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core::chemical Namespace Reference

Namespaces

 carbohydrates
 
 orbitals
 
 rna
 
 sdf
 

Classes

class  Adduct
 Description of optional single-atom residue adducts. More...
 
class  Atom
 basic chemical atom More...
 
class  ICoorAtomID
 Atom 's ID in internal coordinates in a ResidueType. More...
 
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  ChemicalManager
 a class managing different sets of atom_type_set and residue_type_set More...
 
class  CSDAtomType
 Basic "conformational" atom type derived from analysis of Cambridge Structure Database. More...
 
class  CSDAtomTypeSet
 A set of CSDAtomTypes. More...
 
class  Element
 class to describe Elements More...
 
class  ElementSet
 A set of Elements. More...
 
class  IdealBondLengthSet
 A set of Elements. More...
 
class  MMAtomType
 Basic MM atom type. More...
 
class  MMAtomTypeSet
 A set of MMAtomTypes. More...
 
class  Orbital
 basic chemical atom More...
 
class  PatchCase
 A single case of a patch, eg proline Nterminus is a case of NtermProteinFull. More...
 
class  Patch
 A class patching basic ResidueType to create variant types, containing multiple PatchCase. More...
 
class  PatchOperation
 A single operation that needs to be applied in a residue patch. More...
 
class  DeleteAtom
 delete an atom More...
 
class  SetBackboneHeavyatom
 set an atom as backbone heavy atom More...
 
class  SetPolymerConnectAtom
 set an atom as polymer connection More...
 
class  AddConnect
 
class  AddProperty
 add a property to ResidueType 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  AddChi
 Add a chi angle to ResidueType Added by Andy M. Chen in June 2009 This is needed for PTM's, which often result in one or more extra chi angles. More...
 
class  AddProtonChi
 
class  RedefineChi
 Redefine a chi angle Added by Andy M. Chen in June 2009 This is needed for certain PTM's. More...
 
class  AddChiRotamer
 Add a rotamer sample to a chi angle of the ResidueType Added by Andy M. Chen in June 2009 This is needed for PTM's. More...
 
class  AddAtom
 add an atom to ResidueType More...
 
class  AddBond
 add a bond to ResidueType More...
 
class  SetAtomicCharge
 set an atom's charge More...
 
class  SetAtomType
 set atom's chemical type More...
 
class  SetIO_String
 set atom's chemical type More...
 
class  SetMMAtomType
 set atom's MM chemical type More...
 
class  SetICoor
 set an atom's AtomICoord More...
 
class  PrependMainchainAtom
 add a mainchain atom before the first mainchain atom More...
 
class  AppendMainchainAtom
 add a mainchain atom after the last mainchain atom 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  NCAARotLibPath
 set the path to a rotamer library for an NCAA that is not in dunbrack More...
 
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  ResidueSelectorSingle
 A base class for defining a ResidueSelector by a single criterion. More...
 
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_NAME3
 Does the residue have to ANY of these three-letter codes? More...
 
class  Selector_PROPERTY
 Does the residue have ANY of these properties? More...
 
class  Selector_VARIANT_TYPE
 Does the residue have ANY of variant types? More...
 
class  Selector_MATCH_VARIANTS
 Does the residue have ALL of the variant types and no more. More...
 
class  Selector_NO_VARIANTS
 Does the residue have ANY of variant types? More...
 
class  Selector_NAME1
 Does the residue belong to ANY of these AAs? More...
 
class  ResidueSelector
 A class picking out a subset of ResidueType by multiple criteria. More...
 
class  ResidueType
 silly demo class – what would the most familiar residue look like? More...
 
class  ResidueTypeSet
 A collection of ResidueType defined. 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::vector1< AtomOPAtomOPs
 
typedef utility::vector1< AtomCOPAtomCOPs
 
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::access_ptr
< CSDAtomTypeSet
CSDAtomTypeSetAP
 
typedef
utility::pointer::access_ptr
< CSDAtomTypeSet const > 
CSDAtomTypeSetCAP
 
typedef
utility::pointer::owning_ptr
< CSDAtomTypeSet
CSDAtomTypeSetOP
 
typedef
utility::pointer::owning_ptr
< CSDAtomTypeSet const > 
CSDAtomTypeSetCOP
 
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::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
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
< ResidueTypeSet
ResidueTypeSetOP
 
typedef
utility::pointer::access_ptr
< ResidueTypeSet const > 
ResidueTypeSetCAP
 
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_vrt,
  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  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 a AA string name and return its enum type 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, const Atom &atom_type)
 
static basic::Tracer tw ("core.chemical.AtomICoor", basic::t_warning)
 
std::ostream & operator<< (std::ostream &out, const AtomType &atom_type)
 
static basic::Tracer tr ("core.chemical")
 
static basic::Tracer tr ("core.chemical.ChemicalManager")
 
std::string const FA_STANDARD ("fa_standard")
 tag name for querying fullatom chemical type set. More...
 
std::string const CENTROID ("centroid")
 tag name for querying centroid 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...
 
static basic::Tracer tr ("core.chemical")
 
bool CSDAtomTypeSetcontains_atom_type (std::string const &atom_type_name) const
 
static basic::Tracer tr ("core.chemical")
 
static basic::Tracer tr ("core.chemical")
 
static basic::Tracer tr ("core.chemical")
 
std::ostream & operator<< (std::ostream &out, const Orbital &orbital)
 
static basic::Tracer tr ("core.chemical")
 
std::string const patch_linker ("_p:")
 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...
 
static basic::Tracer tr ("core.chemical")
 
std::string expand_icoor_atom_name (std::string name, ResidueType const &rsd)
 helper function More...
 
PatchOperationOP patch_operation_from_patch_file_line (std::string const &line)
 Virtual constructor, returns 0 if no match. More...
 
static basic::Tracer TR_PatchOperations ("core.chemical.PatchOperations.hh")
 
bool operator< (ResConnID const &lhs, ResConnID const &rhs)
 
bool operator== (ResConnID const &lhs, ResConnID const &rhs)
 
bool operator!= (ResConnID const &lhs, ResConnID const &rhs)
 
static basic::Tracer tr ("core.chemical")
 
id::AtomID atom_id_from_icoor_line (std::string const name, ResidueType const &rsd)
 helper fxn More...
 
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)
 function to write out a topology file given a residue type, can be used to More...
 
ResidueSelectorSingleOP residue_selector_single_from_line (std::string const &line)
 create a singe ResidueSelector from an input line. More...
 
