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protocols::kinmatch Namespace Reference

Classes

class  BruteFunGroupTK
 
class  FunGroupTK
 
class  KinFunGroupTK
 
struct  KRSQuery
 

Typedefs

using Reals = utility::vector1< core::Real >
 
using Sizes = utility::vector1< core::Size >
 
using Vec = numeric::xyzVector< Real >
 
using Mat = numeric::xyzMatrix< Real >
 
using Vecs = utility::vector1< Vec >
 

Enumerations

enum  KRSQueryType { CEN, CEN_ANG, CEN_AXS, CEN_AXS_ORI }
 

Functions

template<typename T >
std::string str (T const &t)
 
template<typename T >
std::string lzs (T const &t, int const w)
 
Real sqr (Real const r)
 
Vec xyz (Pose const &p, core::Size const &ia, core::Size const &ir)
 
PoseOP alapose (Pose const &pose_in)
 
vector1< core::Sizeallifnone (vector1< core::Size > v, core::Size n)
 
void dumpcgo (Vec v, string l)
 
void xform_rsd_gl2 (Stub const &s, Residue &rsd)
 

Typedef Documentation

using protocols::kinmatch::Mat = typedef numeric::xyzMatrix<Real>
using protocols::kinmatch::Reals = typedef utility::vector1<core::Real>
using protocols::kinmatch::Sizes = typedef utility::vector1<core::Size>
using protocols::kinmatch::Vec = typedef numeric::xyzVector<Real>
using protocols::kinmatch::Vecs = typedef utility::vector1<Vec>

Enumeration Type Documentation

Enumerator
CEN 
CEN_ANG 
CEN_AXS 
CEN_AXS_ORI 

Function Documentation

PoseOP protocols::kinmatch::alapose ( Pose const &  pose_in)
vector1<core::Size> protocols::kinmatch::allifnone ( vector1< core::Size v,
core::Size  n 
)
void protocols::kinmatch::dumpcgo ( Vec  v,
string  l 
)
template<typename T >
std::string protocols::kinmatch::lzs ( T const &  t,
int const  w 
)
inline
Real protocols::kinmatch::sqr ( Real const  r)
inline
template<typename T >
std::string protocols::kinmatch::str ( T const &  t)
inline

