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Typedefs | Functions
core::pose::motif Namespace Reference

Typedefs

using Xform = xyzTransform< Real >
 
using Vec = xyzVector< Real >
 
using PoseCR = const Pose &
 
using SizeCR = const Size &
 
using AIDs = utility::vector1< core::id::AtomID >
 

Functions

static AIDs get_AIDs (Pose const &pose, core::Size const &ir, utility::vector1< std::string > const &anames)
 
Vec a (Pose const &p, numeric::Size const &i, string const &s)
 
Xform get_backbone_reference_frame (xyzVector< Real > const &N, xyzVector< Real > const &CA, xyzVector< Real > const &C)
 
Xform get_backbone_reference_frame (Pose const &p, numeric::Size const &i)
 
Xform get_nterminal_peptide_bond_reference_frame (xyzVector< Real > const &H, xyzVector< Real > const &N, xyzVector< Real > const &CA)
 
Xform get_nterminal_peptide_bond_reference_frame (Pose const &p, numeric::Size const &i)
 
Xform get_cterminal_peptide_bond_reference_frame (xyzVector< Real > const &O, xyzVector< Real > const &C, xyzVector< Real > const &CA)
 
Xform get_cterminal_peptide_bond_reference_frame (Pose const &p, numeric::Size const &i)
 
AIDs get_nterminal_peptide_bond_reference_frame_atomids (Pose const &p, numeric::Size const &i, bool extra)
 
AIDs get_cterminal_peptide_bond_reference_frame_atomids (Pose const &p, numeric::Size const &i, bool extra)
 
Xform get_sidechain_reference_frame (Pose const &p, numeric::Size const &i)
 
Xform get_frame_ala (PoseCR p, SizeCR i)
 
Xform get_frame_cys (PoseCR p, SizeCR i)
 
Xform get_frame_gly (PoseCR p, SizeCR i)
 
Xform get_frame_ile (PoseCR p, SizeCR i)
 
Xform get_frame_lys (PoseCR p, SizeCR i)
 
Xform get_frame_met (PoseCR p, SizeCR i)
 
Xform get_frame_asn (PoseCR p, SizeCR i)
 
Xform get_frame_pro (PoseCR p, SizeCR i)
 
Xform get_frame_gln (PoseCR p, SizeCR i)
 
Xform get_frame_arg (PoseCR p, SizeCR i)
 
Xform get_frame_ser (PoseCR p, SizeCR i)
 
Xform get_frame_thr (PoseCR p, SizeCR i)
 
Xform get_frame_vee (Vec const &a, Vec const &b, Vec const &c)
 
Xform get_frame_val (PoseCR p, SizeCR i)
 
Xform get_frame_leu (PoseCR p, SizeCR i)
 
Xform get_frame_glu (PoseCR p, SizeCR i)
 
Xform get_frame_asp (PoseCR p, SizeCR i)
 
Xform get_frame_his (PoseCR p, SizeCR i)
 
Xform get_frame_phe (PoseCR p, SizeCR i)
 
Xform get_frame_tyr (PoseCR p, SizeCR i)
 
Xform get_frame_trp (PoseCR p, SizeCR i)
 
AIDs get_backbone_reference_frame_atomids (Pose const &pose, core::Size const &ir)
 
AIDs get_backbone_reference_frame_atomids_with_downstream (Pose const &pose, core::Size const &ir)
 
AIDs get_sidechain_reference_frame_atomids (Pose const &pose, core::Size const &ir)
 
AIDs get_sidechain_reference_frame_atomids_with_downstream (Pose const &pose, core::Size const &ir)
 
AIDs get_atoms_ala (PoseCR p, SizeCR i)
 
AIDs get_atoms_arg (PoseCR p, SizeCR i)
 
AIDs get_atoms_asn (PoseCR p, SizeCR i)
 
AIDs get_atoms_asp (PoseCR p, SizeCR i)
 
AIDs get_atoms_cys (PoseCR p, SizeCR i)
 
AIDs get_atoms_gln (PoseCR p, SizeCR i)
 
AIDs get_atoms_glu (PoseCR p, SizeCR i)
 
