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Rosetta
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Namespaces | |
| jump_selector | |
| movemap | |
| residue_selector | |
| util | |
Classes | |
| class | Enumerate1WithSelector |
| class | PreSelectedResidRange |
Functions | |
| utility::SimpleRange1 | resids (core::pose::Pose const &pose) |
| PreSelectedResidRange | resids (core::pose::Pose const &pose, utility::vector1< select::residue_selector::ResidueSelectorCOP > const &selectors) |
| utility::vector1< Size > | get_residues_from_subset (utility::vector1< bool > const &subset, bool select=true) |
| Get a vector1 of the indexes which are the same value as 'select' in the ResidueSubset. More... | |
| std::set< core::Size > | get_residue_set_from_subset (utility::vector1< bool > const &subset, bool select=true) |
| Get a std::set of the indexes which are the same value as 'select' in the ResidueSubset. More... | |
| utility::vector1< bool > | get_subset_from_residues (utility::vector1< core::Size > const &selection, core::Size total_nres, bool invert=false) |
| Get a vector1 of true/false (a ResidueSubset) from a list of residue numbers. More... | |
| core::select::residue_selector::ResidueSelectorOP | get_residue_selector_from_subset (core::select::residue_selector::ResidueSubset subset) |
| Convert a residue subset back into a residue selector. @detail Not only does this allow one to go from a residue subset back to a selector, but by applying a selector to a pose and using this to go back to a selector, one can turn context-dependent residue selectors into context-independent residue selectors. More... | |
| utility::vector1< bool > | get_neighbor_residues (core::pose::Pose const &pose, utility::vector1< bool > const &residue_positions, core::Real neighbor_dis) |
| Get a boolean vector of neighbor residues given some distance < 10A. More... | |
| void | fill_neighbor_residues (core::pose::Pose const &pose, utility::vector1< bool > &residue_positions, core::Real neighbor_dis=10.0) |
| Fill a boolean vector of residues with neighboring residues. More... | |
| utility::vector1< bool > | trim_neighbors_by_distance (core::pose::Pose const &pose, utility::vector1< bool > const &selection, utility::vector1< bool > const &selection_and_neighbors, core::Real &dist_cutoff) |
| filter neighbors to a certain CB distance. Takes distance from selection to neighbors to trim neighbors. More... | |
| void | filter_neighbors_by_distance (core::pose::Pose const &pose, utility::vector1< bool > const &selection, utility::vector1< bool > &selection_and_neighbors, core::Real &dist_cutoff) |
| filter neighbors to a certain CB distance. Takes distance from selection to neighbors to trim neighbors. More... | |
| utility::vector1< bool > | get_tenA_neighbor_residues (core::pose::Pose const &pose, utility::vector1< bool > const &residue_positions) |
| Get neighbor residues within 10 A CB distance cutoff using the 10 A neighbor graph in energies. Returns ONLY the neighbor residues. More... | |
| void | fill_tenA_neighbor_residues (pose::Pose const &pose, utility::vector1< bool > &residue_positions) |
| Fill neighbor residues within 10 A CB distance cutoff using the 10 A neighbor graph in energies into the boolean vector. More... | |
| std::string | get_pymol_selection_for_atoms (pose::Pose const &pose, utility::vector1< id::AtomID > const &atoms, std::string const &sele_name, bool skip_virts=true) |
| Return a pymol selection of a set of atoms. More... | |
| utility::vector1< bool > | get_master_subunit_selection (pose::Pose const &pose, utility::vector1< bool > const &full_subset) |
| This is for a 'symmetrical' selection (iE Normal selection for symmetrical poses!). Turns off all residues that are not part of the master subunit. More... | |
| void core::select::fill_neighbor_residues | ( | core::pose::Pose const & | pose, |
| utility::vector1< bool > & | residue_positions, | ||
| core::Real | neighbor_dis = 10.0 |
||
| ) |
Fill a boolean vector of residues with neighboring residues.
Uses 10A neighbor graph for neighbors, THEN takes distance from selection to neighbors to trim neighbors. residue_positions includes positions and neighbors. Use a NOT selector to get only the neighbors.
References fill_tenA_neighbor_residues(), and filter_neighbors_by_distance().
Referenced by core::select::residue_selector::NeighborhoodResidueSelector::apply(), protocols::switches::GraftSwitchMover::apply(), protocols::pose_creation::MakeJunctionsMover::assign_seq(), protocols::switches::GraftSwitchMover::get_additional_output(), get_neighbor_residues(), protocols::pose_creation::MergePDBatOverlapMover::merge_junction_sequence(), and protocols::pose_creation::MergePDBatOverlapMover::minimize_overlap().
| void core::select::fill_tenA_neighbor_residues | ( | pose::Pose const & | pose, |
| utility::vector1< bool > & | residue_positions | ||
| ) |
Fill neighbor residues within 10 A CB distance cutoff using the 10 A neighbor graph in energies into the boolean vector.
