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| class | AtomID |
| Atom identifier class. Defined by the atom number and the residue number. More... | |
| class | BondID |
| two more classes, temporary for testing purposes More... | |
| class | StubID |
| class | AtomID_Map |
| Map from Atom identifiers to contained values class. More... | |
| class | AtomID_Map_bool |
| class | AtomID_Map_Real |
| class | AtomID_Map_AtomID |
| class | CacheableAtomID_MapVector |
| AtomID_Map< xyzVector< Real > > More... | |
| class | DOF_ID |
| Kinematics DOF identifier class. More... | |
| class | DOF_ID_Map |
| Map from Atom DOF identifiers to contained values class. More... | |
| class | DOF_ID_Range |
| Kinematics DOF identifier (with range) class. More... | |
| class | EXCN_AtomNotFound |
| class | JumpID |
| class | NamedAtomID |
| Atom identifier class. More... | |
| class | NamedAtomID_Map |
| Map from Atom identifiers to contained values class. More... | |
| class | NamedAtomID_Map_NamedAtomID |
| class | NamedStubID |
| class | PartialAtomID |
| Partial atom identifier class. Defined by an atom index and a residue number, or by an inter-residue-connection index, the number of bonds away from the inter-residue-connection atom, and a residue number. More... | |
| class | SequenceMapping |
| class | TorsionID |
| Torsion identifier class. More... | |
| class | TorsionID_Range |
| Kinematics DOF identifier (with range) class. More... | |
Typedefs | |
| typedef AtomID_Map< bool > | AtomID_Mask |
| typedef utility::pointer::shared_ptr< CacheableAtomID_MapVector > | CacheableAtomID_MapVectorOP |
| typedef utility::pointer::shared_ptr< CacheableAtomID_MapVector const > | CacheableAtomID_MapVectorCOP |
| typedef utility::pointer::weak_ptr< CacheableAtomID_MapVector > | CacheableAtomID_MapVectorAP |
| typedef utility::pointer::weak_ptr< CacheableAtomID_MapVector const > | CacheableAtomID_MapVectorCAP |
| typedef DOF_ID_Map< bool > | DOF_ID_Mask |
| typedef NamedAtomID_Map< bool > | NamedAtomID_Mask |
| typedef utility::pointer::shared_ptr< SequenceMapping > | SequenceMappingOP |
| typedef utility::pointer::shared_ptr< SequenceMapping const > | SequenceMappingCOP |
Enumerations | |
| enum | DOF_Type { INVALID_DOF = 0 , PHI = 1 , THETA , D , RB1 , RB2 , RB3 , RB4 , RB5 , RB6 } |
| DOF (degrees of freedom) type. More... | |
| enum | TorsionType { BB = 1 , CHI , NU , BRANCH , JUMP } |
| Torsion type – used in the TorsionID class. More... | |
| enum | MainchainTorsionType { phi_dihedral = 1 , psi_dihedral , omega_dihedral , omega2_dihedral , omega3_dihedral } |
Variables | |
| AtomID const | GLOBAL_BOGUS_ATOM_ID |
| Globals – may not be used until after core::init is called. More... | |
| AtomID const | GLOBAL_CHAINBREAK_BOGUS_ATOM_ID |
| StubID const | GLOBAL_BOGUS_STUB_ID |
| Global – may not be used until after core::init is called. More... | |
| DOF_ID const | GLOBAL_BOGUS_DOF_ID (AtomID::BOGUS_ATOM_ID(), PHI) |
| Global – may not be used until after core::init is called. More... | |
| NamedAtomID const | GLOBAL_BOGUS_NAMED_ATOM_ID (NamedAtomID::BOGUS_NAMED_ATOM_ID()) |
| Globals – may not be used until after core::init is called. More... | |
| NamedAtomID const | GLOBAL_CHAINBREAK_BOGUS_NAMED_ATOM_ID (NamedAtomID::CHAINBREAK_BOGUS_NAMED_ATOM_ID()) |
| TorsionID const | GLOBAL_BOGUS_TORSION_ID (TorsionID::BOGUS_TORSION_ID()) |
| Globals. More... | |
| PartialAtomID const | GLOBAL_BOGUS_PARTIAL_ATOM_ID |
| Globals – may not be used until after core::init is called. More... | |
| PartialAtomID const | GLOBAL_CHAINBREAK_BOGUS_PARTIAL_ATOM_ID |
| typedef AtomID_Map< bool > core::id::AtomID_Mask |
| typedef utility::pointer::weak_ptr< CacheableAtomID_MapVector > core::id::CacheableAtomID_MapVectorAP |
| typedef utility::pointer::weak_ptr< CacheableAtomID_MapVector const > core::id::CacheableAtomID_MapVectorCAP |
| typedef utility::pointer::shared_ptr< CacheableAtomID_MapVector const > core::id::CacheableAtomID_MapVectorCOP |
| typedef utility::pointer::shared_ptr< CacheableAtomID_MapVector > core::id::CacheableAtomID_MapVectorOP |
| typedef DOF_ID_Map< bool > core::id::DOF_ID_Mask |
| typedef NamedAtomID_Map< bool > core::id::NamedAtomID_Mask |
| typedef utility::pointer::shared_ptr< SequenceMapping const > core::id::SequenceMappingCOP |
| typedef utility::pointer::shared_ptr< SequenceMapping > core::id::SequenceMappingOP |
| enum core::id::DOF_Type |
Torsion type – used in the TorsionID class.
| Enumerator | |
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| BB | |
| CHI | |
| NU | |
| BRANCH | |
| JUMP | |
| void core::id::combine_sequence_mappings | ( | core::id::SequenceMapping & | smap, |
| core::id::SequenceMapping const & | smap_to_add | ||
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combine the input sequence mappings into one utility function added by flo, feb 2011
combine smap_to_add into smap, i.e. smap[j] becomes smap_to_add[ smap[j] ]
References core::id::SequenceMapping::downstream_combine().
| core::id::SequenceMappingOP core::id::combine_sequence_mappings | ( | utility::vector1< core::id::SequenceMapping > const & | smaps | ) |
make one sequence mapping out of all input ones utility function added by flo, feb 2011
combine all input sequence mappings into one. sequentially, that is
Referenced by protocols::seeded_abinitio::adjust_mm_to_length(), and core::pack::task::operation::ReadResfileAndObeyLengthEvents::apply().
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References RB1, RB6, and protocols::hybridization::t.
Referenced by core::optimization::MinimizerMap::reset_jump_rb_deltas(), and core::optimization::symmetry::SymMinimizerMap::reset_jump_rb_deltas().
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References RB1, RB6, and protocols::hybridization::t.
Referenced by core::kinematics::tree::JumpAtom::dof(), core::kinematics::tree::JumpAtom::get_dof_axis_and_end_pos(), and core::kinematics::tree::JumpAtom::set_dof().
References RB1.
Referenced by core::conformation::Conformation::dof_id_from_torsion_id(), and core::kinematics::tree::JumpAtom::setup_min_map().
| AtomID const core::id::GLOBAL_BOGUS_ATOM_ID | ( | AtomID::BOGUS_ATOM_ID() | ) |
| StubID const core::id::GLOBAL_BOGUS_STUB_ID | ( | StubID::BOGUS_STUB_ID() | ) |
| AtomID const core::id::GLOBAL_CHAINBREAK_BOGUS_ATOM_ID | ( | AtomID::CHAINBREAK_BOGUS_ATOM_ID() | ) |
| void core::id::initialize_core_id_globals | ( | ) |
Calling this function ensures that all of the global variables in core::id are initialize before they are needed.