AIDs get_atoms_gly (PoseCR p, SizeCR i)
 
AIDs get_atoms_his (PoseCR p, SizeCR i)
 
AIDs get_atoms_ile (PoseCR p, SizeCR i)
 
AIDs get_atoms_leu (PoseCR p, SizeCR i)
 
AIDs get_atoms_lys (PoseCR p, SizeCR i)
 
AIDs get_atoms_met (PoseCR p, SizeCR i)
 
AIDs get_atoms_phe (PoseCR p, SizeCR i)
 
AIDs get_atoms_pro (PoseCR p, SizeCR i)
 
AIDs get_atoms_ser (PoseCR p, SizeCR i)
 
AIDs get_atoms_thr (PoseCR p, SizeCR i)
 
AIDs get_atoms_trp (PoseCR p, SizeCR i)
 
AIDs get_atoms_tyr (PoseCR p, SizeCR i)
 
AIDs get_atoms_val (PoseCR p, SizeCR i)
 
AIDs get_atoms_ala_downstream (PoseCR p, SizeCR i)
 
AIDs get_atoms_arg_downstream (PoseCR p, SizeCR i)
 
AIDs get_atoms_asn_downstream (PoseCR p, SizeCR i)
 
AIDs get_atoms_asp_downstream (PoseCR p, SizeCR i)
 
AIDs get_atoms_cys_downstream (PoseCR p, SizeCR i)
 
AIDs get_atoms_gln_downstream (PoseCR p, SizeCR i)
 
AIDs get_atoms_glu_downstream (PoseCR p, SizeCR i)
 
AIDs get_atoms_gly_downstream (PoseCR p, SizeCR i)
 
AIDs get_atoms_his_downstream (PoseCR p, SizeCR i)
 
AIDs get_atoms_ile_downstream (PoseCR p, SizeCR i)
 
AIDs get_atoms_leu_downstream (PoseCR p, SizeCR i)
 
AIDs get_atoms_lys_downstream (PoseCR p, SizeCR i)
 
AIDs get_atoms_met_downstream (PoseCR p, SizeCR i)
 
AIDs get_atoms_phe_downstream (PoseCR p, SizeCR i)
 
AIDs get_atoms_pro_downstream (PoseCR p, SizeCR i)
 
AIDs get_atoms_ser_downstream (PoseCR p, SizeCR i)
 
AIDs get_atoms_thr_downstream (PoseCR p, SizeCR i)
 
AIDs get_atoms_trp_downstream (PoseCR p, SizeCR i)
 
AIDs get_atoms_tyr_downstream (PoseCR p, SizeCR i)
 
AIDs get_atoms_val_downstream (PoseCR p, SizeCR i)
 
numeric::xyzTransform< core::Realget_sidechain_reference_frame (Pose const &pose, core::Size const &ir)
 
numeric::xyzTransform< core::Realget_backbone_reference_frame (Pose const &pose, core::Size const &ir)
 
numeric::xyzTransform< core::Realget_nterminal_peptide_bond_reference_frame (Pose const &pose, core::Size const &ir)
 
numeric::xyzTransform< core::Realget_cterminal_peptide_bond_reference_frame (Pose const &pose, core::Size const &ir)
 
numeric::xyzTransform< core::Realget_peptide_bond_reference_frame (Pose const &pose, core::Size const &ir, bool const &n_or_c)
 
numeric::xyzTransform< core::Realget_backbone_reference_frame (numeric::xyzVector< Real > const &N, numeric::xyzVector< Real > const &CA, numeric::xyzVector< Real > const &C)
 
numeric::xyzTransform< core::Realget_nterminal_peptide_bond_reference_frame (numeric::xyzVector< Real > const &H, numeric::xyzVector< Real > const &N, numeric::xyzVector< Real > const &CA)
 
numeric::xyzTransform< core::Realget_cterminal_peptide_bond_reference_frame (numeric::xyzVector< Real > const &O, numeric::xyzVector< Real > const &C, numeric::xyzVector< Real > const &CA)
 
numeric::xyzTransform< core::Realget_frame_ala (Pose const &pose, core::Size const &ir)
 