Referenced by core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::accumulate_seqpos_oversats(), protocols::enzdes::SecondaryMatchProtocol::apply(), protocols::recces::scratch::ThermalSamplingMover::apply(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::assert_calculators(), protocols::noesy_assign::NoesyModule::assign(), protocols::mpi_refinement::MPI_Refine_Master::assign_loop_info(), core::scoring::atomic_depth::AtomicDepth::AtomicDepth(), protocols::peptide_deriver::PeptideDeriverPoseOutputter::begin_receptor_partner_pair(), core::scoring::methods::ProQ_Energy::calculate_feature_vector(), core::scoring::methods::ProQ_Energy::calculate_feature_vector_proq2(), protocols::sparta::GDB::checkFormat(), protocols::pose_length_moves::NearNativeLoopCloser::close_loop(), core::chemical::sdf::MolWriter::compose_atoms(), core::chemical::sdf::MolWriter::compose_bonds(), core::chemical::sdf::MolWriter::compose_metadata(), core::chemical::sdf::MolWriter::compose_properties(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), core::scoring::nmr::convert_string_to_averaging_type(), core::scoring::nmr::pcs::PCSSingleSet::convert_string_to_computation_type(), core::scoring::nmr::NMRSpinlabel::convert_string_to_conformer_filter_type(), core::scoring::nmr::convert_string_to_normalization_type(), core::scoring::nmr::convert_string_to_rate_type(), core::scoring::nmr::convert_string_to_weighting_scheme(), protocols::nonlocal::StarTreeBuilder::do_compute_jump_rmsd(), protocols::enzdes::SecondaryMatchProtocol::do_matching(), protocols::star::emit_intermediate(), core::io::silent::SilentStruct::energies_into_pose(), protocols::indexed_structure_store::extract_residue_entries(), protocols::features::FeaturesReporter::find_tag(), protocols::toolbox::fix_tag_suffix(), protocols::sparta::GDB::FORMAT_str_parser(), protocols::sparta::Sparta::SpartaLib::get_ANN_data(), protocols::ligand_docking::get_interface_deltas(), protocols::mpi_refinement::get_loop_info_full(), protocols::enzdes::enzutil::get_pdb_code_from_pose_tag(), core::scoring::dssp::StrandPairing::hash_value(), protocols::features::JobDataFeatures::insert_string_rows(), protocols::topology_broker::claims::JumpClaim::jump_atom1(), protocols::topology_broker::claims::JumpClaim::jump_atom2(), protocols::sparta::GDB::loadGDB(), protocols::sparta::PDB::loadPDB(), protocols::sparta::ANN::loadWeightBias3(), protocols::forge::components::VarLengthBuild::loop_mover_str(), protocols::recces::RECCES_Mover::more_dump_stuff(), protocols::forge::components::VarLengthBuild::new_secondary_structure_override(), protocols::forge::components::VarLengthBuild::new_sequence_override(), protocols::medal::on_pose_accept(), core::environment::operator<<(), core::pose::full_model_info::operator>>(), core::scoring::methods::ProQ_Energy::output_local_prediction(), protocols::environment::claims::EnvClaim::parse_ctrl_str(), protocols::hbnet::HBNetStapleInterface::parse_my_tag(), protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::parse_target_tag(), protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter::peptide_entry(), protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::peptide_entry(), protocols::peptide_deriver::PeptideDeriverPoseOutputter::peptide_entry(), protocols::flxbb::LayerDesignOperation::pos2select(), protocols::moves::StructureRestrictor::pose_name(), core::fragment::FragmentIO::read_data_from_stream(), protocols::scoring::VDW_CachedRepScreenInfo::read_in_VDW_rep_screen_pose_from_options(), core::conformation::symmetry::SymmData::read_symmetry_data_from_stream(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), protocols::recces::RECCES_Mover::save_data_to_disk(), core::fragment::FragData::secstruct(), protocols::indexed_structure_store::DirectSegmentLookup::segment_lookup(), protocols::dna::seq_to_str(), core::fragment::FragData::sequence(), core::scoring::ScoreFunction::serialize_weights(), protocols::ligand_docking::Rotate_info::set_chain_letter(), protocols::ligand_docking::Translate_info::set_chain_letter(), protocols::abinitio::LoopJumpFoldCst::set_dump_weights_file(), protocols::noesy_assign::CrossPeak::set_elimination_comment(), protocols::noesy_assign::PeakFileFormat_Base::set_filename(), protocols::topology_broker::ClaimerMessage::set_label(), protocols::topology_broker::TopologyClaimer::set_label(), protocols::topology_broker::FragmentClaimer::set_mover_tag(), protocols::jobdist::BasicJob::set_output_file_name(), protocols::topology_broker::SequenceClaimer::set_sequence(), protocols::abinitio::Protocol::set_silentout_file_name(), core::io::silent::SilentStruct::set_tag_from_pose(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_using_user_input_VDW_pose(), core::import_pose::setup_water_bank_for_magnesiums(), core::select::residue_selector::SliceResidueSelector::show_selection_logic(), protocols::sparta::simplifyWhiteSpace(), core::sequence::split_sequence_motif(), core::pose::tag_from_pose(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::three_body_approximate_buried_unsat_calculation(), protocols::nonlocal::BiasedFragmentMover::verify_probabilities_or_die(), protocols::canonical_sampling::MetropolisHastingsMover::write_checkpoint(), and protocols::frag_picker::QuotaDebug::write_summary().

void protocols::kinmatch::xform_rsd_gl2 ( Stub const &  s,
Residue &  rsd 
)
Vec protocols::kinmatch::xyz ( Pose const &  p,
core::Size const &  ia,
core::Size const &  ir 
)
inline