Referenced by core::init::init().
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Referenced by core::pose::Pose::mu(), core::scoring::OmegaTether::omega_index(), and core::pose::Pose::set_mu().
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Referenced by protocols::abinitio::abscript::angle_cpy(), protocols::abinitio::abscript::AbscriptLoopCloserCM::apply(), protocols::minimization_packing::MinMover::apply_dof_tasks_to_movemap(), protocols::environment::bond_torsions(), protocols::indexed_structure_store::extract_residue_entry(), protocols::anchored_design::AnchorMoversData::fix_anchor(), protocols::relax::fix_worst_bad_ramas(), protocols::normalmode::NormalModeMultifunc::get_dofs_map(), core::conformation::carbohydrates::get_reference_atoms(), protocols::forge::remodel::RemodelLoopMover::mark_loop_moveable(), protocols::forge::build::SegmentInsert::movemap(), protocols::forge::build::SegmentRebuild::movemap(), core::pose::Pose::omega(), core::scoring::OmegaTether::omega_index(), protocols::anchored_design::AnchorMoversData::set_movemap(), core::pose::Pose::set_omega(), protocols::simple_moves::RandomOmegaFlipMover::setup_torsion_list(), protocols::simple_moves::RandomTorsionMover::setup_torsion_list(), and protocols::environment::ProtectedConformation::verify_backbone().
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| std::ostream& core::id::operator<< | ( | std::ostream & | os, |
| DOF_ID_Range const & | a | ||
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stream << DOF_ID_Range
| std::ostream& core::id::operator<< | ( | std::ostream & | os, |
| JumpID const & | a | ||
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| std::ostream& core::id::operator<< | ( | std::ostream & | os, |
| NamedAtomID const & | a | ||
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stream << NamedAtomID
| std::ostream& core::id::operator<< | ( | std::ostream & | os, |
| NamedStubID const & | a | ||
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stream << NamedStubID
output operator
| std::ostream& core::id::operator<< | ( | std::ostream & | os, |
| PartialAtomID const & | a | ||
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stream << PartialAtomID
| std::ostream& core::id::operator<< | ( | std::ostream & | os, |
| TorsionID const & | a | ||
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| std::ostream& core::id::operator<< | ( | std::ostream & | os, |
| TorsionID_Range const & | a | ||
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stream << TorsionID_Range
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References core::conformation::membrane::out, and core::id::SequenceMapping::show().
| std::istream& core::id::operator>> | ( | std::istream & | is, |
| NamedAtomID & | e | ||
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input operator >> NamedAtomID
input operator
| std::istream& core::id::operator>> | ( | std::istream & | is, |
| NamedStubID & | s | ||
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input operator >> NamedAtomID
input operator
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Referenced by protocols::loops::loop_closure::ccd::RamaCheckBase::accept_new_conformation(), protocols::abinitio::abscript::angle_cpy(), protocols::abinitio::abscript::AbscriptLoopCloserCM::apply(), protocols::grafting::AnchoredGraftMover::apply(), protocols::grafting::CCDEndsGraftMover::apply(), protocols::idealize::basic_idealize(), protocols::simple_moves::SmallMover::dof_id_ranges(), protocols::simple_moves::ShearMover::dof_id_ranges(), protocols::indexed_structure_store::extract_residue_entry(), protocols::anchored_design::AnchorMoversData::fix_anchor(), protocols::relax::fix_worst_bad_ramas(), protocols::simple_moves::BackboneMover::get_mainchain_TorsionIDs(), core::conformation::carbohydrates::get_reference_atoms(), protocols::simple_moves::SmallMover::move_with_rama(), protocols::forge::build::SegmentInsert::movemap(), protocols::forge::build::SegmentRebuild::movemap(), core::pose::Pose::phi(), core::scoring::OmegaTether::phi_index(), core::pose::Pose::set_phi(), protocols::environment::ProtectedConformation::set_secstruct(), core::kinematics::tree::BondedAtom::setup_min_map(), protocols::simple_moves::RandomTorsionMover::setup_torsion_list(), and protocols::environment::ProtectedConformation::verify_backbone().
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Referenced by core::pose::Pose::phi(), and core::pose::Pose::set_phi().
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Referenced by protocols::loops::loop_closure::ccd::RamaCheckBase::accept_new_conformation(), protocols::abinitio::abscript::angle_cpy(), protocols::abinitio::abscript::AbscriptLoopCloserCM::apply(), protocols::grafting::AnchoredGraftMover::apply(), protocols::grafting::CCDEndsGraftMover::apply(), protocols::environment::bond_torsions(), protocols::simple_moves::SmallMover::dof_id_ranges(), protocols::simple_moves::ShearMover::dof_id_ranges(), protocols::indexed_structure_store::extract_residue_entry(), protocols::anchored_design::AnchorMoversData::fix_anchor(), protocols::simple_moves::BackboneMover::get_mainchain_TorsionIDs(), core::conformation::carbohydrates::get_reference_atoms(), protocols::simple_moves::SmallMover::move_with_rama(), protocols::forge::build::SegmentInsert::movemap(), protocols::forge::build::SegmentRebuild::movemap(), core::pose::Pose::psi(), core::scoring::OmegaTether::psi_index(), core::pose::Pose::set_psi(), protocols::simple_moves::RandomTorsionMover::setup_torsion_list(), and protocols::environment::ProtectedConformation::verify_backbone().
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Referenced by core::pose::Pose::psi(), core::scoring::OmegaTether::psi_index(), and core::pose::Pose::set_psi().
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swap( AtomID_Map, AtomID_Map )
References core::pose::motif::a(), and protocols::match::upstream::b.
Referenced by core::chemical::IdealBondLengthSet::add_bond_length(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::add_to_twobody(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::append_two_body_energy_computations_to_work_vector(), core::chemical::IdealBondLengthSet::contains_bond_length(), core::conformation::parametric::RealValuedParameter::correct_range(), protocols::ub_e2c::ubi_e2c_modeler::CSP_fraction(), core::pack::hbonds::HBondGraphInitializerIG::eval_rot_pair(), core::scoring::rna::TNA_SuitePotential::eval_score(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::evaluate_rotamer_pair_energies(), core::chemical::gasteiger::PossibleAtomTypesForAtom::FinalizeUnhybridized(), core::chemical::find_chi_bonds(), protocols::jd3::JobGenealogist::garbage_collection(), core::chemical::IdealBondLengthSet::get_bond_length(), protocols::simple_moves::SampleSequenceFromProbabilities::get_ranked_positions(), protocols::cyclic_peptide::crosslinker::Thioether_Helper::get_thioether_residues_from_selection(), protocols::indexed_structure_store::FragmentStoreManager::load_grouped_fragment_store(), protocols::hbnet::HBondNetStruct::operator=(), protocols::hotspot_hashing::HotspotStubSet::operator=(), protocols::pockets::SmallMol::operator=(), core::scoring::nmr::order_tensor_parameters(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::prepare_symm_otf_interaction_graph(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::prestore_sc_oversat(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::readMRCandResize(), core::scoring::electron_density::ElectronDensity::readMRCandResize(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::residue_pair_energy(), core::scoring::motif::ResPairMotif::reverse_in_place_unsafe(), protocols::cluster::Cluster::shuffle(), core::scoring::nmr::rdc::RDCMultiSet::solve_tensor_and_compute_score_by_nls(), core::scoring::nmr::pcs::PCSSingleSet::solve_tensor_and_compute_score_by_nls(), protocols::noesy_assign::FragsToAtomDist::swap_atoms(), and core::kinematics::tree::BondedAtom::update_internal_coords().