numeric::xyzTransform< core::Realget_frame_cys (Pose const &pose, core::Size const &ir)
 
numeric::xyzTransform< core::Realget_frame_asp (Pose const &pose, core::Size const &ir)
 
numeric::xyzTransform< core::Realget_frame_glu (Pose const &pose, core::Size const &ir)
 
numeric::xyzTransform< core::Realget_frame_phe (Pose const &pose, core::Size const &ir)
 
numeric::xyzTransform< core::Realget_frame_gly (Pose const &pose, core::Size const &ir)
 
numeric::xyzTransform< core::Realget_frame_his (Pose const &pose, core::Size const &ir)
 
numeric::xyzTransform< core::Realget_frame_ile (Pose const &pose, core::Size const &ir)
 
numeric::xyzTransform< core::Realget_frame_lys (Pose const &pose, core::Size const &ir)
 
numeric::xyzTransform< core::Realget_frame_leu (Pose const &pose, core::Size const &ir)
 
numeric::xyzTransform< core::Realget_frame_met (Pose const &pose, core::Size const &ir)
 
numeric::xyzTransform< core::Realget_frame_asn (Pose const &pose, core::Size const &ir)
 
numeric::xyzTransform< core::Realget_frame_pro (Pose const &pose, core::Size const &ir)
 
numeric::xyzTransform< core::Realget_frame_gln (Pose const &pose, core::Size const &ir)
 
numeric::xyzTransform< core::Realget_frame_arg (Pose const &pose, core::Size const &ir)
 
numeric::xyzTransform< core::Realget_frame_ser (Pose const &pose, core::Size const &ir)
 
numeric::xyzTransform< core::Realget_frame_thr (Pose const &pose, core::Size const &ir)
 
numeric::xyzTransform< core::Realget_frame_val (Pose const &pose, core::Size const &ir)
 
numeric::xyzTransform< core::Realget_frame_trp (Pose const &pose, core::Size const &ir)
 
numeric::xyzTransform< core::Realget_frame_tyr (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_cterminal_peptide_bond_reference_frame_atomids (Pose const &pose, core::Size const &ir, bool extra=false)
 
utility::vector1
< core::id::AtomID
get_nterminal_peptide_bond_reference_frame_atomids (Pose const &pose, core::Size const &ir, bool extra=false)
 
utility::vector1
< core::id::AtomID
get_peptide_bond_reference_frame_atomids (Pose const &pose, core::Size const &ir, bool const &n_or_c, bool extra=false)
 
utility::vector1
< core::id::AtomID
get_atoms_ala (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_cys (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_asp (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_glu (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_phe (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_gly (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_his (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_ile (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_lys (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_leu (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_met (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_asn (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_pro (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_gln (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_arg (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_ser (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_thr (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_val (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_trp (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_tyr (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_ala_downstream (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_cys_downstream (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_asp_downstream (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_glu_downstream (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_phe_downstream (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_gly_downstream (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_his_downstream (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_ile_downstream (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_lys_downstream (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_leu_downstream (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_met_downstream (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_asn_downstream (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_pro_downstream (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_gln_downstream (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_arg_downstream (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_ser_downstream (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_thr_downstream (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_val_downstream (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_trp_downstream (Pose const &pose, core::Size const &ir)
 
utility::vector1
< core::id::AtomID
get_atoms_tyr_downstream (Pose const &pose, core::Size const &ir)
 

Typedef Documentation

using core::pose::motif::AIDs = typedef utility::vector1<core::id::AtomID>
using core::pose::motif::PoseCR = typedef const Pose &
using core::pose::motif::SizeCR = typedef const Size &
using core::pose::motif::Vec = typedef xyzVector<Real>
using core::pose::motif::Xform = typedef xyzTransform<Real>

Function Documentation

Vec core::pose::motif::a ( Pose const &  p,
numeric::Size const &  i,
string const &  s 
)

