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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::ResidueIndexSelectorOP 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 
)

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_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 
)

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().

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::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(), 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(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::calculate(), core::simple_metrics::per_residue_metrics::HbondMetric::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_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().