protocols::kinmatch Namespace Reference

Classes
struct	KRSQuery
class	FunGroupTK
class	BruteFunGroupTK
class	KinFunGroupTK

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::Size >	allifnone (vector1< core::Size > v, core::Size n)
void	dumpcgo (Vec v, string l)
void	xform_rsd_gl2 (Stub const &s, Residue &rsd)

Typedef Documentation

Mat

using protocols::kinmatch::Mat = typedef numeric::xyzMatrix<Real>

Reals

using protocols::kinmatch::Reals = typedef utility::vector1<core::Real>

Sizes

using protocols::kinmatch::Sizes = typedef utility::vector1<core::Size>

Vec

using protocols::kinmatch::Vec = typedef numeric::xyzVector<Real>

Vecs

using protocols::kinmatch::Vecs = typedef utility::vector1<Vec>

Enumeration Type Documentation

KRSQueryType

enum protocols::kinmatch::KRSQueryType

Enumerator
CEN
CEN_ANG
CEN_AXS
CEN_AXS_ORI

Function Documentation

alapose()

PoseOP protocols::kinmatch::alapose

(

Pose const &

pose_in

)

References core::pose::get_restype_for_pose(), core::chemical::ResidueTypeBase::mode(), core::pose::replace_pose_residue_copying_existing_coordinates(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

allifnone()

vector1<core::Size> protocols::kinmatch::allifnone	(	vector1< core::Size >	v,
		core::Size	n
	)

dumpcgo()

void protocols::kinmatch::dumpcgo	(	Vec	v,
		string	l
	)

lzs()

template<typename T >

std::string protocols::kinmatch::lzs ( T const &  t, int const  w  )

inline

References protocols::hybridization::t.

sqr()

Real protocols::kinmatch::sqr ( Real const  r )

inline

Referenced by protocols::kinmatch::KinFunGroupTK::place_c(), and protocols::kinmatch::KinFunGroupTK::place_h().

str()

template<typename T >

std::string protocols::kinmatch::str ( T const &  t )

inline

References protocols::hybridization::t.

Referenced by core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::accumulate_seqpos_oversats(), core::energy_methods::GoapRsdType::add_atmname_using(), protocols::sparta::GDB::addRemark(), protocols::recces::scratch::ThermalSamplingMover::apply(), protocols::enzdes::SecondaryMatchProtocol::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::vip::base_name(), protocols::peptide_deriver::PeptideDeriverPoseOutputter::begin_receptor_partner_pair(), core::energy_methods::ProQ_Energy::calculate_feature_vector(), core::energy_methods::ProQ_Energy::calculate_feature_vector_proq2(), protocols::sic_dock::center_of_geom(), 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(), protocols::sparta::contains(), 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::pdbinfo_manipulations::get_alignpdbinfotosequencesmode_from_string(), 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::pose::get_resnum_list(), core::pose::get_resnum_list_ordered(), protocols::sparta::PDB::getField(), protocols::rosetta_scripts::RosettaScriptsParser::has_double_percent_signs(), protocols::rosetta_scripts::RosettaScriptsParser::has_slash_at_end(), core::scoring::dssp::StrandPairing::hash_value(), protocols::features::JobDataFeatures::insert_string_rows(), core::scoring::bin_transitions::BinTransitionData::is_in_list(), core::pose::is_referencepose_number(), protocols::jd2::archive::NormalizedEvaluatedArchive::is_start_zero_score(), protocols::topology_broker::claims::JumpClaim::jump_atom1(), protocols::topology_broker::claims::JumpClaim::jump_atom2(), protocols::sparta::GDB::loadGDB(), protocols::sparta::PDB::loadPDB(), protocols::sparta::PDB::loadPDB_Entry(), 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::energy_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::io::nmr::read_atom_selection_from_string(), core::fragment::FragmentIO::read_data_from_stream(), core::io::nmr::read_gridsearch_values_from_string(), protocols::scoring::VDW_CachedRepScreenInfo::read_in_VDW_rep_screen_pose_from_options(), core::io::nmr::read_pcs_dataset_params_list(), core::io::nmr::read_pre_dataset_params_list(), core::io::nmr::read_rdc_dataset_params_list(), core::io::nmr::read_rdc_tensor_values_from_string(), core::io::nmr::read_selection_group_from_string(), core::conformation::symmetry::SymmData::read_symmetry_data_from_stream(), core::kinematics::replace_substr(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::report_final_score(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), core::pack::task::operation::ResidueName3Is::ResidueName3Is(), protocols::recces::RECCES_Mover::save_data_to_disk(), core::fragment::FragData::secstruct(), protocols::sparta::section(), 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::quantum_annealing::InteractionGraphSummaryMetric::set_filename(), protocols::noesy_assign::PeakFileFormat_Base::set_filename(), protocols::topology_broker::claims::JumpClaim::set_jump_atom(), 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::environment::DofPassport::show(), core::select::residue_selector::SliceResidueSelector::show_selection_logic(), protocols::sparta::simplifyWhiteSpace(), protocols::sparta::split(), core::sequence::split_sequence_motif(), protocols::sparta::split_WhiteSpace(), protocols::forge::remodel::RemodelData::splitString(), core::io::nmr::strip_brackets(), core::pose::tag_from_pose(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::three_body_approximate_buried_unsat_calculation(), protocols::Tokenize(), protocols::rbsegment_relax::Tokenize(), core::pose::rna::tokenize(), protocols::stepwise::modeler::rna::tokenize(), protocols::sparta::GDB::VARS_str_parser(), protocols::nonlocal::BiasedFragmentMover::verify_probabilities_or_die(), protocols::canonical_sampling::MetropolisHastingsMover::write_checkpoint(), protocols::frag_picker::QuotaDebug::write_summary(), protocols::canonical_sampling::BiasEnergy::Histogram< T >::write_to_string(), and protocols::canonical_sampling::BiasEnergy::write_to_string().