References core::conformation::Residue::has(), core::conformation::Residue::name(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by protocols::normalmode::NormalMode::a_to_i(), protocols::denovo_design::abego_str(), protocols::monte_carlo::GenericMonteCarloMover::adaptation_period(), protocols::monte_carlo::GenericMonteCarloMover::adaptive_movers(), protocols::constraint_movers::ConstraintSetMover::add_constraints(), protocols::denovo_design::components::add_segments_for_chain(), protocols::splice::Splice::add_sequence_constraints_only(), core::membrane::add_shell(), core::scoring::loop_graph::evaluator::SixDTransRotPotential::adjust_near_pi(), protocols::forge::remodel::RemodelGlobalFrame::align_segment(), protocols::evolution::AlignmentGapInserter::alignment_file(), protocols::evolution::AlignmentAAFinder::alignment_file(), protocols::task_operations::DesignAroundOperation::allow_design(), protocols::simple_moves::sidechain_moves::SetChiMover::angle(), protocols::membrane::MPLipidAccessibility::apply(), protocols::normalmode::NormalModeRelaxMover::apply(), protocols::indexed_structure_store::movers::DirectSegmentLookupMover::apply(), protocols::membrane::MPMutateRelaxMover::apply(), protocols::monte_carlo::GenericMonteCarloMover::apply(), protocols::simple_moves::ExplicitWaterMover::apply(), protocols::rosetta_scripts::ParsedProtocol::apply_probability(), protocols::toolbox::apply_superposition_transform(), protocols::sparta::ANN::applyVecNormalization(), protocols::simple_filters::AngleToVector::atm1(), protocols::simple_filters::AngleToVector::atm2(), protocols::constraint_generator::HydrogenBondInfo::atoms(), protocols::protein_interface_design::movers::AddChainBreak::automatic_distance_cutoff(), protocols::evolution::AlignmentAAFinder::available_AAs_file(), protocols::evolution::AlignmentGapInserter::available_AAs_file(), core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_delta_internal_coordinates(), core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_distance_squared(), protocols::denovo_design::connection::calc_approx_loop_length(), protocols::sparta::PDB::calcTriangles(), protocols::normalmode::NormalMode::calculate_Jacobi_correction(), core::scoring::nmr::NMRDummySpinlabelEnsemble::clash_check(), protocols::evolution::AlignmentGapInserter::cleaned_alignment_file(), core::kinematics::tree::BondedAtom::clone(), protocols::simple_moves::BBConRotMover::closure(), protocols::pockets::GenPharmacophore::cluster_KeyFeatures(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::simple_filters::InterRepeatContactFilter::compute(), protocols::simple_filters::IntraRepeatContactFilter::compute(), protocols::rigid::RigidBodyMotionMover::compute_bias(), core::scoring::packing::compute_dec15_score(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::packing::compute_holes_deriv_res(), core::scoring::packing::compute_holes_score(), core::scoring::packing::compute_holes_score_res(), core::scoring::packing::compute_holes_surfs(), protocols::vip::VIP_Mover::compute_number_cavities(), core::scoring::packing::compute_rosettaholes_score(), protocols::denovo_design::filters::PreProlineFilter::compute_simple(), protocols::normalmode::NormalMode::convert_to_torsion_crd(), core::chemical::orbitals::AssignOrbitals::Coordinates_TriganolPlanar_bondedto1atom_helper(), protocols::denovo_design::components::StructureData::copy_data(), protocols::denovo_design::architects::DeNovoArchitectFactory::create_instance(), core::kinematics::Stub::create_orthogonal(), protocols::pockets::dD_dv1(), protocols::pockets