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::Real >	get_sidechain_reference_frame (Pose const &pose, core::Size const &ir)
numeric::xyzTransform< core::Real >	get_backbone_reference_frame (Pose const &pose, core::Size const &ir)
numeric::xyzTransform< core::Real >	get_nterminal_peptide_bond_reference_frame (Pose const &pose, core::Size const &ir)
numeric::xyzTransform< core::Real >	get_cterminal_peptide_bond_reference_frame (Pose const &pose, core::Size const &ir)
numeric::xyzTransform< core::Real >	get_peptide_bond_reference_frame (Pose const &pose, core::Size const &ir, bool const &n_or_c)
numeric::xyzTransform< core::Real >	get_backbone_reference_frame (numeric::xyzVector< Real > const &N, numeric::xyzVector< Real > const &CA, numeric::xyzVector< Real > const &C)
numeric::xyzTransform< core::Real >	get_nterminal_peptide_bond_reference_frame (numeric::xyzVector< Real > const &H, numeric::xyzVector< Real > const &N, numeric::xyzVector< Real > const &CA)
numeric::xyzTransform< core::Real >	get_cterminal_peptide_bond_reference_frame (numeric::xyzVector< Real > const &O, numeric::xyzVector< Real > const &C, numeric::xyzVector< Real > const &CA)
numeric::xyzTransform< core::Real >	get_frame_ala (Pose const &pose, core::Size const &ir)
numeric::xyzTransform< core::Real >	get_frame_cys (Pose const &pose, core::Size const &ir)
numeric::xyzTransform< core::Real >	get_frame_asp (Pose const &pose, core::Size const &ir)
numeric::xyzTransform< core::Real >	get_frame_glu (Pose const &pose, core::Size const &ir)
numeric::xyzTransform< core::Real >	get_frame_phe (Pose const &pose, core::Size const &ir)
numeric::xyzTransform< core::Real >	get_frame_gly (Pose const &pose, core::Size const &ir)
numeric::xyzTransform< core::Real >	get_frame_his (Pose const &pose, core::Size const &ir)
numeric::xyzTransform< core::Real >	get_frame_ile (Pose const &pose, core::Size const &ir)
numeric::xyzTransform< core::Real >	get_frame_lys (Pose const &pose, core::Size const &ir)
numeric::xyzTransform< core::Real >	get_frame_leu (Pose const &pose, core::Size const &ir)
numeric::xyzTransform< core::Real >	get_frame_met (Pose const &pose, core::Size const &ir)
numeric::xyzTransform< core::Real >	get_frame_asn (Pose const &pose, core::Size const &ir)
numeric::xyzTransform< core::Real >	get_frame_pro (Pose const &pose, core::Size const &ir)
numeric::xyzTransform< core::Real >	get_frame_gln (Pose const &pose, core::Size const &ir)
numeric::xyzTransform< core::Real >	get_frame_arg (Pose const &pose, core::Size const &ir)
numeric::xyzTransform< core::Real >	get_frame_ser (Pose const &pose, core::Size const &ir)
numeric::xyzTransform< core::Real >	get_frame_thr (Pose const &pose, core::Size const &ir)
numeric::xyzTransform< core::Real >	get_frame_val (Pose const &pose, core::Size const &ir)
numeric::xyzTransform< core::Real >	get_frame_trp (Pose const &pose, core::Size const &ir)
numeric::xyzTransform< core::Real >	get_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

AIDs

using core::pose::motif::AIDs = typedef utility::vector1<core::id::AtomID>

PoseCR

using core::pose::motif::PoseCR = typedef const Pose &

SizeCR

using core::pose::motif::SizeCR = typedef const Size &

Vec

using core::pose::motif::Vec = typedef xyzVector<Real>

Xform

using core::pose::motif::Xform = typedef xyzTransform<Real>

Function Documentation

a()

