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core::chemical::ResidueTypeBase Class Referenceabstract

A base class for definiting types of residues. More...

#include <ResidueTypeBase.hh>

Inheritance diagram for core::chemical::ResidueTypeBase:
Inheritance graph
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Public Member Functions

TypeSetMode mode () const
 
AtomTypeSet const & atom_type_set () const
 access by reference the atomset for which this residue is constructed More...
 
AtomTypeSetCOP atom_type_set_ptr () const
 access by const pointer the atomset for which this residue is constructed More...
 
ElementSet const & element_set () const
 access by reference the element set for which this residue is constructed More...
 
ElementSetCOP element_set_ptr () const
 access by const pointer the element set for which this residue is constructed More...
 
MMAtomTypeSetCOP mm_atom_types_ptr () const
 
gasteiger::GasteigerAtomTypeSetCOP gasteiger_atom_typeset () const
 
void set_gasteiger_atom_typeset (gasteiger::GasteigerAtomTypeSetCOP setting)
 
orbitals::OrbitalTypeSetCOP orbital_types_ptr () const
 Get the MM atom_type for this atom by its index number in this residue. More...
 
void set_orbital_typeset (orbitals::OrbitalTypeSetCOP setting)
 
bool has_orbital_types () const
 Does this residue type define orbital types? More...
 
virtual Size natoms () const =0
 number of atoms More...
 
virtual Size nheavyatoms () const =0
 number of heavy atoms More...
 
virtual Size nbonds () const =0
 number of bonds More...
 
virtual Size n_virtual_atoms () const =0
 Counts the number of virtual atoms and returns the count. More...
 
virtual bool has (std::string const &atom_name) const =0
 is this atom present in this residue? More...
 
signed long int net_formal_charge () const
 Get the nominal net formal charge on this residue type. More...
 
void net_formal_charge (signed long int charge_in)
 Set the nominal net formal charge on this residue type. More...
 
virtual void show_all_atom_names (std::ostream &out) const =0
 
utility::vector1< std::string >
const & 
get_metal_binding_atoms () const
 
std::string const & get_disulfide_atom_name () const
 Gets disulfide atom name. More...
 
void set_disulfide_atom_name (std::string const &n)
 Sets disulfide atom name. More...
 
std::map< std::string,
std::string > const & 
atom_aliases () const
 returns atom aliases More...
 
std::string const & atom_alias (std::string const &name) const
 returns atom alias More...
 
std::map< std::string,
std::string > const & 
canonical_atom_aliases () const
 returns atom aliases More...
 
std::string const & canonical_atom_alias (std::string const &name) const
 returns atom alias More...
 
Orbital const & orbital (Size const orbital_index) const
 
Orbital const & orbital (std::string const &orbital_name) const
 
orbitals::OrbitalType const & orbital_type (Size const orbital_index) const
 
Size n_orbitals () const
 number of orbitals More...
 
bool has_orbital (std::string const &orbital_name) const
 is this orbital present in this residue? More...
 
core::Size orbital_index (std::string const &name) const
 get orbital index by name More...
 
ResidueProperties const & properties () const
 Access the collection of properties for this ResidueTypeBase. More...
 
void set_properties (ResiduePropertiesOP properties)
 Set the collection of properties for this ResidueTypeBase. More...
 
void add_property (std::string const &property)
 Add a property to this ResidueTypeBase. More...
 
void add_property (core::chemical::ResidueProperty const property)
 Add a property to this ResidueType, by properties enum. More...
 
void set_adduct_flag (bool adduct_in)
 
void add_numeric_property (std::string const &tag, core::Real value)
 Add a numeric property. More...
 
void add_string_property (std::string const &tag, std::string value)
 Add a string property. More...
 
void delete_property (std::string const &property)
 Delete a property of this ResidueType. More...
 
void delete_property (core::chemical::ResidueProperty const property)
 Delete a property of this ResidueType, by properties enum. More...
 
virtual bool is_base_type () const =0
 Is this ResidueTypeBase a base type? More...
 
virtual ResidueTypeCOP get_base_type_cop () const =0
 Get a pointer to this ResidueTypeBase's base ResidueTypeBase. More...
 
void set_metapatched ()
 Set that this is a metapatched ResidueType. More...
 
bool is_metapatched () const
 Get whether this is a metapatched ResidueType. More...
 
bool is_polymer () const
 is polymer? More...
 
bool is_protein () const
 is protein? More...
 
bool is_DNA () const
 is DNA? More...
 
bool is_RNA () const
 is RNA? More...
 
bool is_d_aa () const
 is this a d-amino acid? More...
 
bool is_l_aa () const
 is this an l-amino acid? More...
 
bool is_d_rna () const
 is this a d-RNA? More...
 
bool is_l_rna () const
 is this an l-RNA? More...
 
bool is_peptoid () const
 is peptoid? More...
 
bool is_r_peptoid () const
 Is this a peptoid with a chiral side-chain with "R" chirality? More...
 
bool is_s_peptoid () const
 Is this a peptoid with a chiral side-chain with "S" chirality? More...
 
bool is_achiral_backbone () const
 is this an achiral backbone? More...
 
bool is_achiral_sidechain () const
 Does this have an achiral sidechain? More...
 
bool has_property (std::string const &property) const
 Generic property access. More...
 
bool has_property (ResidueProperty const property) const
 Generic property access, by ResidueProperty. More...
 
core::Real get_numeric_property (std::string const &tag) const
 Get a numeric property, if it exists. More...
 
std::string get_string_property (std::string const &tag) const
 Get a string property, if it exists. More...
 
void add_variant_type (VariantType const variant_type)
 Add a variant type to this ResidueTypeBase. More...
 
void add_variant_type (std::string const &variant_type)
 Add a variant type to this ResidueTypeBase by string. More...
 
void remove_variant_type (VariantType const variant_type)
 Remove a variant type to this ResidueTypeBase. More...
 
void remove_variant_type (std::string const &variant_type)
 Remove a variant type to this ResidueTypeBase by string. More...
 
bool has_variant_type (VariantType const variant_type) const
 Generic variant access. More...
 
bool has_variant_type (std::string const &variant_type) const
 Generic variant access by string. More...
 
void enable_custom_variant_types ()
 Turn on the ability to create VariantTypes "on-the-fly". More...
 
utility::vector1< std::string > variant_types () const
 get all the variant types for this ResidueTypeBase More...
 
utility::vector1< VariantTypevariant_type_enums () const
 Get a vector of VariantType enums for this ResidueTypeBase. More...
 
utility::vector1< std::string >
const & 
custom_variant_types () const
 Get a list of custom VariantType strings for this ResidueTypeBase (by const reference). More...
 
void aa (AA const &type)
 set our aa-type (could be "UNK") More...
 
void aa (std::string const &type)
 set our aa-type (could be "UNK") More...
 
void backbone_aa (std::string const &type)
 AA to use for backbone scoring. More...
 
void backbone_aa (core::chemical::AA const type)
 Set AA to use for backbone scoring directly (without string conversion). More...
 
void base_analogue (std::string const &type)
 NA to use for base-specific generalization (can be more forgiving than na_analogue for new NA backbones) More...
 
void na_analogue (std::string const &type)
 NA to use for fragment sampling and some scoring purposes. More...
 
std::string const & base_name () const
 Get this ResidueTypeBase's base name (shared with other residue types with the same base type). More...
 
std::string const & name () const
 get our (unique) residue name More...
 
void base_name (std::string const &base_name_in)
 Set this ResidueTypeBase's base name (shared with other residue types with the same base type). More...
 
void name (std::string const &name_in)
 set our (unique) residue name More...
 
std::string const & name3 () const
 get our 3letter code. This is set in the ResidueTypeBase .params file through the IO_STRING tag along with the name1 string NOTE: The "name3" is not necessarily three characters long. e.g. Metal ions may be only two characters. More...
 
void name3 (std::string const &name_in)
 set our 3letter code More...
 
char name1 () const
 get our 1letter code. This is set in the ResidueTypeBase .params file through the IO_STRING tag along with the name3 string. More...
 
void name1 (char const code)
 set our 1letter code More...
 
std::string interchangeability_group () const
 get our interchangeability-group id. Used to determine if two residue types are equivalent, except for their variant status. E.g. ResidueTypeBases ALA and ALA_Nterm would be part of the same interchangeability group. This has a degree of subjectivity; are TYR and pTYR in the same interchangeability group? Probably not. This data can be specified in the ResidueTypeBases .params file with the INTERCHANGEABILITY_GROUP tag. More...
 
void interchangeability_group (std::string const &setting)
 set our interchangeability-group id More...
 
void remap_pdb_atom_names (bool rename)
 Turn on geometry-based atom renaming when loading this residue type from PDB files. More...
 
bool remap_pdb_atom_names () const
 Are we using geometry-based atom renaming when loading this residue type from PDB. More...
 
AA const & aa () const
 our traditional residue type, if any More...
 
AA const & backbone_aa () const
 Returns the amino acid type to be used for backbone scoring (rama and p_aa_pp). More...
 
AA const & base_analogue () const
 Returns the nucleic acid type to be used for base features. More...
 
AA const & na_analogue () const
 Returns the nucleic acid type to be used for fragment sampling/scoring. More...
 
void rotamer_library_specification (rotamers::RotamerLibrarySpecificationOP)
 
rotamers::RotamerLibrarySpecificationCOP rotamer_library_specification () const
 
rotamers::RotamerLibrarySpecificationOP rotamer_library_specification_nonconst ()
 Nonconst access to the RotamerLibrarySpecification. More...
 
void strip_rotamer_library_specification ()
 Remove any rotamer library specifications attached to this ResidueTypeBase. More...
 
bool force_nbr_atom_orient () const
 dihedral methods More...
 
void force_nbr_atom_orient (bool force_orient)
 Set force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms. More...
 
std::string const & get_rama_prepro_mainchain_torsion_potential_name (bool const pre_proline_position) const
 Get the key name for the mainchain torsion potential used by the RamaPrePro score term. More...
 
bool mainchain_potentials_match (ResidueTypeBase const &other) const
 Do the rama_prepro mainchain torsion potentials of this residue match another? More...
 
void set_rama_prepro_mainchain_torsion_potential_name (std::string const &name_in, bool const pre_proline_position)
 Set the key name for the mainchain torsion potential used by the RamaPrePro score term. More...
 
std::string const & get_rama_prepro_map_file_name (bool const pre_proline_position) const
 Get the file name for the mainchain torsion potential used by the RamaPrePro score term. More...
 
void set_rama_prepro_map_file_name (std::string const &filename_in, bool const pre_proline_position)
 Set the file name for the mainchain torsion potential used by the RamaPrePro score term. More...
 
bool defines_custom_rama_prepro_map (bool const pre_proline_position) const
 Returns true if and only if (a) this is not a base type, AND (b) there is a rama_prepro_mainchain_torsion_map_file_name_ defined for this ResidueTypeBase (which is presumably different from that of the base type). More...
 
void reset_mainchain_torsion_potential_names ()
 Set the names of the mainchain torsion potential maps to use to "". More...
 
virtual void show (std::ostream &output=std::cout, bool output_atomic_details=false) const =0
 Generate string representation of ResidueTypeBase for debugging purposes. More...
 
utility::vector1< Adduct > const & defined_adducts () const
 get the adducts defined for this residue More...
 
void add_adduct (Adduct &adduct_in)
 
void report_adducts () const
 

Protected Member Functions

 ResidueTypeBase ()
 
 ResidueTypeBase (AtomTypeSetCOP atom_types, ElementSetCOP element_types, MMAtomTypeSetCOP mm_atom_types, orbitals::OrbitalTypeSetCOP orbital_types)
 constructor More...
 
 ResidueTypeBase (ResidueTypeBase const &)=default
 
ResidueTypeBaseoperator= (ResidueTypeBase const &)=default
 Copies <src> into the ResidueTypeBase. More...
 
void atom_type_set (AtomTypeSetCOP setting)
 
utility::vector1< std::string > & metal_binding_atoms ()
 
std::map< std::string,
std::string > & 
atom_aliases ()
 returns atom aliases More...
 
std::map< std::string,
std::string > & 
canonical_atom_aliases ()
 returns atom aliases More...
 
utility::vector1< Orbital > & get_orbitals ()
 
std::map< std::string, int > & get_orbitals_index ()
 
AA const & backbone_aa_raw () const
 
AA const & base_analogue_raw () const
 
AA const & na_analogue_raw () const
 

Private Attributes

TypeSetMode mode_ = INVALID_t
 The TypeSet mode for this ResidueTypeBase. More...
 
AtomTypeSetCOP atom_types_
 The type set for Rosetta Atom types. Required to be non-null for standard ResidueTypes. More...
 
ElementSetCOP elements_
 The set for element objects. – can be null. More...
 
MMAtomTypeSetCOP mm_atom_types_
 The set for MMAtomTypes. – can be null. More...
 
gasteiger::GasteigerAtomTypeSetCOP gasteiger_atom_types_
 The set for GasteigerAtomTypes. – can be null. More...
 
orbitals::OrbitalTypeSetCOP orbital_types_
 The set for OrbitalTypes. – can be null. More...
 
AA aa_ = aa_unk
 standard rosetta aa-type for knowledge-based potentials, may be aa_unk More...
 