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swap( NamedAtomID_Map, NamedAtomID_Map )
References core::pose::motif::a(), and protocols::match::upstream::b.
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Referenced by core::scoring::OmegaTether::phi_index().
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Referenced by core::scoring::OmegaTether::phi_index().
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Referenced by core::scoring::OmegaTether::phi_index().
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References D, PHI, RB1, RB2, RB3, RB4, RB5, RB6, and THETA.
Referenced by core::io::raw_data::ScoreMap::add_arbitrary_string_data_from_pose(), protocols::features::InterfaceDdGMover::add_chain_id(), protocols::antibody::clusters::add_cluster_comments_to_pose(), protocols::abinitio::AbrelaxApplication::add_constraints(), protocols::seeded_abinitio::add_coordinate_constraints(), core::conformation::Conformation::add_disulfide_bond(), protocols::legacy_sewing::SewGraph::add_edges_from_binary(), protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::add_helix_update_moves(), protocols::constraint_movers::CstInfoMover::add_info_for_csts(), protocols::features::InterfaceDdGMover::add_jump_id(), protocols::cyclic_peptide::crosslinker::Thioether_Helper::add_linker_bonds_asymmetric(), core::chemical::MutableResidueType::add_metapatch_connect(), protocols::sewing::movers::AssemblyMover::add_motif_scorers_to_score_file(), protocols::sewing::movers::LigandBindingAssemblyMover::add_motif_scorers_to_score_file(), protocols::relax::membrane::add_mutant_to_vectors(), protocols::pack_daemon::DaemonSet::add_npd_property_calculator_for_state(), core::pose::rna::add_number_base_pairs(), core::pose::rna::add_number_native_base_pairs(), protocols::pack_daemon::DaemonSet::add_pack_daemon(), protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::scoring::methods::NMerSVMEnergy::add_pssm_features(), core::pack::interaction_graph::add_rotamers_to_pose(), core::io::mmtf::add_xbond_information(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::align_and_calculate_rmsd(), protocols::helical_bundle_predict::HelicalBundlePredictApplication::align_to_native_pose(), core::scoring::MembraneTopology::allow_scoring(), protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers::alter_rotamer_set(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites(), protocols::antibody::AntibodyNumberingConverterMover::apply(), protocols::antibody::design::AntibodyDesignMover::apply(), protocols::carbohydrates::CreateGlycanSequonMover::apply(), protocols::carbohydrates::GlycanSampler::apply(), protocols::carbohydrates::GlycanTreeModeler::apply(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::fold_from_loops::movers::ResidueLabelsToPymolSelectionMover::apply(), protocols::ligand_docking::HighResEnsemble::apply(), protocols::ligand_docking::ProtLigEnsemble::apply(), protocols::ligand_docking::WriteLigandMolFile::apply(), protocols::loop_grower::FragmentExtension::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::loophash::LoopHashMoverWrapper::apply(), protocols::membrane::MPQuickRelaxMover::apply(), protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::apply(), protocols::pose_creation::MakePolyXMover::apply(), protocols::pose_sewing::movers::BlockwiseAnalysisMover::apply(), protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::apply(), protocols::pose_sewing::movers::SewAnythingAddMover::apply(), protocols::protein_interface_design::movers::ShoveResidueMover::apply(), protocols::sewing::hashing::AlignmentFileGeneratorMover::apply(), protocols::simple_moves::AddResidueLabelMover::apply(), protocols::simple_moves::BBDihedralSamplerMover::apply(), protocols::simple_moves::DumpPdb::apply(), protocols::simple_moves::DumpSingleResidueRotamers::apply(), protocols::simple_moves::SimpleThreadingMover::apply(), protocols::struct_fragment::StructFragmentMover::apply(), protocols::symmetry::SetupForSequenceSymmetryMover::apply(), protocols::trRosetta_protocols::movers::trRosettaProtocolMover::apply(), protocols::simple_moves::CombinePoseMover::apply(), protocols::protein_interface_design::Revert::apply(), core::select::residue_selector::JumpDownstreamSelector::apply(), core::select::residue_selector::SliceResidueSelector::apply(), protocols::calc_taskop_filters::ConservedPosMutationFilter::apply(), protocols::dna_dock::DNAClashCheckFilter::apply(), protocols::dna_dock::PropagateClashCheckFilter::apply(), protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::apply(), protocols::simple_filters::ResidueBurialFilter::apply(), protocols::simple_filters::SimpleMetricFilter::apply(), protocols::task_operations::InteractingRotamerExplosion::apply(), protocols::task_operations::SequenceMotifTaskOperation::apply(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(), core::chemical::AddConnectAndTrackingVirt::apply(), protocols::protein_interface_design::movers::SecretionOptimizationMover::apply(), protocols::docking::membrane::QuickRelaxPartnersSeparately::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), protocols::nmr::pre::PREMover::apply(), protocols::simple_moves::PeriodicBoxMover::apply(), protocols::splice::Splice::apply(), protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SpliceOut::apply(), protocols::symmetry::DetectSymmetry::apply(), protocols::enzdes::SetCatalyticResPackBehavior::apply(), protocols::hbnet::ConstrainHBondNetwork::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply_coord_cst_to_sctip(), protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply_multi_sequence(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_rama_prepro(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_set_bondangle(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_set_bondlength(), protocols::antibody::design::AntibodyDesignMover::apply_to_cdr(), protocols::match::output::PDBWriter::assemble_outtag(), protocols::toolbox::match_enzdes_util::assemble_remark_line(), protocols::match::output::PDBWriter::assemble_remark_lines(), core::kinematics::inverse::assert_atoms_are_downstream_of_jump(), core::kinematics::inverse::assert_atoms_are_upstream_of_jump(), protocols::fold_from_loops::utils::Nub::assign_disulfides(), core::scoring::epr_deer::DEERDataCache::at(), core::chemical::ResidueType::atom_name(), protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_c_term(), protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_n_term(), core::pack::dunbrack::SingleResidueDunbrackLibrary::bin_rotameric_chi(), protocols::pack_daemon::EntityCorrespondence::bounds_check_entity(), protocols::pack_daemon::EntityCorrespondence::bounds_check_residue(), protocols::hbnet::HBNet::branch_overlapping_networks(), protocols::abinitio::abscript::FragmentJumpCM::build_claims(), protocols::loophash::LoopHashSampler::build_structures(), core::scoring::sc::ShapeComplementarityCalculator::Calc(), protocols::symmetric_docking::SymDockProtocol::calc_fnat(), protocols::nmr::pcs::PCSEnergy::calcualate_total_score_and_tensors(), core::simple_metrics::metrics::DihedralDistanceMetric::calculate(), core::simple_metrics::metrics::SecondaryStructureMetric::calculate(), core::simple_metrics::metrics::SelectedResiduesMetric::calculate(), core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