::dD_dv2(), protocols::pockets::dD_dv3(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_receptor_phores(), core::scoring::func::SmoothStepFunc::dfunc(), core::kinematics::distance(), protocols::frag_picker::scores::AmbigCSScore::do_caching(), protocols::frag_picker::scores::CSScore::do_caching(), core::membrane::enclosing_angles(), protocols::cluster::calibur::Clustering::estimateDist(), protocols::indexed_structure_store::search::PairQueryExecutor::execute_structure(), protocols::indexed_structure_store::search::SingleQueryExecutor::execute_structure(), core::conformation::membrane::ImplicitLipidInfo::f_depth(), core::conformation::membrane::ImplicitLipidInfo::f_depth_gradient(), protocols::pockets::ElectrostaticpotentialGrid::fill_espGrid_values_with_type(), core::chemical::fill_ideal_xyz_from_icoor(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::fill_rotamer_vector(), protocols::canonical_sampling::ParallelTempering::finalize_simulation(), core::chemical::find_chi_bonds(), protocols::pockets::Find_Closest_Intersect_SQ(), protocols::simple_filters::HelixHelixAngleFilter::find_closest_pnts(), protocols::sparta::PDB::findNeighors(), protocols::relax::fix_worst_bad_ramas(), core::scoring::frdc(), core::scoring::frdcDa(), core::scoring::frdcDaR(), core::scoring::frdcR(), core::scoring::func::SmoothStepFunc::func(), protocols::ligand_docking::generate_unique_name(), get_backbone_reference_frame(), core::scoring::motif::get_bins(), core::scoring::magnesium::get_cos_theta(), get_cterminal_peptide_bond_reference_frame(), get_frame_ala(), get_frame_arg(), get_frame_asn(), get_frame_asp(), get_frame_cys(), get_frame_gln(), get_frame_glu(), get_frame_gly(), get_frame_his(), get_frame_ile(), get_frame_leu(), get_frame_lys(), get_frame_met(), get_frame_phe(), get_frame_pro(), get_frame_ser(), get_frame_thr(), get_frame_trp(), get_frame_tyr(), get_frame_val(), core::scoring::magnesium::get_gaussian_deriv(), core::scoring::magnesium::get_gaussian_score(), protocols::cluster::calibur::Clustering::get_neighbor_list(), protocols::vip::VIP_Mover::get_neighbors(), get_nterminal_peptide_bond_reference_frame(), core::import_pose::RNA_DeNovoParameters::get_pairings_from_line(), protocols::indexed_structure_store::StructureStore::get_residues(), protocols::nonlocal::HelixRotate::get_rotation_parameters(), core::scoring::nmr::pcs::PCSData::get_total_number_pcs(), core::scoring::nmr::pcs::PCSMultiSet::get_total_number_pcs(), core::scoring::nmr::pre::PREData::get_total_number_pre(), core::scoring::nmr::rdc::RDCData::get_total_number_rdc(), protocols::sparta::getDiff(), protocols::sparta::PDB::initHBond(), core::import_pose::options::RNA_FragmentMonteCarloOptions::initialize_from_tag(), protocols::constel::NeighTeller::is_neigh_tree(), core::kinematics::jump_distance(), protocols::hybridization::TMalign::Kabsch(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::load_matrix(), core::scoring::dna::lsf_normal(), protocols::ligand_docking::make_atr_rep_grid(), protocols::ligand_docking::make_atr_rep_grid_without_ligands(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::map_phores(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), mybegin(), myend(), protocols::hbnet::HBNet::networks_identical_aa_sequence(), protocols::loop_modeling::operator&(), core::chemical::VDDistanceMatrix::operator()(), core::chemical::HeavyAtomWithPolarHydrogensFilter::operator()(), core::chemical::HeavyAtomWithHydrogensFilter::operator()(), core::scoring::packstat::HTL_EventX::operator()(), core::scoring::motif::RMSandEnergyCMP::operator()(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::operator==(), core::pose::full_model_info::operator==(), protocols::loop_modeling::operator|(), protocols::indexed_structure_store::search::PairQueryExecutor::perform_structure_rmsd(), protocols::indexed_structure_store::search::SingleQueryExecutor::perform_structure_rmsd(), core::scoring::packing::PoseBalls::PoseBalls(), protocols::ligand_docking::print_buried_unsat_Hbonds(), core::scoring::aa_composition_energy::AACompositionEnergySetup::quadratic_fract_out_of_bounds_func(), core::scoring::netcharge_energy::NetChargeEnergySetup::quadratic_out_of_bounds_func(), core::scoring::aa_composition_energy::AACompositionEnergySetup::quadratic_out_of_bounds_func(), core::scoring::motif::random_rotation(), protocols::frag_picker::JCouplingIO::read(), core::chemical::Element::read(), protocols::jumping::read_disulf_pairing_list(), core::scoring::dssp::read_pairing_list(), core::import_pose::RNA_DeNovoParameters::read_parameters_from_file(), protocols::hybridization::TMalign::read_pose(), protocols::topology_broker::PseudocontactShiftEnergyController::read_tag(), protocols::topology_broker::PseudocontactShiftEnergyController_Ts1::read_tag(), protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::read_tag(), protocols::topology_broker::PseudocontactShiftEnergyController_Ts2::read_tag(), protocols::topology_broker::PseudocontactShiftEnergyController_Ts3::read_tag(), protocols::simple_moves::RepeatPropagationMover::repeat_ligand(), protocols::features::SaltBridgeFeatures::report_features(), core::scoring::sc::MolecularSurfaceCalculator::Reset(), protocols::hotspot_hashing::StubGenerator::residueStubOrientFrame(), protocols::task_operations::DesignAroundOperation::resnums_allow_design(), core::chemical::rosetta_retype_fullatom(), protocols::sic_dock::scores::MotifHashRigidScore::score(), core::sequence::ChemicalShiftScoringScheme::score(), protocols::sic_dock::XfoxmScore::score(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::score(), protocols::hotspot_hashing::ComposeSearchPatterns::Searchpoints(), protocols::indexed_structure_store::DirectSegmentLookup::segment_lookup(), core::pack::dunbrack::cenrot::CentroidRotamerSampleData::set_angle(), core::chemical::MutableResidueType::set_atom_type(), core::chemical::MutableResidueType::set_gasteiger_atom_type(), core::chemical::MutableResidueType::set_ideal_xyz(), protocols::qsar::scoring_grid::AtrGrid::set_ligand_rings(), protocols::qsar::scoring_grid::AtrGrid::set_protein_rings(), core::scoring::fiber_diffraction::FiberDiffractionEnergy::setup_for_derivatives(), core::scoring::fiber_diffraction::FiberDiffractionEnergy::setup_for_scoring(), core::scoring::fiber_diffraction::FiberDiffractionEnergyDens::setup_for_scoring(), core::scoring::SS_Killhairpins_Info::setup_killhairpins(), core::scoring::fiber_diffraction::FiberDiffraction::setupBesselOrder(), core::scoring::nmr::pre::PREData::show(), core::scoring::nmr::rdc::RDCData::show(), core::scoring::nmr::pcs::PCSData::show(), core::scoring::nmr::pcs::PCSMultiSet::show(), core::chemical::MutableResidueType::show_all_atom_names(), protocols::loophash::LoopHashMap::sort(), protocols::loophash::sqr(), protocols::hotspot_hashing::stub_from_points(), protocols::hotspot_hashing::stub_to_points(), core::scoring::sc::MolecularSurfaceCalculator::SubDiv(), core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl::svdcmp(), protocols::denovo_design::movers::RotateSegmentMover::target_atoms(), protocols::sparta::PDB::Vec3Norm(), and core::chemical::Element::write().

