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Namespaces | Classes | Functions
core::select Namespace Reference

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< Sizeget_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::Sizeget_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< boolget_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. 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< boolget_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< booltrim_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< boolget_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< boolget_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...
 

Function Documentation

void core::select::fill_neighbor_residues ( core::pose::Pose const &  pose,
utility::vector1< bool > &  residue_positions,
core::Real  neighbor_dis = 10.0 
)
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 
)
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 
)

Convert a residue subset back into a residue selector. 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 
)
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::simple_moves::FoldTreeFromMotif::apply(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::apply(), protocols::protein_interface_design::movers::ShoveResidueMover::apply(), protocols::cyclic_peptide::PeptideCyclizeMover::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::simple_moves::Tumble::apply(), protocols::enzdes::PackRotamersMoverPartGreedy::apply(), protocols::protein_interface_design::movers::TryRotamers::apply(), protocols::protein_interface_design::filters::DisulfideFilter::apply(), core::select::residue_selector::SliceResidueSelector::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), core::select::residue_selector::NeighborhoodResidueSelector::apply(), core::simple_metrics::metrics::SelectedResiduesPyMOLMetric::calculate(), core::simple_metrics::metrics::SelectedResiduesMetric::calculate(), core::simple_metrics::metrics::SecondaryStructureMetric::calculate(), protocols::drug_design::RDKitMetric::calculate(), core::simple_metrics::composite_metrics::CompositeEnergyMetric::calculate(), core::simple_metrics::metrics::SequenceMetric::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(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::calculate(), core::simple_metrics::per_residue_metrics::HbondMetric::calculate(), core::pack::guidance_scoreterms::sap::PerResidueSapScoreMetric::calculate(), core::simple_metrics::metrics::InteractionEnergyMetric::calculate(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::calculate(), core::simple_metrics::per_residue_metrics::WaterMediatedHbondMetric::calculate(), protocols::simple_moves::Tumble::center_of_mass(), protocols::simple_filters::AtomicContactFilter::compute(), protocols::enzdes::RepackWithoutLigandFilter::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::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().

utility::SimpleRange1 core::select::resids ( core::pose::Pose const &  pose)
inline

USAGE: for( core::Size const resid : resids( pose ) )

References core::pose::Pose::size().

Referenced by protocols::simple_filters::ResidueSelectionDistanceFilter::apply(), protocols::pose_length_moves::FixAllLoopsMover::apply(), protocols::denovo_design::residue_selectors::NamedSegmentSelector::apply(), protocols::cyclic_peptide::PeptideStubMover::assign_chain_ids(), protocols::denovo_design::architects::bulge_residues(), protocols::denovo_design::residue_selectors::NamedSegmentSelector::compute_residue_subset(), 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::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::MatcherTask::set_original_scaffold_build_points(), protocols::match::Matcher::set_original_scaffold_build_points(), protocols::match::Matcher::set_original_scaffold_build_points_for_constraint(), and protocols::match::MatcherTask::set_original_scaffold_build_points_for_geometric_constraint().

PreSelectedResidRange core::select::resids ( core::pose::Pose const &  pose,
utility::vector1< select::residue_selector::ResidueSelectorCOP > const &  selectors 
)
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().