ObjexxFCL::FArray2D_int get_residue_path_distances (ResidueType const &res)
 relies on class Graph to find all pairs shortest path information More...
 
static basic::Tracer tr ("core.chemical.ResidueType")
 
std::string strip_whitespace (std::string const &name)
 must be a better place for this, probably already exists! More...
 
static basic::Tracer tr ("core.chemical.ResidueTypeSet")
 
static basic::Tracer TR ("core.chemical.util")
 
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...
 
VariantType const UPPER_TERMINUS ("UPPER_TERMINUS")
 C-terminus cap. More...
 
VariantType const LOWER_TERMINUS ("LOWER_TERMINUS")
 N-terminus cap. 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 ("BRANCH_POINT")
 Variant type used for branched polymers and glycosylations. More...
 
VariantType const BRANCH_LOWER_TERMINUS ("BRANCH_LOWER_TERMINUS")
 Variant type used for branched polymers and glycosylations. More...
 
VariantType const ADDUCT ("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_O2STAR_HYDROGEN ("VIRTUAL_O2STAR_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 ("ACETYLATED_NTERMINUS")
 Acetylated N-terminus cap, written for creating amino acid dipeptides for NCAA rotamer libraries. More...
 
VariantType const METHYLATED_CTERMINUS ("METHYLATED_CTERMINUS")
 Methylated C-terminus cap, written for creating amino acid dipeptides for NCAA rotamer libraries. More...
 
VariantType const SC_ORBITALS ("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 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 SIDECHAIN_CONJUGATION ("SIDECHAIN_CONJUGATION")
 This is used for chemically conjugable residues (LYX, CYX) used for sidechain conjugation (like ubiquitination) More...
 

Variables

Real const MAX_CHEMICAL_BOND_TO_HYDROGEN_LENGTH = { 1.35 }
 Maximum distance between a heavy atom and a hydrogen atom to which it is chemically bound Set in .cc file. More...
 
std::string const RNA = "rna"
 tag name for querying RNA chemical type set. More...
 
std::string const FA_STANDARD
 
std::string const CENTROID
 
std::string const COARSE_TWO_BEAD
 
std::string const HYBRID_FA_STANDARD_CENTROID
 
std::string const COARSE_RNA
 
std::string const patch_linker
 the string used to create new residue names after patching More...
 
VariantType const UPPER_TERMINUS
 
VariantType const LOWER_TERMINUS
 
VariantType const CUTPOINT_UPPER
 
VariantType const CUTPOINT_LOWER
 
VariantType const DISULFIDE
 
VariantType const BRANCH_POINT
 
VariantType const BRANCH_LOWER_TERMINUS
 
VariantType const METHYLATION
 
VariantType const ADDUCT
 
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_O2STAR_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
 
VariantType const METHYLATED_CTERMINUS
 
VariantType const N_ACETYLATION
 
VariantType const C_METHYLAMIDATION
 
VariantType const SC_ORBITALS
 
VariantType const REPLONLY
 
VariantType const OOP_PRE
 
VariantType const OOP_POST
 
VariantType const HBS_PRE
 
VariantType const HBS_POST
 
VariantType const SIDECHAIN_CONJUGATION
 

Typedef Documentation

typedef std::map< std::string, int > core::chemical::AdductMap
typedef utility::keys::Key3Tuple< Size, Size, Size > core::chemical::bondangle_atom_set
typedef utility::keys::Key4Tuple< Size, Size, Size, Size > core::chemical::dihedral_atom_set
typedef utility::keys::Key3Tuple< Size, Size, Size > core::chemical::three_atom_set
typedef utility::keys::Key2Tuple< Size, Size > core::chemical::two_atom_set
typedef std::string core::chemical::VariantType

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

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_vrt 
aa_unk 
num_aa_types 
Enumerator
UnknownBond 
SingleBond 
DoubleBond 
TripleBond 
AromaticBond 
OrbitalBond 
Enumerator
SP2_HYBRID 
SP3_HYBRID 
RING_HYBRID 
UNKNOWN_HYBRID 
HYBRID_MAX 

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)

give a AA string name and return its enum type

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

Referenced by core::chemical::ResidueType::aa(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::flxbb::InterlockAroma::apply(), protocols::protein_interface_design::movers::Splice::apply(), protocols::flxbb::FilterStructs_TotalCharge::apply(), core::pack::task::operation::RestrictYSDesign::apply(), protocols::motifs::MotifDnaPacker::aromatic_motifs(), protocols::motifs::Motif::build_rotamers(), protocols::swa::rna::Correctly_position_cutpoint_phosphate_torsions(), core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_02_from_ASCII(), protocols::hotspot_hashing::HotspotStubSet::create_hotspot_after_pose(), protocols::motifs::MotifDnaPacker::expand_motifs(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::frag_picker::SidechainContactDistCutoff::initialize(), protocols::match::Matcher::initialize_from_file(), protocols::motifs::make_dna_mutations(), protocols::simple_filters::RotamerBoltzmannWeight::parse_def(), protocols::simple_filters::NeighborTypeFilter::parse_my_tag(), protocols::simple_filters::RotamerBoltzmannWeight::parse_my_tag(), core::pack::interaction_graph::SurfacePotential::read_average_res_hASA_database_file(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::read_from_file(), protocols::optimize_weights::PNatAAOptEPositionData::read_from_file(), protocols::noesy_assign::ResonanceList::read_from_stream(), core::scoring::P_AA::read_P_AA(), core::scoring::P_AA::read_P_AA_n(), core::scoring::P_AA::read_P_AA_pp(), core::chemical::ResidueType::rotamer_aa(), and protocols::fldsgn::potentials::SetAACompositionPotential::set_parameters().

AA core::chemical::aa_from_oneletter_code ( char  onelettercode)

give a 1 letter code and return the string name

References oneletter2aa().