AA backbone_aa_ = aa_unk
 
AA na_analogue_ = aa_unp
 
AA base_analogue_ = aa_unp
 
std::string base_name_
 Residue id for the base type (i.e. sans variants). More...
 
std::string name_
 Residue id – Should be unique within a ResidueTypeSet. More...
 
std::string name3_
 PDB-file id, need not be unique NOTE: The "name3" is not necessarily three characters long. e.g. Metal ions may be only two characters. More...
 
char name1_ = ' '
 one-letter code, also not necessarily unique More...
 
std::string interchangeability_group_
 interchangeability group lets a ResidueTypeBase claim to be functionally interchangeable with any other ResidueTypeBase in the same group. This is used by the packer to decide which ResidueTypeBase from a desired group has the right set of variants to be placed at a particular position. E.g. if the interchangeability group is "ALA" and the packer is building rotamers for residue 1, (the N-terminal residue) then, the packer will select the "ALA:NTermProteinFull" ResidueTypeBase and build rotamers for it. More...
 
std::string rama_prepro_mainchain_torsion_potential_name_
 The name of the mainchain torsion potential used by this ResidueTypeBase for the RamaPrePro score term. More...
 
std::string rama_prepro_mainchain_torsion_potential_name_beforeproline_
 The name of the mainchain torsion potential used by this ResidueTypeBase for the RamaPrePro score term. More...
 
std::string rama_prepro_map_file_name_
 The filename of the mainchain torsion potential used by this ResidueTypeBase for the RamaPrePro score term. More...
 
std::string rama_prepro_map_file_name_beforeproline_
 The filename of the mainchain torsion potential used by this ResidueTypeBase for the RamaPrePro score term. More...
 
signed long int net_formal_charge_ = 0
 What is the total formal charge of the ResidueType? (Note that this may be different from the sum of the formal charges on each atom.) More...
 
bool force_nbr_atom_orient_ = false
 
bool remap_pdb_atom_names_ = false
 Should we attempt to rename atoms for this residue type when we read in PDB files? More...
 
utility::pointer::DeepCopyOP
< ResidueProperties
properties_
 Residue properties as defined in the residue topology (.params) files. More...
 
bool is_metapatched_ = false
 Is this ResidueType the product of metapatching? More...
 
utility::pointer::DeepCopyOP
< rotamers::RotamerLibrarySpecification
rotamer_library_specification_
 How to construct a rotamer library for this ResidueTypeBase. More...
 
utility::vector1< std::string > metal_binding_atoms_
 Names of all of the atoms that are able to make a bond to a metal, for metal-binding residue types. More...
 
std::string disulfide_atom_name_ = "NONE"
 Name of the disulfide-forming atom, if any. More...
 
std::map< std::string,
std::string > 
atom_aliases_
 A mapping of alias atom names to canonical atom names Will be added to atom_name_to_vd_ during finalization. More...
 
std::map< std::string,
std::string > 
canonical_atom_aliases_
 A map of canonical atom names to atom aliases (white space included) More...
 
utility::vector1< Adductdefined_adducts_
 Adducts defined for this residue. More...
 
utility::vector1< Orbitalorbitals_
 The orbitals on the ResidueTypeBase, if any. More...
 
std::map< std::string, int > orbitals_index_
 index lookup for orbitals based on atom name Updated in add_orbital() More...
 

Detailed Description

A base class for definiting types of residues.

This class is a base class for the "chemical" information for residues in Rosetta. It's a base class for two different classes. ResidueType, which is the main class used by Rosetta, but which is a fixed-content type, and MutableResidueType, which is a modifiable class. The two type also differ also in how Atoms information is represented. The atom information in MutableResidueType is represented in a molecular graph, which is more convenient for modification, with atoms referenced primarily by "vertex descriptor" in the graph. The atom information in ResidueType is in a struct-of-arrays format, which allows better optimization, with atoms in a defined order. There are also differences in guarantees for each class. ResidueType has certain atom ordering guarantees which MutableResidueType lacks.

To accomodate the two different classes, this base class only stores the common, (non-atom dependent) information, along with some convenient accessors.

See the documentation of each class for more information.

A note on things which belong in this class: Only include things which are atom-independent, and are "primary" information. (Things which can/should be derived from atoms or other info should be placed in the plain ResidueType class, and updated on MutableResidueType -> ResidueType conversion. You can also include (as a virtual method) functions needed for PatchSelector function, but any atom indexing/references should be name-based.

Constructor & Destructor Documentation

core::chemical::ResidueTypeBase::ResidueTypeBase ( )
protecteddefault
core::chemical::ResidueTypeBase::ResidueTypeBase ( AtomTypeSetCOP  atom_types,
ElementSetCOP  element_types,
MMAtomTypeSetCOP  mm_atom_types,
orbitals::OrbitalTypeSetCOP  orbital_types 
)
protected

constructor

We use the AtomTypeSet object to assign atom_types to atoms inside add_atom, and to identify (polar) hydrogens, acceptors, etc. This is protected as we don't want to instantiate a plain ResidueType directly.

References atom_types_, and mode_.

core::chemical::ResidueTypeBase::ResidueTypeBase ( ResidueTypeBase const &  )
protecteddefault

Member Function Documentation

void core::chemical::ResidueTypeBase::aa ( AA const &  type)
inline

set our aa-type (could be "UNK")

References aa_.

Referenced by protocols::minimization_packing::MinimalRotamer::aa(), core::conformation::Residue::aa(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::add_linker_symmetric(), protocols::loops::add_loop(), protocols::motifs::add_motif_bb_constraints(), protocols::stepwise::modeler::align::StepWisePoseAligner::add_to_atom_id_map_after_checks(), protocols::rna::movers::ErraserMinimizerMover::add_virtual_res(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::simple_moves::SetTorsion::apply(), core::select::residue_selector::NumNeighborsSelector::apply(), protocols::farnesyl::InstallFarnesylMover::apply(), protocols::farnesyl::SampleFarnesylMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::calc_taskop_filters::ConservedPosMutationFilter::apply(), protocols::minimization_packing::RotamerizeMover::apply(), protocols::task_operations::SeqprofConsensusOperation::apply(), protocols::denovo_design::movers::FastDesign::apply(), protocols::rna::movers::RNAThreadAndMinimizeMover::apply(), protocols::task_operations::RestrictConservedLowDdgOperation::apply(), core::chemical::Set_AA::apply(), core::chemical::ChiralFlipNaming::apply(), core::pack::rotamer_set::WaterAnchorInfo::attaches_to_residue_type(), protocols::motifs::backbone_stub_match(), protocols::stepwise::modeler::rna::base_atoms_square_deviation(), core::pack::rotamer_set::build_moving_O_bridge_waters(), core::pack::rotamer_set::build_single_edge_waters(), protocols::pose_length_moves::InsertResMover::center_of_mass(), protocols::simple_moves::Tumble::center_of_mass(), core::chemical::sdf::MolWriter::compose_naming(), protocols::matdes::OligomericAverageDegreeFilter::compute(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_burial(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(), core::pack::rotamers::SingleNCAARotamerLibraryCreator::create(), core::scoring::ResidueExclParams::create_excl_info(), core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_02_from_ASCII(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::pack::dunbrack::RotamerLibrary::create_srdl(), core::scoring::constraints::SequenceProfileConstraint::dist(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), core::scoring::methods::RamachandranEnergy2B::eval_dof_derivative(), protocols::stepwise::modeler::figure_out_moving_chain_breaks(), protocols::stepwise::modeler::movemap::figure_out_stepwise_movemap(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::filter_by_sidechain_distance_asymmetric(), protocols::cyclic_peptide::crosslinker::TBMB_Helper::filter_by_sidechain_distance_symmetric(), protocols::magnesium::find_bound_waters_that_are_daughters_in_fold_tree(), protocols::stepwise::modeler::find_downstream_connection_res(), protocols::enzdes::EnzdesFlexBBProtocol::generate_ensemble_for_region(), core::scoring::methods::IdealParametersDatabase::generate_impropers_map_res(), core::chemical::Patch::generates_aa(), core::chemical::rna::get_base_pair_atoms(), protocols::simple_moves::chiral::get_chiral_residue_type(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_last_sidechain_carbon_name(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_max_sidechain_length(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), core::scoring::HydroxylTorsionPotential::get_restag(), core::scoring::methods::get_restag(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_sidechain_amide_name(), core::scoring::dna::get_y_axis_atoms(), protocols::metal_interface::MatchGrafter::graft(), protocols::magnesium::MgHydrater::hydrate_magnesium(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_pose(), protocols::cyclic_peptide::crosslinker::TMA_Helper::is_allowed_residue_type(), protocols::cyclic_peptide::crosslinker::SquarePlanarMetal_Helper::is_allowed_type(), protocols::cyclic_peptide::crosslinker::OctahedralMetal_Helper::is_allowed_type(), protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper::is_allowed_type(), protocols::cyclic_peptide::crosslinker::TrigonalPyramidalMetal_Helper::is_allowed_type(), protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper::is_allowed_type(), core::scoring::methods::ArgCationPiEnergy::is_arg(), core::scoring::constraints::is_aromatic(), protocols::simple_filters::LongestContinuousPolarSegmentFilter::is_counted(), core::scoring::methods::ArgCationPiEnergy::is_his(), core::scoring::methods::ArgCationPiEnergy::is_phe(), core::conformation::Residue::is_similar_aa(), core::conformation::Residue::is_similar_rotamer(), core::scoring::methods::ArgCationPiEnergy::is_trp(), core::scoring::methods::ArgCationPiEnergy::is_tyr(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::liganding_atom_from_restype(), protocols::multistate_design::limit_rotamer_set(), core::scoring::methods::IdealParametersDatabase::lookup_angle(), core::scoring::methods::IdealParametersDatabase::lookup_bondangle_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_bondlength_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_length(), core::scoring::nmr::lookup_pseudoprotons(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), protocols::rna::movers::ErraserMinimizerMover::movemap_setup(), core::pack::dunbrack::SingleResidueDunbrackLibrary::n_rotamer_bins_for_aa(), protocols::denovo_design::DisulfidizeMover::noncanonical_disulfide(), core::import_pose::libraries::one_letter_from_rt(), core::chemical::Selector_AA::operator[](), core::scoring::constraints::parse_NMR_name(), core::scoring::constraints::parse_NMR_name_old(), protocols::hybridization::BackboneTorsionSampler::perturb(), protocols::hybridization::BackboneTorsionPerturbation::perturb(), protocols::rna::movers::ErraserMinimizerMover::process_entire_pose(), protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density(), core::scoring::methods::PoissonBoltzmannEnergy::protein_position_equal_within(), core::chemical::ResidueDatabaseIO::read_residue_type(), protocols::pose_metric_calculators::ChargeCalculator::recompute(), protocols::features::ProteinBondGeometryFeatures::report_intrares_angles(), protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::scoring::constraints::requires_CB_mapping(), core::scoring::methods::pHEnergy::residue_energy(), core::scoring::methods::ReferenceEnergy::residue_energy(), protocols::optimize_weights::IterativeOptEDriver::residue_has_unacceptably_bad_dunbrack_energy(), core::chemical::residue_type_bases_identical(), protocols::match::upstream::DunbrackSCSampler::samples(), core::scoring::ProQPotential::score(), protocols::constraints_additional::SequenceCoupling1BDConstraint::score(), protocols::constraints_additional::SequenceCouplingConstraint::score(), core::scoring::constraints::SequenceProfileConstraint::score(), core::chemical::sdf::MolFileIOMolecule::set_from_extra_data(), core::scoring::methods::MMLJEnergyInter::setup_for_packing(), core::scoring::methods::GoapEnergy::setup_for_scoring(), core::chemical::setup_patch_atomic_charge_reassignments_from_commandline(), protocols::stepwise::modeler::rna::suite_square_deviation(), core::pose::toolbox::AtomLevelDomainMap::update_to_not_move_last_virtual_residue(), protocols::rna::movers::ErraserMinimizerMover::vary_bond_geometry(), core::scoring::rna::RNA_AtomVDW::vdw_atom_list(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::verify_protonated_H1_adenosine_variants(), and core::chemical::write_topology_file().

void core::chemical::ResidueTypeBase::aa ( std::string const &  type)
inline

set our aa-type (could be "UNK")

References aa_, and core::chemical::aa_from_name().

AA const& core::chemical::ResidueTypeBase::aa ( ) const
inline

our traditional residue type, if any

Used for knowledge-based scores, dunbrack, etc. could be "aa_unk".

AA is an enum. There are values for the 20 standard amino acids, the 19 canonical D-amino acids, common beta-amino acids and nucleic acids, and aa_unk as a general catch-all.

References aa_.

Referenced by core::chemical::MutableResidueType::copy_other_info(), and core::chemical::MutableResidueType::placeholder_clone().

void core::chemical::ResidueTypeBase::add_adduct ( Adduct adduct_in)
inline

References defined_adducts_.

void core::chemical::ResidueTypeBase::add_numeric_property ( std::string const &  tag,
core::Real  value 
)

Add a numeric property.

References properties_.

void core::chemical::ResidueTypeBase::add_property ( std::string const &  property)
void core::chemical::ResidueTypeBase::add_property ( core::chemical::ResidueProperty const  property)
void core::chemical::ResidueTypeBase::add_string_property ( std::string const &  tag,
std::string  value 
)

Add a string property.

References properties_.

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

void core::chemical::ResidueTypeBase::add_variant_type ( VariantType const  variant_type)
void core::chemical::ResidueTypeBase::add_variant_type ( std::string const &  variant_type)

Add a variant type to this ResidueTypeBase by string.

References properties_.

std::string const& core::chemical::ResidueTypeBase::atom_alias ( std::string const &  name) const
inline

returns atom alias

References atom_aliases_.

std::map< std::string, std::string > const& core::chemical::ResidueTypeBase::atom_aliases ( ) const
inline
std::map< std::string, std::string >& core::chemical::ResidueTypeBase::atom_aliases ( )
inlineprotected

returns atom aliases

References atom_aliases_.

AtomTypeSet const& core::chemical::ResidueTypeBase::atom_type_set ( ) const
inline
void core::chemical::ResidueTypeBase::atom_type_set ( AtomTypeSetCOP  setting)
protected

References atom_types_, and mode_.

AtomTypeSetCOP core::chemical::ResidueTypeBase::atom_type_set_ptr ( ) const
inline
void core::chemical::ResidueTypeBase::backbone_aa ( std::string const &  type)
inline
void core::chemical::ResidueTypeBase::backbone_aa ( core::chemical::AA const  type)
inline

Set AA to use for backbone scoring directly (without string conversion).