References core::pose::Pose::energies(), and core::scoring::Energies::tenA_neighbor_graph().
Referenced by fill_neighbor_residues(), get_tenA_neighbor_residues(), and protocols::loops::select_loop_residues().
| void core::select::filter_neighbors_by_distance | ( | core::pose::Pose const & | pose, |
| utility::vector1< bool > const & | selection, | ||
| utility::vector1< bool > & | selection_and_neighbors, | ||
| core::Real & | dist_cutoff | ||
| ) |
filter neighbors to a certain CB distance. Takes distance from selection to neighbors to trim neighbors.
References core::conformation::Residue::nbr_atom(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().
Referenced by fill_neighbor_residues(), protocols::loops::filter_loop_neighbors_by_distance(), and trim_neighbors_by_distance().
| utility::vector1< bool > core::select::get_master_subunit_selection | ( | pose::Pose const & | pose, |
| utility::vector1< bool > const & | full_subset | ||
| ) |
This is for a 'symmetrical' selection (iE Normal selection for symmetrical poses!). Turns off all residues that are not part of the master subunit.
Turns off all residues that are not part of the master subunit.
References core::pose::Pose::conformation(), and core::pose::symmetry::is_symmetric().
Referenced by protocols::carbohydrates::GlycanTreeModeler::apply(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::calculate(), core::select::residue_selector::get_cyclic_pose_residue_mappings_from_selectors(), core::select::residue_selector::get_residue_mapping_from_selectors(), and protocols::carbohydrates::GlycanSampler::init_objects().
| utility::vector1< bool > core::select::get_neighbor_residues | ( | core::pose::Pose const & | pose, |
| utility::vector1< bool > const & | residue_positions, | ||
| core::Real | neighbor_dis | ||
| ) |
Get a boolean vector of neighbor residues given some distance < 10A.
References fill_neighbor_residues(), and core::pose::Pose::total_residue().
Referenced by core::select::residue_selector::NeighborhoodResidueSelector::apply().
| std::string core::select::get_pymol_selection_for_atoms | ( | pose::Pose const & | pose, |
| utility::vector1< id::AtomID > const & | atoms, | ||
| std::string const & | sele_name, | ||
| bool | skip_virts | ||
| ) |
Return a pymol selection of a set of atoms.
References protocols::comparative_modeling::features::A, core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), protocols::sparta::contains(), core::chemical::AtomType::is_virtual(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and core::id::to_string().
| core::select::residue_selector::ResidueSelectorOP core::select::get_residue_selector_from_subset | ( | core::select::residue_selector::ResidueSubset | subset | ) |
Convert a residue subset back into a residue selector. @detail Not only does this allow one to go from a residue subset back to a selector, but by applying a selector to a pose and using this to go back to a selector, one can turn context-dependent residue selectors into context-independent residue selectors.
References get_residues_from_subset().
Referenced by protocols::toolbox::pose_manipulation::repack_these_residues(), and core::pack::guidance_scoreterms::sap::SapConstraintHelper::setup_for_symmetry().
| std::set< core::Size > core::select::get_residue_set_from_subset | ( | utility::vector1< bool > const & | subset, |
| bool | select | ||
| ) |
Get a std::set of the indexes which are the same value as 'select' in the ResidueSubset.
Referenced by protocols::hbnet::HBNet::apply(), protocols::switches::GraftSwitchMover::apply(), protocols::hybridization::CartesianSampler::apply_constraints(), protocols::hybridization::CartesianSampler::compute_fragment_bias(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_cartligmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_scmin(), and protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_movable_scs().
| utility::vector1< core::Size > core::select::get_residues_from_subset | ( | utility::vector1< bool > const & | subset, |
| bool | select | ||
| ) |
Get a vector1 of the indexes which are the same value as 'select' in the ResidueSubset.
