
typedef
utility::pointer::access_ptr
< ResidueType
ResidueTypeAP
 
typedef
utility::pointer::access_ptr
< ResidueType const > 
ResidueTypeCAP
 
typedef
utility::pointer::owning_ptr
< ResidueType
ResidueTypeOP
 
typedef
utility::pointer::owning_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::owning_ptr
< ResidueTypeKinWriter
ResidueTypeKinWriterOP
 
typedef
utility::pointer::owning_ptr
< ResidueTypeKinWriter const > 
ResidueTypeKinWriterCOP
 
typedef
utility::pointer::owning_ptr
< ResidueTypeSet
ResidueTypeSetOP
 
typedef
utility::pointer::access_ptr
< ResidueTypeSet const > 
ResidueTypeSetCAP
 
typedef
utility::pointer::owning_ptr
< RingConformerSet
RingConformerSetOP
 
typedef
utility::pointer::owning_ptr
< RingConformerSet const > 
RingConformerSetCOP
 
typedef std::string VariantType
 Notion of Residue variant, eg PHOSPHO, NTERM, TERMINUS, PROTONATION, GLYCOSO ?? More...
 

Enumerations

enum  AA {
  aa_ala = 1, 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_b3cisACPrC, aa_b3cisACPC, aa_b3cisACHC,
  last_beta3_aa = aa_b3cisACHC, 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  BondName {
  UnknownBond =0, SingleBond =1, DoubleBond =2, TripleBond =3,
  AromaticBond =4, OrbitalBond =5
}
 
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  ResidueProperty {
  FIRST_PROPERTY = 1, POLYMER = 1, LIGAND, PROTEIN,
  NA, DNA, RNA, PEPTOID,
  CARBOHYDRATE, LIPID, METAL, SURFACE,
  WATER, VIRTUAL_RESIDUE, TERMINUS, LOWER_TERMINUS,
  UPPER_TERMINUS, BRANCH_LOWER_TERMINUS, BRANCH_POINT, LOWERTERM_TRUNC,
  UPPERTERM_TRUNC, COARSE, ADDUCT, SC_ORBITALS,
  POLAR, CHARGED, AROMATIC, CYCLIC,
  METALBINDING, MEMBRANE, PHOSPHONATE, PHOSPHONATE_UPPER,
  ACETYLATED_NTERMINUS, METHYLATED_CTERMINUS, ALPHA_AA, BETA_AA,
  L_AA, D_AA, TAUTOMER, ALDOSE,
  KETOSE, L_SUGAR, D_SUGAR, OXIROSE,
  OXETOSE, FURANOSE, PYRANOSE, SEPTANOSE,
  ALPHA_SUGAR, BETA_SUGAR, SIALIC_ACID, ALDONIC_ACID,
  _2_KETOALDONIC_ACID, _3_KETOALDONIC_ACID, _4_KETOALDONIC_ACID, _5_KETOALDONIC_ACID,
  _6_KETOALDONIC_ACID, _7_KETOALDONIC_ACID, _8_KETOALDONIC_ACID, URONIC_ACID,
  _1_DEOXY_SUGAR, _2_DEOXY_SUGAR, _3_DEOXY_SUGAR, _4_DEOXY_SUGAR,
  _5_DEOXY_SUGAR, _6_DEOXY_SUGAR, _7_DEOXY_SUGAR, _8_DEOXY_SUGAR,
  _9_DEOXY_SUGAR, _1_AMINO_SUGAR, _2_AMINO_SUGAR, _3_AMINO_SUGAR,
  _4_AMINO_SUGAR, _5_AMINO_SUGAR, _6_AMINO_SUGAR, _7_AMINO_SUGAR,
  _8_AMINO_SUGAR, _9_AMINO_SUGAR, _1_ACETYLAMINO_SUGAR, _2_ACETYLAMINO_SUGAR,
  _3_ACETYLAMINO_SUGAR, _4_ACETYLAMINO_SUGAR, _5_ACETYLAMINO_SUGAR, _6_ACETYLAMINO_SUGAR,
  _7_ACETYLAMINO_SUGAR, _8_ACETYLAMINO_SUGAR, _9_ACETYLAMINO_SUGAR, _1_PHOSPHATE,
  _2_PHOSPHATE, _3_PHOSPHATE, _4_PHOSPHATE, _5_PHOSPHATE,
  _6_PHOSPHATE, _7_PHOSPHATE, _8_PHOSPHATE, _9_PHOSPHATE,
  N_RESIDUE_PROPERTIES = _9_PHOSPHATE
}
 Enumerators for all the properties that can be assigned to a ResidueType. More...
 
enum  CPParameter { q = 1, PHI, THETA }
 Enumerators for the three Cremer-Pople "ring-puckering" parameters used to describe 4-, 5-, and 6-membered ring conformers. More...
 
enum  Hybridization {
  SP2_HYBRID = 1, SP3_HYBRID, RING_HYBRID, UNKNOWN_HYBRID,
  HYBRID_MAX = UNKNOWN_HYBRID
}
 

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 > & name2aa ()
 map that converts string name to AA enum More...
 
std::map< char, AA > & 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 > & 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 > & aa2oneletter ()
 vector that maps AA enum to one letter char More...
 
AA aa_from_name (std::string const &name)
 Give an AA string name, return its enum type. More...
 
bool is_canonical_D_aa (AA 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...
 
AA get_L_equivalent (AA 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 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, intparse_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...
 
void error_check_requested_adducts (AdductMap const &add_map, ResidueTypeCOPs const &rsd_types)
 Make sure requested adducts exist in some residue. More...
 
std::ostream & operator<< (std::ostream &out, Atom const &atom)
 
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, AtomICoor const &start, ResidueType const &rsd_type, core::Size indent)
 
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...
 
BondName convert_to_BondName (std::string const &id)
 
std::ostream & operator<< (std::ostream &out, Bond const &bond)
 
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)
 Determine which bonds are in rings, and set the BondRingness property of each. More...
 
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...
 
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 centroid chemical type set. More...
 
std::string const CENTROID_ROT ("centroid_rot")
 tag name for querying centroid_rot chemical type set. More...
 
std::string const COARSE_TWO_BEAD ("coarse_two_bead")
 tag name for querying coarse-grained 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...
 
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)
 
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)
 
std::ostream & operator<< (std::ostream &out, const Orbital &orbital)
 
std::string const patch_linker (":")
 the string used to generate new residue names 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...
 
std::string tag_from_line (std::string const &line)
 handy function, return the first word from a line More...
 
PatchCaseOP case_from_lines (utility::vector1< std::string > const &lines)
 create a PatchCase from input lines More...
 
std::string expand_icoor_atom_name (std::string name, ResidueType const &rsd)
 
PatchOperationOP patch_operation_from_patch_file_line (std::string const &line)
 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)
 
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::AtomTypeSetCAP atom_types, chemical::ElementSetCAP elements, chemical::MMAtomTypeSetCAP mm_atom_types, chemical::orbitals::OrbitalTypeSetCAP orbital_atom_types,chemical::ResidueTypeSetCAP rsd_type_set)
 virtual constructor for ResidueType objects More...
 