Referenced by core::sequence::AnnotatedSequence::aa(), protocols::noesy_assign::ResonanceList::aa_from_resid(), core::pack::task::operation::RestrictAbsentCanonicalAASRLT::aas_to_keep(), protocols::forge::components::BDR::allowed_surface_aa(), protocols::forge::remodel::RemodelMover::allowed_surface_aa(), core::pose::Pose::annotated_sequence(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::swa::monte_carlo::RNA_AddMover::apply(), protocols::toolbox::task_operations::ThreadSequenceOperation::apply(), protocols::toolbox::task_operations::JointSequenceOperation::apply(), protocols::rna::RNA_HelixAssembler::build_on_base_pair(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_binding_data(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), core::scoring::dna::DirectReadoutPotential::DirectReadoutPotential(), core::pack::task::operation::DisallowIfNonnativeRLT::disallow_aas(), core::pack::task::operation::DisallowIfNonnative::disallow_aas(), protocols::frag_picker::scores::ProfileScoreSubMatrix::do_caching(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), protocols::flxbb::LayerDesignOperation::get_restrictions(), protocols::forge::remodel::RemodelData::getLoopsToBuildFromFile(), core::pack::task::PIKAA::initialize_from_tokens(), core::pack::task::NOTAA::initialize_from_tokens(), core::sequence::ProfSimScoringScheme::initialize_parameters(), core::pack::task::operation::RestrictAbsentCanonicalAAS::keep_aas(), protocols::sasa_scores::load_avge_polynomial_coefficients(), protocols::noesy_assign::MethylNameLibrary::load_database_table(), protocols::protein_interface_design::ReportPSSMDifferences::load_pssm_data(), protocols::optimize_weights::IterativeOptEDriver::load_pssm_data(), protocols::sasa_scores::load_sasapack_polynomial_coefficients(), protocols::protein_interface_design::movers::PlaceOnLoop::loop_length(), protocols::pmut_scan::PointMutScanDriver::make_mutant_structure(), core::fragment::make_pose_from_sequence_(), protocols::analysis::InterfaceAnalyzerMover::mut_to_gly(), core::scoring::nv::NVlookup::NVlookup(), core::fragment::picking_old::vall::VallResidue::order_vector(), protocols::frag_picker::VallResidue::order_vector(), protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::ParallelBetaPairingPreferenceFilter(), protocols::multistate_design::PosType::PosType(), protocols::pack_daemon::EntityFunc::process_AA_SET_line(), protocols::forge::components::BDR::process_continuous_design_string(), protocols::forge::remodel::RemodelMover::process_continuous_design_string(), protocols::forge::components::BDR::process_insert_design_string(), protocols::forge::remodel::RemodelMover::process_insert_design_string(), protocols::pack_daemon::EntityFunc::process_SET_CONDITION_line(), protocols::dna::DnaInterfacePacker::protein_scan(), core::sequence::MatrixScoringScheme::read_data(), core::io::PositionDdGInfo::read_ddg_predictions_file(), core::sequence::SequenceProfile::read_from_checkpoint(), core::sequence::SequenceProfile::read_from_file(), protocols::noesy_assign::ResonanceList::read_from_stream(), protocols::read_in_mutations(), core::scoring::methods::NMerPSSMEnergy::read_nmer_pssm(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::read_params(), core::pack::task::TARGET::residue_action(), core::pose::residue_types_from_sequence(), core::sequence::MatrixScoringScheme::score(), protocols::frag_picker::scores::HydrophobicityProfileSimilarity::score(), protocols::toolbox::task_operations::RestrictConservedLowDdgOperation::seqprof_wt_aa(), protocols::noesy_assign::FragsToAtomDist::swap_atoms(), and core::sequence::MatrixScoringScheme::values_for_aa().

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

Add additional parameter files not present in <atom-set-name>/extras.txt. Called by ChemicalManager at time of AtomTypeSet creation.

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

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

VariantType const core::chemical::ADDUCT ( "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 
)
VariantType const core::chemical::BRANCH_LOWER_TERMINUS ( "BRANCH_LOWER_TERMINUS"  )

Variant type used for branched polymers and glycosylations.

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

Variant type used for branched polymers and glycosylations.

VariantType const core::chemical::C_METHYLAMIDATION ( "C_METHYLAMIDATION"  )
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(), 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::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.

bool core::chemical::CSDAtomTypeSetcontains_atom_type ( std::string const &  atom_type_name) const
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

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 ( std::map< std::string, int > const &  add_map,
ResidueTypeCOPs const &  rsd_types 
)

Make sure requested adducts exist in some residue.

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

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

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

Make sure any adducts requested actually exist.

Make sure requested adducts exist in some residue.

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

Referenced by core::chemical::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.

ObjexxFCL::FArray2D_int core::chemical::get_residue_path_distances ( ResidueType const &  res)
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"  )
VariantType const core::chemical::LOWER_TERMINUS ( "LOWER_TERMINUS"  )

N-terminus cap.

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

Modify atom_type properties from the command line. Called by ChemicalManager at time of AtomTypeSet creation.

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

Referenced by core::chemical::ChemicalManager::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 protocols::noesy_assign::MethylNames::aa_name(), core::pack::task::ResidueLevelTask_::allow_noncanonical_aa(), core::pose::Pose::annotated_sequence(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::swa::rna::base_atoms_square_deviation(), protocols::fldsgn::filters::CoreDunbrackFilter::compute(), core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_10_from_ASCII(), protocols::dna::dna_base_partner(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_atom(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_magnetic_anisotropy_deriv_for_src_base(), protocols::swa::rna::get_max_centroid_to_atom_distance(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), protocols::swa::rna::Get_num_side_chain_atom_from_res_name(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_ring_current_deriv_for_src_base(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::swa::rna::Is_virtual_base(), protocols::protein_interface_design::movers::PlaceOnLoop::loop_length(), protocols::toolbox::pose_metric_calculators::SequenceComparison::measure_sequence_recovery(), operator<<(), protocols::noesy_assign::MethylNameLibrary::operator[](), protocols::optimize_weights::IterativeOptEDriver::output_weighted_unfolded_energies(), protocols::swa::rna::phosphate_base_phosphate_square_deviation(), protocols::swa::rna::phosphate_square_deviation(), 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::RotamericSingleResidueDunbrackLibrary< T >::read_from_file(), protocols::noesy_assign::ResonanceList::read_from_stream(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::read_params(), core::chemical::ResidueDatabaseIO::read_residue_type(), read_topology_file(), core::scoring::methods::EnvSmoothEnergy::representative_atom_name(), core::scoring::methods::MembraneEnvSmoothEnergy::representative_atom_name(), core::pack::task::ResidueLevelTask_::restrict_absent_nas(), protocols::swa::rna::setup_suite_atom_id_map(), protocols::swa::rna::suite_square_deviation(), protocols::swa::rna::StepWiseRNA_PoseSetup::verify_protonated_H1_adenosine_variants(), and protocols::noesy_assign::Resonance::write_to_stream().

