Rosetta Protocols  2014.35
Classes | Typedefs | Enumerations | Functions
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< 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 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 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::sparta::Sparta::SpartaLib::get_ANN_data(), protocols::enzdes::enzutil::get_pdb_code_from_pose_tag(), 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::environment::claims::EnvClaim::parse_ctrl_str(), 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 
)
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::modeler::align::StepWisePoseAligner::add_coordinate_constraints_from_map(), protocols::simple_moves::AddCavitiesMover::add_suckers(), protocols::simple_moves::symmetry::DetectSymmetry::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::toolbox::task_operations::InteractingRotamerExplosion::apply(), protocols::contact_map::ContactMap::apply(), protocols::idealize::basic_idealize(), protocols::toolbox::SelectResiduesByLayer::calc_sc_neighbors(), protocols::antibody_legacy::CDRH3Modeler::CDR_H3_filter(), 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::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::hotspot_hashing::HotspotStub::get_nearest_residue(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives::get_xyz(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), protocols::features::HBondFeatures::insert_site_atoms_row(), 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::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(), protocols::environment::CoMTrackerCM::update_tracking_residue(), and protocols::simple_moves::symmetry::SymmetrySlider::very_far_away().