ResidueTypeOP read_topology_file (utility::io::izstream &data, chemical::AtomTypeSetCAP atom_types, chemical::ElementSetCAP elements, chemical::MMAtomTypeSetCAP mm_atom_types, chemical::orbitals::OrbitalTypeSetCAP orbital_atom_types, chemical::ResidueTypeSetCAP rsd_type_set)
 
void write_topology_file (ResidueType const &rsd, std::string filename="")
 writes a .params file from a given ResidueType object More...
 
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...
 
core::Real get_rpp_charge (std::string const &type)
 Get charge for atom type based on Rosetta++ aaproperties_pack.cc values. 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)
 
ResiduePropertyoperator++ (ResidueProperty &property)
 
ResidueSelectorSingleOP residue_selector_single_from_line (std::string const &line)
 create a singe ResidueSelector from an input line. More...
 
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)
 
utility::vector1< std::string > get_lines_from_file_data (std::string const &filename)
 Local method that opens a file and returns its data as a list of lines after checking for errors. More...
 
utility::vector1< RingConformerread_conformers_from_database_file_for_ring_size (std::string const &filename, core::Size ring_size)
 Return a list of ring conformers, read from a database file. More...
 
std::ostream & operator<< (std::ostream &output, RingConformer const &object_to_output)
 
std::ostream & operator<< (std::ostream &output, RingConformerSet const &object_to_output)
 
static std::string const chr_chains ("ABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890abcdefghijklmnopqrstuvwxyz")
 
core::chemical::ResidueTypeSetCAP rsd_set_from_cmd_line ()
 
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. Called by ChemicalManager at time of AtomTypeSet creation. 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. Called by ChemicalManager at time of AtomTypeSet creation. More...
 
std::string formatted_icoord_tree (core::chemical::ResidueType const &restype)
 Return a string representing the Icoord tree of the Restype. More...
 
void print_chis (std::ostream &out, ResidueType const &res)
 Utility to examine chi output. More...
 
std::string fixup_patches (std::string string_in)
 
VariantType const UPPER_TERMINUS_VARIANT ("UPPER_TERMINUS")
 C-terminus cap. More...
 
VariantType const LOWER_TERMINUS_VARIANT ("LOWER_TERMINUS")
 N-terminus cap. More...
 
VariantType const UPPERTERM_TRUNC_VARIANT ("UPPERTERM_TRUNC")
 C-terminus truncation. More...
 
VariantType const LOWERTERM_TRUNC_VARIANT ("LOWERTERM_TRUNC")
 N-terminus truncation. More...
 
VariantType const CUTPOINT_LOWER ("CUTPOINT_LOWER")
 for use during loop modeling, at positions before a cutpoint More...
 
VariantType const CUTPOINT_UPPER ("CUTPOINT_UPPER")
 for use during loop modeling, at positions after a cutpoint More...
 
VariantType const DISULFIDE ("DISULFIDE")
 
VariantType const BRANCH_POINT_VARIANT ("BRANCH_POINT")
 Variant type used for branched polymers and glycosylations. More...
 
VariantType const BRANCH_LOWER_TERMINUS_VARIANT ("BRANCH_LOWER_TERMINUS")
 Variant type used for branched polymers and glycosylations. More...
 
VariantType const ADDUCT_VARIANT ("ADDUCT")
 
VariantType const METHYLATION ("METHYLATION")
 
VariantType const CENTROID_HA ("CENTROID_WITH_HA")
 
VariantType const PROTONATED ("PROTONATED")
 
VariantType const DEPROTONATED ("DEPROTONATED")
 
VariantType const SPECIAL_ROT ("SPECIAL_ROT")
 Generic variant type that allows for differential scoring of a set of residues/rotamers. More...
 
VariantType const VIRTUAL_PHOSPHATE ("VIRTUAL_PHOSPHATE")
 
VariantType const VIRTUAL_RNA_RESIDUE ("VIRTUAL_RNA_RESIDUE")
 
VariantType const VIRTUAL_O2PRIME_HYDROGEN ("VIRTUAL_O2PRIME_HYDROGEN")
 
VariantType const PHOSPHORYLATION ("PHOSPHORYLATION")
 
VariantType const ACETYLATION ("ACETYLATION")
 
VariantType const SULFATION ("SULFATION")
 
VariantType const CARBOXYLATION ("CARBOXYLATION")
 
VariantType const HYDROXYLATION ("HYDROXYLATION")
 
VariantType const DIMETHYLATION ("DIMETHYLATION")
 
VariantType const TRIMETHYLATION ("TRIMETHYLATION")
 
VariantType const DIIODINATION ("DIIODINATION")
 
VariantType const ACETYLATED_NTERMINUS_VARIANT ("ACETYLATED_NTERMINUS")
 Acetylated N-terminus cap, written for creating amino acid dipeptides for NCAA rotamer libraries. More...
 
VariantType const METHYLATED_CTERMINUS_VARIANT ("METHYLATED_CTERMINUS")
 Methylated C-terminus cap, written for creating amino acid dipeptides for NCAA rotamer libraries. More...
 
VariantType const SC_ORBITALS_VARIANT ("SC_ORBITALS")
 
VariantType const N_ACETYLATION ("N_ACETYLATION")
 Cap extensions at termini to include peptide bonds, written for stepwise assembly (SWA) code. More...
 
VariantType const C_METHYLAMIDATION ("C_METHYLAMIDATION")
 
VariantType const REPLONLY ("REPLONLY")
 @ brief only the repulsive energy will be considered during structure calculations More...
 
VariantType const NTERM_CONNECT ("NTERM_CONNECT")
 N-terminal connect and C-terminal connect. More...
 
VariantType const CTERM_CONNECT ("CTERM_CONNECT")
 
VariantType const OOP_PRE ("OOP_PRE")
 @ brief oop_pre patch, used for oligooxopiperazines (OOPs) More...
 
VariantType const OOP_POST ("OOP_POST")
 @ brief oop_post patch, used for oligooxopiperazines (OOPs) More...
 
VariantType const HBS_PRE ("HBS_PRE")
 @ brief hbs_pre patch, used for hydrogen bond surrogates More...
 
VariantType const HBS_POST ("HBS_POST")
 @ brief hbs_post patch, used for hydrogen bond surrogates More...
 
VariantType const C1_MODIFIED_SUGAR ("C1_MODIFIED_SUGAR")
 @ brief variant for any saccharide residue modified at the 1 position More...
 
VariantType const C2_MODIFIED_SUGAR ("C2_MODIFIED_SUGAR")
 @ brief variant for any saccharide residue modified at the 2 position More...
 
VariantType const C3_MODIFIED_SUGAR ("C3_MODIFIED_SUGAR")
 @ brief variant for any saccharide residue modified at the 3 position More...
 