xform_rsd_gl2()

void protocols::kinmatch::xform_rsd_gl2	(	Stub const &	s,
		Residue &	rsd
	)

References core::kinematics::Stub::global2local(), core::conformation::Residue::natoms(), core::conformation::Residue::set_xyz(), and core::conformation::Residue::xyz().

xyz()

Vec protocols::kinmatch::xyz ( Pose const &  p, core::Size const &  ia, core::Size const &  ir  )

inline

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

Referenced by protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::add(), 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::pose_sewing::movers::SewAnythingAddMover::align(), protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::helical_bundle::FitSimpleHelix::apply(), protocols::RotamerDump::RotamerDumpMover::apply(), protocols::simple_moves::CombinePoseMover::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(), 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(), protocols::cryst::MakeLatticeMover::build_lattice_of_virtuals(), protocols::cryst::MakeLayerMover::build_layer_of_virtuals(), core::select::util::calc_sc_neighbors(), core::scoring::constraints::AtomToAxisConstraint::calc_xyzs(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::calculate_free_ligand_score(), protocols::pose_sewing::calculate_motif_score_bt_residues(), core::scoring::constraints::RTConstraint::calculate_rt(), core::scoring::packstat::cavity_distance_constraint(), core::conformation::membrane::membrane_geometry::DoubleVesicle::center(), 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::MembranePotential::compute_membrane_embedding(), core::scoring::packstat::compute_sasa(), core::scoring::packstat::compute_sasa_generic(), core::scoring::packing::PoseBalls::compute_smooth_nb(), core::scoring::packstat::MultiProbePerSphereAccumulator::compute_surrounding_sasa(), core::scoring::packstat::compute_surrounding_sasa(), protocols::simple_moves::ConcatenatePosesMover::concatenate_poses(), protocols::mpi_refinement::constrain_residue(), protocols::ligand_docking::ga_ligand_dock::constraint_relax(), protocols::sic_dock::ConstraintSetScore::ConstraintSetScore(), core::scoring::TMscore::convert_FArray2D_to_vector0(), protocols::normalmode::NormalMode::convert_to_torsion_crd(), protocols::frag_picker::DiversifyCrmsdByClustering::copy_coordinates(), protocols::frag_picker::DiversifyCrmsdSelector::copy_coordinates(), core::conformation::membrane::MembraneGeometry::corrected_coordinate(), core::conformation::membrane::MembraneGeometry::corrected_xyz(), protocols::md::CartesianMD::cst_on_pose_simple(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_all_ligand_phores(), 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::AngleConstraint::dist(), core::scoring::constraints::AtomPairConstraint::dist(), core::scoring::constraints::AtomToAxisConstraint::dist(), core::scoring::constraints::CoordinateConstraint::dist(), core::scoring::constraints::DihedralConstraint::dist(), core::scoring::constraints::DihedralPairConstraint::dist(), core::scoring::constraints::DistancePairConstraint::dist(), core::scoring::constraints::LocalCoordinateConstraint::dist(), core::scoring::constraints::NamedAngleConstraint::dist(), core::scoring::constraints::NamedDihedralConstraint::dist(), core::scoring::constraints::NonResidueTypeConstraint::dist(), core::scoring::constraints::ResidueTypeConstraint::dist(), protocols::constraints_additional::COMCoordinateConstraint::dist(), core::scoring::constraints::AmbiguousNMRConstraint::dist(