Referenced by protocols::enzdes::PackRotamersMoverPartGreedy::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::apply(), protocols::protein_interface_design::movers::ShoveResidueMover::apply(), protocols::protein_interface_design::movers::TryRotamers::apply(), protocols::simple_moves::SixDoFGridDockMover::apply(), protocols::simple_moves::Tumble::apply(), core::select::residue_selector::NeighborhoodResidueSelector::apply(), core::select::residue_selector::SliceResidueSelector::apply(), protocols::protein_interface_design::filters::DisulfideFilter::apply(), protocols::cyclic_peptide::PeptideCyclizeMover::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::simple_moves::FoldTreeFromMotif::apply(), core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric::calculate(), core::simple_metrics::composite_metrics::CompositeEnergyMetric::calculate(), core::simple_metrics::metrics::InteractionEnergyMetric::calculate(), core::simple_metrics::metrics::SecondaryStructureMetric::calculate(), core::simple_metrics::metrics::SelectedResiduesMetric::calculate(), core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::calculate(), core::simple_metrics::metrics::SequenceMetric::calculate(), core::simple_metrics::per_residue_metrics::HbondMetric::calculate(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::calculate(), core::simple_metrics::per_residue_metrics::PerResidueEnergyMetric::calculate(), core::simple_metrics::per_residue_metrics::PerResidueSasaMetric::calculate(), core::simple_metrics::per_residue_metrics::SidechainNeighborCountMetric::calculate(), core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::calculate(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::calculate(), protocols::drug_design::RDKitMetric::calculate(), protocols::simple_moves::Tumble::center_of_mass(), protocols::enzdes::RepackWithoutLigandFilter::compute(), protocols::simple_filters::AtomicContactFilter::compute(), protocols::contact_map::ContactMap::fill_contacts(), protocols::contact_map::ContactMap::fill_contacts_all_atom2(), core::select::residue_selector::get_cyclic_pose_residue_mappings_from_selectors(), core::select::residue_selector::get_residue_mapping_from_selectors(), get_residue_selector_from_subset(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::get_residues(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::initialize(), protocols::backrub::BackrubMover::pivot_residues(), protocols::glycan_docking::GlycanDockProtocol::record_pose_metrics(), protocols::protein_interface_design::filters::DisulfideFilter::report(), protocols::pose_reporters::RMSDReporter::report_property(), protocols::protein_interface_design::filters::DisulfideFilter::report_sm(), protocols::toolbox::pose_manipulation::rigid_body_move(), protocols::idealize::IdealizeMover::setup_idealize_constraints(), and protocols::calc_taskop_movers::DesignRepackMover::target_residues().
| utility::vector1< bool > core::select::get_subset_from_residues | ( | utility::vector1< core::Size > const & | selection, |
| core::Size | total_nres, | ||
| bool | invert = false |
||
| ) |
Get a vector1 of true/false (a ResidueSubset) from a list of residue numbers.
If invert is true, residues not in the selection are true in the returned vector.
| utility::vector1< bool > core::select::get_tenA_neighbor_residues | ( | pose::Pose const & | pose, |
| utility::vector1< bool > const & | residue_positions | ||
| ) |
Get neighbor residues within 10 A CB distance cutoff using the 10 A neighbor graph in energies. Returns ONLY the neighbor residues.
References fill_tenA_neighbor_residues().
Referenced by protocols::antibody::GraftedStemOptimizer::get_stem_movemap(), and protocols::antibody::GraftedStemOptimizer::get_stem_taskfactory().
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inline |
USAGE: for( core::Size const resid : resids( pose ) )
References core::pose::Pose::size().
Referenced by core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::add_longrange_twobody_energies_multithreaded(), protocols::hbnet::add_network_resids_to_pose(), core::select::jump_selector::JumpForResidue::apply(), protocols::denovo_design::residue_selectors::NamedSegmentSelector::apply(), protocols::simple_filters::ResidueSelectionDistanceFilter::apply(), protocols::pose_length_moves::FixAllLoopsMover::apply(), protocols::cyclic_peptide::PeptideStubMover::assign_chain_ids(), protocols::denovo_design::architects::bulge_residues(), protocols::ligand_docking::ga_ligand_dock::compute_nhbonds(), protocols::denovo_design::residue_selectors::NamedSegmentSelector::compute_residue_subset(), protocols::denovo_design::residue_selectors::NamedSegmentSelector::compute_residue_subset_for_segment(), protocols::denovo_design::movers::AlignResiduesMover::delete_residues(), protocols::cyclic_peptide::dump_debug_output(), protocols::pose_length_moves::AnalyzeLoopModeling::generate_lookback_rmsd(), protocols::pose_length_moves::PossibleLoop::generate_output_pose(), protocols::cyclic_peptide::PeptideStubMover::get_anchor_rsd(), protocols::denovo_design::components::get_strand_residues(), protocols::pockets::PocketGrid::getRelaxResidues(), protocols::indexed_structure_store::SSHashedFragmentStore::max_rmsd_in_region(), protocols::hbnet::HBNet::place_rots_on_pose(), protocols::simple_filters::ResidueSelectionDistanceFilter::report(), core::pack::task::operation::RestrictYSDesign::RestrictYSDesign(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::set_nonpivot_res_to_sweep(), protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber::set_nonpivot_res_to_sweep(), protocols::match::Matcher::set_original_scaffold_build_points(), protocols::match::MatcherTask::set_original_scaffold_build_points(), protocols::match::Matcher::set_original_scaffold_build_points_for_constraint(), protocols::match::MatcherTask::set_original_scaffold_build_points_for_geometric_constraint(), and core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::set_twobody_energies_multithreaded().
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inline |
USAGES: for( core::Size const resid : resids( pose, {s1, s2} ) )
| utility::vector1< bool > core::select::trim_neighbors_by_distance | ( | core::pose::Pose const & | pose, |
| utility::vector1< bool > const & | selection, | ||
| utility::vector1< bool > const & | all_neighbors, | ||
| core::Real & | dist_cutoff | ||
| ) |
filter neighbors to a certain CB distance. Takes distance from selection to neighbors to trim neighbors.
References filter_neighbors_by_distance().
1.9.1