::calculate(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::calculate(), protocols::pose_sewing::simple_metrics::BlockwiseShapeCompMetric::calculate(), protocols::quantum_annealing::InteractionGraphSummaryMetric::calculate(), protocols::pose_sewing::calculate_bw_pose_compat_motifs(), protocols::pose_sewing::calculate_bw_window_motifs(), protocols::nmr::pre::PREEnergy::calculate_total_score(), protocols::antibody::clusters::CDRClusterEnumManager::cdr_cluster_enum_to_string(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::check_backbones_match(), protocols::docking::DockingEnsemblePrepackProtocol::check_ensemble_member_compatibility(), protocols::helical_bundle_predict::HelicalBundlePredictApplication::check_ignore_residues_reasonable(), protocols::antibody::CDRSetOptionsParser::check_line_len(), protocols::antibody::design::CDRGraftDesignOptionsParser::check_line_len(), protocols::antibody::design::CDRSeqDesignOptionsParser::check_line_len(), protocols::relax::membrane::check_mutants_ok(), protocols::features::FeaturesReporter::check_relevant_residues_range(), protocols::loop_grower::LoopPartialSolutionStore::cluster_check(), protocols::pockets::GenPharmacophore::cluster_KeyFeatures(), protocols::toolbox::match_enzdes_util::InvrotTarget::collect_all_inverse_rotamers(), protocols::optimize_weights::IterativeOptEDriver::collect_decoy_discrimination_data(), core::pack::task::ResfileContents::commands_for_residue(), protocols::simple_filters::SimpleMetricFilter::compare_composites(), core::pack::compare_mingraph_and_energy_graph(), core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), protocols::rigid::UniformRigidBodyMover::complex_type_gen(), protocols::backrub::BackrubMover::complex_type_generator_for_backrub_mover(), core::chemical::sdf::MolWriter::compose_atoms(), core::chemical::sdf::MolWriter::compose_nbr_atom(), protocols::features::InterfaceDdGMover::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::simple_filters::NMerSVMEnergyFilter::compute(), protocols::frag_picker::FragmentScoreFilter::compute(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_burial(), core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::compute_deltas(), core::pack::rotamer_set::RotamerSets::compute_energies(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::compute_energies(), core::scoring::MembranePotential::compute_membrane_embedding(), protocols::simple_moves::ConcatenatePosesMover::concatenate_poses(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::confirm_is_cyclic_peptide(), protocols::forge::remodel::RemodelMover::confirm_sequence(), protocols::enzdes::PoseFoundResiduesCombination::construct_and_dump_outpose(), protocols::jd3::job_distributors::VanillaJobDistributor::construct_job_result_input_list(), protocols::frag_picker::convert_binary_checkpoint(), protocols::cyclic_peptide::CycpepRigidBodyPermutationMover::copy_cycpep_pose_coordinates_to_original_pose(), core::chemical::ResidueType::copy_other_info(), core::chemical::correct_conn(), core::pack::rotamers::SingleNCAARotamerLibraryCreator::create(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::create_atom_id_map(), protocols::calc_taskop_movers::ConsensusDesignMover::create_consensus_design_task(), core::pack::dunbrack::RotamerLibrary::create_fa_dunbrack_libraries_10_from_ASCII(), protocols::toolbox::ResidueNetwork::create_from_pose(), core::scoring::ScoringManager::create_nmer_pssm(), protocols::match::output::ProcessorFactory::create_output_writer(), core::io::pdb::create_records_from_sfr(), core::pack::dunbrack::RotamerLibrary::create_rotameric_dunlib(), protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::create_segment_file(), core::pack::dunbrack::RotamerLibrary::create_semi_rotameric_dunlib(), protocols::pack_daemon::DynamicAggregateFunction::create_variable_vector_expressions(), core::chemical::gasteiger::PossibleAtomTypesForAtom::CreateAtomicEnvironmentToTypesMap(), protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_projected_deltaE_of_considered_substitution(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), core::chemical::MutableResidueType::delete_child_proton(), protocols::loophash::LoopHashLibrary::delete_db(), protocols::electron_density::density_grid_search(), core::io::HeaderInformation::deposition_date(), protocols::match::Matcher::desymmeterize_upstream_restype_for_constraint(), protocols::antibody::AntibodyInfo::detect_and_set_regular_CDR_H3_stem_type_new_rule(), core::conformation::Conformation::detect_disulfides(), protocols::match::MatcherTask::determine_all_match_relevant_downstream_atoms(), protocols::match::output::OutputWriter::determine_redundant_upstream_matchres(), protocols::multistage_rosetta_scripts::MRSJobQueen::determine_validity_of_stage_tags(), LigandDiscoverySearch::discover(), protocols::pack_daemon::DynamicAggregateFunctionDriver::distribute_jobs_to_remote_daemons(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::io::mmcif::dump_cif(), protocols::toolbox::match_enzdes_util::InvrotTree::dump_invrots_tree_as_multimodel_pdbs(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::dump_pdbs(), protocols::electron_density::dump_points_to_search_to_pdb_or_txt(), protocols::electron_density::DockPDBIntoDensityMover::dump_RBfitDB_to_pdbs(), protocols::grafting::simple_movers::KeepRegionMover::end(), core::scoring::ScoringManager::energy_method(), protocols::simple_moves::DumpSingleResidueRotamers::enumerate_aa_rotamer(), protocols::enzdes::EnzdesFlexibleRegion::EnzdesFlexibleRegion(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::erode_points(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::eval_docked_pose(), protocols::enzdes::EnzdesScorefileFilter::examine_pose(), protocols::hotspot_hashing::movers::PlaceProbeMover::execute_one_search(), protocols::match::upstream::FullChiSampleSet::expand_non_dunbrack_chi(), protocols::match::upstream::FullChiSampleSet::expand_samples_for_nrchi_wi_nrchi_bin(), core::scoring::ScoringManager::factory_register(), protocols::jd2::EnsembleJobInputter::fill_jobs(), protocols::features::DatabaseJobInputter::fill_jobs(), core::pack::rotamers::SingleLigandRotamerLibrary::fill_missing_atoms(), protocols::loop_grower::LoopPartialSolutionStore::filter(), protocols::docking::membrane::MPDockingMover::finalize_setup(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::find_biggest_skeleton(), protocols::splice::Splice::find_dbase_entry(), protocols::splice::SpliceIn::find_dbase_entry(), protocols::splice::SpliceInTail::find_dbase_entry(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface(), protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(), core::scoring::hbonds::find_hb_paths(), protocols::denovo_design::components::find_orientations_and_lengths(), protocols::protein_interface_design::movers::SecretionOptimizationMover::find_tm_regions(), core::chemical::gasteiger::PossibleAtomTypesForAtom::FindPossibleAtomTypesForAtom(), protocols::noesy_assign::CrossPeak::fold_resonance(), protocols::noesy_assign::CrossPeak::folder(), core::kinematics::Stub::from_four_points(), protocols::pack_daemon::DynamicAggregateFunction::function_expression(), protocols::pack_daemon::EntityFunc::function_expression(), protocols::legacy_sewing::LegacyEnumerateAssemblyMover::generate_assembly(), protocols::sewing::hashing::EdgeMapGenerator::generate_edge_file(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::generate_perturbed_structures(), core::pack::interaction_graph::generate_rotamers_from_packer_solution_description(), protocols::match::output::WriteUpstreamHitKinemage::geom_id(), protocols::features::InterfaceFeatures::get_all_pose_chains(), core::pack::interaction_graph::get_annealable_graph_summary(), core::import_pose::libraries::ChunkSet::get_atom_id_domain_map_for_rosetta_library_chunk(), protocols::analysis::GlycanInfoMover::get_attachment_point_string(), protocols::antibody::AntibodyInfo::get_CDR_end(), protocols::antibody::AntibodyInfo::get_CDR_start(), core::pose::get_chain_id_from_chain(), protocols::sewing::data_storage::SmartAssembly::get_comprehensive_assembly_string(), protocols::sewing::data_storage::SmartAssembly::get_comprehensive_forward_assembly(), protocols::sewing::data_storage::SmartAssembly::get_comprehensive_reverse_assembly(), protocols::hbnet::HBNet::get_file_name(), core::kinematics::get_foldtree_which_partitions(), protocols::sewing::data_storage::SmartAssembly::get_forward_assembly(), protocols::glycan_docking::get_glycolig_subset_with_torsions(), protocols::qsar::scoring_grid::GridManager::get_grids(), protocols::jd3::dag_node_managers::get_index_of_last_element_with_token(), core::pose::get_jump_id_from_chain_id(), protocols::antibody::AntibodyInfo::get_landmark_resnum(), protocols::ligand_docking::InterfaceScoreCalculator::get_ligand_docking_scores(), protocols::ligand_docking::get_ligand_grid_scores(), protocols::ligand_docking::get_ligand_travel(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::get_loop_index(), protocols::trRosetta_protocols::movers::trRosettaProtocolMover::get_minimization_mode_string_from_enum(), protocols::legacy_sewing::SewGraph::get_model_node(), protocols::motif_grafting::movers::MotifMatch::get_motif_ranges(), protocols::stepwise::monte_carlo::get_move_type_string(), protocols::abinitio::abscript::AbscriptStageMover::get_name(), protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler::get_name(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::get_name(), protocols::stepwise::sampler::rna::RNA_KIC_Sampler::get_name(), protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler::get_name(), protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::get_name(), protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler::get_name(), protocols::stepwise::sampler::StepWiseSamplerOneDOF::get_name(), protocols::stepwise::sampler::StepWiseSamplerOneTorsion::get_name(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), core::conformation::carbohydrates::GlycanTreeSet::get_node(), core::conformation::carbohydrates::GlycanTree::get_node(), protocols::legacy_sewing::SewGraph::get_node_indices_from_model_id(), protocols::fold_from_loops::utils::Nub::get_nub_pieces(), protocols::jobdist::PlainSilentFileJobDistributor::get_output_filename(), protocols::jobdist::PlainPdbJobDistributor::get_output_filename(), protocols::jobdist::PlainRawJobDistributor::get_output_filename(), core::scoring::get_pairwise_atom_energies(), core::pose::get_pdb2pose_numbering_as_stdmap(), protocols::pdbinfo_manipulations::get_pose_sequences(), core::select::get_pymol_selection_for_atoms(), protocols::ligand_docking::get_radius_of_gyration(), protocols::trRosetta_protocols::movers::trRosettaProtocolMover::get_randomization_mode_string_from_enum(), core::pack::task::get_resfile_commands(), core::pose::carbohydrates::get_resnums_from_glycan_positions(), protocols::sewing::data_storage::SmartAssembly::get_reverse_assembly(), core::chemical::rna::get_rna_base_coordinate_system(), core::scoring::carbohydrates::CHIEnergyFunction::get_sampling_data(), core::scoring::carbohydrates::OmegaPreferencesFunction::get_sampling_data(), protocols::motif_grafting::movers::MotifMatch::get_scaffold2motif_size_change(), protocols::motif_grafting::movers::MotifMatch::get_scaffold_ranges(), core::pose::get_sha1_hash_excluding_chain(), core::pose::get_sha1_hash_excluding_chains(), core::pose::get_sha1_hash_from_chain(), core::pose::get_sha1_hash_from_chains(), core::scoring::get_single_atom_energies(), protocols::antibody::PDBLandmark::get_string(), protocols::features::get_struct_id_with_highest_score_from_score_data(), protocols::features::get_struct_id_with_nth_lowest_score_from_job_data(), protocols::features::get_struct_id_with_nth_lowest_score_from_score_data(), protocols::simple_moves::bb_sampler::SugarBBSampler::get_torsion(), protocols::canonical_sampling::MetricRecorder::get_torsion_ids(), core::conformation::carbohydrates::GlycanTreeSet::get_tree(), core::pose::Pose::glycan_tree_branch_sequence(), core::pose::carbohydrates::glycosylate_pose(), protocols::jd2::JobDistributor::go_main(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_pose_energies_table(), core::kinematics::FoldTree::hash_value(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::identical_info_consistency_check(), protocols::optimize_weights::WrapperOptEMultifunc::init(), protocols::membrane::MPQuickRelaxMover::init_from_cmd(), protocols::carbohydrates::GlycanSampler::init_objects(), core::scoring::nmr::pcs::PCSData::init_pcs_data_from_file(), core::scoring::nmr::pre::PREData::init_pre_data_from_file(), core::scoring::nmr::rdc::RDCData::init_rdc_data_from_file(), protocols::fldsgn::topology::HelixPairing::initialize(), protocols::fldsgn::topology::StrandPairing::initialize(), protocols::abinitio::abscript::RigidChunkCM::initialize(), protocols::pack_daemon::IterativeVectorExpression::initialize(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst::initialize_from_command_line(), protocols::pack_daemon::EntityCorrespondence::initialize_from_correspondence_file(), protocols::match::Matcher::initialize_from_file(), protocols::match::downstream::ActiveSiteGrid::initialize_from_gridlig_file(), core::scoring::hbonds::HBondDatabase::initialize_HBEval(), core::conformation::membrane::ImplicitLipidInfo::initialize_implicit_lipid_parameters(), core::pose::datacache::CacheableDataType::initialize_name_map(), protocols::calc_taskop_movers::CreateSequenceMotifMover::initialize_objects(), protocols::qsar::scoring_grid::PCSMultiGrid::initialize_pcs_data_from_input_file(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), protocols::match::MatcherTask::initialize_scaffold_active_site_residue_list_from_command_line(), protocols::pack_daemon::EntityFunc::initialize_scanner_and_function_names(), protocols::tcr::initialize_template_db_files(), core::environment::FoldTreeSketch::insert_cut(), core::environment::FoldTreeSketch::insert_jump(), core::scoring::methods::EnergyMethodOptions::insert_score_function_method_options_rows(), protocols::features::ScoreTypeFeatures::insert_score_type_rows(), core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator::InterfaceDeltaEnergeticsCalculator(), protocols::environment::introduce_datamap_cuts(), protocols::sewing::hashing::Hasher::iterate_over_basis_pairs(), protocols::sewing::data_storage::SmartAssembly::iterate_over_basis_pairs(), protocols::fold_from_loops::utils::Nub::join_pieces(), protocols::optimize_weights::load_component_weights(), protocols::loophash::LoopHashLibrary::load_db(