VariantType const C4_MODIFIED_SUGAR ("C4_MODIFIED_SUGAR")
 @ brief variant for any saccharide residue modified at the 4 position More...
 
VariantType const C5_MODIFIED_SUGAR ("C5_MODIFIED_SUGAR")
 @ brief variant for any saccharide residue modified at the 5 position More...
 
VariantType const C6_MODIFIED_SUGAR ("C6_MODIFIED_SUGAR")
 @ brief variant for any saccharide residue modified at the 6 position More...
 
VariantType const C7_MODIFIED_SUGAR ("C7_MODIFIED_SUGAR")
 @ brief variant for any saccharide residue modified at the 7 position More...
 
VariantType const C8_MODIFIED_SUGAR ("C8_MODIFIED_SUGAR")
 @ brief variant for any saccharide residue modified at the 8 position More...
 
VariantType const C9_MODIFIED_SUGAR ("C9_MODIFIED_SUGAR")
 @ brief variant for any saccharide residue modified at the 9 position More...
 
VariantType const SIDECHAIN_CONJUGATION ("SIDECHAIN_CONJUGATION")
 This is used for chemically conjugable residues (LYX, CYX) used for sidechain conjugation (like ubiquitination) More...
 

Variables

static basic::Tracer TR ("core.chemical.Atom")
 
static basic::Tracer tw ("core.chemical.AtomICoor", basic::t_warning)
 
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...
 
static basic::Tracer tr ("core.chemical")
 
static basic::Tracer TR ("core.chemical.Bond")
 
static basic::Tracer TR ("core.chemical.bond_support")
 
static basic::Tracer TR ("core.chemical.ChemicalManager")
 
std::string const FA_RNA = "rna"
 tag name for querying RNA chemical type set. More...
 
std::string const FA_STANDARD
 
std::string const CENTROID
 
std::string const CENTROID_ROT
 
std::string const COARSE_TWO_BEAD
 
std::string const HYBRID_FA_STANDARD_CENTROID
 
std::string const COARSE_RNA
 
static basic::Tracer tr ("core.chemical.ElementSet")
 
static basic::Tracer TR ("core.chemical.icoor_support")
 
static basic::Tracer tr ("core.chemical")
 
static basic::Tracer tr ("core.chemical")
 
static basic::Tracer tr ("core.chemical")
 
std::string const patch_linker
 the string used to create new residue names after patching More...
 
static basic::Tracer tr ("core.chemical")
 
static basic::Tracer TR_PatchOperations ("core.chemical.PatchOperations.hh")
 
static basic::Tracer tr ("core.chemical")
 
static basic::Tracer TR ("core.chemical.residue_support")
 
static basic::Tracer tr ("core.chemical.ResidueType")
 
static basic::Tracer tr ("core.chemical.ResidueTypeSet")
 
static basic::Tracer TR ("core.chemical.util")
 
VariantType const UPPER_TERMINUS_VARIANT
 
VariantType const LOWER_TERMINUS_VARIANT
 
VariantType const UPPERTERM_TRUNC_VARIANT
 
VariantType const LOWERTERM_TRUNC_VARIANT
 
VariantType const CUTPOINT_UPPER
 
VariantType const CUTPOINT_LOWER
 
VariantType const DISULFIDE
 
VariantType const BRANCH_POINT_VARIANT
 
VariantType const BRANCH_LOWER_TERMINUS_VARIANT
 
VariantType const METHYLATION
 
VariantType const ADDUCT_VARIANT
 
VariantType const CENTROID_HA
 
VariantType const PROTONATED
 
VariantType const DEPROTONATED
 
VariantType const SPECIAL_ROT
 
VariantType const VIRTUAL_PHOSPHATE
 
VariantType const VIRTUAL_RNA_RESIDUE
 
VariantType const VIRTUAL_O2PRIME_HYDROGEN
 
VariantType const PHOSPHORYLATION
 
VariantType const ACETYLATION
 
VariantType const SULFATION
 
VariantType const CARBOXYLATION
 
VariantType const HYDROXYLATION
 
VariantType const DIMETHYLATION
 
VariantType const TRIMETHYLATION
 
VariantType const DIIODINATION
 
VariantType const ACETYLATED_NTERMINUS_VARIANT
 
VariantType const METHYLATED_CTERMINUS_VARIANT
 
VariantType const N_ACETYLATION
 
VariantType const C_METHYLAMIDATION
 
VariantType const SC_ORBITALS_VARIANT
 
VariantType const REPLONLY
 
VariantType const NTERM_CONNECT
 
VariantType const CTERM_CONNECT
 
VariantType const OOP_PRE
 
VariantType const OOP_POST
 
VariantType const HBS_PRE
 
VariantType const HBS_POST
 
VariantType const C1_MODIFIED_SUGAR
 
VariantType const C2_MODIFIED_SUGAR
 
VariantType const C3_MODIFIED_SUGAR
 
VariantType const C4_MODIFIED_SUGAR
 
VariantType const C5_MODIFIED_SUGAR
 
VariantType const C6_MODIFIED_SUGAR
 
VariantType const C7_MODIFIED_SUGAR
 
VariantType const C8_MODIFIED_SUGAR
 
VariantType const C9_MODIFIED_SUGAR
 
VariantType const SIDECHAIN_CONJUGATION
 

Typedef Documentation

typedef boost::graph_traits<AcceptorAtomGraph>::edge_iterator core::chemical::AcceptorAtomEIter
typedef boost::graph_traits<AcceptorAtomGraph>::vertex_iterator core::chemical::AcceptorAtomVIter
typedef std::map< std::string, int > core::chemical::AdductMap
typedef boost::graph_traits<ResidueGraph>::adjacency_iterator core::chemical::AdjacentIter
typedef boost::graph_traits<APolarHydrogenGraph>::vertex_iterator core::chemical::APolarHydrogenVIter
typedef boost::graph_traits<AromaticAtomGraph>::edge_iterator core::chemical::AromaticAtomEIter
typedef boost::graph_traits<AromaticAtomGraph>::vertex_iterator core::chemical::AromaticAtomVIter
typedef ResidueGraph::edge_descriptor core::chemical::ED
typedef boost::graph_traits<ResidueGraph>::edge_iterator core::chemical::EIter
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<HydrogenAtomGraph>::edge_iterator core::chemical::HHydrogenAtomEIter
typedef HydrogenAtomGraph::edge_descriptor core::chemical::HydrogenAtomED
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 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 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 boost::graph_traits<ResidueGraph>::out_edge_iterator core::chemical::OutEdgeIter
typedef boost::graph_traits<PolarHydrogenGraph>::edge_iterator core::chemical::PolarHydrogenEIter
typedef boost::graph_traits<PolarHydrogenGraph>::vertex_iterator core::chemical::PolarHydrogenVIter
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

Notion of Residue variant, eg PHOSPHO, NTERM, TERMINUS, PROTONATION, GLYCOSO ??