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

References backbone_aa_.

AA const& core::chemical::ResidueTypeBase::backbone_aa ( ) const
inline

Returns the amino acid type to be used for backbone scoring (rama and p_aa_pp).

References aa_, core::chemical::aa_unk, and backbone_aa_.

AA const& core::chemical::ResidueTypeBase::backbone_aa_raw ( ) const
inlineprotected
void core::chemical::ResidueTypeBase::base_analogue ( std::string const &  type)
inline
AA const& core::chemical::ResidueTypeBase::base_analogue ( ) const
inline

Returns the nucleic acid type to be used for base features.

References aa_, core::chemical::aa_unp, and base_analogue_.

AA const& core::chemical::ResidueTypeBase::base_analogue_raw ( ) const
inlineprotected

References base_analogue_.

std::string const& core::chemical::ResidueTypeBase::base_name ( ) const
inline

Get this ResidueTypeBase's base name (shared with other residue types with the same base type).

References base_name_.

Referenced by protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_residue_info_to_sfr(), core::chemical::ChiralFlipNaming::apply(), protocols::simple_moves::MutateResidue::break_a_disulfide(), core::simple_metrics::metrics::SequenceMetric::calculate(), core::pack::palette::PackerPalette::decide_what_to_do_with_base_type(), protocols::ligand_docking::HighResDocker::enable_ligand_rotamer_packing(), protocols::ligand_docking::ProtLigEnsemble::enable_ligand_rotamer_packing(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_last_sidechain_carbon_name(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_max_sidechain_length(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), core::scoring::HydroxylTorsionPotential::get_restag(), protocols::cyclic_peptide::crosslinker::TMA_Helper::get_sidechain_amide_name(), core::pose::toolbox::AtomID_Mapper::initialize(), protocols::cyclic_peptide::crosslinker::TMA_Helper::is_allowed_residue_type(), protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper::is_allowed_type(), protocols::cyclic_peptide::crosslinker::Metal_HelperBase::liganding_atom_from_restype(), protocols::simple_moves::MutateResidue::make_mutation(), core::pose::MiniPose::MiniPose(), core::chemical::Selector_BASENAME::operator[](), core::chemical::Patch::patched_name(), core::chemical::MutableResidueType::placeholder_clone(), core::chemical::residue_type_bases_identical(), core::chemical::mainchain_potential::MainchainScoreTable::set_dimension_and_ntorsions_for_restype(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_chainbreak_variants(), core::chemical::MutableResidueType::show(), core::chemical::ResidueType::show(), protocols::stepwise::modeler::virtualize_side_chains(), and core::chemical::write_topology_file().

void core::chemical::ResidueTypeBase::base_name ( std::string const &  base_name_in)
inline

Set this ResidueTypeBase's base name (shared with other residue types with the same base type).

References base_name_.

std::string const& core::chemical::ResidueTypeBase::canonical_atom_alias ( std::string const &  name) const
inline
std::map< std::string, std::string > const& core::chemical::ResidueTypeBase::canonical_atom_aliases ( ) const
inline
std::map< std::string, std::string >& core::chemical::ResidueTypeBase::canonical_atom_aliases ( )
inlineprotected

returns atom aliases

References canonical_atom_aliases_.

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

Get a list of custom VariantType strings for this ResidueTypeBase (by const reference).

This ONLY includes custom, on-the-fly variants, not standard variants.

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

References properties_.

Referenced by protocols::cyclic_peptide::RamaMutationSelector::apply(), and core::pack::palette::PackerPalette::get_types_on_residue().

utility::vector1< Adduct > const& core::chemical::ResidueTypeBase::defined_adducts ( ) const
inline
bool core::chemical::ResidueTypeBase::defines_custom_rama_prepro_map ( bool const  pre_proline_position) const

Returns true if and only if (a) this is not a base type, AND (b) there is a rama_prepro_mainchain_torsion_map_file_name_ defined for this ResidueTypeBase (which is presumably different from that of the base type).

If pre_proline_position is true, checks rama_prepro_mainchain_torsion_map_file_name_beforeproline_ instead of rama_prepro_mainchain_torsion_potential_name_.

References is_base_type(), rama_prepro_map_file_name_, and rama_prepro_map_file_name_beforeproline_.

void core::chemical::ResidueTypeBase::delete_property ( std::string const &  property)

Delete a property of this ResidueType.

This is needed for deleting properties, which occurs in certain PTMs.

References properties_.

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

void core::chemical::ResidueTypeBase::delete_property ( core::chemical::ResidueProperty const  property)

Delete a property of this ResidueType, by properties enum.

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

References core::chemical::NO_PROPERTY, and properties_.

ElementSet const& core::chemical::ResidueTypeBase::element_set ( ) const
inline

access by reference the element set for which this residue is constructed

References elements_.

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

ElementSetCOP core::chemical::ResidueTypeBase::element_set_ptr ( ) const
inline

access by const pointer the element set for which this residue is constructed

References elements_.

Referenced by core::chemical::MutableResidueType::placeholder_clone(), core::chemical::residue_type_bases_identical(), and core::chemical::MutableResidueType::set_atom_type().

void core::chemical::ResidueTypeBase::enable_custom_variant_types ( )

Turn on the ability to create VariantTypes "on-the-fly".

"Custom" VariantTypes as strings are permitted for the enzdes and metalloproteins cases. Do not enable unless you have a good reason to, as string look-ups are less efficient and more error-prone.

References properties_.

Referenced by core::chemical::MutableResidueType::add_metapatch_connect(), core::chemical::AddConnectAndTrackingVirt::apply(), and core::chemical::MutableResidueType::delete_child_proton().

bool core::chemical::ResidueTypeBase::force_nbr_atom_orient ( ) const
inline

dihedral methods

Return force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms

References force_nbr_atom_orient_.

Referenced by core::chemical::SetOrientAtom::apply(), core::chemical::residue_type_bases_identical(), core::chemical::ResidueType::select_orient_atoms(), and core::chemical::write_topology_file().

void core::chemical::ResidueTypeBase::force_nbr_atom_orient ( bool  force_orient)
inline

Set force_nbr_atom_orient_, used to control orient atoms selected by select_orient_atoms.

References force_nbr_atom_orient_.

gasteiger::GasteigerAtomTypeSetCOP core::chemical::ResidueTypeBase::gasteiger_atom_typeset ( ) const
virtual ResidueTypeCOP core::chemical::ResidueTypeBase::get_base_type_cop ( ) const
pure virtual

Get a pointer to this ResidueTypeBase's base ResidueTypeBase.

NOTE: Behavior when is_base_type() == true varies by subclass!

Implemented in core::chemical::ResidueType, and core::chemical::MutableResidueType.

Referenced by get_rama_prepro_mainchain_torsion_potential_name(), and get_rama_prepro_map_file_name().

std::string const& core::chemical::ResidueTypeBase::get_disulfide_atom_name ( ) const
inline

Gets disulfide atom name.

Author
Andrew M. Watkins (amw57.nosp@m.9@ny.nosp@m.u.edu).

References disulfide_atom_name_.

Referenced by protocols::cyclic_peptide::TryDisulfPermutations::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), core::chemical::ConnectSulfurAndMakeVirtualProton::apply(), core::chemical::ConnectSulfurAndMakeVirtualProton::changes_connections_on(), core::scoring::disulfides::FullatomDisulfideEnergy::defines_score_for_residue_pair(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::scoring::disulfides::DisulfideAtomIndices::DisulfideAtomIndices(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed(), protocols::denovo_design::DisulfidizeMover::find_current_disulfides(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides(), core::conformation::Conformation::fix_disulfides(), core::conformation::form_disulfide(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_connectivity_annotation_info(), core::conformation::get_disulf_partner(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_ssbond_record(), core::conformation::is_disulfide_bond(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), core::chemical::residue_type_bases_identical(), and core::chemical::write_topology_file().

utility::vector1< std::string > const& core::chemical::ResidueTypeBase::get_metal_binding_atoms ( ) const
inline
core::Real core::chemical::ResidueTypeBase::get_numeric_property ( std::string const &  tag) const

Get a numeric property, if it exists.

References name3_, and properties_.

Referenced by protocols::qsar::scoring_grid::LigandPropertyScore::score().

utility::vector1< Orbital >& core::chemical::ResidueTypeBase::get_orbitals ( )
inlineprotected
std::map< std::string, int >& core::chemical::ResidueTypeBase::get_orbitals_index ( )
inlineprotected
std::string const & core::chemical::ResidueTypeBase::get_rama_prepro_mainchain_torsion_potential_name ( bool const  pre_proline_position) const

Get the key name for the mainchain torsion potential used by the RamaPrePro score term.

Get the key name for the mainchain torsion potential.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (in which case this function returns the string stored in the base ResidueTypeBase), though this can be overridden.

Note
Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we're interested in.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (in which case this function returns the string stored in the base ResidueTypeBase), though this can be overridden.

References get_base_type_cop(), is_base_type(), rama_prepro_mainchain_torsion_potential_name_, and rama_prepro_mainchain_torsion_potential_name_beforeproline_.

Referenced by core::chemical::residue_type_bases_identical(), core::chemical::ResidueType::update_derived_data(), and core::chemical::write_topology_file().

std::string const & core::chemical::ResidueTypeBase::get_rama_prepro_map_file_name ( bool const  pre_proline_position) const

Get the file name for the mainchain torsion potential used by the RamaPrePro score term.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (in which case this function returns the string stored in the base ResidueTypeBase), though this can be overridden.

Note
Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we're interested in.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (in which case this function returns the string stored in the base ResidueTypeBase), though this can be overridden.

References get_base_type_cop(), is_base_type(), rama_prepro_map_file_name_, and rama_prepro_map_file_name_beforeproline_.

Referenced by core::scoring::ResidueExclParams::create_excl_info(), core::chemical::residue_type_bases_identical(), core::chemical::ResidueType::update_derived_data(), and core::chemical::write_topology_file().

std::string core::chemical::ResidueTypeBase::get_string_property ( std::string const &  tag) const

Get a string property, if it exists.

References name3_, and properties_.

virtual bool core::chemical::ResidueTypeBase::has ( std::string const &  atom_name) const
pure virtual
bool core::chemical::ResidueTypeBase::has_orbital ( std::string const &  orbital_name) const
inline

is this orbital present in this residue?

References orbitals_index_.

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

bool core::chemical::ResidueTypeBase::has_orbital_types ( ) const
inline

Does this residue type define orbital types?

References orbital_types_.

bool core::chemical::ResidueTypeBase::has_property ( std::string const &  property) const
bool core::chemical::ResidueTypeBase::has_property ( ResidueProperty const  property) const

Generic property access, by ResidueProperty.

References properties_.

bool core::chemical::ResidueTypeBase::has_variant_type ( VariantType const  variant_type) const

Generic variant access.

References properties_.