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

bool core::chemical::operator== ( ResConnID const &  lhs,
ResConnID const &  rhs 
)
std::istream & core::chemical::operator>> ( std::istream &  is,
AA &  aa 
)

input operator for AA enum type

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

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

AdductMap core::chemical::parse_adduct_string ( utility::options::StringVectorOption &  add_vec)

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

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

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

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 protocols::swa::phi(), and tr().

Referenced by case_from_lines().

VariantType const core::chemical::PHOSPHORYLATION ( "PHOSPHORYLATION"  )
VariantType const core::chemical::PROTONATED ( "PROTONATED"  )
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 rosetta_database/chemical/residue_type_sets/fa_standard/residue_types/???.params These files contain information about each basic ResidueType which can be patched to created various variant types.

References core::id::D, protocols::abinitio::filename(), get_residue_path_distances(), name_from_aa(), protocols::swa::phi(), protocols::swa::rotate(), core::kinematics::Stub::spherical(), strip_whitespace(), and tr().

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

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

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

create a singe ResidueSelector from an input line.

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

std::string core::chemical::residue_type_all_patches_name ( ResidueType const &  rsd_type)
std::string core::chemical::residue_type_base_name ( ResidueType const &  rsd_type)
core::chemical::ResidueTypeSetCAP core::chemical::rsd_set_from_cmd_line ( )
VariantType const core::chemical::SC_ORBITALS ( "SC_ORBITALS"  )
utility::vector1< std::string > core::chemical::setup_aa2name ( )

setup the vector that maps AA enum to string name

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

Referenced by aa2oneletter().

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

setup the map that converts string name to AA enum

References aa_ala, aa_arg, aa_asn, aa_asp, aa_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_val, aa_vrt, na_ade, na_cyt, na_gua, na_rad, na_rcy, na_rgu, na_thy, and na_ura.

Referenced by name2aa().

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

setup the map the converts one letter char to AA enum

References aa_ala, aa_arg, aa_asn, aa_asp, aa_cys, aa_gln, aa_glu, aa_gly, aa_his, aa_ile, aa_leu, aa_lys, aa_met, aa_phe, aa_pro, aa_ser, aa_thr, aa_trp, aa_tyr, aa_unk, aa_val, 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

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

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

Referenced by core::chemical::ResidueType::add_actcoord_atom(), core::chemical::ResidueType::add_atom(), core::chemical::AtomTypeSet::add_parameters_from_file(), core::chemical::ResidueType::add_property(), core::chemical::Patch::apply(), core::scoring::hbonds::assign_abase_derivs(), core::chemical::ResidueType::atom_index(), core::scoring::automorphic_rmsd(), core::scoring::CA_gdtmm(), core::scoring::CA_maxsub(), core::scoring::CA_rmsd(), core::scoring::CA_rmsd_symmetric(), core::chemical::ResidueType::calculate_icoor(), protocols::noesy_assign::CrossPeakList::calibrate(), protocols::canonical_sampling::canonical_sampling_main(), core::chemical::ResidueType::debug_dump_icoor(), core::chemical::ResidueType::delete_property(), core::scoring::gdtha(), core::scoring::gdtsc(), core::scoring::hbonds::hb_energy_deriv(), core::scoring::hbonds::hbond_compute_energy(), core::scoring::hbonds::make_hbBasetoAcc_unitvector(), OPT_1GRP_KEY(), patch_operation_from_patch_file_line(), core::chemical::ResidueType::print_bondangles(), core::chemical::ResidueType::print_dihedrals(), core::chemical::ResidueType::print_pretty_path_distances(), core::chemical::CSDAtomTypeSet::read_file(), core::chemical::MMAtomTypeSet::read_file(), core::chemical::ElementSet::read_file(), core::chemical::Patch::read_file(), core::chemical::AtomTypeSet::read_file(), core::fragment::ConstantLengthFragSet::read_fragment_stream(), read_topology_file(), core::chemical::ResidueType::report_adducts(), core::chemical::ChemicalManager::residue_type_set(), core::chemical::ResidueType::set_lower_connect_atom(), core::chemical::ResidueType::set_upper_connect_atom(), core::chemical::ResidueType::setup_atom_ordering(), core::fragment::SecstructSRFD::steal(), protocols::noesy_assign::CrossPeakList::update_decoy_compatibility_score(), protocols::vip::VIP_Mover::VIP_Mover(), core::scoring::xyz_gdtmm(), and core::chemical::ResidueType::~ResidueType().

static basic::Tracer core::chemical::tr ( "core.chemical.ChemicalManager"  )
static
static basic::Tracer core::chemical::tr ( "core.chemical.ResidueTypeSet"  )
static
static basic::Tracer core::chemical::tr ( "core.chemical"  )
static
static basic::Tracer core::chemical::tr ( "core.chemical.ResidueType"  )
static
static basic::Tracer core::chemical::tr ( "core.chemical"  )
static
static basic::Tracer core::chemical::TR_PatchOperations ( "core.chemical.PatchOperations.hh"  )
static
VariantType const core::chemical::TRIMETHYLATION ( "TRIMETHYLATION"  )
static basic::Tracer core::chemical::tw ( "core.chemical.AtomICoor"  ,
basic::t_warning   
)
static
VariantType const core::chemical::UPPER_TERMINUS ( "UPPER_TERMINUS"  )

C-terminus cap.

VariantType const core::chemical::VIRTUAL_O2STAR_HYDROGEN ( "VIRTUAL_O2STAR_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)

function to write out a topology file given a residue type, can be used to

writes a .params file from a given ResidueType object

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(), protocols::abinitio::filename(), core::chemical::ResidueType::force_nbr_atom_orient(), core::chemical::ResidueType::icoor(), core::chemical::ResidueType::is_aromatic(), core::chemical::ResidueType::is_charged(), core::chemical::ResidueType::is_DNA(), core::chemical::ResidueType::is_ligand(), core::chemical::ResidueType::is_lower_terminus(), 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::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::AtomICoor::phi(), core::chemical::ResidueType::proton_chi_extra_samples(), core::chemical::ResidueType::proton_chi_samples(), 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
VariantType const core::chemical::ACETYLATION
VariantType const core::chemical::ADDUCT
VariantType const core::chemical::BRANCH_LOWER_TERMINUS
VariantType const core::chemical::BRANCH_POINT
VariantType const core::chemical::C_METHYLAMIDATION
VariantType const core::chemical::CARBOXYLATION
std::string const core::chemical::CENTROID