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::dist(), core::scoring::constraints::RTConstraint::dist(), protocols::frag_picker::scores::AtomBasedConstraintsScore::do_caching(), protocols::md::CartesianMD::do_MD(), core::energy_methods::SmoothEnvEnergy::eval_residue_derivatives(), core::energy_methods::ArgCationPiEnergy::eval_residue_pair_derivatives(), core::scoring::MembranePotential::evaluate_env(), core::conformation::membrane::MembraneGeometry::f1_pore(), core::conformation::membrane::MembraneGeometry::f2_pore(), core::conformation::membrane::membrane_geometry::Bicelle::f_bicelle(), core::conformation::membrane::membrane_geometry::DoubleVesicle::f_deriv(), core::conformation::membrane::membrane_geometry::DoubleVesicle::f_double_vesicle(), core::conformation::membrane::membrane_geometry::Bicelle::f_transition(), core::conformation::membrane::membrane_geometry::DoubleVesicle::f_transition(), core::conformation::membrane::membrane_geometry::Slab::f_transition(), core::conformation::membrane::membrane_geometry::Vesicle::f_transition(), core::conformation::membrane::membrane_geometry::Bicelle::f_transition_deriv(), core::conformation::membrane::membrane_geometry::DoubleVesicle::f_transition_deriv(), core::conformation::membrane::membrane_geometry::Slab::f_transition_deriv(), core::conformation::membrane::membrane_geometry::Vesicle::f_transition_deriv(), core::conformation::membrane::membrane_geometry::Bicelle::f_transition_deriv_m(), core::conformation::membrane::membrane_geometry::Bicelle::f_transition_f1(), core::conformation::membrane::membrane_geometry::DoubleVesicle::f_transition_f1(), core::conformation::membrane::membrane_geometry::Slab::f_transition_f1(), core::conformation::membrane::membrane_geometry::Vesicle::f_transition_f1(), core::conformation::membrane::membrane_geometry::Bicelle::f_transition_f2(), core::conformation::membrane::membrane_geometry::DoubleVesicle::f_transition_f2(), core::conformation::membrane::membrane_geometry::Slab::f_transition_f2(), core::conformation::membrane::membrane_geometry::Vesicle::f_transition_f2(), core::conformation::membrane::membrane_geometry::Vesicle::f_vesicle(), core::conformation::membrane::membrane_geometry::DoubleVesicle::f_vesicle_deriv(), core::conformation::membrane::membrane_geometry::Vesicle::f_vesicle_deriv(), core::conformation::membrane::membrane_geometry::DoubleVesicle::f_vesicle_membrane(), core::conformation::membrane::membrane_geometry::Bicelle::fa_elec_lipid(), core::conformation::membrane::membrane_geometry::DoubleVesicle::fa_elec_lipid(), core::conformation::membrane::membrane_geometry::Slab::fa_elec_lipid(), core::conformation::membrane::membrane_geometry::Vesicle::fa_elec_lipid(), core::conformation::membrane::membrane_geometry::Bicelle::fa_elec_lipid_deriv(), core::conformation::membrane::membrane_geometry::DoubleVesicle::fa_elec_lipid_deriv(), core::conformation::membrane::membrane_geometry::Slab::fa_elec_lipid_deriv(), core::conformation::membrane::membrane_geometry::Vesicle::fa_elec_lipid_deriv(), core::scoring::Membrane_FAPotential::fa_projection(), protocols::frag_picker::scores::FragmentCrmsd::fill_CA_coords(), protocols::frag_picker::scores::FragmentCrmsdResDepth::fill_CA_coords(), protocols::frag_picker::scores::FragmentDME::fill_CA_coords(), protocols::toolbox::fill_CA_coords(), core::scoring::constraints::BigBinConstraint::fill_f1_f2(), protocols::constraints_additional::BindingSiteConstraint::fill_f1_f2(), protocols::constraints_additional::COMCoordinateConstraint::fill_f1_f2(), core::scoring::constraints::AngleConstraint::fill_f1_f2(), core::scoring::constraints::AtomPairConstraint::fill_f1_f2(), core::scoring::constraints::AtomToAxisConstraint::fill_f1_f2(), core::scoring::constraints::AmbiguousConstraint::fill_f1_f2(), core::scoring::constraints::AmbiguousNMRConstraint::fill_f1_f2(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::fill_f1_f2(), core::scoring::constraints::BackboneStubConstraint::fill_f1_f2(), core::scoring::constraints::BackboneStubLinearConstraint::fill_f1_f2(), core::scoring::constraints::BasePairConstraint::fill_f1_f2(), core::scoring::constraints::CoordinateConstraint::fill_f1_f2(), core::scoring::constraints::DihedralConstraint::fill_f1_f2(), core::scoring::constraints::DihedralPairConstraint::fill_f1_f2(), core::scoring::constraints::DistancePairConstraint::fill_f1_f2(), core::scoring::constraints::KofNConstraint::fill_f1_f2(), core::scoring::constraints::LocalCoordinateConstraint::fill_f1_f2(), core::scoring::constraints::MultiConstraint::fill_f1_f2(), core::scoring::constraints::RTConstraint::fill_f1_f2(), protocols::constraints_additional::AmbiguousMultiConstraint::fill_f1_f2(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_cartmin(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_ligmin_helper(), protocols::metal_interface::find_closest_atom(), protocols::splice::Splice::fold_tree(), 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::topology_broker::CoordConstraintClaimer::generate_constraints(), protocols::toolbox::DistanceResidueNetwork::generate_edges(), core::scoring::hbonds::HBond::get_AHDangle(), core::scoring::hbonds::HBond::get_BAHangle(), core::scoring::hbonds::HBond::get_BAtorsion(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_chi_weight(), protocols::simple_moves::AddCavitiesMover::get_closest_heavy_atom(), core::scoring::hbonds::HBond::get_HAdist(), core::scoring::loop_graph::get_loop_atom(), protocols::hotspot_hashing::HotspotStub::get_nearest_residue(), protocols::simple_moves::AtomHash::get_neighborcount(), 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::kinematics::Stub::global2local(), core::conformation::membrane::membrane_geometry::Bicelle::h_bicelle(), core::conformation::membrane::membrane_geometry::Bicelle::h_bicelle_deriv_wrt_r(), core::chemical::Orbital::ideal_xyz(), core::conformation::membrane::MembraneInfo::in_membrane(), core::conformation::membrane::MembraneInfo::in_membrane_atom(), core::energy_methods::FaMPEnvEnergy::init(), core::energy_methods::FaMPSolvEnergy::init(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::inv_dist6(), protocols::hydrate::is_inside(), core::scoring::sc::ElectrostaticComplementarityCalculator::is_within_radius(), core::kinematics::Stub::local2global(), protocols::frag_picker::scores::MakeFragmentAllAtomCrmsd::make(), protocols::frag_picker::scores::MakeFragmentCrmsd::make(), protocols::frag_picker::scores::MakeFragmentCrmsdResDepth::make(), protocols::frag_picker::scores::MakeFragmentDME::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(), protocols::nmr::pcs::PCSLigandTransformMover::next_ligand_position(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::scoring::constraints::CoordinateConstraint::non_virtual_score(), protocols::helical_bundle::FitSimpleHelixMultiFunc::operator()(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), 