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::cluster::calibur::__cmp(), 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::sic_dock::Rose::align_c(), protocols::sic_dock::Rose::align_n(), protocols::forge::remodel::RemodelGlobalFrame::align_segment(), protocols::evolution::AlignmentAAFinder::alignment_file(), protocols::evolution::AlignmentGapInserter::alignment_file(), protocols::task_operations::DesignAroundOperation::allow_design(), protocols::environment::ang_delta(), protocols::loops::loop_mover::ang_delta(), protocols::simple_moves::sidechain_moves::SetChiMover::angle(), protocols::rigid::angle_between(), protocols::abinitio::abscript::angle_diff(), core::scoring::motif::angle_distance(), protocols::membrane::MPLipidAccessibility::apply(), protocols::normalmode::NormalModeRelaxMover::apply(), protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::apply(), protocols::membrane::MPMutateRelaxMover::apply(), protocols::protein_interface_design::movers::SecretionOptimizationMover::apply(), protocols::indexed_structure_store::movers::DirectSegmentLookupMover::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(), protocols::simple_moves::BBGaussianMover::cholesky_bw(), protocols::simple_moves::BBGaussianMover::cholesky_fw(), core::scoring::nmr::NMRDummySpinlabelEnsemble::clash_check(), protocols::evolution::AlignmentGapInserter::cleaned_alignment_file(), protocols::simple_moves::BBConRotMover::closure(), protocols::pockets::GenPharmacophore::cluster_KeyFeatures(), protocols::loophash::cmp(), core::optimization::cmp_particles(), protocols::membrane::com(), protocols::indexed_structure_store::ResidueEntry::comp_id(), protocols::indexed_structure_store::StructureEntry::comp_id(), protocols::hbnet::NetworkStateScoreComparator::compare(), core::scoring::compare_by_abs(), protocols::motif_grafting::movers::compare_motif2scaffold_data_by_scaffold_low2high(), protocols::topology_broker::compare_sequence_claim_priority(), 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::splice::SampleRotamersFromPDB::concatenate_rot_matrix(), 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(), protocols::protein_interface_design::movers::SecretionOptimizationMover::DesignAroundApply(), core::scoring::func::SmoothStepFunc::dfunc(), core::scoring::dimer_pairing_pointer_sorter(), core::kinematics::distance(), protocols::frag_picker::scores::AmbigCSScore::do_caching(), protocols::frag_picker::scores::CSScore::do_caching(), core::optimization::DOF_Node_sorter(), core::optimization::symmetry::DOF_Node_sorter(), protocols::evaluation::dump_matrix_no(), protocols::toolbox::dump_matrix_no(), core::membrane::enclosing_angles(), protocols::genetic_algorithm::eq_OP_deref(), protocols::cluster::calibur::Clustering::estD(), protocols::cluster::calibur::Clustering::estimateDist(), protocols::indexed_structure_store::search::PairQueryExecutor::execute_structure(), protocols::indexed_structure_store::search::SingleQueryExecutor::execute_structure(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_atom_neighbor_stuff(), protocols::pockets::ElectrostaticpotentialGrid::fill_espGrid_values_with_type(), core::chemical::fill_ideal_xyz_from_icoor(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::fill_rotamer_vector(), protocols::sic_dock::XfoxmScore::fillarray(), core::chemical::rdkit::final_neutralize(), protocols::canonical_sampling::ParallelTempering::finalize_simulation(), core::chemical::find_chi_bonds(), protocols::pockets::Find_Closest_Intersect_SQ(), protocols::simple_filters::HelixHelixAngleFilter::find_closest_pnts(), core::chemical::VDDistanceMatrix::find_max_over(), protocols::sparta::PDB::findNeighors(), protocols::relax::fix_worst_bad_ramas(), core::scoring::frdc(), core::scoring::frdcDa(), core::scoring::frdcDaR(), core::scoring::frdcR(), core::kinematics::Stub::from_four_points(), core::scoring::func::SmoothStepFunc::func(), core::conformation::membrane::MembraneGeometry::g_radius_gradient_dx(), core::conformation::membrane::MembraneGeometry::g_radius_gradient_dy(), core::conformation::membrane::MembraneGeometry::g_radius_gradient_dz(), protocols::ligand_docking::generate_unique_name(), get_backbone_reference_frame(), core::scoring::motif::get_bins(), core::scoring::dssp::get_CA_vectors(), protocols::jumping::get_CA_vectors(), protocols::vip::VIP_Mover::get_cav_approx(), core::scoring::magnesium::get_cos_theta(), get_cterminal_peptide_bond_reference_frame(), core::scoring::packstat::Octree2D::get_cube(), protocols::simple_moves::BBConRotMover::get_determinant(), 