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

Enumeration Type Documentation

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

Enumerator
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 
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_b3cisACPrC 
aa_b3cisACPC 
aa_b3cisACHC 
last_beta3_aa 
aa_h2o 
aa_vrt 
aa_unp 
aa_unk 
num_aa_types 

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 
Enumerator
UnknownBondOrder 
SingleBondOrder 
DoubleBondOrder 
TripleBondOrder 
OrbitalBondOrder 
PseudoBondOrder 
Enumerator
UnknownRingness 
BondNotInRing 
BondInRing 

Enumerators for the three Cremer-Pople "ring-puckering" parameters used to describe 4-, 5-, and 6-membered ring conformers.

Enumerator
PHI 
THETA 
Enumerator
SP2_HYBRID 
SP3_HYBRID 
RING_HYBRID 
UNKNOWN_HYBRID 
HYBRID_MAX 

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

Enumerator
FIRST_PROPERTY 
POLYMER 
LIGAND 
PROTEIN 
NA 
DNA 
RNA 
PEPTOID 
CARBOHYDRATE 
LIPID 
METAL 
SURFACE 
WATER 
VIRTUAL_RESIDUE 
TERMINUS 
LOWER_TERMINUS 
UPPER_TERMINUS 
BRANCH_LOWER_TERMINUS 
BRANCH_POINT 
LOWERTERM_TRUNC 
UPPERTERM_TRUNC 
COARSE 
ADDUCT 
SC_ORBITALS 
POLAR 
CHARGED 
AROMATIC 
CYCLIC 
METALBINDING 
MEMBRANE 
PHOSPHONATE 
PHOSPHONATE_UPPER 
ACETYLATED_NTERMINUS 
METHYLATED_CTERMINUS 
ALPHA_AA 
BETA_AA 
L_AA 
D_AA 
TAUTOMER 
ALDOSE 
KETOSE 
L_SUGAR 
D_SUGAR 
OXIROSE 
OXETOSE 
FURANOSE 
PYRANOSE 
SEPTANOSE 
ALPHA_SUGAR 
BETA_SUGAR 
SIALIC_ACID 
ALDONIC_ACID 
_2_KETOALDONIC_ACID 
_3_KETOALDONIC_ACID 
_4_KETOALDONIC_ACID 
_5_KETOALDONIC_ACID 
_6_KETOALDONIC_ACID 
_7_KETOALDONIC_ACID 
_8_KETOALDONIC_ACID 
URONIC_ACID 
_1_DEOXY_SUGAR 
_2_DEOXY_SUGAR 
_3_DEOXY_SUGAR 
_4_DEOXY_SUGAR 
_5_DEOXY_SUGAR 
_6_DEOXY_SUGAR 
_7_DEOXY_SUGAR 
_8_DEOXY_SUGAR 
_9_DEOXY_SUGAR 
_1_AMINO_SUGAR 
_2_AMINO_SUGAR 
_3_AMINO_SUGAR 
_4_AMINO_SUGAR 
_5_AMINO_SUGAR 
_6_AMINO_SUGAR 
_7_AMINO_SUGAR 
_8_AMINO_SUGAR 
_9_AMINO_SUGAR 
_1_ACETYLAMINO_SUGAR 
_2_ACETYLAMINO_SUGAR 
_3_ACETYLAMINO_SUGAR 
_4_ACETYLAMINO_SUGAR 
_5_ACETYLAMINO_SUGAR 
_6_ACETYLAMINO_SUGAR 
_7_ACETYLAMINO_SUGAR 
_8_ACETYLAMINO_SUGAR 
_9_ACETYLAMINO_SUGAR 
_1_PHOSPHATE 
_2_PHOSPHATE 
_3_PHOSPHATE 
_4_PHOSPHATE 
_5_PHOSPHATE 
_6_PHOSPHATE 
_7_PHOSPHATE 
_8_PHOSPHATE 
_9_PHOSPHATE 
N_RESIDUE_PROPERTIES 

Function Documentation

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

vector that maps AA enum to string name

References setup_aa2name().

Referenced by name_from_aa().

utility::vector1< char >& 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)
AA core::chemical::aa_from_oneletter_code ( char  onelettercode)
VariantType const core::chemical::ACETYLATED_NTERMINUS_VARIANT ( "ACETYLATED_NTERMINUS"  )

Acetylated N-terminus cap, written for creating amino acid dipeptides for NCAA rotamer libraries.

VariantType const core::chemical::ACETYLATION ( "ACETYLATION"  )
void core::chemical::add_atom_type_set_parameters_from_command_line ( std::string const &  atom_type_set_tag,
AtomTypeSet atom_type_set 
)
VariantType const core::chemical::ADDUCT_VARIANT ( "ADDUCT"  )
ResidueTypeOP core::chemical::apply_adducts_to_residue ( ResidueType const &  rsd,
utility::vector1< bool > &  add_mask 
)
id::AtomID core::chemical::atom_id_from_icoor_line ( std::string const  name,
ResidueType const &  rsd 
)
gasteiger::GasteigerAtomTypeData::Properties core::chemical::bond_order_to_property ( const core::Size BOND_ORDER_OR_AROMATIC)
VariantType const core::chemical::BRANCH_LOWER_TERMINUS_VARIANT ( "BRANCH_LOWER_TERMINUS"  )

Variant type used for branched polymers and glycosylations.

VariantType const core::chemical::BRANCH_POINT_VARIANT ( "BRANCH_POINT"  )

Variant type used for branched polymers and glycosylations.

VariantType const core::chemical::C1_MODIFIED_SUGAR ( "C1_MODIFIED_SUGAR"  )

@ brief variant for any saccharide residue modified at the 1 position

VariantType const core::chemical::C2_MODIFIED_SUGAR ( "C2_MODIFIED_SUGAR"  )

@ brief variant for any saccharide residue modified at the 2 position

VariantType const core::chemical::C3_MODIFIED_SUGAR ( "C3_MODIFIED_SUGAR"  )

@ brief variant for any saccharide residue modified at the 3 position

VariantType const core::chemical::C4_MODIFIED_SUGAR ( "C4_MODIFIED_SUGAR"  )

@ brief variant for any saccharide residue modified at the 4 position

VariantType const core::chemical::C5_MODIFIED_SUGAR ( "C5_MODIFIED_SUGAR"  )

@ brief variant for any saccharide residue modified at the 5 position

VariantType const core::chemical::C6_MODIFIED_SUGAR ( "C6_MODIFIED_SUGAR"  )

@ brief variant for any saccharide residue modified at the 6 position

VariantType const core::chemical::C7_MODIFIED_SUGAR ( "C7_MODIFIED_SUGAR"  )

@ brief variant for any saccharide residue modified at the 7 position

VariantType const core::chemical::C8_MODIFIED_SUGAR ( "C8_MODIFIED_SUGAR"  )

@ brief variant for any saccharide residue modified at the 8 position

VariantType const core::chemical::C9_MODIFIED_SUGAR ( "C9_MODIFIED_SUGAR"  )

@ brief variant for any saccharide residue modified at the 9 position

VariantType const core::chemical::C_METHYLAMIDATION ( "C_METHYLAMIDATION"  )
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(), utility::graph::breadth_first_search_prune(), core::chemical::ResidueType::graph(), core::chemical::ResidueType::name(), core::chemical::ResidueType::natoms(), and TR.