Referenced by protocols::jumping::JumpSample::add_chainbreaks(), protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps(), core::chemical::MutableResidueType::add_metapatch_connect(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::stepwise::modeler::rna::sugar::SugarVirtualizeMover::apply(), protocols::stepwise::modeler::rna::sugar::SugarInstantiateMover::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), core::pack::task::operation::OptCysHG::apply(), core::chemical::AddConnectAndTrackingVirt::apply(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::apply_Aform_torsions_to_five_prime_phosphate(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::apply_Aform_torsions_to_three_prime_phosphate(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_peptide_plane_variants(), protocols::mainchain_potential::GenerateMainchainPotential::apply_protein_patches(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_virtual_phosphate_variants(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_virtual_phosphate_variants(), core::pose::rna::apply_virtual_rna_residue_variant_type(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), protocols::rna::movers::RNA_LoopCloser::check_closure(), protocols::rna::denovo::RNA_FragmentMonteCarlo::check_fold_tree_cutpoints_ok(), protocols::stepwise::modeler::rna::check_instantiated_O2Prime_hydrogen(), protocols::stepwise::modeler::protein::InputStreamWithResidueInfo::cleanup_pose(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoASP(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoGLU(), protocols::stepwise::modeler::rna::create_standard_o2prime_pack_task(), protocols::enzdes::EnzdesBaseProtocol::cst_minimize(), core::pack::palette::PackerPalette::decide_what_to_do_with_base_type(), core::pack::palette::PackerPalette::decide_what_to_do_with_existing_type(), protocols::stepwise::modeler::declare_chemical_bonds_at_cutpoints(), core::chemical::MutableResidueType::delete_child_proton(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), core::scoring::Ramachandran2B::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::Ramachandran::eval_rama_score_residue_nonstandard_connection(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::figure_out_dof_ids_and_offsets(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::figure_out_loop(), protocols::stepwise::modeler::figure_out_moving_chain_breaks(), protocols::stepwise::modeler::figure_out_moving_partition_res(), core::pose::rna::figure_out_reasonable_rna_fold_tree(), protocols::stepwise::modeler::movemap::figure_out_stepwise_movemap(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::figure_out_which_cutpoints_were_affected(), protocols::stepwise::modeler::packer::figure_out_working_interface_res(), protocols::abinitio::abscript::find_disulfide_partner(), core::scoring::methods::find_relevant_connections(), core::scoring::methods::find_relevant_connections_onersd(), protocols::stepwise::modeler::find_root_without_virtual_ribose(), core::pose::fix_up_residue_type_variants_at_floating_base(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_calc_rms_atom_id_map(), protocols::rna::movers::RNA_LoopCloser::get_cutpoints_closed(), protocols::rna::denovo::get_default_allowed_bulge_res(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_movable_scs(), core::chemical::ResidueTypeSet::get_residue_type_with_custom_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), core::conformation::get_root_atomno(), core::pack::palette::PackerPalette::get_types_on_residue(), protocols::cyclic_peptide::PeptideStubMover::handle_lower_terminus(), protocols::cyclic_peptide::PeptideStubMover::handle_upper_terminus(), core::conformation::Residue::has_variant_type(), core::pose::rna::has_virtual_rna_residue_variant_type(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::initialize_phosphate_move_list(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_pose_level_screeners(), protocols::stepwise::modeler::is_cutpoint_closed(), core::pose::rna::is_cutpoint_closed_torsion(), core::pose::rna::is_cutpoint_open(), core::pose::rna::is_torsion_valid(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::let_neighboring_chis_minimize(), core::scoring::methods::IdealParametersDatabase::lookup_bondangle_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), protocols::ncbb::ResidueReplacementRebuildMover::make_new_pose(), core::pose::make_pose_from_sequence(), protocols::stepwise::modeler::make_variants_match(), protocols::stepwise::sampler::rna::modeler_sugar_at_five_prime(), protocols::stepwise::sampler::rna::modeler_sugar_at_three_prime(), core::chemical::Selector_VARIANT_TYPE::operator[](), core::chemical::Selector_MATCH_VARIANTS::operator[](), protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::pose_has_chainbreak(), protocols::stepwise::monte_carlo::mover::AddMover::prepend_residue(), core::scoring::Ramachandran2B::RamaE(), core::scoring::Ramachandran2B::RamaE_Lower(), core::scoring::Ramachandran2B::RamaE_Upper(), protocols::stepwise::modeler::rna::remove_all_variant_types(), protocols::toolbox::pose_manipulation::remove_chainbreaks_according_to_jumps(), core::import_pose::remove_cutpoints_closed(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::remove_extraneous_virtuals(), protocols::stepwise::modeler::rna::remove_virtual_O2Prime_hydrogen(), core::scoring::methods::pHEnergy::residue_energy(), core::scoring::methods::ReferenceEnergy::residue_energy(), core::import_pose::RNA_BasePairHandler::RNA_BasePairHandler(), protocols::rna::movers::RNA_LoopCloser::rna_ccd_close(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_disulfides(), core::import_pose::setup_fold_trees(), protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap(), core::pose::toolbox::AtomLevelDomainMap::setup_movemap(), protocols::stepwise::modeler::protein::setup_protein_backbone_atom_id_map(), protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::setup_sugar_modeling(), core::pose::rna::setup_three_prime_phosphate_based_on_next_residue(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_virtual_phosphate_variants(), protocols::stepwise::modeler::split_pose(), core::pose::update_block_stack_variants(), protocols::rna::denovo::movers::RNA_FragmentMover::update_insert_map(), core::pose::toolbox::AtomLevelDomainMap::update_to_move_internal_phosphates(), core::pose::toolbox::AtomLevelDomainMap::update_to_not_move_virtual_o2prime(), core::pose::toolbox::AtomLevelDomainMap::update_to_not_move_virtual_phosphates(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::verify_protonated_H1_adenosine_variants(), core::pose::rna::virtualize_5prime_phosphates(), protocols::rna::denovo::virtualize_bulges(), and core::pose::rna::virtualize_free_rna_moieties().

bool core::chemical::ResidueTypeBase::has_variant_type ( std::string const &  variant_type) const

Generic variant access by string.

References properties_.

std::string core::chemical::ResidueTypeBase::interchangeability_group ( ) const
inline

get our interchangeability-group id. Used to determine if two residue types are equivalent, except for their variant status. E.g. ResidueTypeBases ALA and ALA_Nterm would be part of the same interchangeability group. This has a degree of subjectivity; are TYR and pTYR in the same interchangeability group? Probably not. This data can be specified in the ResidueTypeBases .params file with the INTERCHANGEABILITY_GROUP tag.

References interchangeability_group_.

Referenced by core::chemical::SetInterchangeabilityGroup_String::apply(), core::chemical::ChiralFlipNaming::apply(), core::chemical::sdf::MolWriter::compose_naming(), core::chemical::MutableResidueType::placeholder_clone(), core::chemical::residue_type_bases_identical(), core::chemical::sdf::MolFileIOMolecule::set_from_extra_data(), and core::chemical::write_topology_file().

void core::chemical::ResidueTypeBase::interchangeability_group ( std::string const &  setting)
inline

set our interchangeability-group id

References interchangeability_group_.

bool core::chemical::ResidueTypeBase::is_achiral_backbone ( ) const
inline
bool core::chemical::ResidueTypeBase::is_achiral_sidechain ( ) const
inline

Does this have an achiral sidechain?

Includes gly and aib, and most (but not all) peptoids.

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

References core::chemical::ACHIRAL_SIDECHAIN, core::chemical::ResidueProperties::has_property(), and properties().

virtual bool core::chemical::ResidueTypeBase::is_base_type ( ) const
pure virtual
bool core::chemical::ResidueTypeBase::is_d_aa ( ) const
inline
bool core::chemical::ResidueTypeBase::is_d_rna ( ) const
inline
bool core::chemical::ResidueTypeBase::is_DNA ( ) const
inline
bool core::chemical::ResidueTypeBase::is_l_aa ( ) const
inline
bool core::chemical::ResidueTypeBase::is_l_rna ( ) const
inline
bool core::chemical::ResidueTypeBase::is_metapatched ( ) const
inline

Get whether this is a metapatched ResidueType.

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

References is_metapatched_.

Referenced by core::chemical::residue_type_bases_identical().

bool core::chemical::ResidueTypeBase::is_peptoid ( ) const
inline

is peptoid?

References core::chemical::ResidueProperties::has_property(), core::chemical::PEPTOID, and properties().

Referenced by protocols::cyclic_peptide::DeclareBond::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::ncbb::SecStructMinimizeMover::apply(), protocols::simple_moves::CoupledMover::apply(), core::chemical::ChiralFlipNaming::apply(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_sample_cis_peptide_bond(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_phipsi_RMSD(), core::conformation::check_good_cutpoint_neighbour(), core::pack::rotamers::SingleNCAARotamerLibraryCreator::create(), core::pack::palette::PackerPalette::decide_what_to_do_with_base_type(), core::pack::palette::PackerPalette::decide_what_to_do_with_existing_type(), protocols::stepwise::modeler::figure_out_moving_chain_breaks(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), core::pose::get_constraints_from_link_records(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_torsion_records(), protocols::cyclic_peptide::PeptideStubMover::handle_lower_terminus(), protocols::cyclic_peptide::PeptideStubMover::handle_upper_terminus(), core::scoring::methods::RamaPreProEnergy::is_allowed_type(), core::conformation::Residue::is_peptoid(), protocols::stepwise::modeler::is_protein(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::is_supported_restype(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::mutate_to_alanine(), core::conformation::Residue::orient_onto_residue_peptoid(), core::conformation::Residue::place(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), protocols::simple_moves::CyclizationMover::setup_connections(), protocols::simple_moves::RandomOmegaFlipMover::setup_torsion_list(), and protocols::simple_moves::RandomTorsionMover::setup_torsion_list().

bool core::chemical::ResidueTypeBase::is_polymer ( ) const
inline

is polymer?

References core::chemical::ResidueProperties::has_property(), core::chemical::POLYMER, and properties().

Referenced by protocols::helical_bundle_predict::HelicalBundlePredictApplication::align_to_native_pose(), protocols::simple_moves::MissingDensityToJumpMover::apply(), core::select::residue_selector::BinSelector::apply(), protocols::loophash::BackboneSegment::apply_to_pose(), core::chemical::gasteiger::assign_gasteiger_atom_types(), core::chemical::ResidueType::atom_depends_on_lower_polymeric_connection(), core::chemical::ResidueType::atom_depends_on_polymeric_connection(), core::chemical::ResidueType::atom_depends_on_upper_polymeric_connection(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::calculate_jump(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_burial(), protocols::ligand_docking::constrain_ligand_torsions(), core::scoring::ResidueExclParams::create_excl_info(), core::pack::palette::PackerPalette::decide_what_to_do_with_base_type(), core::pack::palette::PackerPalette::decide_what_to_do_with_existing_type(), core::chemical::rna::default_jump_atom(), core::chemical::ResidueType::define_mainchain_atoms(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), protocols::hybridization::discontinued_lower(), protocols::hybridization::discontinued_upper(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_derivatives(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), protocols::loops::find_non_protein_chunks(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::fragment_check(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_calc_rms_atom_id_map(), core::pose::full_model_info::FullModelParameters::get_cutpoint_open_from_pdb_info(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_rmsd_res_and_superimpose_res_in_pose(), core::conformation::get_root_residue_root_atomno(), protocols::loophash::get_rt_over_leap_fast(), core::conformation::Residue::has_lower_connect(), core::chemical::ResidueType::has_polymer_dependent_groups(), core::conformation::Residue::has_upper_connect(), protocols::stepwise::modeler::align::StepWiseClusterer::initialize_parameters(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_residue_level_screeners(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_sampler(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_screeners(), protocols::toolbox::rigid_body::initialize_stub(), core::conformation::Residue::is_polymer(), core::conformation::Residue::is_polymer_bonded(), core::pose::make_pose_from_sequence(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_3_verify_sufficient_backbone_atoms(), core::conformation::Residue::place(), core::io::serialization::read_binary(), core::chemical::ResidueDatabaseIO::report_residue_type(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_chainbreak_variants(), protocols::stepwise::monte_carlo::mover::AddMover::setup_initial_torsions(), protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), core::pose::rna::update_map(), core::chemical::ResidueType::update_polymer_dependent_groups(), and core::chemical::write_topology_file().

bool core::chemical::ResidueTypeBase::is_protein ( ) const
inline

is protein?

References core::chemical::ResidueProperties::has_property(), properties(), and core::chemical::PROTEIN.

Referenced by protocols::toolbox::pose_manipulation::add_chainbreaks_according_to_jumps(), protocols::hybridization::add_constraints(), protocols::motifs::add_motif_sc_constraints(), protocols::hybridization::HybridizeProtocol::align_by_domain(), protocols::cyclic_peptide::SymmetricCycpepAlign::align_to_origin(), protocols::cyclic_peptide::SymmetricCycpepAlign::align_to_zaxis(), protocols::stepwise::modeler::packer::SideChainCopier::apply(), protocols::dna::DesignProteinBackboneAroundDNA::apply(), protocols::dna::RestrictDesignToProteinDNAInterface::apply(), protocols::task_operations::InteractingRotamerExplosion::apply(), protocols::rbsegment_relax::OptimizeThreadingMover::apply(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::motifs::MotifDnaPacker::apply(), protocols::task_operations::JointSequenceOperation::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::ncbb::ResidueReplacementRebuildMover::apply(), protocols::calc_taskop_filters::ConservedPosMutationFilter::apply(), protocols::task_operations::SeqprofConsensusOperation::apply(), protocols::simple_moves::CoupledMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::task_operations::RestrictConservedLowDdgOperation::apply(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_peptide_plane_variants(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_terminus_variants_at_protein_rna_boundaries(), core::chemical::ResidueType::atom_index(), core::chemical::MutableResidueType::autodetermine_chi_bonds(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), core::pack::rotamer_set::build_rotated_water_rotamers(), protocols::toolbox::CA_superimpose(), protocols::flexpep_docking::FlexPepDockingPoseMetrics::calc_phipsi_RMSD(), core::simple_metrics::metrics::DihedralDistanceMetric::calculate(), protocols::hybridization::FragmentBiasAssigner::chainbreak(), protocols::simple_filters::LongestContinuousPolarSegmentFilter::compute(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), protocols::optimize_weights::IterativeOptEDriver::compute_rotamer_energies_for_assigned_pdbs(), protocols::stepwise::modeler::protein::contains_protein(), protocols::cyclic_peptide::SymmetricCycpepAlign::count_protein_residues(), protocols::calc_taskop_movers::ConsensusDesignMover::create_consensus_design_task(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::create_random_fragments(), core::scoring::hbonds::create_rotamer_descriptor(), protocols::calc_taskop_movers::ConsensusDesignMover::create_sequence_profile_constraints(), core::pack::palette::PackerPalette::decide_what_to_do_with_base_type(), core::pack::palette::PackerPalette::decide_what_to_do_with_existing_type(), core::chemical::rna::default_jump_atom(), core::scoring::methods::dfire::DFIRE_Energy::defines_residue_pair_energy(), protocols::dna::DnaInterfaceFinder::determine_dna_interface(), protocols::dna::DnaInterfaceFinder::determine_interface(), protocols::dna::DnaInterfaceFinder::determine_protein_interface(), protocols::rna::movers::determine_residues_to_rebuild(), protocols::hybridization::discontinued_lower(), protocols::hybridization::discontinued_upper(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), protocols::cyclic_peptide::SymmetricCycpepAlign::do_trim_to_single_repeat(), protocols::loops::extract_secondary_structure_chunks(), protocols::stepwise::modeler::figure_out_moving_chain_breaks(), protocols::stepwise::modeler::protein::figure_out_protein_modeling_info(), core::pose::rna::figure_out_reasonable_rna_fold_tree(), protocols::stepwise::modeler::movemap::figure_out_stepwise_movemap(), protocols::stepwise::modeler::packer::figure_out_working_interface_res(), protocols::pmut_scan::PointMutScanDriver::fill_mutations_list(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood(), protocols::rna::movers::find_nearby_res(), protocols::loops::find_non_protein_chunks(), core::scoring::cryst::fix_bfactorsMissing(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::fix_phi_psi_offsets(), protocols::stepwise::modeler::fix_protein_jump_atom(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), protocols::constraint_movers::AddConstraintsToCurrentConformationMover::generate_coordinate_constraints(), protocols::stepwise::modeler::protein::get_bridge_res(), protocols::match::BfactorMPM::get_ca_bfactors(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_calc_rms_atom_id_map(), core::scoring::elec::FA_ElecEnergy::get_countpair_representative_atom(), core::pose::full_model_info::FullModelParameters::get_cutpoint_open_from_pdb_info(), protocols::hybridization::InsertChunkMover::get_local_sequence_mapping(), core::scoring::HydroxylTorsionPotential::get_restag(), core::scoring::methods::get_restag(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::get_stepwise_jump_atom(), core::pose::rna::get_suite_torsion_info(), core::sequence::ABEGOManager::get_symbols(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_torsion_records(), core::scoring::bin_transitions::BinTransitionData::has_property(), protocols::dna::DnaInterfacePacker::init_standard(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::initialize(), protocols::dna::DnaInterfaceMultiStateDesign::initialize(), core::scoring::FACTSRsdTypeInfo::initialize_intrascale(), protocols::stepwise::modeler::align::StepWiseClusterer::initialize_parameters(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::initialize_phi_psi_offsets(), protocols::toolbox::rigid_body::initialize_stub(), core::scoring::methods::RamaPreProEnergy::is_allowed_type(), protocols::stepwise::modeler::is_protein(), core::conformation::Residue::is_protein(), core::scoring::is_protein_sidechain_heavyatom(), protocols::stepwise::modeler::protein::just_protein(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::let_neighboring_chis_minimize(), protocols::features::ResidueConformationFeatures::load_conformation(), protocols::features::ProteinResidueConformationFeatures::load_conformation(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), protocols::ncbb::ResidueReplacementRebuildMover::make_new_pose(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::make_pose(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), protocols::match::AddAllPositionsMPM::modified_match_positions(), protocols::match::RemoveNorCTermMPM::modified_match_positions(), protocols::loops::native_loop_core_CA_rmsd(), protocols::stepwise::modeler::output_movemap(), protocols::hybridization::MRMover::pack_missing_sidechains(), protocols::hybridization::BackboneTorsionSampler::perturb(), protocols::hybridization::BackboneTorsionPerturbation::perturb(), protocols::comparative_modeling::pick_loops_chainbreak(), protocols::rna::movers::ErraserMinimizerMover::pose_preliminaries(), protocols::motifs::MotifSearch::position_vector_setup(), protocols::motifs::LigandMotifSearch::position_vector_setup(), protocols::toolbox::DecoySetEvaluation::push_back(), protocols::hybridization::TMalign::read_pose(), protocols::pose_metric_calculators::HPatchCalculator::recompute(), protocols::pose_metric_calculators::SurfaceCalculator::recompute(), protocols::pose_metric_calculators::ChargeCalculator::recompute(), protocols::pose_metric_calculators::PackstatCalculator::recompute(), protocols::pose_metric_calculators::NonlocalContactsCalculator::recompute(), protocols::toolbox::pose_manipulation::remove_non_protein_residues(), core::pose::remove_nonprotein_residues(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::RotamericSingleResidueDunbrackLibrary(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::save_phi_psi_offsets(), protocols::cyclic_peptide::SymmetricCycpepAlign::select_protein_residues(), core::pose::set_ss_from_phipsi(), protocols::simple_moves::CyclizationMover::setup_connections(), core::import_pose::setup_fold_trees(), protocols::enzdes::EnzdesScorefileFilter::setup_pose_metric_calculators(), protocols::stepwise::modeler::protein::setup_protein_backbone_atom_id_map(), protocols::simple_moves::RandomOmegaFlipMover::setup_torsion_list(), protocols::simple_moves::RandomTorsionMover::setup_torsion_list(), core::pose::transfer_phi_psi(), core::pose::rna::update_map(), protocols::rna::movers::ErraserMinimizerMover::vary_bond_geometry(), and protocols::stepwise::modeler::virtualize_side_chains().