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::magnesium::MgOrbitalFrameFinder::point_orbitals_to_closest_ligands(), protocols::electron_density::pose_spherical_samples(), protocols::toolbox::DecoySetEvaluation::push_back(), protocols::toolbox::DecoySetEvaluation::push_back_CA_xyz(), core::conformation::membrane::membrane_geometry::DoubleVesicle::r_alpha(), core::conformation::membrane::membrane_geometry::Slab::r_alpha(), core::conformation::membrane::membrane_geometry::Vesicle::r_alpha(), core::conformation::membrane::membrane_geometry::Bicelle::r_alpha_m(), core::conformation::membrane::MembraneGeometry::r_alpha_p_x(), core::conformation::membrane::MembraneGeometry::r_alpha_p_y(), core::conformation::membrane::MembraneGeometry::r_alpha_p_z(), core::io::serialization::read_binary(), protocols::legacy_sewing::read_native_residue_file(), protocols::qsar::scoring_grid::HbaGrid::refresh(), protocols::qsar::scoring_grid::HbdGrid::refresh(), protocols::qsar::scoring_grid::VdwGrid::refresh(), core::io::pose_from_sfr::PoseFromSFRBuilder::remember_unrecognized_res(), protocols::features::SaltBridgeFeatures::report_features(), protocols::pose_sewing::filters::CoreScorer::report_sm(), core::conformation::membrane::MembraneInfo::residue_z_position(), core::scoring::retrieve_coordinates(), core::energy_methods::RNA_StubCoordinateEnergy::RNA_StubCoordinateEnergy(), core::pack::RTMin::rtmin(), protocols::md::Rattle::run_rattle1(), protocols::md::Rattle::run_rattle2(), protocols::constraints_additional::COMCoordinateConstraint::score(), core::scoring::constraints::AngleConstraint::score(), core::scoring::constraints::AtomPairConstraint::score(), core::scoring::constraints::AtomToAxisConstraint::score(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::score(), core::scoring::constraints::BigBinConstraint::score(), core::scoring::constraints::CoordinateConstraint::score(), core::scoring::constraints::DihedralConstraint::score(), core::scoring::constraints::DihedralPairConstraint::score(), core::scoring::constraints::DistancePairConstraint::score(), core::scoring::constraints::NamedAngleConstraint::score(), core::scoring::constraints::NamedDihedralConstraint::score(), core::scoring::constraints::LocalCoordinateConstraint::score(), core::scoring::MembranePotential::score_normal_center(), core::scoring::packstat::search_x(), protocols::electron_density::DockPDBIntoDensityMover::setMultiNative(), protocols::antibody::snugdock::SnugDockProtocol::setup_ab_ag_foldtree(), protocols::constraints_additional::BindingSiteConstraint::setup_for_derivatives(), protocols::constraints_additional::COMCoordinateConstraint::setup_for_derivatives(), core::scoring::constraints::Constraints::setup_for_derivatives(), protocols::constraints_additional::BindingSiteConstraint::setup_for_scoring(), protocols::constraints_additional::COMCoordinateConstraint::setup_for_scoring(), core::scoring::constraints::Constraints::setup_for_scoring(), core::scoring::constraints::MultiConstraint::setup_for_scoring(), core::scoring::constraints::NamedAngleConstraint::setup_for_scoring(), core::scoring::constraints::NamedAtomPairConstraint::setup_for_scoring(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::symmetrize_hbonds_graph(), core::scoring::MembranePotential::termini_penalty(), protocols::sewing::data_storage::SmartAssembly::transform_segments(), protocols::sewing::hashing::Hasher::transform_segments(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen(), protocols::md::CartesianMD::VelocityVerlet_Integrator(), and protocols::mpi_refinement::StructAvrgMover::weighted_average().