Referenced by find_nbr_dist().

VariantType const core::chemical::CARBOXYLATION ( "CARBOXYLATION"  )
PatchCaseOP core::chemical::case_from_lines ( utility::vector1< std::string > const &  lines)

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(), tag, and tag_from_line().

Referenced by core::chemical::Patch::read_file().

std::string const core::chemical::CENTROID ( "centroid"  )

tag name for querying centroid chemical type set.

VariantType const core::chemical::CENTROID_HA ( "CENTROID_WITH_HA"  )
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.

std::string const core::chemical::COARSE_TWO_BEAD ( "coarse_two_bead"  )

tag name for querying coarse-grained chemical type set.

LightWeightResidueGraph core::chemical::convert_residuetype_to_light_graph ( ResidueType const &  res)
BondName core::chemical::convert_to_BondName ( std::string const &  id)
Real core::chemical::create_bond_length ( gasteiger::GasteigerAtomTypeData const &  atom1,
gasteiger::GasteigerAtomTypeData const &  atom2,
BondName  bond_type 
)
VariantType const core::chemical::CTERM_CONNECT ( "CTERM_CONNECT"  )
VariantType const core::chemical::CUTPOINT_LOWER ( "CUTPOINT_LOWER"  )

for use during loop modeling, at positions before a cutpoint

VariantType const core::chemical::CUTPOINT_UPPER ( "CUTPOINT_UPPER"  )

for use during loop modeling, at positions after a cutpoint

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(), and tr.

Referenced by read_topology_file().

VariantType const core::chemical::DEPROTONATED ( "DEPROTONATED"  )
VariantType const core::chemical::DIIODINATION ( "DIIODINATION"  )
VariantType const core::chemical::DIMETHYLATION ( "DIMETHYLATION"  )
VariantType const core::chemical::DISULFIDE ( "DISULFIDE"  )
void core::chemical::error_check_requested_adducts ( AdductMap const &  add_map,
ResidueTypeCOPs const &  rsd_types 
)

Make sure requested adducts exist in some residue.

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.

References core::chemical::ResidueType::defined_adducts(), and utility_exit_with_message.

Referenced by core::chemical::ResidueTypeSet::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 
)
void core::chemical::find_bonds_in_rings ( ResidueType res)
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(), begin, 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, TR, and utility_exit_with_message.

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

std::string core::chemical::fixup_patches ( std::string  string_in)
std::string core::chemical::formatted_icoord_tree ( core::chemical::ResidueType const &  restype)

Return a string representing the Icoord tree of the Restype.

Mainly intended for debugging purposes.

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

Referenced by print_chis().

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  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, and aa_val.

std::string core::chemical::get_element_color ( std::string const &  element)
AA core::chemical::get_L_equivalent ( AA  aa)
utility::vector1< std::string > core::chemical::get_lines_from_file_data ( std::string const &  filename)

Local method that opens a file and returns its data as a list of lines after checking for errors.

Blank and commented lines are not returned and the file is closed before returning the lines.

References utility::io::izstream::close(), file_exists(), getline(), utility::io::izstream::good(), trim(), and utility_exit_with_message.

Referenced by read_conformers_from_database_file_for_ring_size().

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().

core::Real core::chemical::get_rpp_charge ( std::string const &  type)

Get charge for atom type based on Rosetta++ aaproperties_pack.cc values.

References TR.

Referenced by rosetta_recharge_fullatom().

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

Does a ResidueGraph have a given vertex descriptor?

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

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 
)
VariantType const core::chemical::HBS_POST ( "HBS_POST"  )

@ brief hbs_post patch, used for hydrogen bond surrogates

VariantType const core::chemical::HBS_PRE ( "HBS_PRE"  )

@ brief hbs_pre patch, used for hydrogen bond surrogates

std::string const core::chemical::HYBRID_FA_STANDARD_CENTROID ( "hybrid_fa_standard_centroid"  )

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

VariantType const core::chemical::HYDROXYLATION ( "HYDROXYLATION"  )
bool core::chemical::is_canonical_D_aa ( AA  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::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::bbdep_nrchi_score(), core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::methods::CartesianBondedEnergy::eval_improper_torsion_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_improper_torsions(), 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_residue_pair_derivatives(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::eval_rotameric_energy_deriv(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_torsion_energies(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_improper_torsions_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_singleres_torsion_energies(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::fill_rotamer_vector(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::fill_rotamer_vector_bbdep(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::fill_rotamer_vector_bbind(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_phi_from_rsd(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_psi_from_rsd(), core::scoring::methods::get_restag(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::get_rotamer_from_chi_static(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::interpolate_rotamers(), core::scoring::Ramachandran::is_canonical_d_aminoacid(), core::scoring::P_AA::is_canonical_d_aminoacid(), core::scoring::methods::RamachandranEnergy::residue_energy(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), core::pack::task::ResidueLevelTask_::ResidueLevelTask_(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::rotamer_energy_deriv(), and core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T >::rotamer_energy_deriv_bbdep().

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().

VariantType const core::chemical::LOWER_TERMINUS_VARIANT ( "LOWER_TERMINUS"  )

N-terminus cap.

VariantType const core::chemical::LOWERTERM_TRUNC_VARIANT ( "LOWERTERM_TRUNC"  )

N-terminus truncation.

VariantType const core::chemical::METHYLATED_CTERMINUS_VARIANT ( "METHYLATED_CTERMINUS"  )

Methylated C-terminus cap, written for creating amino acid dipeptides for NCAA rotamer libraries.

VariantType const core::chemical::METHYLATION ( "METHYLATION"  )
void core::chemical::modify_atom_properties_from_command_line ( std::string const &  atom_type_set_tag,
AtomTypeSet atom_type_set 
)
VariantType const core::chemical::N_ACETYLATION ( "N_ACETYLATION"  )

Cap extensions at termini to include peptide bonds, written for stepwise assembly (SWA) code.

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

map that converts string name to AA enum

References setup_name2aa().

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

std::string core::chemical::name_from_aa ( AA  aa)

give a enum type and return the string name

References aa2name(), and num_aa_types.

Referenced by core::pack::task::ResidueLevelTask_::allow_noncanonical_aa(), core::pose::Pose::annotated_sequence(), core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_10_from_ASCII(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), 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(), core::scoring::methods::get_restag(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), operator<<(), core::scoring::rna::chemical_shift::print_chemical_shift_data(), core::pack::interaction_graph::SurfacePotential::read_average_res_hASA_database_file(), core::pack::dunbrack::RotamerLibrary::read_from_binary(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::read_from_file(), core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T >::read_from_file(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >::read_from_file(), core::chemical::ResidueDatabaseIO::read_residue_type(), read_topology_file(), core::scoring::methods::EnvSmoothEnergy::representative_atom_name(), core::scoring::methods::MembraneEnvSmoothEnergy::representative_atom_name(), core::scoring::membrane::FaMPEnvSmoothEnergy::representative_atom_name(), and core::pack::task::ResidueLevelTask_::restrict_absent_nas().