bool core::chemical::ResidueTypeBase::is_r_peptoid ( ) const
inline

Is this a peptoid with a chiral side-chain with "R" chirality?

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

References core::chemical::ResidueProperties::has_property(), properties(), and core::chemical::R_PEPTOID.

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

bool core::chemical::ResidueTypeBase::is_RNA ( ) const
inline

is RNA?

References core::chemical::ResidueProperties::has_property(), properties(), and core::chemical::RNA.

Referenced by core::import_pose::add_block_stack_variants(), core::pose::rna::add_chi_constraints(), core::pose::rna::add_virtual_O2Prime_hydrogen(), protocols::stepwise::monte_carlo::mover::AddMover::append_residue(), protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::apply(), protocols::stepwise::modeler::packer::SideChainCopier::apply(), protocols::stepwise::legacy::modeler::rna::apply_chi_cst(), protocols::simple_moves::apply_ideal_coordinates_for_alternative_pucker(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_terminus_variants_at_protein_rna_boundaries(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_virtual_phosphate_variants(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_virtual_phosphate_variants(), core::pose::rna::assert_phosphate_nomenclature_matches_mini(), core::chemical::MutableResidueType::autodetermine_chi_bonds(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), core::import_pose::RNA_BasePairHandler::check_base_pairs(), protocols::stepwise::modeler::rna::check_instantiated_O2Prime_hydrogen(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::copy_rna_chi(), core::pose::correctly_add_2prime_connection_variants(), core::pose::correctly_add_cutpoint_variants(), protocols::stepwise::modeler::align::create_alignment_id_map_legacy(), core::scoring::methods::IdealParametersDatabase::create_parameters_for_restype(), core::pack::palette::PackerPalette::decide_what_to_do_with_base_type(), core::chemical::rna::default_jump_atom(), core::pose::rna::detect_base_contacts(), core::pose::rna::detect_phosphate_contacts(), core::pose::rna::detect_sugar_contacts(), protocols::rna::movers::determine_residues_to_rebuild(), protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks(), protocols::stepwise::modeler::rna::sugar::VirtualSugarJustInTimeInstantiator::do_the_modeler(), core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative(), core::pose::rna::extract_rna_chains(), protocols::stepwise::modeler::figure_out_moving_chain_breaks(), core::pose::rna::figure_out_reasonable_rna_fold_tree(), core::pose::rna::figure_out_rna_chains(), protocols::stepwise::modeler::movemap::figure_out_stepwise_movemap(), protocols::stepwise::modeler::packer::figure_out_working_interface_res(), core::pose::fix_up_residue_type_variants_at_floating_base(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_calc_rms_atom_id_map(), core::pose::full_model_info::FullModelParameters::get_cutpoint_open_from_pdb_info(), core::scoring::methods::FreeDOF_Energy::get_hbond_energy(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_reference_xyz(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_reference_xyz_average(), core::scoring::methods::get_restag(), core::io::silent::SilentStructFactory::get_silent_struct_out(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::get_stepwise_jump_atom(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_wc_near_o2prime(), core::scoring::constraints::BasePairConstraint::init_subsidiary_constraints(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_moving_residue_pose_list(), protocols::stepwise::modeler::align::StepWiseClusterer::initialize_parameters(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_pose_level_screeners(), core::import_pose::libraries::RNA_ChunkLibrary::initialize_rna_chunk_library(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_sampler(), core::chemical::ResidueType::is_NA(), core::conformation::Residue::is_RNA(), core::scoring::rna::StackElecEnergy::is_rna_base(), core::pose::rna::is_torsion_valid(), protocols::stepwise::modeler::rna::just_rna(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::let_neighboring_chis_minimize(), core::pose::rna::mutate_position(), protocols::rna::denovo::movers::RNA_Minimizer::o2prime_trials(), protocols::stepwise::modeler::rna::o2prime_trials(), protocols::stepwise::modeler::output_movemap(), protocols::rna::movers::RNA_LoopCloser::passes_fast_scan(), core::pose::pdbslice(), protocols::stepwise::monte_carlo::mover::AddMover::prepend_residue(), core::import_pose::put_in_cutpoint(), core::scoring::constraints::BasePairConstraint::read_def(), core::pose::rna::remove_upper_lower_variants_from_RNA(), core::pose::toolbox::AtomID_Mapper::renumber_after_variant_changes(), core::import_pose::RNA_BasePairHandler::RNA_BasePairHandler(), core::import_pose::RNA_BasePairHandler::setup_base_pair_constraints(), core::pose::rna::setup_base_pair_constraints(), protocols::rna::denovo::setup_coarse_chainbreak_constraints(), core::import_pose::setup_fold_trees(), protocols::stepwise::monte_carlo::mover::AddMover::setup_initial_torsions(), protocols::rna::denovo::movers::RNA_Minimizer::setup_movemap(), core::pose::rna::setup_three_prime_phosphate_based_on_next_residue(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_virtual_phosphate_variants(), protocols::stepwise::modeler::split_pose(), protocols::rna::denovo::movers::RNA_FragmentMover::update_insert_map(), core::pose::rna::update_map(), core::pose::toolbox::AtomLevelDomainMap::update_to_move_internal_phosphates(), core::pose::rna::virtualize_5prime_phosphates(), protocols::rna::denovo::virtualize_bulges(), core::pose::rna::virtualize_free_rna_moieties(), protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::virtualize_poor_scoring_o2prime_hydrogens(), and protocols::stepwise::modeler::virtualize_side_chains().

bool core::chemical::ResidueTypeBase::is_s_peptoid ( ) const
inline

Is this a peptoid with a chiral side-chain with "S" chirality?

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

References core::chemical::ResidueProperties::has_property(), properties(), and core::chemical::S_PEPTOID.

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

bool core::chemical::ResidueTypeBase::mainchain_potentials_match ( ResidueTypeBase const &  other) const
utility::vector1< std::string >& core::chemical::ResidueTypeBase::metal_binding_atoms ( )
inlineprotected
MMAtomTypeSetCOP core::chemical::ResidueTypeBase::mm_atom_types_ptr ( ) const
inline
TypeSetMode core::chemical::ResidueTypeBase::mode ( ) const
inline

References mode_.

Referenced by core::pose::add_custom_variant_type_to_pose_residue(), core::scoring::rna::data::RNA_DMS_Potential::add_probe_to_pose(), core::pose::add_variant_type_to_pose_residue(), core::pose::add_variant_type_to_residue(), protocols::kinmatch::alapose(), protocols::seeded_abinitio::GrowPeptides::append_residues_cterminally(), protocols::seeded_abinitio::GrowPeptides::append_residues_nterminally(), protocols::matdes::SchemePlaceMotifsMover::apply(), protocols::cyclic_peptide::FlipChiralityMover::apply(), protocols::simple_moves::RepulsiveOnlyMover::apply(), protocols::simple_moves::ModifyVariantTypeMover::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::simple_moves::ReportEffectivePKA::apply(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), core::pose::rna::assert_phosphate_nomenclature_matches_mini(), core::pack::rotamer_set::build_anchorless_water_rotamers(), core::pack::rotamer_set::build_fixed_O_water_rotamers_independent(), core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::pack::rotamer_set::build_moving_O_water_rotamers_independent(), core::pack::rotamer_set::build_single_anchor_water_rotamers_independet(), core::scoring::rna::RNP_LowResPairDistPotential::calc_rnp_pair_dist_score(), protocols::fldsgn::BluePrintBDR::centroid_build(), protocols::forge::components::BDR::centroid_build(), protocols::ligand_docking::HighResDocker::enable_ligand_rotamer_packing(), protocols::ligand_docking::ProtLigEnsemble::enable_ligand_rotamer_packing(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_dof_derivative(), core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::find_disulfides(), core::util::generate_replacement_restype(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), core::pose::toolbox::AtomID_Mapper::initialize(), protocols::magnesium::instantiate_water_at_octahedral_vertex(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent_helper(), protocols::simple_moves::MutateResidue::make_mutation(), protocols::environment::ProtectedConformation::match_variants(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), core::pose::rna::mutate_position(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::orient_rotamer_to_symmetric_partner(), protocols::magnesium::MgWaterHydrogenPacker::pack_mg_water_hydrogens_in_pose(), core::scoring::motif::Xfres::place_sidechain_in_pose(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), protocols::stepwise::modeler::rna::phosphate::position_five_prime_phosphate_SLOW(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), core::pose::remove_variant_type_from_pose_residue(), core::pose::remove_variant_type_from_residue(), core::pack::dunbrack::cenrot::CenRotDunEnergy::residue_energy(), core::scoring::disulfides::CentroidDisulfideEnergy::residue_pair_energy(), core::scoring::rna::RNA_VDW_Energy::residue_pair_energy(), core::scoring::methods::HybridVDW_Energy::residue_pair_energy(), core::scoring::rna::RNP_LowResPairDistEnergy::residue_pair_energy(), core::scoring::rna::RNP_LowResEnergy::residue_pair_energy(), core::chemical::residue_type_bases_identical(), core::scoring::rna::RNP_LowResEnergy::setup_for_scoring(), protocols::constraints_additional::COMCoordinateConstraint::setup_for_scoring(), protocols::constraints_additional::BindingSiteConstraint::setup_for_scoring(), core::pose::Pose::virtual_to_real(), and core::io::serialization::write_binary().

Size core::chemical::ResidueTypeBase::n_orbitals ( ) const
virtual Size core::chemical::ResidueTypeBase::n_virtual_atoms ( ) const
pure virtual

Counts the number of virtual atoms and returns the count.

The virtual count is not stored in the resiude type. This count is performed on the fly, and can hurt performance if reapeatedly carried out. Not intended for use in large loops – instead, call once and store the value.

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

Implemented in core::chemical::ResidueType, and core::chemical::MutableResidueType.

void core::chemical::ResidueTypeBase::na_analogue ( std::string const &  type)
inline
AA const& core::chemical::ResidueTypeBase::na_analogue ( ) const
inline

Returns the nucleic acid type to be used for fragment sampling/scoring.

References aa_, core::chemical::aa_unp, and na_analogue_.

AA const& core::chemical::ResidueTypeBase::na_analogue_raw ( ) const
inlineprotected
std::string const& core::chemical::ResidueTypeBase::name ( ) const
inline

get our (unique) residue name

References name_.