static AIDs core::pose::motif::get_AIDs ( Pose const &  pose,
core::Size const &  ir,
utility::vector1< std::string > const &  anames 
)
static
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_ala ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_ala ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_ala_downstream ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_ala_downstream ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_arg ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_arg ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_arg_downstream ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_arg_downstream ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_asn ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_asn ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_asn_downstream ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_asn_downstream ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_asp ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_asp ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_asp_downstream ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_asp_downstream ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_cys ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_cys ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_cys_downstream ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_cys_downstream ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_gln ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_gln ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_gln_downstream ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_gln_downstream ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_glu ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_glu ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_glu_downstream ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_glu_downstream ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_gly ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_gly ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_gly_downstream ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_gly_downstream ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_his ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_his ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_his_downstream ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_his_downstream ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_ile ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_ile ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_ile_downstream ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_ile_downstream ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_leu ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_leu ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_leu_downstream ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_leu_downstream ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_lys ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_lys ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_lys_downstream ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_lys_downstream ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_met ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_met ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_met_downstream ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_met_downstream ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_phe ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_phe ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_phe_downstream ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_phe_downstream ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_pro ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_pro ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_pro_downstream ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_pro_downstream ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_ser ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_ser ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_ser_downstream ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_ser_downstream ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_thr ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_thr ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_thr_downstream ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_thr_downstream ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_trp ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_trp ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_trp_downstream ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_trp_downstream ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_tyr ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_tyr ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_tyr_downstream ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_tyr_downstream ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_val ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_val ( PoseCR  p,
SizeCR  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_val_downstream ( Pose const &  pose,
core::Size const &  ir 
)
AIDs core::pose::motif::get_atoms_val_downstream ( PoseCR  p,
SizeCR  i 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_backbone_reference_frame ( Pose const &  pose,
core::Size const &  ir 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_backbone_reference_frame ( numeric::xyzVector< Real > const &  N,
numeric::xyzVector< Real > const &  CA,
numeric::xyzVector< Real > const &  C 
)
Xform core::pose::motif::get_backbone_reference_frame ( xyzVector< Real > const &  N,
xyzVector< Real > const &  CA,
xyzVector< Real > const &  C 
)
Xform core::pose::motif::get_backbone_reference_frame ( Pose const &  p,
numeric::Size const &  i 
)
utility::vector1< core::id::AtomID > core::pose::motif::get_backbone_reference_frame_atomids ( Pose const &  pose,
core::Size const &  ir 
)
utility::vector1< core::id::AtomID > core::pose::motif::get_backbone_reference_frame_atomids_with_downstream ( Pose const &  pose,
core::Size const &  ir 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_cterminal_peptide_bond_reference_frame ( Pose const &  pose,