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

Referenced by protocols::simple_moves::ConstrainToIdealMover::add_bond_angle_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_dihedral_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_length_constraint(), protocols::metal_interface::AddZincSiteConstraints::add_constraints(), protocols::stepwise::modeler::align::StepWisePoseAligner::add_coordinate_constraints_from_map(), protocols::mpi_refinement::add_init_dev_penalty(), protocols::simple_moves::AtomHash::add_point(), core::scoring::power_diagram::PowerDiagram::add_single_atom_to_power_diagram(), protocols::simple_moves::AddCavitiesMover::add_suckers(), core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::pose::addVirtualResAsRoot(), protocols::RotamerDump::RotamerDumpMover::apply(), protocols::symmetry::DetectSymmetry::apply(), protocols::simple_moves::CombinePoseMover::apply(), protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::task_operations::InteractingRotamerExplosion::apply(), protocols::helical_bundle::FitSimpleHelix::apply(), protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator::apply(), protocols::rna::movers::RNAIdealizeMover::apply(), protocols::contact_map::ContactMap::apply(), protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::apply(), protocols::cryst::UpdateCrystInfo::apply(), protocols::simple_moves::ExplicitWaterMover::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply_coord_cst_to_sctip(), core::conformation::membrane::MembraneInfo::atom_z_position(), protocols::idealize::basic_idealize(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::scoring::atomic_depth::AtomicDepth::boundbox(), core::pack::rotamer_set::build_fixed_O_water_rotamers_independent(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), core::scoring::calc_atom_masks(), core::select::util::SelectResiduesByLayer::calc_sc_neighbors(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::calculate_free_ligand_score(), core::scoring::constraints::RTConstraint::calculate_rt(), core::scoring::packstat::cavity_distance_constraint(), protocols::antibody_legacy::CDRH3Modeler::CDR_H3_filter(), protocols::simple_moves::PeriodicBoxMover::check_virial_pressure(), protocols::scoring::ImplicitFastClashCheck::clash_check_trimer(), protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd(), protocols::simple_moves::ExplicitWaterMover::cluster_rotset(), core::pose::compare_atom_coordinates(), core::scoring::CenRotEnvPairPotential::compute_centroid_environment(), core::scoring::SmoothEnvPairPotential::compute_centroid_environment(), core::scoring::ChemicalShiftAnisotropy::compute_csascore(), core::scoring::CenRotEnvPairPotential::compute_dcentroid_environment(), core::scoring::SmoothEnvPairPotential::compute_dcentroid_environment(), core::scoring::DipolarCoupling::compute_dcscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::membrane::FaMPEnvEnergy::compute_fa_proj_coord(), core::scoring::MembranePotential::compute_membrane_embedding(), core::scoring::packstat::compute_sasa(), core::scoring::packstat::compute_sasa_generic(), core::scoring::packing::PoseBalls::compute_smooth_nb(), protocols::simple_moves::ConcatenatePosesMover::concatenate_poses(), protocols::mpi_refinement::constrain_residue(), protocols::sic_dock::ConstraintSetScore::ConstraintSetScore(), protocols::normalmode::NormalMode::convert_to_torsion_crd(), protocols::frag_picker::DiversifyCrmsdByClustering::copy_coordinates(), protocols::frag_picker::DiversifyCrmsdSelector::copy_coordinates(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_don_orientation_vector(), protocols::md::CartesianMD::cst_on_pose_simple(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_receptor_phores(), core::chemical::detect_ld_chirality_from_polymer_residue(), core::io::determine_glycan_links(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::determine_largest_nbr_atom_distance(), protocols::helical_bundle::FitSimpleHelixMultiFunc::dfunc(), core::scoring::constraints::DistancePairConstraint::dist(), core::scoring::constraints::DihedralConstraint::dist(), core::scoring::constraints::DihedralPairConstraint::dist(), core::scoring::constraints::NamedDihedralConstraint::dist(), core::scoring::constraints::NamedAngleConstraint::dist(), protocols::constraints_additional