protocols::kinmatch Namespace Reference

Classes
struct	KRSQuery
class	FunGroupTK
class	BruteFunGroupTK
class	KinFunGroupTK

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

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, Size const &ia, Size const &ir)
PoseOP	alapose (Pose const &pose_in)
vector1< Size >	allifnone (vector1< Size > v, Size n)
void	dumpcgo (Vec v, string l)
void	xform_rsd_gl2 (Stub const &s, Residue &rsd)

Typedef Documentation

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

Definition at line 79 of file FunGroupTK.cc.

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

Definition at line 76 of file FunGroupTK.cc.

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

Definition at line 77 of file FunGroupTK.cc.

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

Definition at line 78 of file FunGroupTK.cc.

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

Definition at line 80 of file FunGroupTK.cc.

Enumeration Type Documentation

enum protocols::kinmatch::KRSQueryType

Enumerator
CEN
CEN_ANG
CEN_AXS
CEN_AXS_ORI

Definition at line 37 of file FunGroupTK.hh.

Function Documentation

PoseOP protocols::kinmatch::alapose

(

Pose const &

pose_in)

Definition at line 110 of file FunGroupTK.cc.

References core::pose::Pose::n_residue(), core::chemical::ResidueTypeSet::name_map(), core::pose::replace_pose_residue_copying_existing_coordinates(), core::pose::Pose::residue(), and core::conformation::Residue::residue_type_set().

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

Definition at line 119 of file FunGroupTK.cc.

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

Definition at line 128 of file FunGroupTK.cc.

template<typename T >

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

inline

Definition at line 93 of file FunGroupTK.cc.

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

inline

Definition at line 104 of file FunGroupTK.cc.

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

template<typename T >

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

inline

Definition at line 85 of file FunGroupTK.cc.

Referenced by protocols::enzdes::SecondaryMatchProtocol::apply(), protocols::noesy_assign::NoesyModule::assign(), protocols::sparta::GDB::checkFormat(), protocols::nonlocal::StarTreeBuilder::do_compute_jump_rmsd(), protocols::enzdes::SecondaryMatchProtocol::do_matching(), protocols::star::emit_intermediate(), protocols::features::FeaturesReporter::find_tag(), protocols::toolbox::fix_tag_suffix(), protocols::sparta::GDB::FORMAT_str_parser(), protocols::sparta::Sparta::SpartaLib::get_ANN_data(), protocols::enzdes::enzutil::get_pdb_code_from_pose_tag(), core::scoring::dssp::StrandPairing::hash_value(), protocols::sparta::GDB::loadGDB(), protocols::sparta::PDB::loadPDB(), protocols::sparta::ANN::loadWeightBias3(), protocols::forge::components::VarLengthBuild::loop_mover_str(), protocols::loops::FoldTreeFromLoops::loop_str(), protocols::forge::components::VarLengthBuild::new_secondary_structure_override(), protocols::forge::components::VarLengthBuild::new_sequence_override(), protocols::medal::on_pose_accept(), protocols::flxbb::LayerDesignOperation::pos2select(), protocols::moves::StructureRestrictor::pose_name(), core::fragment::FragmentIO::read_data(), core::conformation::symmetry::SymmData::read_symmetry_data_from_stream(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), core::fragment::FragData::secstruct(), protocols::dna::seq_to_str(), core::fragment::FragData::sequence(), core::scoring::ScoreFunction::serialize_weights(), protocols::abinitio::LoopJumpFoldCst::set_dump_weights_file(), protocols::noesy_assign::CrossPeak::set_elimination_comment(), protocols::noesy_assign::PeakFileFormat_Base::set_filename(), protocols::topology_broker::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(), core::pose::tag_from_pose(), protocols::nonlocal::BiasedFragmentMover::verify_probabilities_or_die(), and protocols::frag_picker::QuotaDebug::write_summary().

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

Definition at line 132 of file FunGroupTK.cc.

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

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

inline

Definition at line 106 of file FunGroupTK.cc.

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

Referenced by protocols::simple_moves::ConstrainToIdealMover::add_bond_angle_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_constraint(), protocols::simple_moves::AddCavitiesMover::add_suckers(), core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), core::pose::addVirtualResAsRoot(), protocols::RotamerDump::RotamerDumpMover::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::contact_map::ContactMap::apply(), protocols::idealize::basic_idealize(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::pack::rotamer_set::build_fixed_O_water_rotamers_independent(), core::io::pdb::build_pose_as_is1(), core::scoring::calc_atom_masks(), core::scoring::packstat::cavity_distance_constraint(), protocols::antibody::CDRH3Modeler::CDR_H3_filter(), protocols::loops::loop_closure::ccd::check_torsions(), protocols::scoring::ImplicitFastClashCheck::clash_check_trimer(), protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd(), core::pose::compare_atom_coordinates(), core::scoring::ChemicalShiftAnisotropy::compute_csascore(), core::scoring::SmoothEnvPairPotential::compute_dcentroid_environment(), core::scoring::DipolarCoupling::compute_dcscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDa(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsDaR(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nlsR(), core::scoring::MembranePotential::compute_membrane_embedding(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::scoring::packstat::compute_sasa(), core::scoring::packstat::compute_sasa_generic(), core::scoring::packing::PoseBalls::compute_smooth_nb(), 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::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::determine_largest_nbr_atom_distance(), core::scoring::constraints::CoordinateConstraint::dist(), core::scoring::constraints::AtomPairConstraint::dist(), core::scoring::constraints::LocalCoordinateConstraint::dist(), core::scoring::disulfides::DisulfideMatchingPotential::disulfide_RT(), protocols::frag_picker::scores::AtomBasedConstraintsScore::do_caching(), core::scoring::methods::LinearChainbreakEnergy::do_score_dev(), core::scoring::methods::LinearChainbreakEnergy::do_score_ovp(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::methods::LinearChainbreakEnergy::eval_atom_derivative(), core::scoring::methods::SmoothEnvEnergy::eval_residue_derivatives(), core::scoring::methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::MembranePotential::evaluate_env(), 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::toolbox::fill_CA_coords(), protocols::frag_picker::scores::FragmentDME::fill_CA_coords(), protocols::frag_picker::scores::FragmentCrmsd::fill_CA_coords(), protocols::frag_picker::scores::FragmentCrmsdResDepth::fill_CA_coords(), core::scoring::constraints::DihedralPairConstraint::fill_f1_f2(), core::scoring::constraints::DistancePairConstraint::fill_f1_f2(), core::scoring::constraints::DihedralConstraint::fill_f1_f2(), core::scoring::constraints::AngleConstraint::fill_f1_f2(), protocols::constraints_additional::BindingSiteConstraint::fill_f1_f2(), core::scoring::constraints::CoordinateConstraint::fill_f1_f2(), core::scoring::constraints::AtomPairConstraint::fill_f1_f2(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::fill_f1_f2(), core::scoring::constraints::LocalCoordinateConstraint::fill_f1_f2(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), protocols::enzdes::PredesignPerturbMover::find_geometric_center_for_constrained_lig_atoms(), protocols::loophash::FastGapMover::find_next_gap(), 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::hybridization::generate_centroid_constraints(), protocols::topology_broker::CoordConstraintClaimer::generate_constraints(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::get_acceptor_base_atm_xyz(), core::scoring::geometric_solvation::GeometricSolEnergy::get_acceptor_base_atm_xyz(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_params(), protocols::hotspot_hashing::HotspotStub::get_nearest_residue(), core::pack::get_residue_current_energy(), core::scoring::packstat::SimplePDB::get_spheres(), core::chemical::Orbital::ideal_xyz(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), protocols::features::HBondFeatures::insert_site_atoms_row(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::inv_dist6(), 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::MakeFragmentAllAtomCrmsd::make(), protocols::frag_picker::scores::MakeFragmentCrmsdResDepth::make(), core::pack::min_pack(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::dna::PDBOutput::output_hbond_info(), protocols::match::NumNeighborsMPM::passes_com_vector_criterion(), protocols::hotspot_hashing::StubGenerator::placeResidueOnPose(), protocols::toolbox::DecoySetEvaluation::push_back(), protocols::toolbox::DecoySetEvaluation::push_back_CA_xyz(), core::io::serialization::read_binary(), protocols::qsar::scoring_grid::HbaGrid::refresh(), protocols::qsar::scoring_grid::HbdGrid::refresh(), protocols::qsar::scoring_grid::VdwGrid::refresh(), protocols::features::SaltBridgeFeatures::report_features(), core::scoring::methods::CenHBEnergy::residue_pair_energy(), core::scoring::retrieve_coordinates(), protocols::simple_moves::symmetry::SymmetrySlider::rg(), 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::AngleConstraint::score(), core::scoring::constraints::AtomPairConstraint::score(), core::scoring::constraints::CoordinateConstraint::score(), core::scoring::constraints::LocalCoordinateConstraint::score(), core::scoring::MembranePotential::score_normal_center(), core::scoring::packstat::search_x(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), protocols::constraints_additional::BindingSiteConstraint::setup_for_scoring(), protocols::features::strand_assembly::StrandBundleFeatures::sheet_torsion(), core::scoring::MembranePotential::termini_penalty(), protocols::hybridization::FoldTreeHybridize::translate_virt_to_CoM(), core::scoring::NeighborList::update_from_wide_nblist(), and protocols::simple_moves::symmetry::SymmetrySlider::very_far_away().