VariantType const core::chemical::NTERM_CONNECT ( "NTERM_CONNECT"  )

N-terminal connect and C-terminal connect.

std::map< char, AA >& 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)
bool core::chemical::oneletter_code_specifies_aa ( char  onelettercode)
VariantType const core::chemical::OOP_POST ( "OOP_POST"  )

@ brief oop_post patch, used for oligooxopiperazines (OOPs)

VariantType const core::chemical::OOP_PRE ( "OOP_PRE"  )

@ brief oop_pre patch, used for oligooxopiperazines (OOPs)

bool core::chemical::operator!= ( ResConnID const &  lhs,
ResConnID const &  rhs 
)
ResidueProperty & core::chemical::operator++ ( ResidueProperty &  property)
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 &  out,
Bond const &  bond 
)
std::ostream & core::chemical::operator<< ( std::ostream &  output,
ResidueProperties const &  object_to_output 
)
std::ostream & core::chemical::operator<< ( std::ostream &  out,
Atom const &  atom 
)
std::ostream& core::chemical::operator<< ( std::ostream &  out,
Element const &  obj 
)
inline
std::ostream& core::chemical::operator<< ( std::ostream &  out,
ElectronConfiguration const &  obj 
)
inline
std::ostream & core::chemical::operator<< ( std::ostream &  output,
RingConformer const &  object_to_output 
)
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,
RingConformerSet const &  object_to_output 
)
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.

References utility::options::StringVectorOption::size().

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

std::string const core::chemical::patch_linker ( ":"  )

the string used to generate new residue names

PatchOperationOP core::chemical::patch_operation_from_patch_file_line ( std::string const &  line)

Virtual constructor, returns 0 if no match.

References l, mean, path, numeric::conversions::radians(), radians(), radius, runtime_assert, tag, tr, and utility_exit_with_message.

Referenced by case_from_lines().

VariantType const core::chemical::PHOSPHORYLATION ( "PHOSPHORYLATION"  )
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,
AtomICoor const &  start,
ResidueType const &  rsd_type,
core::Size  indent 
)
void core::chemical::print_chis ( std::ostream &  out,
ResidueType const &  res 
)
VariantType const core::chemical::PROTONATED ( "PROTONATED"  )
utility::vector1< RingConformer > core::chemical::read_conformers_from_database_file_for_ring_size ( std::string const &  filename,
core::Size  ring_size 
)
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,
chemical::ResidueTypeSetCAP  rsd_type_set 
)
ResidueTypeOP core::chemical::read_topology_file ( utility::io::izstream data,
chemical::AtomTypeSetCAP  atom_types,
chemical::ElementSetCAP  elements,
chemical::MMAtomTypeSetCAP  mm_atom_types,
chemical::orbitals::OrbitalTypeSetCAP  orbital_atom_types,
chemical::ResidueTypeSetCAP  rsd_type_set 
)

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, "ROTAMER_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.

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.

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"

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

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

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 also the CHI_ROTAMERS and NCAA_ROTLIB_PATH tags for alternate ways to provide 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.

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" No examples currently found in the database (10/13).

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.

References aa_ser, aa_thr, utility::io::izstream::close(), convert_to_BondName(), define_mainchain_atoms(), numeric::conversions::degrees(), basic::options::OptionKeys::corrections::chemical::expand_st_chi2sampling, FA_STANDARD, utility::io::izstream::filename(), filename(), getline(), l, mean, name_from_aa(), basic::options::option, basic::options::OptionKeys::corrections::chemical::parse_charge, parse_charge, utility::file::FileName::path(), path, numeric::conversions::radians(), radians(), radius, core::kinematics::Stub::spherical(), strip_whitespace(), tag, tr, utility_exit_with_message, and utility::file::FileName::vol().

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().

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(), utility::to_string(), and TR.

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

VariantType const core::chemical::REPLONLY ( "REPLONLY"  )

@ brief only the repulsive energy will be considered during structure calculations

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.

Assumes:

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

References angle, core::chemical::ResidueType::atom_name(), core::id::D, utility::graph::depth_first_search_sort(), core::chemical::ResidueType::has(), core::chemical::ResidueType::natoms(), core::id::PHI, core::chemical::ResidueType::set_icoor(), core::id::THETA, torsion(), TR, and utility_exit_with_message.

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

ResidueSelectorSingleOP core::chemical::residue_selector_single_from_line ( std::string const &  line)

create a singe ResidueSelector from an input line.

References l, and tag.

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

std::string core::chemical::residue_type_all_patches_name ( ResidueType const &  rsd_type)

helper function, returns the name of all added patches

References core::chemical::ResidueType::name(), and patch_linker.

Referenced by core::util::add_covalent_linkage_helper(), and core::io::pdb::build_pose_as_is1().

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 core::scoring::hbonds::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(), get_rpp_charge(), core::chemical::ResidueType::graph(), core::chemical::ResidueType::name(), TR, and type.

Referenced by 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 AromaticBond, core::chemical::Atom::atom_type_index(), core::chemical::ResidueType::atom_type_set(), core::chemical::element::Br, core::chemical::element::C, core::chemical::element::Ca, core::chemical::element::Cl, DoubleBond, core::chemical::Atom::element_type(), core::chemical::element::F, core::chemical::element::Fe, core::chemical::ResidueType::graph(), core::chemical::element::H, 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(), core::scoring::hbonds::t, TripleBond, utility_exit_with_message, and core::chemical::element::Zn.

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

core::chemical::ResidueTypeSetCAP core::chemical::rsd_set_from_cmd_line ( )
VariantType const core::chemical::SC_ORBITALS_VARIANT ( "SC_ORBITALS"  )
utility::vector1< std::string > core::chemical::setup_aa2name ( )

setup the vector that maps AA enum to string name

References begin, core::sequence::end, 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 begin, core::sequence::end, num_aa_types, and oneletter2aa().

Referenced by aa2oneletter().

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_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().

VariantType const core::chemical::SIDECHAIN_CONJUGATION ( "SIDECHAIN_CONJUGATION"  )

This is used for chemically conjugable residues (LYX, CYX) used for sidechain conjugation (like ubiquitination)

VariantType const core::chemical::SPECIAL_ROT ( "SPECIAL_ROT"  )

Generic variant type that allows for differential scoring of a set of residues/rotamers.

std::string core::chemical::strip_whitespace ( std::string const &  name)
inline
VariantType const core::chemical::SULFATION ( "SULFATION"  )
std::string core::chemical::tag_from_line ( std::string const &  line)

handy function, return the first word from a line

References l, and tag.