Referenced by core::chemical::MutableResidueType::add_actcoord_atom(), core::chemical::MutableResidueType::add_atom(), core::chemical::MutableResidueType::add_atom_alias(), core::chemical::MutableResidueType::add_bond(), core::chemical::MutableResidueType::add_chi(), protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::legacy_sewing::Assembly::add_loop_segment(), core::chemical::MutableResidueType::add_metapatch_connect(), protocols::pack_daemon::DaemonSet::add_pack_daemon(), protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::pack::dunbrack::RotamerConstraint::add_residue(), core::scoring::GenBondedExclInfo::add_residue_exclude_torsions(), core::pack::rotamer_set::UnboundRotamersOperation::alter_rotamer_set(), core::conformation::Conformation::append_residue_by_bond(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::oop::OopPatcher::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::carbohydrates::IdealizeAnomericHydrogens::apply(), protocols::antibody::AntibodyModelerProtocol::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::denovo_design::movers::DeclareStructureDataCovalentBondMover::apply(), protocols::simple_moves::CopyRotamerMover::apply(), protocols::minimization_packing::DisulfideOptimizationMover::apply(), protocols::task_operations::RestrictNativeResiduesOperation::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::simple_moves::sidechain_moves::SidechainMover::apply(), core::chemical::DeleteAtom::apply(), core::chemical::SetBackboneHeavyatom::apply(), core::chemical::Patch::apply(), core::chemical::SetPolymerConnectAtom::apply(), core::chemical::AddChi::apply(), core::chemical::RedefineChi::apply(), core::chemical::DeleteTerminalChi::apply(), core::chemical::ClearChiRotamers::apply(), core::chemical::AddAtom::apply(), core::chemical::AddBond::apply(), core::chemical::SetAtomicCharge::apply(), core::chemical::SetFormalCharge::apply(), core::chemical::SetAtomType::apply(), core::chemical::SetMMAtomType::apply(), core::chemical::ChangeAncestory::apply(), core::chemical::ResetBondLength::apply(), core::chemical::PrependMainchainAtom::apply(), core::chemical::AppendMainchainAtom::apply(), core::chemical::ReplaceMainchainAtom::apply(), core::chemical::SetNbrAtom::apply(), core::chemical::ConnectSulfurAndMakeVirtualProton::apply(), core::chemical::ChiralFlipNaming::apply(), core::chemical::AddConnectAndTrackingVirt::apply(), core::chemical::SetVirtualShadow::apply(), core::chemical::SetDisulfideAtomName::apply(), core::chemical::apply_adducts_to_residue(), protocols::simple_moves::CopyRotamerMover::apply_from_template_pose(), core::chemical::MutableResidueType::assign_internal_coordinates(), core::chemical::MutableResidueType::assign_neighbor_atom(), core::chemical::MutableResidueType::atom_base(), core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_name(), core::chemical::MutableResidueType::autodetermine_chi_bonds(), core::scoring::automorphic_rmsd(), core::chemical::MutableResidueType::bond(), core::pack::rotamers::SingleLigandRotamerLibrary::build_base_rotamers(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), core::scoring::lkball::LKB_ResidueInfo::build_waters(), core::chemical::MutableICoorRecord::buildable(), core::scoring::sc::ElectrostaticComplementarityCalculator::Calc(), core::scoring::sc::MolecularSurfaceCalculator::Calc(), core::simple_metrics::metrics::SequenceMetric::calculate(), core::scoring::SplitUnfoldedTwoBodyPotential::calculate_residue_emap(), core::chemical::calculate_rigid_matrix(), core::chemical::MutableResidueType::change_bond_type(), protocols::features::ProteinResidueConformationFeatures::check_num_requested_atoms(), core::chemical::check_residue_has_atom(), core::chemical::clean_up_dangling_connect(), core::chemical::sdf::MolWriter::compose_metadata(), core::chemical::sdf::MolWriter::compose_naming(), protocols::simple_filters::MutationsFilter::compute(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::compute(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_burial(), core::conformation::Residue::connect_atom(), core::chemical::ResidueType::copy_atom_info(), core::chemical::ResidueType::copy_other_info(), core::pack::rotamers::SingleNCAARotamerLibraryCreator::create(), core::scoring::etable::count_pair::CountPairFactory::create_count_pair_function_and_invoke(), core::scoring::ResidueExclParams::create_excl_info(), protocols::legacy_sewing::create_model_from_pose(), core::chemical::ResidueType::define_mainchain_atoms(), core::chemical::MutableResidueType::delete_atom(), core::chemical::MutableResidueType::delete_chi(), core::chemical::MutableResidueType::delete_child_proton(), core::chemical::MutableResidueType::delete_nu(), core::chemical::MutableResidueType::delete_ring(), protocols::relax::delete_virtual_residues(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::chemical::detect_ld_chirality_from_polymer_residue(), core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), core::import_pose::atom_tree_diffs::dump_reference_pose(), core::chemical::MutableResidueType::dump_vd_info(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), protocols::match::upstream::FullChiSampleSet::expand_non_dunbrack_chi(), core::pack::rotamers::SingleResidueRotamerLibrary::expand_proton_chis(), core::chemical::fill_ideal_xyz_from_icoor(), core::pack::rotamers::SingleBasicRotamerLibrary::fill_rotamer_vector(), core::chemical::find_nbr_dist(), core::scoring::methods::IdealParametersDatabase::generate_impropers_map_res(), core::scoring::mm::MMBondAngleResidueTypeParamSet::get(), core::pose::motif::get_AIDs(), core::conformation::get_anchor_and_root_atoms(), protocols::simple_moves::chiral::get_chiral_residue_type(), core::scoring::elec::GroupElec::get_group(), core::scoring::elec::CountPairRepMap::get_map(), core::chemical::ResidueType::get_metal_binding_atoms(), protocols::hbnet::HBNet::get_native_networks(), core::scoring::GenBondedExclInfo::get_residue_data(), core::chemical::ResidueTypeSet::get_residue_type_with_custom_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), core::scoring::methods::get_restag(), core::scoring::SplitUnfoldedTwoBodyPotential::get_restype_emap(), core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), core::scoring::FACTSRsdTypeMap::get_type_info(), core::scoring::lkball::LKB_ResidueInfo::get_water_builder(), core::chemical::has_assigned_coords(), core::chemical::ICoorAtomID::ICoorAtomID(), protocols::topology_broker::TopologyBroker::initialize_cuts(), core::chemical::ResidueType::initialize_derived_data(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_generic_polymer_bond_sampler(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_ligand_bond_sampler(), core::scoring::FACTSRsdTypeInfo::initialize_parameters(), core::scoring::lkball::LKBallDatabase::initialize_residue_type(), protocols::features::HBondFeatures::insert_site_row(), core::pack::dunbrack::load_unboundrot(), core::chemical::make_centroid(), protocols::ncbb::ResidueReplacementRebuildMover::make_new_pose(), protocols::rotamer_recovery::RRComparerAutomorphicRMSD::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerElecDensDiff::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerRotBins::measure_rotamer_recovery(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), core::pose::MiniPose::MiniPose(), protocols::rna::movers::ErraserMinimizerMover::movemap_setup(), core::pose::rna::mutate_position(), core::conformation::Residue::name(), core::pose::named_atom_id_to_atom_id(), core::scoring::nmr::NMRDummySpinlabelConformer::NMRDummySpinlabelConformer(), core::import_pose::libraries::one_letter_from_rt(), core::conformation::Residue::orient_onto_residue(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_3_verify_sufficient_backbone_atoms(), core::chemical::Patch::patched_name(), core::chemical::ResidueType::perform_checks(), core::chemical::MutableResidueType::placeholder_clone(), core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff(), protocols::backrub::positions_incompatible_with_task(), core::chemical::pretty_print_atomicoor(), core::chemical::print_chis(), core::chemical::ResidueDatabaseIO::read_residue_type(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), core::io::pose_from_sfr::remap_names_on_geometry(), core::pose::remove_virtual_residues(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::chemical::ResidueDatabaseIO::report_residue_type_bond(), core::chemical::ResidueDatabaseIO::report_residue_type_chi(), core::chemical::ResidueDatabaseIO::report_residue_type_chi_rotamer(), core::chemical::ResidueDatabaseIO::report_residue_type_cut_bond(), core::chemical::ResidueDatabaseIO::report_residue_type_icoor(), core::chemical::ResidueDatabaseIO::report_residue_type_properties(), core::chemical::ResidueDatabaseIO::report_residue_type_proton_chi(), core::chemical::ResidueDatabaseIO::report_residue_type_variant(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), protocols::rna::movers::ERRASER2Protocol::resample_full_model(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::residue_conformations_redundant(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::chemical::residue_type_all_patches_name(), core::chemical::residue_type_base_name(), core::chemical::residue_type_bases_identical(), core::chemical::ResidueType::ResidueType(), protocols::rna::movers::RNA_LoopCloser::rna_ccd_close(), core::scoring::rna::rna_residue_type_to_num(), core::chemical::rosetta_recharge_fullatom(), core::pack::rotamers::rotamer_information_from_PDB_stream(), protocols::ligand_docking::rotamers_for_trials(), core::scoring::ResidueExclParams::rsd1type(), core::scoring::ResidueExclParams::rsd2type(), core::scoring::ResidueExclParams::same_rsdpairs(), protocols::match::upstream::DunbrackSCSampler::samples(), protocols::relax::RepeatProteinRelax::seal_jumps(), core::chemical::ResidueType::select_orient_atoms(), core::chemical::MutableResidueType::set_backbone_heavyatom(), core::chemical::mainchain_potential::MainchainScoreTable::set_dimension_and_ntorsions_for_restype(), core::chemical::sdf::MolFileIOMolecule::set_from_extra_data(), protocols::match::set_ligpose_rotamer(), core::scoring::lkball::LKBallDatabase::setup_atom_weights(), core::scoring::GenericBondedPotential::setup_for_scoring(), core::chemical::setup_patch_atomic_charge_reassignments_from_commandline(), core::scoring::lkball::setup_water_builders_for_residue_type(), core::chemical::MutableResidueType::show(), core::chemical::ResidueType::show(), core::chemical::RerootRestypeVisitor::start_vertex(), core::pack::rotamers::SingleResidueRotamerLibraryFactory::type_for_residuetype(), core::chemical::MutableResidueType::update_atom_type_set(), core::chemical::ResidueType::update_derived_data(), core::pose::rna::update_edge_hbond_numbers(), core::chemical::MutableResidueType::validate_residue_type(), core::io::serialization::write_binary(), core::chemical::write_graphviz(), core::chemical::ResidueTypeKinWriter::write_kin_header(), core::chemical::ResidueDatabaseIO::write_residuetype_to_database(), and core::chemical::write_topology_file().

void core::chemical::ResidueTypeBase::name ( std::string const &  name_in)
inline

set our (unique) residue name

References name_, and properties_.

char core::chemical::ResidueTypeBase::name1 ( ) const
inline

get our 1letter code. This is set in the ResidueTypeBase .params file through the IO_STRING tag along with the name3 string.

References name1_.

Referenced by core::chemical::SetIO_String::apply(), core::simple_metrics::metrics::SequenceMetric::calculate(), core::pose::Pose::chain_sequence(), core::pose::full_model_info::check_full_model_info_OK(), protocols::relax::membrane::check_mutants_ok(), core::chemical::sdf::MolWriter::compose_naming(), protocols::simple_filters::BuriedSurfaceAreaFilter::compute(), protocols::simple_filters::BuriedSurfaceAreaFilter::compute_residue_selection(), protocols::rna::denovo::create_rna_vall_torsions(), core::chemical::rna::default_jump_atom(), core::pose::rna::detect_base_contacts(), protocols::contact_map::ContactMap::fill_contacts(), protocols::contact_map::ContactMap::fill_contacts_all_atom2(), core::pose::rna::get_number_native_base_pairs(), protocols::loophash::get_rt_over_leap_without_foldtree_bs(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_torsion_records(), core::scoring::constraints::BasePairConstraint::init_subsidiary_constraints(), core::conformation::Residue::name1(), core::import_pose::libraries::one_letter_from_rt(), core::chemical::Selector_NAME1::operator[](), protocols::score_filters::ScoreCutoffFilter::output_residue_pair_energies(), core::chemical::ResidueType::perform_checks(), core::chemical::MutableResidueType::placeholder_clone(), protocols::rna::denovo::print_hbonds(), protocols::hybridization::TMalign::read_pose(), core::chemical::ResidueDatabaseIO::read_residue_type(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::scoring::methods::HRFDynamicsEnergy::residue_energy(), core::scoring::methods::CovalentLabelingFAEnergy::residue_energy(), core::chemical::residue_type_bases_identical(), core::scoring::rna::rna_residue_type_to_num(), core::pose::Pose::sequence(), core::chemical::sdf::MolFileIOMolecule::set_from_extra_data(), core::pose::rna::setup_base_pair_constraints(), core::chemical::setup_patch_atomic_charge_reassignments_from_commandline(), core::chemical::MutableResidueType::show(), core::chemical::ResidueType::show(), core::scoring::rna::RNA_AtomVDW::vdw_atom_list(), core::chemical::ResidueTypeKinWriter::write_kin_header(), and core::chemical::write_topology_file().

void core::chemical::ResidueTypeBase::name1 ( char const  code)
inline

set our 1letter code

References name1_.

std::string const& core::chemical::ResidueTypeBase::name3 ( ) const
inline

get our 3letter code. This is set in the ResidueTypeBase .params file through the IO_STRING tag along with the name1 string NOTE: The "name3" is not necessarily three characters long. e.g. Metal ions may be only two characters.

If you need three characters, the PDB convention is to right pad.

References name3_.