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_initial_pool(), protocols::loophash::LoopHashLibrary::load_mergeddb(), protocols::denovo_design::components::SheetDB::load_sheetlist_from_file(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::load_template_pool(), core::scoring::mm::MMBondAngleLibrary::lookup(), core::scoring::mm::MMTorsionLibrary::lookup(), protocols::loophash::LoopHashLibrary::LoopHashLibrary(), protocols::motifs::IRCollection::make_motif_filename(), protocols::membrane::MPMutateRelaxMover::make_mutations(), protocols::task_operations::RestrictToInterfaceOperation::make_name(), protocols::task_operations::RestrictToNeighborhoodOperation::make_name(), protocols::denovo_design::components::make_strand_info_str(), protocols::fold_from_loops::utils::map_by_residue_subsets(), protocols::fldsgn::MatchResidues::map_ss_segments(), core::conformation::map_string_to_torsion_bin_string(), protocols::jd2::MPIFileBufJobDistributor::master_go(), protocols::splice::min_seg(), protocols::legacy_sewing::Model::model_begin(), protocols::legacy_sewing::Model::model_end(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::legacy_sewing::HashEdge::model_resnum(), protocols::match::SecondaryStructureMPM::modified_match_positions(), protocols::match::NumNeighborsMPM::modified_match_positions(), protocols::match::BfactorMPM::modified_match_positions(), protocols::pose_creation::MergePDBMover::Overlap::name(), core::chemical::ICoorAtomID::name(), protocols::jd3::chunk_library::ChunkLibraryJobQueen::next_batch_of_larval_jobs_from_prelim(), protocols::jd3::full_model::FullModelJobQueen::next_batch_of_larval_jobs_from_prelim(), protocols::jd3::standard::StandardJobQueen::next_batch_of_larval_jobs_from_prelim(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::next_generation(), protocols::canonical_sampling::TemperingBase::observe_after_metropolis(), protocols::canonical_sampling::TrialCounterObserver::observe_after_metropolis(), core::scoring::func::FourPointsFunc::operator()(), core::environment::LengthChecker::operator()(), core::scoring::epr_deer::DEERDataCache::operator[](), protocols::relax::LocalRelax::optimization_loop(), protocols::optimize_weights::IterativeOptEDriver::optimize_weights(), protocols::membrane::MPMutateRelaxMover::output_filename(), protocols::score_filters::ScoreCutoffFilter::output_residue_pair_energies(), core::scoring::rna::output_rna_motif(), core::scoring::rna::output_rna_motifs(), IdentifyLigandMotifs::output_single_motif_to_MotifLibrary(), protocols::match::output::WriteUpstreamHitKinemage::output_upstream_coordinates(), protocols::loop_grower::LoopPartialSolutionStore::parametercheck_filter(), protocols::constraint_generator::parse_custom_torsion(), core::scoring::epr_deer::DEERIO::parse_input(), protocols::sewing::hashing::AlignmentFileGeneratorMover::parse_ligands_tag(), protocols::ligand_docking::Rotate::parse_my_tag(), protocols::abinitio::abscript::AbscriptMover::parse_my_tag(), protocols::simple_moves::SixDoFGridDockMover::parse_my_tag(), protocols::helical_bundle_predict::HBPHelixAssignments::parse_psipred_file_contents(), core::scoring::constraints::ConstraintIO::parse_residue(), core::pack::task::operation::ExtraRotamers::parse_tag(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_1_split_and_merge_residues_as_necessary(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_quick_and_dirty_resolve_residue_types(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_resolve_residue_types(), core::scoring::nmr::pcs::PCSSingle::PCSSingle(), protocols::ligand_docking::ga_ligand_dock::Pharmacophore::Pharmacophore(), protocols::cyclic_peptide_predict::PNearCalculator::PNearCalculator(), protocols::flxbb::LayerDesignOperation::pos2select(), protocols::legacy_sewing::Assembly::pose_num(), protocols::legacy_sewing::Model::pose_number(), protocols::task_operations::RestrictConservedLowDdgOperation::position_ala_ddG(), protocols::task_operations::RestrictConservedLowDdgOperation::position_untouchable(), protocols::jd3::job_distributors::VanillaJobDistributor::potentially_discard_some_job_results(), protocols::jd3::job_distributors::VanillaJobDistributor::potentially_output_some_job_results(), core::scoring::nmr::pre::PRESingle::PRESingle(), protocols::vardist_solaccess::VarSolDistSasaCalculator::print(), protocols::match::downstream::AtomDistanceSecMatchRPE::print(), protocols::match::downstream::AtomAngleSecMatchRPE::print(), protocols::match::downstream::AtomDihedralSecMatchRPE::print(), core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator::print(), core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator::print(), core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator::print(), core::pose::metrics::simple_calculators::SasaCalculator2::print(), core::pose::metrics::simple_calculators::SasaCalculatorLegacy::print(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::print(), protocols::denovo_design::calculators::CavityCalculator::print(), protocols::mean_field::EnergiesByTaskCalculator::print(), protocols::pose_metric_calculators::CatPiCalculator::print(), protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator::print(), protocols::pose_metric_calculators::HPatchCalculator::print(), protocols::pose_metric_calculators::InterGroupNeighborsCalculator::print(), protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator::print(), protocols::pose_metric_calculators::NeighborsByDistanceCalculator::print(), protocols::pose_metric_calculators::PackstatCalculator::print(), protocols::pose_metric_calculators::PiPiCalculator::print(), protocols::pose_metric_calculators::ResidueDecompositionCalculator::print(), protocols::pose_metric_calculators::RotamerBoltzCalculator::print(), protocols::pose_metric_calculators::SaltBridgeCalculator::print(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::print(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::print(), protocols::pose_metric_calculators::SurfaceCalculator::print(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::print(), protocols::simple_pose_metric_calculators::NumberHBondsCalculator::print(), protocols::fldsgn::NcontactsCalculator::print(), protocols::pose_metric_calculators::FragQualCalculator::print(), protocols::ligand_docking::ProtLigPair_info::print_mut_string(), protocols::antibody::design::AntibodyDesignMover::print_str_vec(), protocols::ligand_docking::ProtLigPair_info::print_string(), protocols::pockets::FingerprintBase::print_to_pdb(), protocols::pack_daemon::EntityFunc::process_AA_SET_line(), protocols::pack_daemon::DynamicAggregateFunction::process_ENTITY_FUNCTION_line(), protocols::pack_daemon::DynamicAggregateFunction::process_FITNESS_line(), protocols::pack_daemon::DynamicAggregateFunction::process_NPD_PROPERTY_line(), protocols::toolbox::match_enzdes_util::EnzConstraintIO::process_pdb_header(), protocols::pack_daemon::DynamicAggregateFunction::process_POSE_ENERGY_line(), protocols::pack_daemon::DynamicAggregateFunction::process_POSE_ENERGY_VECTOR_line(), protocols::pack_daemon::DynamicAggregateFunction::process_SCALAR_EXPRESSION_line(), protocols::pack_daemon::EntityFunc::process_SCORE_line(), protocols::pack_daemon::EntityFunc::process_SET_CONDITION_line(), protocols::pack_daemon::DynamicAggregateFunction::process_STATE_line(), protocols::pack_daemon::