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

VariantType const core::chemical::TRIMETHYLATION ( "TRIMETHYLATION"  )
VariantType const core::chemical::UPPER_TERMINUS_VARIANT ( "UPPER_TERMINUS"  )

C-terminus cap.

VariantType const core::chemical::UPPERTERM_TRUNC_VARIANT ( "UPPERTERM_TRUNC"  )

C-terminus truncation.

VariantType const core::chemical::VIRTUAL_O2PRIME_HYDROGEN ( "VIRTUAL_O2PRIME_HYDROGEN"  )
VariantType const core::chemical::VIRTUAL_PHOSPHATE ( "VIRTUAL_PHOSPHATE"  )
VariantType const core::chemical::VIRTUAL_RNA_RESIDUE ( "VIRTUAL_RNA_RESIDUE"  )
void core::chemical::write_topology_file ( ResidueType const &  rsd,
std::string  filename 
)

writes a .params file from a given ResidueType object

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

References core::chemical::ResidueType::aa(), core::chemical::ResidueType::actcoord_atoms(), core::chemical::ResidueType::atom(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::atom_type(), core::chemical::ICoorAtomID::atomno(), core::chemical::ResidueConnection::atomno(), core::chemical::Atom::charge(), core::chemical::ResidueType::chi_atoms(), core::chemical::AtomICoor::d(), numeric::conversions::degrees(), degrees(), core::chemical::ResidueType::force_nbr_atom_orient(), core::chemical::Atom::formal_charge(), core::chemical::ResidueType::icoor(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_aromatic(), core::chemical::ResidueType::is_beta_aa(), core::chemical::ResidueType::is_charged(), core::chemical::ResidueType::is_d_aa(), core::chemical::ResidueType::is_DNA(), core::chemical::ResidueType::is_l_aa(), core::chemical::ResidueType::is_ligand(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_metal(), core::chemical::ResidueType::is_metalbinding(), core::chemical::ResidueType::is_polar(), core::chemical::ResidueType::is_polymer(), core::chemical::ResidueType::is_protein(), core::chemical::ResidueType::is_proton_chi(), core::chemical::ResidueType::is_RNA(), core::chemical::ResidueType::is_surface(), core::chemical::ResidueType::is_terminus(), core::chemical::ResidueType::is_upper_terminus(), core::chemical::ResidueType::lower_connect(), core::chemical::ResidueType::mm_atom_type(), core::chemical::ResidueType::n_nus(), core::chemical::MMAtomType::name(), core::chemical::AtomType::name(), core::chemical::ResidueType::name(), core::chemical::ResidueType::name1(), core::chemical::ResidueType::name3(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nbr_atom(), core::chemical::ResidueType::nbr_radius(), core::chemical::ResidueType::nbrs(), core::chemical::ResidueType::nchi(), core::chemical::ResidueType::nu_atoms(), out, core::chemical::AtomICoor::phi(), core::chemical::ResidueType::proton_chi_extra_samples(), core::chemical::ResidueType::proton_chi_samples(), numeric::conversions::radians(), core::chemical::AtomICoor::stub_atom1(), core::chemical::AtomICoor::stub_atom2(), core::chemical::AtomICoor::stub_atom3(), core::chemical::AtomICoor::theta(), core::chemical::ICoorAtomID::type(), and core::chemical::ResidueType::upper_connect().

Variable Documentation

VariantType const core::chemical::ACETYLATED_NTERMINUS_VARIANT
VariantType const core::chemical::ACETYLATION
VariantType const core::chemical::ADDUCT_VARIANT
VariantType const core::chemical::BRANCH_LOWER_TERMINUS_VARIANT
VariantType const core::chemical::BRANCH_POINT_VARIANT
VariantType const core::chemical::C1_MODIFIED_SUGAR
VariantType const core::chemical::C2_MODIFIED_SUGAR
VariantType const core::chemical::C3_MODIFIED_SUGAR
VariantType const core::chemical::C4_MODIFIED_SUGAR
VariantType const core::chemical::C5_MODIFIED_SUGAR
VariantType const core::chemical::C6_MODIFIED_SUGAR
VariantType const core::chemical::C7_MODIFIED_SUGAR
VariantType const core::chemical::C8_MODIFIED_SUGAR
VariantType const core::chemical::C9_MODIFIED_SUGAR
VariantType const core::chemical::C_METHYLAMIDATION
VariantType const core::chemical::CARBOXYLATION
std::string const core::chemical::CENTROID
VariantType const core::chemical::CENTROID_HA
std::string const core::chemical::CENTROID_ROT
std::string const core::chemical::COARSE_RNA
std::string const core::chemical::COARSE_TWO_BEAD
VariantType const core::chemical::CTERM_CONNECT
VariantType const core::chemical::CUTPOINT_LOWER
VariantType const core::chemical::CUTPOINT_UPPER
VariantType const core::chemical::DEPROTONATED
VariantType const core::chemical::DIIODINATION
VariantType const core::chemical::DIMETHYLATION
VariantType const core::chemical::DISULFIDE

Referenced by core::pack::task::operation::NoRepackDisulfides::apply(), core::pack::task::operation::OptCysHG::apply(), core::io::pdb::build_pose_as_is1(), core::conformation::change_cys_state(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::conformation::disulfide_bonds(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::disulfides_changed(), core::scoring::MembranePotential::evaluate_pair(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), core::scoring::EnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::conformation::Conformation::fix_disulfides(), core::conformation::form_disulfide(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), and core::scoring::membrane::MPPairEnergy::residue_pair_energy().

std::string const core::chemical::FA_RNA = "rna"
std::string const core::chemical::FA_STANDARD

Referenced by core::chemical::IdealBondLengthSet::add_bond_length(), core::pose::addVirtualResAsRoot(), core::import_pose::build_pose_as_is2(), core::io::pdb::build_pose_from_pdb_as_is(), core::scoring::geometric_solvation::compute_exact_geosol(), core::chemical::IdealBondLengthSet::contains_bond_length(), core::chemical::ChemicalManager::create_residue_type_set(), core::scoring::geometric_solvation::DatabaseOccSolEne::DatabaseOccSolEne(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::scoring::ScoringManager::etable(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::ExactOccludedHbondSolEnergy(), core::io::silent::SilentStruct::fill_pose(), core::import_pose::PDBSilentStruct::fill_pose(), core::io::raw_data::DecoyStruct::fill_pose(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), core::conformation::form_disulfide(), core::chemical::IdealBondLengthSet::get_bond_length(), core::scoring::ScoringManager::get_MMBondAngleLibrary(), core::scoring::ScoringManager::get_MMBondLengthLibrary(), core::scoring::ScoringManager::get_MMLJLibrary(), core::scoring::ScoringManager::get_MMTorsionLibrary(), core::pack::interaction_graph::RotamerDotsRadiusData::get_NACCESS_SASA_radii(), core::pack::interaction_graph::RotamerDotsRadiusData::get_NACCESS_SASA_radii_with_expanded_polars(), core::pack::interaction_graph::RotamerDotsRadiusData::get_ROSETTA_SASA_radii(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::conformation::Conformation::is_fullatom(), core::scoring::ScoringManager::memb_etable(), core::conformation::orient_residue_for_ideal_bond(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), core::import_pose::pose_from_pdb(), core::import_pose::pose_from_pdbstring(), core::io::pdb::pose_from_pose(), core::import_pose::poseOPs_from_pdbs(), core::import_pose::poses_from_pdbs(), read_topology_file(), core::pack::dunbrack::RotamerLibrary::rsd_library_already_loaded(), core::pack::task::operation::util::select_coord_for_residue(), and core::util::switch_to_residue_type_set().

VariantType const core::chemical::HBS_POST
VariantType const core::chemical::HBS_PRE
std::string const core::chemical::HYBRID_FA_STANDARD_CENTROID
VariantType const core::chemical::HYDROXYLATION
VariantType const core::chemical::LOWER_TERMINUS_VARIANT
VariantType const core::chemical::LOWERTERM_TRUNC_VARIANT
Real const core::chemical::MAX_CHEMICAL_BOND_TO_HYDROGEN_LENGTH = { 1.35 }

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

S-H bond length in CYS.

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

VariantType const core::chemical::METHYLATED_CTERMINUS_VARIANT
VariantType const core::chemical::METHYLATION
VariantType const core::chemical::N_ACETYLATION
VariantType const core::chemical::NTERM_CONNECT
VariantType const core::chemical::OOP_POST
VariantType const core::chemical::OOP_PRE
std::string const core::chemical::patch_linker
VariantType const core::chemical::PHOSPHORYLATION
VariantType const core::chemical::PROTONATED
VariantType const core::chemical::REPLONLY

Referenced by core::scoring::methods::RG_Energy_Fast::calculate_rg_score(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::RamachandranEnergy::eval_dof_derivative(), core::scoring::methods::P_AA_pp_Energy::eval_dof_derivative(), core::pack::dunbrack::DunbrackEnergy::eval_dof_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_dof_derivative(), core::scoring::etable::TableLookupEtableEnergy::eval_intrares_energy(), core::scoring::etable::AnalyticEtableEnergy::eval_intrares_energy(), core::scoring::methods::CenRotEnvEnergy::eval_residue_derivatives(), core::scoring::methods::SmoothEnvEnergy::eval_residue_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::scoring::methods::RamachandranEnergy::eval_residue_dof_derivative(), core::scoring::methods::YHHPlanarityEnergy::eval_residue_dof_derivative(), core::scoring::methods::OmegaTetherEnergy::eval_residue_dof_derivative(), core::scoring::methods::P_AA_pp_Energy::eval_residue_dof_derivative(), core::pack::dunbrack::DunbrackEnergy::eval_residue_dof_derivative(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_dof_derivative(), core::scoring::methods::CenRotPairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::disulfides::FullatomDisulfideEnergy::eval_residue_pair_derivatives(), core::scoring::methods::PairEnergy::eval_residue_pair_derivatives(), core::scoring::SecondaryStructurePotential::identify_ss(), core::scoring::disulfides::FullatomDisulfideEnergy::old_eval_atom_derivative(), core::scoring::methods::OmegaTetherEnergy::old_eval_dof_derivative(), core::scoring::methods::RamachandranEnergy::residue_energy(), core::scoring::methods::OmegaTetherEnergy::residue_energy(), core::scoring::methods::YHHPlanarityEnergy::residue_energy(), core::scoring::methods::P_AA_pp_Energy::residue_energy(), core::pack::dunbrack::DunbrackEnergy::residue_energy(), core::scoring::methods::EnvEnergy::residue_energy(), core::pack::dunbrack::cenrot::CenRotDunEnergy::residue_energy(), core::scoring::methods::CenRotEnvEnergy::residue_energy(), core::scoring::methods::SmoothEnvEnergy::residue_energy(), core::scoring::methods::ReferenceEnergyNoncanonical::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::methods::ReferenceEnergy::residue_energy(), core::scoring::disulfides::DisulfideMatchingEnergy::residue_pair_energy(), core::scoring::disulfides::CentroidDisulfideEnergy::residue_pair_energy(), core::scoring::methods::CenPairEnergy::residue_pair_energy(), core::scoring::methods::SmoothCenPairEnergy::residue_pair_energy(), core::scoring::methods::CenRotPairEnergy::residue_pair_energy(), core::scoring::methods::PairEnergy::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy(), core::scoring::disulfides::FullatomDisulfideEnergy::residue_pair_energy_ext(), core::scoring::methods::RG_LocalEnergy::setup_for_derivatives(), core::scoring::methods::RG_Energy_Fast::setup_for_derivatives(), and core::scoring::disulfides::FullatomDisulfideEnergy::setup_for_minimizing_for_residue_pair().

VariantType const core::chemical::SC_ORBITALS_VARIANT
VariantType const core::chemical::SIDECHAIN_CONJUGATION
VariantType const core::chemical::SPECIAL_ROT
VariantType const core::chemical::SULFATION
basic::Tracer core::chemical::TR("core.chemical.bond_support")
static
basic::Tracer core::chemical::tr("core.chemical.ElementSet")
static
basic::Tracer core::chemical::tr("core.chemical")
static
basic::Tracer core::chemical::TR("core.chemical.Bond")
static
basic::Tracer core::chemical::tr("core.chemical")
static
basic::Tracer core::chemical::TR("core.chemical.Atom")
static
basic::Tracer core::chemical::TR("core.chemical.util")
static
basic::Tracer core::chemical::tr("core.chemical")
static
basic::Tracer core::chemical::TR("core.chemical.icoor_support")
static
basic::Tracer core::chemical::TR("core.chemical.residue_support")
static
basic::Tracer core::chemical::tr("core.chemical")
static
basic::Tracer core::chemical::tr("core.chemical")
static
basic::Tracer core::chemical::tr("core.chemical.ResidueTypeSet")
static
basic::Tracer core::chemical::tr("core.chemical.ResidueType")
static
basic::Tracer core::chemical::TR("core.chemical.ChemicalManager")
static
basic::Tracer core::chemical::tr("core.chemical")
static
basic::Tracer core::chemical::TR_PatchOperations("core.chemical.PatchOperations.hh")
static
VariantType const core::chemical::TRIMETHYLATION
basic::Tracer core::chemical::tw("core.chemical.AtomICoor", basic::t_warning)
static
VariantType const core::chemical::UPPER_TERMINUS_VARIANT
VariantType const core::chemical::UPPERTERM_TRUNC_VARIANT
VariantType const core::chemical::VIRTUAL_O2PRIME_HYDROGEN
VariantType const core::chemical::VIRTUAL_PHOSPHATE
VariantType const core::chemical::VIRTUAL_RNA_RESIDUE