::COMCoordinateConstraint::dist(), core::scoring::constraints::AtomPairConstraint::dist(), core::scoring::constraints::AngleConstraint::dist(), core::scoring::constraints::LocalCoordinateConstraint::dist(), core::scoring::constraints::CoordinateConstraint::dist(), core::scoring::disulfides::DisulfideMatchingPotential::disulfide_RT(), protocols::frag_picker::scores::AtomBasedConstraintsScore::do_caching(), protocols::md::CartesianMD::do_MD(), core::scoring::methods::LinearChainbreakEnergy::do_score_dev(), core::scoring::methods::LinearChainbreakEnergy::do_score_ovp(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::methods::BranchEnergy::eval_atom_derivative(), protocols::rna::AlignmentEnergy::eval_atom_derivative(), core::scoring::methods::LinearChainbreakEnergy::eval_atom_derivative(), core::scoring::hbonds::NPDHBondEnergy::eval_atom_derivative(), core::scoring::methods::SmoothEnvEnergy::eval_residue_derivatives(), core::scoring::methods::CenRotEnvEnergy::eval_residue_derivatives(), core::scoring::methods::ArgCationPiEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CenRotPairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_score(), protocols::metal_interface::AddZincSiteConstraints::evaluate_constraints(), core::scoring::MembranePotential::evaluate_env(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(), core::scoring::methods::ShortRangeTwoBodyEnergy::evaluate_rotamer_pair_energies(), core::scoring::methods::PairEnergy::evaluate_rotamer_pair_energies(), protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf(), core::scoring::Membrane_FAPotential::fa_projection(), protocols::frag_picker::scores::FragmentDME::fill_CA_coords(), protocols::frag_picker::scores::FragmentCrmsd::fill_CA_coords(), protocols::frag_picker::scores::FragmentCrmsdResDepth::fill_CA_coords(), protocols::toolbox::fill_CA_coords(), core::scoring::constraints::DistancePairConstraint::fill_f1_f2(), core::scoring::constraints::DihedralConstraint::fill_f1_f2(), core::scoring::constraints::DihedralPairConstraint::fill_f1_f2(), core::scoring::constraints::AtomPairConstraint::fill_f1_f2(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::fill_f1_f2(), protocols::constraints_additional::COMCoordinateConstraint::fill_f1_f2(), protocols::constraints_additional::BindingSiteConstraint::fill_f1_f2(), core::scoring::constraints::LocalCoordinateConstraint::fill_f1_f2(), core::scoring::constraints::AngleConstraint::fill_f1_f2(), core::scoring::constraints::RTConstraint::fill_f1_f2(), core::scoring::constraints::CoordinateConstraint::fill_f1_f2(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), protocols::simple_moves::ExplicitWaterMover::find_closest(), protocols::simple_filters::HelixHelixAngleFilter::find_closest_res(), protocols::enzdes::PredesignPerturbMover::find_geometric_center_for_constrained_lig_atoms(), protocols::loophash::FastGapMover::find_next_gap(), protocols::splice::fix_chain_break_residue(), protocols::frag_picker::scores::FragmentAllAtomCrmsd::FragmentAllAtomCrmsd(), protocols::frag_picker::scores::FragmentCrmsd::FragmentCrmsd(), protocols::frag_picker::scores::FragmentCrmsdResDepth::FragmentCrmsdResDepth(), protocols::frag_picker::scores::FragmentDME::FragmentDME(), protocols::generalized_kinematic_closure::GeneralizedKIC::generate_bridgeobjects_data_from_atomlist(), protocols::hybridization::generate_centroid_constraints(), protocols::topology_broker::CoordConstraintClaimer::generate_constraints(), protocols::toolbox::DistanceResidueNetwork::generate_edges(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_chi_weight(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_params(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), protocols::membrane::scoring::FaWaterToBilayerEnergy::get_menv_params_for_residue(), protocols::hotspot_hashing::HotspotStub::get_nearest_residue(), protocols::simple_moves::AtomHash::get_neighborcount(), protocols::hydrate::get_ready_for_sew_packing(), core::pack::get_residue_current_energy(), core::io::pose_from_sfr::PoseFromSFRBuilder::get_rsd_type(), core::scoring::packstat::SimplePDB::get_spheres(), protocols::sewing::scoring::MotifScorer::get_stub(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::get_xyz(), core::chemical::Orbital::ideal_xyz(), core::scoring::membrane::FaMPEnvEnergy::init(), core