DynamicAggregateFunction::process_STATE_VECTOR_line(), protocols::pack_daemon::EntityFunc::process_SUB_EXPRESSION_line(), protocols::pack_daemon::DynamicAggregateFunction::process_VECTOR_EXPRESSION_line(), protocols::pack_daemon::DynamicAggregateFunction::process_VECTOR_VARIABLE_line(), protocols::network::NetworkQueue::process_work_unit(), core::pack::task::operation::ExtraChiCutoffRLT::provide_xml_schema(), core::select::residue_selector::ResiduePropertySelector::provide_xml_schema(), core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric::provide_xml_schema(), core::simple_metrics::composite_metrics::ElectrostaticSimilarityMetric::provide_xml_schema(), core::simple_metrics::metrics::ResidueSummaryMetric::provide_xml_schema(), core::simple_metrics::metrics::RMSDMetric::provide_xml_schema(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::provide_xml_schema(), protocols::coupled_moves::CoupledMovesProtocol::provide_xml_schema(), protocols::enzdes::EnzScoreFilter::provide_xml_schema(), protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator::provide_xml_schema(), protocols::fold_from_loops::constraint_generator::SegmentedAtomPairConstraintGenerator::provide_xml_schema(), protocols::fold_from_loops::filters::ConstraintFulfilmentFilter::provide_xml_schema(), protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::provide_xml_schema(), protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter::provide_xml_schema(), protocols::fold_from_loops::movers::DisplayPoseLabelsMover::provide_xml_schema(), protocols::fold_from_loops::movers::LabelPoseFromResidueSelectorMover::provide_xml_schema(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::provide_xml_schema(), protocols::fold_from_loops::movers::ResidueLabelsToPymolSelectionMover::provide_xml_schema(), protocols::fold_from_loops::movers::SavePDBInfoMover::provide_xml_schema(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::provide_xml_schema(), protocols::fold_from_loops::NubInitioMover::provide_xml_schema(), protocols::fold_from_loops::selectors::ConstraintResidueSelector::provide_xml_schema(), protocols::fold_from_loops::selectors::CutpointResidueSelector::provide_xml_schema(), protocols::mean_field::GenMeanFieldMover::provide_xml_schema(), protocols::motif_grafting::movers::MotifGraftMover::provide_xml_schema(), protocols::moves::PyMOLMover::provide_xml_schema(), protocols::recon_design::FitnessFilter::provide_xml_schema(), protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter::provide_xml_schema(), protocols::simple_filters::SimpleMetricFilter::provide_xml_schema(), protocols::struct_fragment::StructFragmentMover::provide_xml_schema(), core::conformation::parametric::SizeValuedParameter::provide_xsd_information(), core::conformation::parametric::RealValuedParameter::provide_xsd_setting_information(), protocols::loop_grower::LoopPartialSolutionStore::push(), protocols::jd3::job_distributors::JobExtractor::query_job_queen_for_more_jobs_for_current_node(), protocols::glycan_docking::GlycanDockProtocol::ramp_score_weight(), core::environment::FoldTreeSketch::range_check(), core::scoring::nmr::rdc::RDCSingle::RDCSingle(), core::chemical::gasteiger::GasteigerAtomTypeSet::read_bond_file(), core::sequence::SequenceProfile::read_from_checkpoint(), core::sequence::SequenceProfile::read_from_file(), protocols::noesy_assign::PeakFileFormat::read_header(), core::chemical::carbohydrates::read_linkage_conformers_from_database_file(), core::scoring::methods::NMerRefEnergy::read_nmer_table(), protocols::pack_daemon::DynamicAggregateFunction::read_state_vector_file(), core::conformation::symmetry::SymmetricConformation::recalculate_transforms(), protocols::pose_metric_calculators::ResidueDecompositionByChainCalculator::recompute(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::match::output::PDBWriter::record_match(), protocols::match::output::CloudPDBWriter::record_match(), protocols::match::upstream::ProteinUpstreamBuilder::recover_hits(), protocols::pack_daemon::MPIMultistateFitnessFunction::recover_poses_from_states(), protocols::loop_grower::LoopGrower::refine_cycle(), protocols::electron_density::DockPDBIntoDensityMover::refine_RBfitResultDB(), core::environment::FoldTreeSketch::remove_cycles(), protocols::legacy_sewing::remove_models_from_dssp(), protocols::toolbox::match_enzdes_util::EnzdesCstParamCache::remove_seqpos_from_template_res(), core::chemical::rename_atoms(), core::environment::FoldTreeSketch::render(), protocols::toolbox::pose_manipulation::repack_this_residue(), protocols::indexed_structure_store::filters::FragmentLookupFilter::report(), protocols::simple_filters::TotalSasaFilter::report(), protocols::mean_field::GenMeanFieldMover::report_aa_matrix(), protocols::legacy_sewing::SewGraph::report_binary_stats(), protocols::features::ModelFeatures::report_features(), protocols::indexed_structure_store::filters::FragmentLookupFilter::report_sm(), core::scoring::Energies::require_context_graph_(), core::scoring::symmetry::SymmetricEnergies::require_context_graph_(), core::pack::task::IGEdgeReweightContainer::res_res_weight(), protocols::loop_grower::LoopGrower::rescoresolutionset(), core::pose::residue_types_from_sequence(), protocols::enzdes::SecondaryMatchProtocol::residues_compatible(), core::pose::ResidueIndexDescriptionPoseNum::resolve_index(), core::pose::ResidueIndexDescriptionPDB::resolve_index(), core::pose::ResidueIndexDescriptionChainEnd::resolve_index(), core::io::pose_to_sfr::restrict_prec(), core::pack::task::operation::rotamer_sampling_data_xml_schema_attributes(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::run(), protocols::antibody::design::AntibodyDesignMover::run_basic_mc_algorithm(), protocols::frag_picker::run_command(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::run_docking(), core::io::external::PsiPredInterface::run_psipred(), core::io::external::PsiPredInterface::run_psipred_prob(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), protocols::match::upstream::DunbrackSCSampler::samples(), protocols::simple_moves::SaveProbabilitiesMetricMover::save_aa_probabilities_to_file(), protocols::monte_carlo::GenericSimulatedAnnealer::save_checkpoint_file(), protocols::loophash::LoopHashLibrary::save_db(), protocols::electron_density::DockPDBIntoDensityMover::score_and_dump_natives(), core::pack::annealer::SequenceSymmetricAnnealer::search_pose_for_residue_subsets(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::select_points(), protocols::pack_daemon::PackDaemon::select_rotamer_subset(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), protocols::moves::PyMOLMover::send_any(), protocols::moves::PyMOLMover::send_foldtree(), protocols::moves::PyMOLMover::send_hbonds(), protocols::moves::PyMOLMover::send_membrane_planes(), protocols::moves::PyMOLMover::send_movemap(), protocols::moves::PyMOLMover::send_polars(), protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst::seqpos_for_geomcst(), protocols::features::serialize_ids(), protocols::hbnet::HBNet::set_constraints(), protocols::antibody::AntibodyInfo::set_default(), protocols::helical_bundle_predict::HBPHelix::set_end_position(), protocols::splice::Splice::set_fold_tree(), core::select::residue_selector::ResidueIndexSelector::set_index(), core::select::residue_selector::ResidueIndexSelector::set_index_range(), protocols::match::set_ligpose_rotamer(), protocols::frag_picker::FragmentPicker::set_max_threads(), core::scoring::Energies::set_owner(), core::simple_metrics::per_residue_metrics::LoadedProbabilitiesMetric::set_probabilities_from_lines(), protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::set_rmsd_residues_to_ignore_native(), protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::set_rmsd_residues_to_ignore_prediction(), protocols::features::DatabaseJobInputter::set_struct_ids_from_sql(), protocols::environment::ProtectedConformation::set_stub_transform(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::set_thresh(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_up_terminal_disulfide_variants(), protocols::cyclic_peptide::crosslinker::set_up_thioether_variants(), protocols::rna::setup::RNA_CSA_JobDistributor::set_updates(), core::simple_metrics::SimpleMetricData::set_value(), protocols::antibody::AntibodyInfo::setup_CDRsInfo(), core::pack::annealer::SequenceSymmetricAnnealer::setup_for_linked_residues(), core::scoring::carbohydrates::CHIEnergyFunction::setup_for_sampling(), core::scoring::carbohydrates::OmegaPreferencesFunction::setup_for_sampling(), core::conformation::carbohydrates::GlycanTree::setup_glycan_nodes(), protocols::optimize_weights::IterativeOptEDriver::setup_pdbnames_next_round(), protocols::simple_moves::PeriodicBoxMover::setup_pose(), protocols::enzdes::EnzdesScorefileFilter::setup_pose_metric_calculators(), protocols::tcr::TCRmodel::setup_templates(), protocols::cryst::MakeLatticeMover::setup_xtal_symminfo(), protocols::cryst::MakeLayerMover::setup_xtal_symminfo(), core::simple_metrics::SimpleMetricData::show(), protocols::ligand_docking::ga_ligand_dock::AtomProperties::show(), core::kinematics::MoveMap::show(), protocols::recces::sampler::rna::MC_RNA_KIC_Sampler::show(), protocols::glycan_docking::GlycanDockProtocol::show(), protocols::antibody::design::AntibodyDesignMover::show(), core::select::residue_selector::SliceResidueSelector::show_selection_logic(), protocols::match::output::PDBWriter::signature_string(), protocols::pose_sewing::data_storage::TerminalDSSPSortedPoseVector::simultaneously_populate_and_write_segment_file_pdb_using_stored_motifs(), protocols::loop_grower::LoopGrower::single_grow(), protocols::loop_grower::LoopPartialSolutionStore::skeleton_filter(), protocols::task_operations::ConservativeDesignOperation::skip_resid(), protocols::enzdes::EnzdesFlexibleRegion::sort_ensemble_by_designability(), core::pose::RID_FileSource::source_string(), core::pack::task::ResfileContents::specialized_commands_exist_for_residue(), protocols::splice::SpliceOut::SpliceOutFilter(), core::sequence::split_sequence_motif(), protocols::grafting::simple_movers::KeepRegionMover::start(), core::id::TorsionID::str(), core::scoring::superimpose_polymer_heavyatoms(), core::scoring::superimpose_pose(), protocols::docking::membrane::MPFindInterfaceMover::superimpose_upstream_partner(), core::pack::interaction_graph::DensePDEdge::swap_edge_energies(), core::pack::interaction_graph::FASTEREdge::swap_edge_energies(), protocols::optimize_weights::IterativeOptEDriver::test_weight_sensitivity(), core::pack::annealer::Value::to_string(), core::select::residue_selector::ResidueRange::to_string(), protocols::noesy_assign::CrossPeak::tolerance(), protocols::antibody::design::transform_sequence_to_mutation_set(), protocols::motifs::IRCollection::try_for_more(), protocols::moves::UDPSocketClient::UDPSocketClient(), core::kinematics::tree::BondedAtom::update_internal_coords(), core::conformation::symmetry::SymmetryInfo::update_nmonomer_jumps(), core::pack::annealer::SequenceSymmetricAnnealer::update_shared_residue_map(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::update_tags(), protocols::symmetry::SetupForSequenceSymmetryMover::validate_residue_selectors(), protocols::pack_daemon::DynamicAggregateFunction::variable_expression(), protocols::pack_daemon::EntityFunc::variable_expression(), protocols::pack_daemon::IterativeVectorExpression::vector_values(), protocols::pack_daemon::DynamicAggregateFunctionDriver::verify_remote_daemon_set_initialization_successful(), protocols::pack_daemon::DynamicAggregateFunction::verify_variable_name_or_throw(), protocols::pack_daemon::DynamicAggregateFunction::verify_vector_arguments(), core::select::residue_selector::SelectorLogicParser::visit(), core::select::residue_selector::SliceResidueSelector::wrap_index(), protocols::sewing::hashing::BasisMapGenerator::write_alignments_to_file(), protocols::sewing::hashing::EdgeMapGenerator::write_edges_for_segment(), protocols::noesy_assign::PeakFileFormat::write_header(), protocols::match::output::CloudPDBWriter::write_match_groups(), protocols::simple_moves::DumpSingleResidueRotamers::write_poses_to_pdbs(), protocols::loop_grower::LoopGrower::write_to_disk(), protocols::loop_grower::LoopPartialSolutionStore::writelpsstore(), core::scoring::func::FourPointsFunc::xyz(), protocols::abinitio::abscript::RigidChunkCM::yield_claims(), and protocols::loops::loop_mover::LoopCM::yield_claims().
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| AtomID const core::id::GLOBAL_BOGUS_ATOM_ID(AtomID::BOGUS_ATOM_ID()) |
Globals – may not be used until after core::init is called.
Referenced by core::scoring::constraints::SequenceProfileConstraint::atom(), protocols::constraints_additional::SequenceCouplingConstraint::atom(), core::scoring::constraints::MembraneSpanConstraint::atom(), core::scoring::constraints::MembraneSpanTermZConstraint::atom(), core::scoring::constraints::NonResidueTypeConstraint::atom(), core::scoring::constraints::ResidueCouplingConstraint::atom(), core::scoring::constraints::ResidueTypeConstraint::atom(), core::scoring::constraints::ResidueTypeLinkingConstraint::atom(), core::chemical::ICoorAtomID::buildable(), protocols::backrub::BackrubSegment::end_bond_angle_key(), core::conformation::Residue::inter_residue_connection_partner(), and core::pose::named_atom_id_to_atom_id().
| DOF_ID const core::id::GLOBAL_BOGUS_DOF_ID | ( | AtomID::BOGUS_ATOM_ID() | , |
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Global – may not be used until after core::init is called.
Referenced by core::kinematics::AtomTree::bond_length_dof_id(), core::conformation::Conformation::dof_id_from_atom_ids(), core::conformation::Conformation::dof_id_from_torsion_id(), and core::kinematics::AtomTree::torsion_angle_dof_id().
| NamedAtomID const core::id::GLOBAL_BOGUS_NAMED_ATOM_ID | ( | NamedAtomID::BOGUS_NAMED_ATOM_ID() | ) |
Globals – may not be used until after core::init is called.
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Globals – may not be used until after core::init is called.
| StubID const core::id::GLOBAL_BOGUS_STUB_ID(StubID::BOGUS_STUB_ID()) |
Global – may not be used until after core::init is called.
| TorsionID const core::id::GLOBAL_BOGUS_TORSION_ID | ( | TorsionID::BOGUS_TORSION_ID() | ) |
Globals.
Global – may not be used until after core::init is called.
| AtomID const core::id::GLOBAL_CHAINBREAK_BOGUS_ATOM_ID(AtomID::CHAINBREAK_BOGUS_ATOM_ID()) |
| NamedAtomID const core::id::GLOBAL_CHAINBREAK_BOGUS_NAMED_ATOM_ID | ( | NamedAtomID::CHAINBREAK_BOGUS_NAMED_ATOM_ID() | ) |
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1.9.1