Referenced by protocols::abinitio::StructureStore::add(), protocols::topology_broker::add_cmdline_claims(), protocols::flexpep_docking::FlexPepDockingProtocol::addLowResStatistics(), core::pose::addVirtualResAsRoot(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply(), protocols::ub_e2c::ubi_e2c_modeler::apply(), protocols::loops::loop_closure::ccd::ShortLoopClosure::apply(), protocols::medal::MedalMover::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::domain_assembly::AssembleLinkerMover::apply(), protocols::loophash::Mover_LoopHashRefine::apply(), protocols::loophash::FastGapMover::apply(), protocols::docking::DockingEnsemblePrepackProtocol::apply(), protocols::floppy_tail::FloppyTailMover::apply(), protocols::antibody2::ModelCDRH3::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::loophash::LoopHashDiversifier::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::jd2::parser::FragmentReader::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::loophash::LoopHashLibrary::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::antibody::GraftMover::apply(), protocols::antibody::CDRH3Modeler::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::grafting::AnchoredGraftMover::apply(), protocols::antibody::CloseOneMover::apply(), protocols::anchored_design::AnchoredPerturbMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::components::VarLengthBuild::apply(), core::scoring::AtomVDW::AtomVDW(), protocols::analysis::InterfaceAnalyzerMover::calc_centroid_dG(), core::import_pose::centroid_pose_from_pdb(), protocols::simple_filters::EnergyPerResidueFilter::compute(), protocols::simple_filters::ScoreTypeFilter::compute(), protocols::simple_filters::ResidueSetChainEnergyFilter::compute(), protocols::simple_moves::GunnCost::compute_gunn(), protocols::swa::StepWiseScreener::convert_to_centroid(), protocols::swa::protein::StepWiseProteinScreener::convert_to_centroid(), core::scoring::saxs::SAXSEnergyCreator::create_energy_method(), core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph(), protocols::loophash::MPI_LoopHashRefine_Master::create_loophash_WUs(), core::scoring::disulfides::CentroidDisulfidePotential::disulfide_params(), protocols::abinitio::AbrelaxApplication::do_rerun(), protocols::ub_e2c::ubi_e2c_modeler::evaluate_native(), core::io::raw_data::DecoyStruct::fill_pose(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), protocols::noesy_assign::NoesyModule::generate_constraint_files(), protocols::abinitio::AbrelaxApplication::generate_extended_pose(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), protocols::seeded_abinitio::GrowPeptides::grow_from_verteces(), protocols::constraints_additional::BindingSiteConstraint::init(), protocols::topology_broker::RigidChunkClaimer::init_after_reading(), protocols::ub_e2c::ubi_e2c_modeler::init_d77_perturbation(), protocols::jd2::archive::ArchiveBase::init_from_decoy_set(), protocols::ub_e2c::ubi_e2c_modeler::init_k48r_perturbation(), protocols::swa::StepWiseScreener::initialize_ghost_pose(), protocols::swa::protein::StepWiseProteinScreener::initialize_ghost_pose(), core::conformation::Conformation::is_centroid(), protocols::docking::DockingEnsemble::load_ensemble(), protocols::features::PoseConformationFeatures::load_sequence(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::loophash::LoopHashRelaxProtocol::manual_call(), protocols::ub_e2c::ubi_e2c_modeler::monoub_apply(), protocols::ub_e2c::ubi_e2c_modeler::monoub_first_perturbation(), protocols::topology_broker::RigidChunkClaimer::new_decoy(), protocols::scoring::methods::saxs::PDDFEnergy::PDDFEnergy(), protocols::checkpoint::pose_from_binary_silent_file(), core::import_pose::pose_from_pdb(), core::import_pose::poseOPs_from_pdbs(), protocols::RBSegmentRelaxImpl::RBSegmentRelaxImpl(), protocols::topology_broker::CoordConstraintClaimer::read_cst_pose(), protocols::topology_broker::StartStructClaimer::read_tag(), protocols::comparative_modeling::rebuild_loops_until_closed(), protocols::toolbox::pose_metric_calculators::ClashCountCalculator::recompute(), protocols::toolbox::pose_metric_calculators::FragQualCalculator::recompute(), protocols::checkpoint::CheckPointer::recover_checkpoint(), core::scoring::disulfides::CentroidDisulfideEnergy::residue_pair_energy(), core::chemical::ChemicalManager::residue_type_set(), protocols::ub_e2c::ubi_e2c_modeler::restore_cter(), protocols::flexpep_docking::FlexPepDockingAbInitio::restorePSER(), protocols::topology_broker::RigidChunkClaimer::RigidChunkClaimer(), core::pack::dunbrack::RotamerLibrary::rsd_library_already_loaded(), protocols::loophash::WorkUnit_LoopHash::run(), protocols::abinitio::run_boinc_debug(), protocols::symmetric_docking::SymDockProtocol::score_only(), protocols::abinitio::AbrelaxApplication::setup(), protocols::abinitio::AbrelaxApplication::setup_fold(), protocols::constraints_additional::BindingSiteConstraint::setup_for_scoring(), protocols::docking::TemperedDocking::setup_objects(), protocols::docking::DockingProtocol::setup_objects(), protocols::abinitio::ResolutionSwitcher::start_pose(), protocols::star::to_centroid(), protocols::flexpep_docking::FlexPepDockingLowRes::to_centroid(), protocols::flexpep_docking::FlexPepDockingAbInitio::to_centroid(), protocols::medal::to_centroid(), and protocols::jobdist::universal_main().

VariantType const core::chemical::CENTROID_HA
std::string const core::chemical::COARSE_RNA
std::string const core::chemical::COARSE_TWO_BEAD
VariantType const core::chemical::CUTPOINT_LOWER