Referenced by protocols::loops::add_loop(), core::chemical::MutableResidueType::add_metalbinding_atom(), protocols::comparative_modeling::StealSideChainsMover::apply(), protocols::dna::WatsonCrickRotamerCouplings::apply(), protocols::farnesyl::SampleFarnesylMover::apply(), protocols::dna_dock::PropagateClashCheckFilter::apply(), protocols::enzdes::AddRigidBodyLigandConfs::apply(), core::chemical::SetIO_String::apply(), core::chemical::ChiralFlipNaming::apply(), core::chemical::MutableResidueType::atom_vertex(), protocols::forge::remodel::RemodelEnzdesCstModule::blueprint_cst_definition(), protocols::ligand_docking::MoveMapBuilder::build(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), core::chemical::rotamers::NCAARotamerLibrarySpecification::cache_tag(), protocols::features::strand_assembly::cal_shortest_dis_between_facing_aro_in_sw(), core::simple_metrics::metrics::SequenceMetric::calculate(), core::scoring::SplitUnfoldedTwoBodyPotential::calculate_residue_emap(), core::chemical::AutomorphismIterator::can_pair(), core::pose::full_model_info::check_full_model_info_OK(), protocols::features::strand_assembly::check_heading_direction(), protocols::features::strand_assembly::check_LR(), protocols::features::strand_assembly::check_PA(), protocols::features::strand_assembly::check_whether_sheets_are_connected_with_near_bb_atoms(), core::chemical::sdf::MolWriter::compose_metadata(), core::chemical::sdf::MolWriter::compose_naming(), protocols::simple_filters::ResidueIEFilter::compute(), protocols::simple_filters::BuriedSurfaceAreaFilter::compute(), protocols::simple_filters::ResidueIEFilter::compute_resnums(), protocols::flxbb::constraints_sheet(), protocols::enzdes::PoseFoundResiduesCombination::construct_and_dump_outpose(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoASP(), protocols::flexpep_docking::FlexPepDockingAbInitio::convertPSERtoGLU(), protocols::features::strand_assembly::count_AA_w_direction(), protocols::features::strand_assembly::count_AA_wo_direction(), core::pack::rotamers::SingleNCAARotamerLibraryCreator::create(), core::scoring::ResidueExclParams::create_excl_info(), core::chemical::ResidueType::debug_dump_icoor(), core::chemical::rna::default_jump_atom(), core::chemical::MutableResidueType::delete_actcoord_atom(), core::chemical::MutableResidueType::delete_metalbinding_atom(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), protocols::features::strand_assembly::determine_core_heading_surface_heading_by_distance(), protocols::features::strand_assembly::determine_heading_direction_by_vector(), core::pack::rotamer_set::RotamerSubset::different_resgroup(), core::pack::rotamer_set::different_resgroup(), core::scoring::constraints::NonResidueTypeConstraint::dist(), core::scoring::constraints::ResidueTypeConstraint::dist(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::dof_id_ranges(), protocols::simple_moves::sidechain_moves::SidechainMover::dof_id_ranges(), core::scoring::methods::dfire::DFIRE_Potential::eval_dfire_pair_energy(), protocols::stepwise::modeler::StepWiseMinimizer::figure_out_working_minimize_res(), core::io::pose_from_sfr::PoseFromSFRBuilder::fill_name_map(), protocols::cyclic_peptide::crosslinker::TMA_Helper::filter_by_sidechain_distance_symmetric(), protocols::enzdes::SecondaryMatchProtocol::find_all_allowed_positions(), protocols::magnesium::fix_water_jump(), protocols::ligand_docking::frac_atoms_within(), protocols::constraint_generator::ResidueTypeConstraintGenerator::generate_residue_type_constraints(), protocols::features::strand_assembly::get_aro_residues_in_this_sheet(), core::chemical::rna::get_base_pair_atoms(), core::pose::get_constraints_from_link_records(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::get_fixed_pt(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_link_record(), core::scoring::elec::CountPairRepMap::get_map(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_residue_information(), core::scoring::HydroxylTorsionPotential::get_restag(), core::scoring::methods::get_restag(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_ssbond_record(), protocols::canonical_sampling::MetricRecorder::get_torsion_ids(), protocols::simple_moves::DOFHistogramRecorder::insert_dofs_by_residue(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::is_residue_allowed(), core::conformation::Residue::is_similar_rotamer(), protocols::ligand_docking::LigandBaseProtocol::make_movemap(), core::conformation::Residue::name3(), protocols::legacy_sewing::Assembly::native_positions(), core::pack::task::operation::ResidueName3Is::operator()(), core::chemical::Selector_NAME3::operator[](), orbital_index(), core::scoring::constraints::parse_NMR_name_old(), core::chemical::ResidueType::perform_checks(), core::chemical::MutableResidueType::placeholder_clone(), protocols::features::strand_assembly::prepare_and_write_number_of_electrostatic_interactions_of_residues_to_files(), protocols::dna::DnaChains::print(), protocols::ligand_docking::print_buried_unsat_Hbonds(), protocols::match::output::print_node(), core::conformation::print_node(), protocols::viewer::print_node(), protocols::match::MatcherMover::process_pose(), core::scoring::aa_composition_energy::AACompositionPropertiesSet::properties_match_this(), protocols::dna::DnaInterfacePacker::protein_scan(), core::chemical::ResidueDatabaseIO::read_residue_type(), report_adducts(), protocols::features::ScreeningFeatures::report_features(), core::chemical::ResidueDatabaseIO::report_residue_type(), core::scoring::methods::UnfoldedStateEnergy::residue_energy(), core::chemical::residue_type_bases_identical(), core::chemical::sdf::MolFileIOMolecule::set_from_extra_data(), protocols::simple_moves::CyclizationMover::setup_connections(), core::conformation::setup_corresponding_atoms(), core::scoring::methods::GoapEnergy::setup_for_scoring(), protocols::magnesium::MgMonteCarlo::setup_mg_water_fold_tree(), core::chemical::setup_patch_atomic_charge_reassignments_from_commandline(), core::scoring::hbonds::HBond::show(), core::chemical::MutableResidueType::show(), core::chemical::ResidueType::show(), protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(), protocols::magnesium::update_mg_hoh_fold_tree(), protocols::features::strand_assembly::write_beta_sheet_capping_info_to_a_file(), core::chemical::ResidueTypeKinWriter::write_kin_header(), protocols::features::strand_assembly::write_number_of_electrostatic_interactions_of_residues_to_files(), protocols::features::strand_assembly::write_p_aa_pp_of_AAs_to_a_file(), protocols::features::strand_assembly::write_phi_psi_of_each_residue_to_a_file(), protocols::features::strand_assembly::write_rama_of_AAs_to_a_file(), core::chemical::write_topology_file(), and protocols::features::strand_assembly::WriteToDB_turn_AA().

void core::chemical::ResidueTypeBase::name3 ( std::string const &  name_in)
inline

set our 3letter code

References name3_.

virtual Size core::chemical::ResidueTypeBase::natoms ( ) const
pure virtual
virtual Size core::chemical::ResidueTypeBase::nbonds ( ) const
pure virtual
signed long int core::chemical::ResidueTypeBase::net_formal_charge ( ) const
inline

Get the nominal net formal charge on this residue type.

This may not match the sum of the formal charges on the atoms

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

References net_formal_charge_.

Referenced by core::chemical::SetNetFormalCharge::apply(), core::scoring::netcharge_energy::NetChargeEnergy::calculate_energy(), core::chemical::residue_type_bases_identical(), and core::chemical::write_topology_file().

void core::chemical::ResidueTypeBase::net_formal_charge ( signed long int  charge_in)
inline

Set the nominal net formal charge on this residue type.

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

References net_formal_charge_.

virtual Size core::chemical::ResidueTypeBase::nheavyatoms ( ) const
pure virtual

number of heavy atoms

Implemented in core::chemical::ResidueType, and core::chemical::MutableResidueType.

ResidueTypeBase& core::chemical::ResidueTypeBase::operator= ( ResidueTypeBase const &  )
protecteddefault
Orbital const & core::chemical::ResidueTypeBase::orbital ( Size const  orbital_index) const
Orbital const & core::chemical::ResidueTypeBase::orbital ( std::string const &  orbital_name) const

References orbital_index(), and orbitals_.

core::Size core::chemical::ResidueTypeBase::orbital_index ( std::string const &  name) const
orbitals::OrbitalType const & core::chemical::ResidueTypeBase::orbital_type ( Size const  orbital_index) const
orbitals::OrbitalTypeSetCOP core::chemical::ResidueTypeBase::orbital_types_ptr ( ) const
inline

Get the MM atom_type for this atom by its index number in this residue.

References orbital_types_.

Referenced by core::chemical::MutableResidueType::add_orbital(), core::chemical::MutableResidueType::placeholder_clone(), and core::chemical::residue_type_bases_identical().

ResidueProperties const& core::chemical::ResidueTypeBase::properties ( ) const
inline

Access the collection of properties for this ResidueTypeBase.

References properties_.

Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::simple_moves::hbs::HbsPatcher::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), core::select::residue_selector::ResiduePropertySelector::apply(), core::chemical::AddConnectAndTrackingVirt::apply(), core::chemical::sdf::MolWriter::compose_rosetta_properties(), protocols::toolbox::pose_manipulation::construct_poly_uniq_restype_pose(), protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(), protocols::enzdes::EnzdesBaseProtocol::cst_minimize(), core::conformation::form_disulfide_helper(), protocols::simple_moves::chiral::get_chiral_residue_type(), core::chemical::ResidueTypeSet::get_residue_type_with_custom_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_added(), core::chemical::ResidueTypeSet::get_residue_type_with_variant_removed(), core::chemical::ResidueType::has_sc_orbitals(), protocols::abinitio::abscript::RigidChunkCM::initialize(), core::chemical::ResidueType::initialize_derived_data(), core::chemical::ResidueType::is_acetylated_nterminus(), is_achiral_backbone(), is_achiral_sidechain(), core::chemical::ResidueType::is_adduct(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_aramid(), core::chemical::ResidueType::is_aromatic(), core::chemical::ResidueType::is_beta_aa(), core::chemical::ResidueType::is_branch_point(), core::chemical::ResidueType::is_canonical_aa(), core::chemical::ResidueType::is_canonical_nucleic(), core::chemical::ResidueType::is_carbohydrate(), core::chemical::ResidueType::is_charged(), core::chemical::ResidueType::is_coarse(), core::chemical::ResidueType::is_cyclic(), is_d_aa(), is_d_rna(), core::chemical::ResidueType::is_disulfide_bonded(), is_DNA(), core::chemical::ResidueType::is_gamma_aa(), core::chemical::ResidueType::is_inverted_virtual_residue(), is_l_aa(), is_l_rna(), core::chemical::ResidueType::is_ligand(), core::chemical::ResidueType::is_lipid(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_membrane(), core::chemical::ResidueType::is_meta_aramid(), core::chemical::ResidueType::is_metal(), core::chemical::ResidueType::is_metalbinding(), core::chemical::ResidueType::is_methylated_cterminus(), core::chemical::ResidueType::is_n_methylated(), core::chemical::ResidueType::is_oligourea(), core::chemical::ResidueType::is_ortho_aramid(), core::chemical::ResidueType::is_para_aramid(), is_peptoid(), core::chemical::ResidueType::is_PNA(), core::chemical::ResidueType::is_polar(), is_polymer(), core::chemical::ResidueType::is_post_methylene_meta_aramid(), core::chemical::ResidueType::is_post_methylene_ortho_aramid(), core::chemical::ResidueType::is_post_methylene_para_aramid(), core::chemical::ResidueType::is_pre_methylene_meta_aramid(), core::chemical::ResidueType::is_pre_methylene_ortho_aramid(), core::chemical::ResidueType::is_pre_methylene_para_aramid(), core::chemical::ResidueType::is_pre_methylene_post_methylene_meta_aramid(), core::chemical::ResidueType::is_pre_methylene_post_methylene_ortho_aramid(), core::chemical::ResidueType::is_pre_methylene_post_methylene_para_aramid(), is_protein(), core::chemical::ResidueType::is_purine(), core::chemical::ResidueType::is_pyrimidine(), is_r_peptoid(), is_RNA(), is_s_peptoid(), core::chemical::ResidueType::is_sidechain_amine(), core::chemical::ResidueType::is_sidechain_thiol(), core::chemical::ResidueType::is_solvent(), core::chemical::ResidueType::is_sri(), core::chemical::ResidueType::is_surface(), core::chemical::ResidueType::is_terminus(), core::chemical::ResidueType::is_TNA(), core::chemical::ResidueType::is_TP3(), core::chemical::ResidueType::is_triazolemer(), core::chemical::ResidueType::is_upper_terminus(), core::chemical::ResidueType::is_virtual_residue(), core::chemical::ResidueType::is_virtualizable_by_packer(), core::chemical::ResidueType::is_VRT1(), core::chemical::ResidueType::is_water(), core::chemical::ResidueType::lower_connect(), core::chemical::ResidueType::lower_connect_atom(), protocols::environment::ProtectedConformation::match_variants(), core::chemical::ResidueTypeSelector::match_variants(), core::pose::MiniPose::MiniPose(), core::chemical::Selector_MATCH_VARIANTS::operator[](), core::chemical::Selector_NO_VARIANTS::operator[](), core::chemical::ResidueType::perform_checks(), core::chemical::MutableResidueType::placeholder_clone(), protocols::stepwise::modeler::rna::remove_all_variant_types(), protocols::toolbox::match_enzdes_util::CovalentConnectionReplaceInfo::remove_covalent_connection_from_pose(), core::chemical::ResidueDatabaseIO::report_residue_type_properties(), core::chemical::ResidueDatabaseIO::report_residue_type_variant(), core::chemical::ResidueType::requires_actcoord(), core::scoring::methods::ReferenceEnergyNoncanonical::residue_energy(), core::chemical::residue_type_bases_identical(), core::chemical::ResidueType::self_pointer_updates(), set_properties(), core::chemical::MutableResidueType::show(), core::chemical::ResidueType::show(), core::chemical::ResidueType::update_ring_conformer_sets(), core::chemical::ResidueType::upper_connect(), core::chemical::ResidueType::upper_connect_atom(), core::chemical::variants_match_with_exceptions(), core::pose::Pose::virtual_to_real(), and core::chemical::write_topology_file().

void core::chemical::ResidueTypeBase::remap_pdb_atom_names ( bool  rename)
inline
bool core::chemical::ResidueTypeBase::remap_pdb_atom_names ( ) const
inline

Are we using geometry-based atom renaming when loading this residue type from PDB.