::scoring::membrane::FaMPSolvEnergy::init(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), protocols::features::HBondFeatures::insert_site_atoms_row(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::inv_dist6(), protocols::hydrate::is_inside(), core::io::pose_from_sfr::PoseFromSFRBuilder::is_residue_type_recognized(), protocols::features::strand_assembly::judge_facing(), protocols::loops::loop_closure::ccd::load_coords_and_torsions(), protocols::frag_picker::scores::MakeFragmentDME::make(), protocols::frag_picker::scores::MakeFragmentCrmsd::make(), protocols::frag_picker::scores::MakeFragmentCrmsdResDepth::make(), protocols::frag_picker::scores::MakeFragmentAllAtomCrmsd::make(), protocols::sewing::hashing::LigandBindingResPlacer::make_aligned_residue(), protocols::normalmode::NormalMode::make_Hessian_ANM(), protocols::normalmode::NormalMode::make_Hessian_TNM(), core::scoring::power_diagram::PowerDiagram::make_initial_power_diagram(), core::pack::min_pack_optimize(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), protocols::helical_bundle::FitSimpleHelixMultiFunc::operator()(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::dna::PDBOutput::output_hbond_info(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_resolve_residue_types(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_3_verify_sufficient_backbone_atoms(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_5_note_discarded_atoms(), protocols::match::NumNeighborsMPM::passes_com_vector_criterion(), protocols::cryst::MakeLatticeMover::place_near_origin(), protocols::hotspot_hashing::StubGenerator::placeResidueOnPose(), protocols::membrane::pose_tm_com(), protocols::electron_density::DockIntoDensityMover::poseSphericalSamples(), core::scoring::elec::FA_GrpElecEnergy::precalc_context(), protocols::toolbox::DecoySetEvaluation::push_back(), protocols::toolbox::DecoySetEvaluation::push_back_CA_xyz(), core::io::serialization::read_binary(), protocols::legacy_sewing::read_native_residue_file(), protocols::qsar::scoring_grid::HbdGrid::refresh(), protocols::qsar::scoring_grid::HbaGrid::refresh(), protocols::qsar::scoring_grid::VdwGrid::refresh(), protocols::features::SaltBridgeFeatures::report_features(), core::scoring::methods::CenHBEnergy::residue_pair_energy(), core::conformation::membrane::MembraneInfo::residue_z_position(), core::scoring::retrieve_coordinates(), protocols::symmetry::SymmetrySlider::rg(), core::scoring::rna::RNA_StubCoordinateEnergy::RNA_StubCoordinateEnergy(), core::pack::RTMin::rtmin(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), core::scoring::constraints::DistancePairConstraint::score(), core::scoring::constraints::DihedralPairConstraint::score(), core::scoring::constraints::DihedralConstraint::score(), core::scoring::constraints::NamedAngleConstraint::score(), core::scoring::constraints::NamedDihedralConstraint::score(), core::scoring::constraints::AtomPairConstraint::score(), core::scoring::constraints::AngleConstraint::score(), core::scoring::constraints::LocalCoordinateConstraint::score(), core::scoring::constraints::CoordinateConstraint::score(), core::scoring::MembranePotential::score_normal_center(), core::scoring::packstat::search_x(), core::scoring::nmr::NMRGridSearch::set_grid_search_center(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), protocols::antibody::snugdock::SnugDockProtocol::setup_ab_ag_foldtree(), protocols::constraints_additional::BindingSiteConstraint::setup_for_scoring(), protocols::carbohydrates::RingPlaneFlipMover::setup_movable_torsion_pairs(), protocols::features::strand_assembly::StrandBundleFeatures::sheet_torsion(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::symmetrize_hbonds_graph(), core::scoring::MembranePotential::termini_penalty(), protocols::sewing::hashing::Hasher::transform_segments(), protocols::sewing::data_storage::SmartAssembly::transform_segments(), protocols::hybridization::FoldTreeHybridize::translate_virt_to_CoM(), core::scoring::NeighborList::update_from_wide_nblist(), protocols::environment::CoMTrackerCM::update_tracking_residue(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen(), protocols::md::CartesianMD::VelocityVerlet_Integrator(), protocols::symmetry::SymmetrySlider::very_far_away(), and protocols::mpi_refinement::StructAvrgMover::weighted_average().