Referenced by protocols::abinitio::KinematicControl::add_chainbreak_variants(), protocols::topology_broker::TopologyBroker::add_chainbreak_variants(), protocols::jumping::JumpSample::add_chainbreaks(), protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps(), protocols::ligand_docking::MinimizeBackbone::add_cut_points(), core::util::add_cutpoint_variants(), protocols::forge::methods::add_cutpoint_variants(), protocols::loops::add_cutpoint_variants(), protocols::loops::add_single_cutpoint_variant(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::rna::RNA_LoopCloser::apply(), protocols::antibody2::LHSnugFitLegacy::apply(), protocols::antibody2::H3PerturbCCD::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::antibody2::LHRepulsiveRampLegacy::apply(), protocols::grafting::AnchoredGraftMover::apply(), protocols::antibody::LoopRlxMover::apply(), protocols::swa::rna::StepWiseRNA_PoseSetup::apply_cutpoint_variants(), protocols::swa::StepWisePoseSetup::apply_cutpoint_variants(), protocols::loops::apply_sequence_mapping(), protocols::swa::rna::apply_virtual_rna_residue_variant_type(), core::conformation::Conformation::backbone_torsion_angle_atoms(), protocols::idealize::basic_idealize(), protocols::LoopRebuild::build_loop_with_ccd_closure(), core::pack::rotamer_set::RotamerSets::build_rotamers(), protocols::analysis::LoopAnalyzerMover::calculate_all_chainbreaks(), protocols::swa::rna::StepWiseRNA_ResidueSampler::Chain_break_screening_general(), protocols::topology_broker::TopologyBroker::check_chainbreak_variants(), protocols::rna::RNA_LoopCloser::check_closure(), protocols::antibody::CloseOneMover::close_one_loop_stem(), protocols::abinitio::copy_side_chains(), protocols::forge::methods::cyclize_pose(), protocols::anchored_design::dump_cutpoint_info(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), protocols::swa::rna::StepWiseRNA_Minimizer::figure_out_actual_five_prime_chain_break_res(), protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_dof_ids_and_offsets(), protocols::swa::protein::StepWiseProteinLoopBridger::figure_out_loop(), protocols::swa::protein::StepWiseProteinCCD_Closer::figure_out_loop(), protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_which_cutpoints_were_affected(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), core::scoring::methods::DistanceChainbreakEnergy::finalize_total_energy(), core::scoring::methods::LinearChainbreakEnergy::finalize_total_energy(), protocols::seeded_abinitio::DefineMovableLoops::find_loops(), protocols::seeded_abinitio::CloseFold::find_loops(), protocols::swa::rna::get_default_allowed_bulge_res(), protocols::rna::RNA_LoopCloser::get_extra_cutpoints(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::get_previously_closed_cutpoint_from_imported_silent_file(), protocols::swa::Is_close_chain_break(), protocols::swa::rna::Is_close_chain_break(), core::scoring::rna::RNA_TorsionPotential::Is_cutpoint_closed_torsion(), core::scoring::rna::is_cutpoint_open(), core::scoring::methods::is_lower_cutpoint(), protocols::rna::RNA_LoopCloser::local_minimize_at_chainbreaks(), core::scoring::methods::IdealParametersDatabase::lookup_angle_legacy(), core::scoring::methods::IdealParametersDatabase::lookup_bondangle_buildideal(), protocols::antibody2::RefineOneCDRLoopCentroid::loop_centroid_relax(), protocols::antibody::CDRH3Modeler::loop_centroid_relax(), protocols::antibody::CDRH3Modeler::loop_fa_relax(), protocols::forge::methods::make_star_foldtree(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::forge::build::BuildManager::modify(), protocols::swa::rna::remove_chain_break_jump_point(), protocols::jumping::JumpSample::remove_chainbreaks(), protocols::toolbox::pose_manipulation::remove_chainbreaks_according_to_jumps(), protocols::rna::remove_cutpoint_closed(), core::util::remove_cutpoint_variants(), protocols::forge::methods::remove_cutpoint_variants(), protocols::loops::remove_cutpoint_variants(), protocols::rna::remove_cutpoints_closed(), protocols::rna::RNA_LoopCloser::remove_variants_at_extra_cutpoints(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::antibody::AntibodyModeler::repulsive_ramp(), protocols::rna::RNA_LoopCloser::rna_ccd_close(), protocols::antibody::CDRH3Modeler::scored_frag_close(), protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(), protocols::seeded_abinitio::SeedFoldTree::set_foldtree(), protocols::loops::set_loop_cutpoint_in_pose_fold_tree(), protocols::swa::rna::setup_chain_break_jump_point(), protocols::rna::RNA_StructureParameters::setup_chainbreak_variants(), protocols::jumping::MembraneJump::setup_fold_tree(), core::conformation::setup_links(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::rna::RNA_LoopCloser::setup_variants_at_extra_cutpoints(), protocols::rna::RNA_StructureParameters::setup_virtual_phosphate_variants(), protocols::rna::RNA_StructureParameters::setup_virtual_phosphate_variants_OLD(), protocols::antibody::AntibodyModeler::snugfit_mcm_protocol(), protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(), and protocols::rna::virtualize_5prime_phosphates().