References remap_pdb_atom_names_.

void core::chemical::ResidueTypeBase::remove_variant_type ( VariantType const  variant_type)

Remove a variant type to this ResidueTypeBase.

References properties_.

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

void core::chemical::ResidueTypeBase::remove_variant_type ( std::string const &  variant_type)

Remove a variant type to this ResidueTypeBase by string.

References properties_.

void core::chemical::ResidueTypeBase::report_adducts ( ) const
void core::chemical::ResidueTypeBase::reset_mainchain_torsion_potential_names ( )

Set the names of the mainchain torsion potential maps to use to "".

Also resets the mainchain torsion potential filename strings.

References rama_prepro_mainchain_torsion_potential_name_, rama_prepro_mainchain_torsion_potential_name_beforeproline_, rama_prepro_map_file_name_, and rama_prepro_map_file_name_beforeproline_.

void core::chemical::ResidueTypeBase::rotamer_library_specification ( rotamers::RotamerLibrarySpecificationOP  rotlibspec)
rotamers::RotamerLibrarySpecificationCOP core::chemical::ResidueTypeBase::rotamer_library_specification ( ) const
rotamers::RotamerLibrarySpecificationOP core::chemical::ResidueTypeBase::rotamer_library_specification_nonconst ( )
void core::chemical::ResidueTypeBase::set_adduct_flag ( bool  adduct_in)
void core::chemical::ResidueTypeBase::set_disulfide_atom_name ( std::string const &  n)
inline

Sets disulfide atom name.

Author
Andrew M. Watkins (amw57.nosp@m.9@ny.nosp@m.u.edu).

References disulfide_atom_name_.

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

void core::chemical::ResidueTypeBase::set_gasteiger_atom_typeset ( gasteiger::GasteigerAtomTypeSetCOP  setting)
void core::chemical::ResidueTypeBase::set_metapatched ( )
inline

Set that this is a metapatched ResidueType.

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

References is_metapatched_.

void core::chemical::ResidueTypeBase::set_orbital_typeset ( orbitals::OrbitalTypeSetCOP  setting)
inline

References orbital_types_.

void core::chemical::ResidueTypeBase::set_properties ( ResiduePropertiesOP  properties)

Set the collection of properties for this ResidueTypeBase.

References properties(), and properties_.

void core::chemical::ResidueTypeBase::set_rama_prepro_mainchain_torsion_potential_name ( std::string const &  name_in,
bool const  pre_proline_position 
)

Set the key name for the mainchain torsion potential used by the RamaPrePro score term.

Set the key name for the mainchain torsion potential.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (pointing the function to the base type), though this can be overridden using this function.

Note
Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we're interested in.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (pointing the function to the base type), though this can be overridden using this function.

References rama_prepro_mainchain_torsion_potential_name_, and rama_prepro_mainchain_torsion_potential_name_beforeproline_.

Referenced by core::chemical::RamaPreproResname::apply(), and core::chemical::ResidueType::update_derived_data().

void core::chemical::ResidueTypeBase::set_rama_prepro_map_file_name ( std::string const &  filename_in,
bool const  pre_proline_position 
)

Set the file name for the mainchain torsion potential used by the RamaPrePro score term.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (pointing the function to the base type), though this can be overridden using this function.

Note
Different maps are used for preproline positions and non-preproline positions. The boolean determines which map we're interested in.

Stored internally as a string for base residue types. Empty string is stored by default for derived residue types (pointing the function to the base type), though this can be overridden using this function.

References rama_prepro_map_file_name_, and rama_prepro_map_file_name_beforeproline_.

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

virtual void core::chemical::ResidueTypeBase::show ( std::ostream &  output = std::cout,
bool  output_atomic_details = false 
) const
pure virtual

Generate string representation of ResidueTypeBase for debugging purposes.

Implemented in core::chemical::ResidueType, and core::chemical::MutableResidueType.

virtual void core::chemical::ResidueTypeBase::show_all_atom_names ( std::ostream &  out) const
pure virtual
void core::chemical::ResidueTypeBase::strip_rotamer_library_specification ( )

Remove any rotamer library specifications attached to this ResidueTypeBase.

After this operation, the rotamer_library_specification() method returns a NULL pointer.

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

References rotamer_library_specification_.

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

utility::vector1< VariantType > core::chemical::ResidueTypeBase::variant_type_enums ( ) const

Get a vector of VariantType enums for this ResidueTypeBase.

This ONLY includes standard, enum-based variants, not on-the-fly custom variants.

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

References properties_.

Referenced by protocols::cyclic_peptide::RamaMutationSelector::apply(), core::pack::palette::PackerPalette::decide_what_to_do_with_existing_type(), and core::chemical::ResidueTypeSet::get_residue_type_with_custom_variant_added().

utility::vector1< std::string > core::chemical::ResidueTypeBase::variant_types ( ) const

get all the variant types for this ResidueTypeBase

This will include both on-the-fly custom variants defined by string AND string equivalents of standard, enumerated variants. – rhiju (merging roccomoretti/restypeset_fiddle)

References properties_.

Referenced by protocols::loops::apply_sequence_mapping(), core::pose::rna::mutate_position(), and core::chemical::write_topology_file().

Member Data Documentation

AA core::chemical::ResidueTypeBase::aa_ = aa_unk
private

standard rosetta aa-type for knowledge-based potentials, may be aa_unk

Referenced by aa(), backbone_aa(), base_analogue(), and na_analogue().

std::map< std::string, std::string > core::chemical::ResidueTypeBase::atom_aliases_
private

A mapping of alias atom names to canonical atom names Will be added to atom_name_to_vd_ during finalization.

Referenced by atom_alias(), and atom_aliases().

AtomTypeSetCOP core::chemical::ResidueTypeBase::atom_types_
private

The type set for Rosetta Atom types. Required to be non-null for standard ResidueTypes.

Referenced by atom_type_set(), atom_type_set_ptr(), and ResidueTypeBase().

AA core::chemical::ResidueTypeBase::backbone_aa_ = aa_unk
private

Referenced by backbone_aa(), and backbone_aa_raw().

AA core::chemical::ResidueTypeBase::base_analogue_ = aa_unp
private

Referenced by base_analogue(), and base_analogue_raw().

std::string core::chemical::ResidueTypeBase::base_name_
private

Residue id for the base type (i.e. sans variants).

Does not accumulate VariantType names (e.g. "ALA").

Referenced by base_name().

std::map< std::string, std::string > core::chemical::ResidueTypeBase::canonical_atom_aliases_
private

A map of canonical atom names to atom aliases (white space included)

Referenced by canonical_atom_alias(), and canonical_atom_aliases().

utility::vector1< Adduct > core::chemical::ResidueTypeBase::defined_adducts_
private

Adducts defined for this residue.

Referenced by add_adduct(), defined_adducts(), and report_adducts().

std::string core::chemical::ResidueTypeBase::disulfide_atom_name_ = "NONE"
private

Name of the disulfide-forming atom, if any.

Referenced by get_disulfide_atom_name(), and set_disulfide_atom_name().

ElementSetCOP core::chemical::ResidueTypeBase::elements_
private

The set for element objects. – can be null.

Referenced by element_set(), and element_set_ptr().

bool core::chemical::ResidueTypeBase::force_nbr_atom_orient_ = false
private

Controls which atoms are selected by "select_orient_atoms", used to overlay residues during packing.

Referenced by force_nbr_atom_orient().

gasteiger::GasteigerAtomTypeSetCOP core::chemical::ResidueTypeBase::gasteiger_atom_types_
private

The set for GasteigerAtomTypes. – can be null.

Referenced by gasteiger_atom_typeset(), and set_gasteiger_atom_typeset().

std::string core::chemical::ResidueTypeBase::interchangeability_group_
private

interchangeability group lets a ResidueTypeBase claim to be functionally interchangeable with any other ResidueTypeBase in the same group. This is used by the packer to decide which ResidueTypeBase from a desired group has the right set of variants to be placed at a particular position. E.g. if the interchangeability group is "ALA" and the packer is building rotamers for residue 1, (the N-terminal residue) then, the packer will select the "ALA:NTermProteinFull" ResidueTypeBase and build rotamers for it.

Referenced by interchangeability_group().

bool core::chemical::ResidueTypeBase::is_metapatched_ = false
private

Is this ResidueType the product of metapatching?

False by default; true if and only if a metapatch contributed to this ResidueType.

Referenced by is_metapatched(), and set_metapatched().

utility::vector1< std::string > core::chemical::ResidueTypeBase::metal_binding_atoms_
private

Names of all of the atoms that are able to make a bond to a metal, for metal-binding residue types.

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

Referenced by get_metal_binding_atoms(), and metal_binding_atoms().

MMAtomTypeSetCOP core::chemical::ResidueTypeBase::mm_atom_types_
private

The set for MMAtomTypes. – can be null.

Referenced by mm_atom_types_ptr().

TypeSetMode core::chemical::ResidueTypeBase::mode_ = INVALID_t
private

The TypeSet mode for this ResidueTypeBase.

Referenced by atom_type_set(), mode(), and ResidueTypeBase().

AA core::chemical::ResidueTypeBase::na_analogue_ = aa_unp
private

Referenced by na_analogue(), and na_analogue_raw().

char core::chemical::ResidueTypeBase::name1_ = ' '
private

one-letter code, also not necessarily unique

Referenced by name1().

std::string core::chemical::ResidueTypeBase::name3_
private

PDB-file id, need not be unique NOTE: The "name3" is not necessarily three characters long. e.g. Metal ions may be only two characters.

Referenced by get_numeric_property(), get_string_property(), and name3().

std::string core::chemical::ResidueTypeBase::name_
private

Residue id – Should be unique within a ResidueTypeSet.

Accumulates VariantType names (e.g. "ALA:NtermProteinFull").

Referenced by name().

signed long int core::chemical::ResidueTypeBase::net_formal_charge_ = 0
private

What is the total formal charge of the ResidueType? (Note that this may be different from the sum of the formal charges on each atom.)

Referenced by net_formal_charge().

orbitals::OrbitalTypeSetCOP core::chemical::ResidueTypeBase::orbital_types_
private

The set for OrbitalTypes. – can be null.

Referenced by has_orbital_types(), orbital_type(), orbital_types_ptr(), and set_orbital_typeset().

utility::vector1< Orbital > core::chemical::ResidueTypeBase::orbitals_
private

The orbitals on the ResidueTypeBase, if any.

Referenced by get_orbitals(), n_orbitals(), orbital(), and orbital_type().

std::map< std::string, int > core::chemical::ResidueTypeBase::orbitals_index_
private

index lookup for orbitals based on atom name Updated in add_orbital()

Referenced by get_orbitals_index(), has_orbital(), and orbital_index().

utility::pointer::DeepCopyOP< ResidueProperties > core::chemical::ResidueTypeBase::properties_
private
std::string core::chemical::ResidueTypeBase::rama_prepro_mainchain_torsion_potential_name_
private

The name of the mainchain torsion potential used by this ResidueTypeBase for the RamaPrePro score term.

If blank, the base type's mainchain torsion potential is used.

Note
This one is for maps used if this residue is not immediately before a proline.

Referenced by get_rama_prepro_mainchain_torsion_potential_name(), mainchain_potentials_match(), reset_mainchain_torsion_potential_names(), and set_rama_prepro_mainchain_torsion_potential_name().

std::string core::chemical::ResidueTypeBase::rama_prepro_mainchain_torsion_potential_name_beforeproline_
private

The name of the mainchain torsion potential used by this ResidueTypeBase for the RamaPrePro score term.

If blank, the base type's mainchain torsion potential is used.

Note
This one is for maps used if this residue occurs before a proline.

Referenced by get_rama_prepro_mainchain_torsion_potential_name(), mainchain_potentials_match(), reset_mainchain_torsion_potential_names(), and set_rama_prepro_mainchain_torsion_potential_name().

std::string core::chemical::ResidueTypeBase::rama_prepro_map_file_name_
private

The filename of the mainchain torsion potential used by this ResidueTypeBase for the RamaPrePro score term.

If blank, the base type's file is used. If that's blank too, then this ResidueTypeBase isn't scored by RamaPrePro.

Note
This one is for maps used if this residue is not immediately before a proline.

Referenced by defines_custom_rama_prepro_map(), get_rama_prepro_map_file_name(), mainchain_potentials_match(), reset_mainchain_torsion_potential_names(), and set_rama_prepro_map_file_name().

std::string core::chemical::ResidueTypeBase::rama_prepro_map_file_name_beforeproline_
private

The filename of the mainchain torsion potential used by this ResidueTypeBase for the RamaPrePro score term.

If blank, the base type's file is used. If that's blank too, then this ResidueTypeBase isn't scored by RamaPrePro.

Note
This one is for maps used if this residue occurs before a proline.

Referenced by defines_custom_rama_prepro_map(), get_rama_prepro_map_file_name(), mainchain_potentials_match(), reset_mainchain_torsion_potential_names(), and set_rama_prepro_map_file_name().

bool core::chemical::ResidueTypeBase::remap_pdb_atom_names_ = false
private

Should we attempt to rename atoms for this residue type when we read in PDB files?

Referenced by remap_pdb_atom_names().

utility::pointer::DeepCopyOP< rotamers::RotamerLibrarySpecification > core::chemical::ResidueTypeBase::rotamer_library_specification_
private

The documentation for this class was generated from the following files: