protocols::kinmatch Namespace Reference

Classes
class	BruteFunGroupTK
class	FunGroupTK
class	KinFunGroupTK
struct	KRSQuery

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

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

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

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

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

Enumeration Type Documentation

enum protocols::kinmatch::KRSQueryType

Enumerator
CEN
CEN_ANG
CEN_AXS
CEN_AXS_ORI

Function Documentation

PoseOP protocols::kinmatch::alapose

(

Pose const &

pose_in

)

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
	)

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

References numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

template<typename T >

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

inline

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

inline

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

Referenced by protocols::enzdes::SecondaryMatchProtocol::apply(), protocols::noesy_assign::NoesyModule::assign(), protocols::sparta::GDB::checkFormat(), protocols::environment::claims::JumpClaim::ctrl_strength(), 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(), protocols::environment::claims::JumpClaim::init_strength(), 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::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(), protocols::rotamer_recovery::RRReporterSQLite::report_rotamer_recovery_full(), protocols::dna::seq_to_str(), 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(), 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
	)

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

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

Referenced by protocols::simple_moves::ConstrainToIdealMover::add_bond_angle_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_constraint(), protocols::metal_interface::AddZincSiteConstraints::add_constraints(), protocols::stepwise::sampling::general::StepWisePoseAligner::add_coordinate_constraints_from_map(), protocols::simple_moves::AddCavitiesMover::add_suckers(), protocols::simple_moves::symmetry::DetectSymmetry::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::contact_map::ContactMap::apply(), protocols::idealize::basic_idealize(), protocols::toolbox::SelectResiduesByLayer::calc_sc_neighbors(), protocols::antibody_legacy::CDRH3Modeler::CDR_H3_filter(), protocols::loops::loop_closure::ccd::check_torsions(), protocols::scoring::ImplicitFastClashCheck::clash_check_trimer(), protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd(), protocols::sic_dock::ConstraintSetScore::ConstraintSetScore(), protocols::normalmode::NormalMode::convert_to_torsion_crd(), protocols::frag_picker::DiversifyCrmsdByClustering::copy_coordinates(), protocols::frag_picker::DiversifyCrmsdSelector::copy_coordinates(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO::determine_largest_nbr_atom_distance(), protocols::frag_picker::scores::AtomBasedConstraintsScore::do_caching(), protocols::metal_interface::AddZincSiteConstraints::evaluate_constraints(), protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf(), 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(), protocols::constraints_additional::BindingSiteConstraint::fill_f1_f2(), protocols::constraints_additional::COMCoordinateConstraint::fill_f1_f2(), 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(), protocols::toolbox::DistanceResidueNetwork::generate_edges(), protocols::hotspot_hashing::HotspotStub::get_nearest_residue(), protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternatives::get_xyz(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), protocols::features::HBondFeatures::insert_site_atoms_row(), protocols::features::strand_assembly::SandwichFeatures::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::normalmode::NormalMode::make_Hessian_ANM(), protocols::normalmode::NormalMode::make_Hessian_TNM(), 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(), protocols::qsar::scoring_grid::HbdGrid::refresh(), protocols::qsar::scoring_grid::HbaGrid::refresh(), protocols::qsar::scoring_grid::VdwGrid::refresh(), protocols::features::SaltBridgeFeatures::report_features(), protocols::md::CartesianMD::report_MD(), protocols::simple_moves::symmetry::SymmetrySlider::rg(), protocols::constraints_additional::COMCoordinateConstraint::score(), 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(), protocols::hybridization::FoldTreeHybridize::translate_virt_to_CoM(), and protocols::simple_moves::symmetry::SymmetrySlider::very_far_away().