VariantType const core::chemical::CUTPOINT_UPPER

Referenced by protocols::abinitio::KinematicControl::add_chainbreak_variants(), protocols::topology_broker::TopologyBroker::add_chainbreak_variants(), protocols::jumping::JumpSample::add_chainbreaks(), protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps(), protocols::ligand_docking::MinimizeBackbone::add_cut_points(), core::util::add_cutpoint_variants(), protocols::forge::methods::add_cutpoint_variants(), protocols::loops::add_cutpoint_variants(), protocols::loops::add_single_cutpoint_variant(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::rna::RNA_LoopCloser::apply(), protocols::antibody2::LHSnugFitLegacy::apply(), protocols::antibody2::H3PerturbCCD::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::antibody2::LHRepulsiveRampLegacy::apply(), protocols::grafting::AnchoredGraftMover::apply(), protocols::antibody::LoopRlxMover::apply(), protocols::swa::rna::StepWiseRNA_PoseSetup::apply_cutpoint_variants(), protocols::swa::StepWisePoseSetup::apply_cutpoint_variants(), protocols::loops::apply_sequence_mapping(), protocols::swa::rna::StepWiseRNA_PoseSetup::apply_virtual_phosphate_variants(), protocols::swa::StepWisePoseSetup::apply_virtual_phosphate_variants(), protocols::swa::rna::apply_virtual_rna_residue_variant_type(), core::conformation::Conformation::backbone_torsion_angle_atoms(), protocols::idealize::basic_idealize(), protocols::LoopRebuild::build_loop_with_ccd_closure(), core::pack::rotamer_set::RotamerSets::build_rotamers(), protocols::analysis::LoopAnalyzerMover::calculate_all_chainbreaks(), protocols::swa::rna::StepWiseRNA_ResidueSampler::Chain_break_screening_general(), protocols::topology_broker::TopologyBroker::check_chainbreak_variants(), protocols::rna::RNA_LoopCloser::check_closure(), protocols::antibody::CloseOneMover::close_one_loop_stem(), protocols::abinitio::copy_side_chains(), protocols::forge::methods::cyclize_pose(), protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo::diversify_backbone_only_rotamers(), protocols::anchored_design::dump_cutpoint_info(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), protocols::swa::rna::StepWiseRNA_Minimizer::figure_out_actual_five_prime_chain_break_res(), protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_dof_ids_and_offsets(), protocols::swa::protein::StepWiseProteinLoopBridger::figure_out_loop(), protocols::swa::protein::StepWiseProteinCCD_Closer::figure_out_loop(), protocols::coarse_rna::CoarseRNA_LoopCloser::figure_out_which_cutpoints_were_affected(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), core::scoring::methods::DistanceChainbreakEnergy::finalize_total_energy(), core::scoring::methods::LinearChainbreakEnergy::finalize_total_energy(), protocols::seeded_abinitio::DefineMovableLoops::find_loops(), protocols::seeded_abinitio::CloseFold::find_loops(), protocols::swa::rna::get_default_allowed_bulge_res(), protocols::rna::RNA_LoopCloser::get_extra_cutpoints(), protocols::swa::rna::StepWiseRNA_JobParameters_Setup::get_previously_closed_cutpoint_from_imported_silent_file(), protocols::swa::Is_close_chain_break(), protocols::swa::rna::Is_close_chain_break(), core::scoring::rna::RNA_TorsionPotential::Is_cutpoint_closed_torsion(), core::scoring::rna::is_cutpoint_open(), core::scoring::methods::is_upper_cutpoint(), protocols::rna::RNA_LoopCloser::local_minimize_at_chainbreaks(), core::scoring::methods::IdealParametersDatabase::lookup_angle_legacy(), core::scoring::methods::IdealParametersDatabase::lookup_bondangle_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), protocols::antibody2::RefineOneCDRLoopCentroid::loop_centroid_relax(), protocols::antibody::CDRH3Modeler::loop_centroid_relax(), protocols::antibody::CDRH3Modeler::loop_fa_relax(), protocols::forge::methods::make_star_foldtree(), protocols::enzdes::EnzdesFlexibleRegion::minimize_region(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::forge::build::BuildManager::modify(), protocols::swa::rna::remove_chain_break_jump_point(), protocols::jumping::JumpSample::remove_chainbreaks(), protocols::toolbox::pose_manipulation::remove_chainbreaks_according_to_jumps(), protocols::rna::remove_cutpoint_closed(), core::util::remove_cutpoint_variants(), protocols::forge::methods::remove_cutpoint_variants(), protocols::loops::remove_cutpoint_variants(), protocols::rna::remove_cutpoints_closed(), protocols::rna::RNA_LoopCloser::remove_variants_at_extra_cutpoints(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::antibody::AntibodyModeler::repulsive_ramp(), protocols::rna::RNA_LoopCloser::rna_ccd_close(), protocols::antibody::CDRH3Modeler::scored_frag_close(), protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(), protocols::seeded_abinitio::SeedFoldTree::set_foldtree(), protocols::loops::set_loop_cutpoint_in_pose_fold_tree(), protocols::swa::rna::setup_chain_break_jump_point(), protocols::rna::RNA_StructureParameters::setup_chainbreak_variants(), protocols::jumping::MembraneJump::setup_fold_tree(), core::conformation::setup_links(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::rna::RNA_LoopCloser::setup_variants_at_extra_cutpoints(), protocols::rna::RNA_StructureParameters::setup_virtual_phosphate_variants(), protocols::rna::RNA_StructureParameters::setup_virtual_phosphate_variants_OLD(), protocols::antibody::AntibodyModeler::snugfit_mcm_protocol(), protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(), and protocols::rna::virtualize_5prime_phosphates().

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(), protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::protein_interface_design::movers::Splice::apply(), core::io::pdb::build_pose_as_is1(), core::conformation::change_cys_state(), protocols::sasa_scores::compute_avge_scores(), protocols::sasa_scores::compute_sasapack_scores(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(), 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::FullatomDisulfideEnergyContainer::find_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::conformation::Conformation::fix_disulfides(), protocols::protein_interface_design::movers::Splice::fold_tree(), core::conformation::form_disulfide(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), protocols::enzdes::EnzdesFlexBBProtocol::modified_task(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), and protocols::swa::StepWisePoseSetup::setup_disulfides().

