Rosetta 3.4
Classes | Typedefs | Enumerations | Functions
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< RealVec
typedef numeric::xyzMatrix< RealMat
typedef utility::vector1< VecVecs

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 const sqr (Real const r)
Vec xyz (Pose const &p, Size const &ia, Size const &ir)
PoseOP alapose (Pose const &pose_in)
vector1< Sizeallifnone (vector1< Size > v, Size n)
void dumpcgo (Vec v, string l)
void xform_rsd_gl2 (Stub const &s, Residue &rsd)

Typedef Documentation


Enumeration Type Documentation

Enumerator:
CEN 
CEN_ANG 
CEN_AXS 
CEN_AXS_ORI 

Function Documentation

PoseOP protocols::kinmatch::alapose ( Pose const &  pose_in)
vector1<Size> protocols::kinmatch::allifnone ( vector1< Size v,
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 const protocols::kinmatch::sqr ( Real const  r) [inline]
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::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::enzdes::enzutil::get_pdb_code_from_pose_tag(), 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::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(), protocols::dna::seq_to_str(), core::fragment::FragData::sequence(), core::scoring::ScoreFunction::serialize_weights(), protocols::abinitio::LoopJumpFoldCst::set_dump_weights_file(), protocols::noesy_assign::PeakFileFormat_Base::set_filename(), protocols::topology_broker::JumpClaim::set_jump_atom(), protocols::topology_broker::TopologyClaimer::set_label(), protocols::topology_broker::ClaimerMessage::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(), 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,
Size const &  ia,
Size const &  ir 
) [inline]

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

Referenced by protocols::simple_moves::AddCavitiesMover::add_suckers(), core::scoring::sc::ShapeComplementarityCalculator::AddResidue(), core::pose::addVirtualResAsRoot(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::RotamerDump::RotamerDumpMover::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::antibody2::CDR_H3_filter(), 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::SmoothEnvPairPotential::compute_dcentroid_environment(), 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(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_don_orientation_vector(), protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO::determine_largest_nbr_atom_distance(), core::scoring::constraints::LocalCoordinateConstraint::dist(), core::scoring::constraints::CoordinateConstraint::dist(), core::scoring::constraints::AtomPairConstraint::dist(), protocols::frag_picker::scores::AtomBasedConstraintsScore::do_caching(), core::scoring::methods::LinearChainbreakEnergy::eval_atom_derivative(), core::scoring::methods::ChainbreakEnergy::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(), protocols::toolbox::fill_CA_coords(), protocols::constraints_additional::BindingSiteConstraint::fill_f1_f2(), core::scoring::constraints::LocalCoordinateConstraint::fill_f1_f2(), core::scoring::constraints::DihedralPairConstraint::fill_f1_f2(), core::scoring::constraints::DihedralConstraint::fill_f1_f2(), core::scoring::constraints::CoordinateConstraint::fill_f1_f2(), core::scoring::constraints::AtomPairConstraint::fill_f1_f2(), core::scoring::constraints::AngleConstraint::fill_f1_f2(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::fill_f1_f2(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), 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::forge::constraints::InverseRotamersRCG::generate_remodel_constraints(), protocols::hotspot_hashing::HotspotStub::get_nearest_residue(), core::pack::get_residue_current_energy(), core::scoring::packstat::SimplePDB::get_spheres(), 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::MakeFragmentCrmsdResDepth::make(), protocols::frag_picker::scores::MakeFragmentCrmsd::make(), protocols::frag_picker::scores::MakeFragmentAllAtomCrmsd::make(), core::pack::min_pack(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), protocols::match::NumNeighborsMPM::passes_com_vector_criterion(), protocols::toolbox::DecoySetEvaluation::push_back(), protocols::toolbox::DecoySetEvaluation::push_back_CA_xyz(), core::io::serialization::read_binary(), protocols::qsar::scoring_grid::VdwGrid::refresh(), 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::LocalCoordinateConstraint::score(), core::scoring::constraints::DihedralPairConstraint::score(), core::scoring::constraints::DihedralConstraint::score(), core::scoring::constraints::CoordinateConstraint::score(), core::scoring::constraints::AtomPairConstraint::score(), core::scoring::constraints::AngleConstraint::score(), 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(), core::scoring::MembranePotential::termini_penalty(), protocols::comparative_modeling::hybridize::FoldTreeHybridize::translate_virt_to_CoM(), and protocols::simple_moves::symmetry::SymmetrySlider::very_far_away().

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