core::Size const &  ir 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_cterminal_peptide_bond_reference_frame ( numeric::xyzVector< Real > const &  O,
numeric::xyzVector< Real > const &  C,
numeric::xyzVector< Real > const &  CA 
)
Xform core::pose::motif::get_cterminal_peptide_bond_reference_frame ( xyzVector< Real > const &  O,
xyzVector< Real > const &  C,
xyzVector< Real > const &  CA 
)
Xform core::pose::motif::get_cterminal_peptide_bond_reference_frame ( Pose const &  p,
numeric::Size const &  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_cterminal_peptide_bond_reference_frame_atomids ( Pose const &  pose,
core::Size const &  ir,
bool  extra = false 
)
AIDs core::pose::motif::get_cterminal_peptide_bond_reference_frame_atomids ( Pose const &  p,
numeric::Size const &  i,
bool  extra 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_frame_ala ( Pose const &  pose,
core::Size const &  ir 
)
Xform core::pose::motif::get_frame_ala ( PoseCR  p,
SizeCR  i 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_frame_arg ( Pose const &  pose,
core::Size const &  ir 
)
Xform core::pose::motif::get_frame_arg ( PoseCR  p,
SizeCR  i 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_frame_asn ( Pose const &  pose,
core::Size const &  ir 
)
Xform core::pose::motif::get_frame_asn ( PoseCR  p,
SizeCR  i 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_frame_asp ( Pose const &  pose,
core::Size const &  ir 
)
Xform core::pose::motif::get_frame_asp ( PoseCR  p,
SizeCR  i 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_frame_cys ( Pose const &  pose,
core::Size const &  ir 
)
Xform core::pose::motif::get_frame_cys ( PoseCR  p,
SizeCR  i 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_frame_gln ( Pose const &  pose,
core::Size const &  ir 
)
Xform core::pose::motif::get_frame_gln ( PoseCR  p,
SizeCR  i 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_frame_glu ( Pose const &  pose,
core::Size const &  ir 
)
Xform core::pose::motif::get_frame_glu ( PoseCR  p,
SizeCR  i 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_frame_gly ( Pose const &  pose,
core::Size const &  ir 
)
Xform core::pose::motif::get_frame_gly ( PoseCR  p,
SizeCR  i 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_frame_his ( Pose const &  pose,
core::Size const &  ir 
)
Xform core::pose::motif::get_frame_his ( PoseCR  p,
SizeCR  i 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_frame_ile ( Pose const &  pose,
core::Size const &  ir 
)
Xform core::pose::motif::get_frame_ile ( PoseCR  p,
SizeCR  i 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_frame_leu ( Pose const &  pose,
core::Size const &  ir 
)
Xform core::pose::motif::get_frame_leu ( PoseCR  p,
SizeCR  i 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_frame_lys ( Pose const &  pose,
core::Size const &  ir 
)
Xform core::pose::motif::get_frame_lys ( PoseCR  p,
SizeCR  i 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_frame_met ( Pose const &  pose,
core::Size const &  ir 
)
Xform core::pose::motif::get_frame_met ( PoseCR  p,
SizeCR  i 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_frame_phe ( Pose const &  pose,
core::Size const &  ir 
)
Xform core::pose::motif::get_frame_phe ( PoseCR  p,
SizeCR  i 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_frame_pro ( Pose const &  pose,
core::Size const &  ir 
)
Xform core::pose::motif::get_frame_pro ( PoseCR  p,
SizeCR  i 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_frame_ser ( Pose const &  pose,
core::Size const &  ir 
)
Xform core::pose::motif::get_frame_ser ( PoseCR  p,
SizeCR  i 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_frame_thr ( Pose const &  pose,
core::Size const &  ir 
)
Xform core::pose::motif::get_frame_thr ( PoseCR  p,
SizeCR  i 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_frame_trp ( Pose const &  pose,
core::Size const &  ir 
)
Xform core::pose::motif::get_frame_trp ( PoseCR  p,
SizeCR  i 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_frame_tyr ( Pose const &  pose,
core::Size const &  ir 
)
Xform core::pose::motif::get_frame_tyr ( PoseCR  p,
SizeCR  i 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_frame_val ( Pose const &  pose,
core::Size const &  ir 
)
Xform core::pose::motif::get_frame_val ( PoseCR  p,
SizeCR  i 
)
Xform core::pose::motif::get_frame_vee ( Vec const &  a,
Vec const &  b,
Vec const &  c 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_nterminal_peptide_bond_reference_frame ( Pose const &  pose,
core::Size const &  ir 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_nterminal_peptide_bond_reference_frame ( numeric::xyzVector< Real > const &  H,
numeric::xyzVector< Real > const &  N,
numeric::xyzVector< Real > const &  CA 
)
Xform core::pose::motif::get_nterminal_peptide_bond_reference_frame ( xyzVector< Real > const &  H,
xyzVector< Real > const &  N,
xyzVector< Real > const &  CA 
)
Xform core::pose::motif::get_nterminal_peptide_bond_reference_frame ( Pose const &  p,
numeric::Size const &  i 
)
utility::vector1<core::id::AtomID> core::pose::motif::get_nterminal_peptide_bond_reference_frame_atomids ( Pose const &  pose,
core::Size const &  ir,
bool  extra = false 
)
AIDs core::pose::motif::get_nterminal_peptide_bond_reference_frame_atomids ( Pose const &  p,
numeric::Size const &  i,
bool  extra 
)
numeric::xyzTransform<core::Real> core::pose::motif::get_peptide_bond_reference_frame ( Pose const &  pose,
core::Size const &  ir,
bool const &  n_or_c 
)
inline
utility::vector1<core::id::AtomID> core::pose::motif::get_peptide_bond_reference_frame_atomids ( Pose const &  pose,
core::Size const &  ir,
bool const &  n_or_c,
bool  extra = false 
)
inline
numeric::xyzTransform<core::Real> core::pose::motif::get_sidechain_reference_frame ( Pose const &  pose,
core::Size const &  ir 
)
Xform core::pose::motif::get_sidechain_reference_frame ( Pose const &  p,
numeric::Size const &  i 
)
utility::vector1< core::id::AtomID > core::pose::motif::get_sidechain_reference_frame_atomids ( Pose const &  pose,
core::Size const &  ir 
)
utility::vector1< core::id::AtomID > core::pose::motif::get_sidechain_reference_frame_atomids_with_downstream ( Pose const &  pose,
core::Size const &  ir 
)