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

Referenced by core::chemical::IdealBondLengthSet::add_bond_length(), core::pose::addVirtualResAsRoot(), protocols::topology_broker::MembraneTopologyClaimer::addVirtualResAsRootMembrane(), protocols::relax::MiniRelax::apply(), protocols::seeded_abinitio::GrowPeptides::apply(), protocols::protein_interface_design::movers::DockAndRetrieveSidechains::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::ligand_docking::AddHydrogen::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::ub_e2c::ubi_e2c_modeler::apply(), protocols::simple_filters::SAXSScoreFilter::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::domain_assembly::AssembleLinkerMover::apply(), protocols::antibody2::ModelCDRH3::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::loophash::LoopHashDiversifier::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::match::MatcherMover::apply(), protocols::antibody::GraftMover::apply(), protocols::antibody::CDRH3Modeler::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::symmetric_docking::SymDockProtocol::apply(), protocols::relax::FastRelax::apply(), protocols::flxbb::FlxbbDesign::apply(), protocols::antibody::CloseOneMover::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::relax::FastRelax::batch_apply(), core::import_pose::build_pose_as_is2(), core::io::pdb::build_pose_from_pdb_as_is(), protocols::MakeRotLib::calc_std_dev(), protocols::docking::DockingEnsemble::calculate_highres_ref_energy(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::forge::components::BDR::centroid_build(), protocols::forge::remodel::RemodelMover::centroid_build(), protocols::optimize_weights::IterativeOptEDriver::collect_ddG_of_mutation_data(), protocols::simple_filters::EnergyPerResidueFilter::compute(), protocols::simple_filters::ScoreTypeFilter::compute(), protocols::simple_filters::ResidueSetChainEnergyFilter::compute(), core::scoring::geometric_solvation::compute_exact_geosol(), protocols::toolbox::pose_manipulation::construct_poly_ala_pose(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(), core::chemical::IdealBondLengthSet::contains_bond_length(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoASP(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoGLU(), core::scoring::geometric_solvation::DatabaseOccSolEne::DatabaseOccSolEne(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::abinitio::AbrelaxApplication::do_rerun(), protocols::enzdes::EnzdesBaseProtocol::EnzdesBaseProtocol(), core::scoring::ScoringManager::etable(), protocols::ub_e2c::ubi_e2c_modeler::evaluate_native(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::ExactOccludedHbondSolEnergy(), core::io::silent::SilentStruct::fill_pose(), core::import_pose::PDBSilentStruct::fill_pose(), core::io::raw_data::DecoyStruct::fill_pose(), core::io::silent::BinaryProteinSilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), protocols::protein_interface_design::movers::DisulfideMover::form_disulfide(), core::conformation::form_disulfide(), protocols::swa::protein::generate_beta_database_test(), protocols::ligand_docking::generate_unique_name(), core::chemical::IdealBondLengthSet::get_bond_length(), protocols::simple_moves::chiral::get_chiral_residue_type(), protocols::enzdes::AddOrRemoveMatchCsts::get_EnzConstraintIO_for_cstfile(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::get_instance(), 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(), protocols::simple_moves::AddCavitiesMover::get_suck_res(), protocols::motifs::MotifSearch::incorporate_motifs(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::match::initialize_atomtype_2_probe_radius_map(), protocols::match::MatcherTask::initialize_enzdes_input_data_from_command_line(), core::conformation::Conformation::is_fullatom(), protocols::ligand_docking::LigandDockMain::LigandDockMain(), protocols::features::PoseConformationFeatures::load_sequence(), protocols::loophash::LoopHashRelaxProtocol::manual_call(), core::scoring::ScoringManager::memb_etable(), protocols::MakeRotLib::min_rotamers(), protocols::ub_e2c::ubi_e2c_modeler::monoub_apply(), protocols::motifs::Motif::Motif(), core::conformation::orient_residue_for_ideal_bond(), protocols::frag_picker::FragmentCandidate::output_silent(), protocols::fldsgn::BluePrintBDR::parse_my_tag(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), protocols::checkpoint::pose_from_binary_silent_file(), protocols::comparative_modeling::ThreadingJobInputter::pose_from_job(), 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(), protocols::motifs::MotifSearch::protein_dna_motif(), protocols::motifs::LigandMotifSearch::protein_dna_motif(), protocols::jumping::ResiduePairJumpSetup::read_file(), protocols::topology_broker::FibrilModelingClaimer::read_tag(), protocols::topology_broker::RigidChunkClaimer::read_tag(), protocols::topology_broker::MetalloClaimer::read_tag(), protocols::abinitio::IterativeBase::reassign_noesy_data(), protocols::checkpoint::CheckPointer::recover_checkpoint(), protocols::features::RotamerFeatures::report_features(), protocols::relax::WorkUnit_BatchRelax_and_PostRescore::rescore_all_decoys(), core::chemical::ChemicalManager::residue_type_set(), protocols::rbsegment_relax::restore_pose_from_rbsegs(), core::pack::dunbrack::RotamerLibrary::rsd_library_already_loaded(), core::pack::task::operation::util::select_coord_for_residue(), protocols::forge::constraints::InvrotTreeRCG::set_cstfile(), protocols::relax::WorkUnit_BatchRelax_and_PostRescore::set_defaults(), protocols::pack_daemon::DaemonSet::set_entity_resfile(), protocols::ligand_docking::LigandDesign::set_fragments(), protocols::ligand_docking::GrowLigand::set_fragments(), protocols::abinitio::AbrelaxApplication::setup_fold(), protocols::docking::DockingProtocol::setup_objects(), protocols::rbsegment_relax::setup_pose_from_rbsegs(), protocols::motifs::single_residue_from_stream(), protocols::topology_broker::TopologyBroker::switch_to_fullatom(), and protocols::flexpep_docking::FlexPepDockingLowRes::to_allatom().

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
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::etable::BaseEtableEnergy< Derived >::atomic_interaction_cutoff(), and core::scoring::hackelec::HackElecEnergy::hydrogen_interaction_cutoff().

VariantType const core::chemical::METHYLATED_CTERMINUS
VariantType const core::chemical::METHYLATION
VariantType const core::chemical::N_ACETYLATION
VariantType const core::chemical::OOP_POST
VariantType const core::chemical::OOP_PRE
std::string const core::chemical::patch_linker

the string used to create new residue names after patching

Referenced by core::chemical::Patch::apply(), residue_type_all_patches_name(), and residue_type_base_name().

VariantType const core::chemical::PHOSPHORYLATION
VariantType const core::chemical::PROTONATED
VariantType const core::chemical::REPLONLY

Referenced by protocols::simple_moves::RepulsiveOnlyMover::apply(), 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::scoring::etable::TableLookupEtableEnergy::eval_intrares_energy(), core::scoring::etable::AnalyticEtableEnergy::eval_intrares_energy(), core::scoring::methods::SmoothEnvEnergy::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::scoring::methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::PairEnergy::eval_residue_pair_derivatives(), core::scoring::disulfides::FullatomDisulfideEnergy::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::OmegaTetherEnergy::residue_energy(), core::scoring::methods::RamachandranEnergy::residue_energy(), core::scoring::methods::YHHPlanarityEnergy::residue_energy(), core::scoring::methods::P_AA_pp_Energy::residue_energy(), core::scoring::methods::SmoothEnvEnergy::residue_energy(), core::pack::dunbrack::DunbrackEnergy::residue_energy(), core::scoring::methods::EnvEnergy::residue_energy(), core::scoring::methods::ReferenceEnergy::residue_energy(), core::scoring::methods::ReferenceEnergyNoncanonical::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::disulfides::DisulfideMatchingEnergy::residue_pair_energy(), core::scoring::disulfides::CentroidDisulfideEnergy::residue_pair_energy(), core::scoring::methods::SmoothCenPairEnergy::residue_pair_energy(), core::scoring::methods::CenPairEnergy::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_Energy_Fast::setup_for_derivatives(), and core::scoring::disulfides::FullatomDisulfideEnergy::setup_for_minimizing_for_residue_pair().

std::string const core::chemical::RNA = "rna"
VariantType const core::chemical::SC_ORBITALS
VariantType const core::chemical::SIDECHAIN_CONJUGATION
VariantType const core::chemical::SPECIAL_ROT
VariantType const core::chemical::SULFATION
VariantType const core::chemical::TRIMETHYLATION
VariantType const core::chemical::UPPER_TERMINUS
VariantType const core::chemical::VIRTUAL_O2STAR_HYDROGEN
VariantType const core::chemical::VIRTUAL_PHOSPHATE
VariantType const core::chemical::VIRTUAL_RNA_RESIDUE