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(), get_frame_vee(), 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::scoring::packstat::old::get_orientation(), 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::simple_moves::BBConRotMover::get_xyz(), protocols::sparta::PDB::getBondAngle(), protocols::sparta::getDiff(), protocols::sparta::PDB::getDihedralAngle(), protocols::sparta::PDB::getOneAAName(), protocols::sparta::PDB::getThreeAAName(), core::scoring::hbonds::HBond::hbond_energy_comparer(), protocols::sparta::PDB::initHBond(), core::import_pose::options::RNA_FragmentMonteCarloOptions::initialize_from_tag(), core::scoring::epr_deer::Simulated4PDEERTraceFactory::initialize_kernel(), protocols::sic_dock::invstub(), core::scoring::iprod(), protocols::constel::NeighTeller::is_neigh_tree(), protocols::evaluation::PCA::jacobi(), protocols::toolbox::jacobi(), core::scoring::jacobi(), protocols::cluster::calibur::jacobi3(), core::scoring::jacobi3(), core::kinematics::jump_distance(), protocols::hybridization::TMalign::Kabsch(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::load_matrix(), core::scoring::dna::lsf_normal(), protocols::genetic_algorithm::lt_OP_deref(), protocols::ligand_docking::make_atr_rep_grid(), protocols::ligand_docking::make_atr_rep_grid_without_ligands(), protocols::sic_dock::XfoxmScore::makebinary(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::map_phores(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), protocols::cluster::Exemplar::min_heap(), protocols::sic_dock::multstubs(), core::scoring::mvmul(), mybegin(), myend(), protocols::hbnet::HBNet::networks_identical_aa_sequence(), protocols::loop_modeling::operator&(), core::scoring::packstat::OrderCavBallOnX::operator()(), core::scoring::packstat::OrderCavBallOnRmE::operator()(), core::scoring::packstat::OrderCavBallOnR::operator()(), core::scoring::packstat::OrderCavBallOnRmAnb::operator()(), core::scoring::packstat::OrderCBC::operator()(), protocols::ligand_docking::ga_ligand_dock::DensStructInfoComp::operator()(), protocols::pack_daemon::EntityHistoryLT::operator()(), core::scoring::packstat::HTL_EventX::operator()(), protocols::hbnet::compare_net_vec::operator()(), protocols::hbnet::compare_hbond_residues::operator()(), protocols::hbnet::compare_hbond_resnums::operator()(), protocols::jd3::compare_job_nodes::operator()(), core::scoring::motif::RMSandEnergyCMP::operator()(), core::pose::PDBPoseMap::no_segID_comp::operator()(), core::scoring::motif::MyPred::operator()(), protocols::dna::ResTypeSequence_lt::operator()(), core::scoring::packstat::OrderSphereOnX::operator()(), core::scoring::packstat::OrderSphereOnID::operator()(), protocols::environment::Comparator::operator()(), comparator::operator()(), protocols::ligand_docking::ga_ligand_dock::StructInfoComp::operator()(), protocols::ligand_docking::ga_ligand_dock::StructInfoCompdH::operator()(), core::import_pose::atom_tree_diffs::ScoreLessThanComparator::operator()(), core::chemical::VDDistanceMatrix::operator()(), core::chemical::HeavyAtomWithPolarHydrogensFilter::operator()(), core::chemical::HeavyAtomWithHydrogensFilter::operator()(), protocols::protein_interface_design::movers::SecretionOptimizationMover::tm_region::operator<(), protocols::simple_filters::SecretionPredictionFilter::tm_region::operator<(), protocols::hbnet::HBondNetStruct::operator<(), protocols::hbnet::HBondResStruct::operator<(), core::kinematics::operator<<(), boost::tuples::operator==(), protocols::hbnet::HBondResStruct::operator==(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::operator==(), protocols::loop_modeling::operator|(), protocols::evaluation::PCA::oprod(), protocols::toolbox::oprod(), protocols::indexed_structure_store::search::SingleQueryExecutor::perform_structure_rmsd(), protocols::indexed_structure_store::search::PairQueryExecutor::perform_structure_rmsd(), protocols::canonical_sampling::CanonicalSamplingMover::periodic_range(), protocols::fldsgn::topology::pointer_sorter(), core::scoring::packing::PoseBalls::PoseBalls(), protocols::ligand_docking::print_buried_unsat_Hbonds(), protocols::cluster::calibur::print_matrix(), core::energy_methods::ResidualDipolarCouplingEnergy_Rohl::pythag(), core::scoring::aa_composition_energy::AACompositionEnergySetup::quadratic_fract_out_of_bounds_func(), core::scoring::aa_composition_energy::AACompositionEnergySetup::quadratic_out_of_bounds_func(), core::scoring::netcharge_energy::NetChargeEnergySetup::quadratic_out_of_bounds_func(), core::scoring::motif::random_rotation(), core::chemical::Element::read(), protocols::frag_picker::JCouplingIO::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_Ts2::read_tag(), protocols::topology_broker::PseudocontactShiftEnergyController_Ts3::read_tag(), protocols::topology_broker::PseudocontactShiftEnergyController_Ts4::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::evaluation::ROTATE(), protocols::toolbox::ROTATE(), core::scoring::ROTATE(), protocols::cluster::calibur::ROTATE(), core::sequence::ChemicalShiftScoringScheme::score(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::score(), protocols::sic_dock::XfoxmScore::score(), protocols::sic_dock::scores::MotifHashRigidScore::score(), core::scoring::constraints::MembraneSpanTermZConstraint::score_delta(), protocols::hotspot_hashing::ComposeSearchPatterns::Searchpoints(), protocols::indexed_structure_store::DirectSegmentLookup::segment_lookup(), protocols::pose_selectors::AndSelector::selection_operation(), protocols::pose_selectors::OrSelector::selection_operation(), 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::energy_methods::FiberDiffractionEnergy::setup_for_derivatives(), core::energy_methods::FiberDiffractionEnergy::setup_for_scoring(), core::energy_methods::FiberDiffractionEnergyDens::setup_for_scoring(), core::scoring::SS_Killhairpins_Info::setup_killhairpins(), core::scoring::fiber_diffraction::FiberDiffraction::setupBesselOrder(), core::scoring::nmr::pcs::PCSData::show(), core::scoring::nmr::pcs::PCSMultiSet::show(), core::scoring::nmr::pre::PREData::show(), core::scoring::nmr::rdc::RDCData::show(), core::chemical::MutableResidueType::show_all_atom_names(), protocols::loophash::LoopHashMap::sort(), protocols::fldsgn::topology::sort_by_length(), protocols::ddg::sort_numerically_ascending(), protocols::loophash::sqr(), core::kinematics::Stub::Stub(), protocols::hotspot_hashing::stub_from_points(), protocols::hotspot_hashing::stub_to_points(), core::scoring::sc::MolecularSurfaceCalculator::SubDiv(), core::energy_methods::ResidualDipolarCouplingEnergy_Rohl::svdcmp(), core::id::swap(), protocols::denovo_design::movers::RotateSegmentMover::target_atoms(), protocols::cluster::calibur::Clustering::trueD(), core::conformation::membrane::membrane_geometry::Bicelle::update_edge_steepness(), protocols::normalmode::NormalMode::update_inertia_tensor(), protocols::sparta::PDB::Vec3Norm(), and core::chemical::Element::write().

get_AIDs()

static AIDs core::pose::motif::get_AIDs ( Pose const &  pose, core::Size const &  ir, utility::vector1< std::string > const &  anames  )

static

References core::chemical::ResidueType::atom_index(), core::id::AtomID::BOGUS_ATOM_ID(), core::chemical::ResidueType::has(), core::chemical::ResidueTypeBase::name(), and core::pose::Pose::residue_type().

Referenced by get_atoms_ala(), get_atoms_ala_downstream(), get_atoms_arg(), get_atoms_arg_downstream(), get_atoms_asn(), get_atoms_asn_downstream(), get_atoms_asp(), get_atoms_asp_downstream(), get_atoms_cys(), get_atoms_cys_downstream(), get_atoms_gln(), get_atoms_gln_downstream(), get_atoms_glu(), get_atoms_glu_downstream(), get_atoms_gly(), get_atoms_gly_downstream(), get_atoms_his(), get_atoms_his_downstream(), get_atoms_ile(), get_atoms_ile_downstream(), get_atoms_leu(), get_atoms_leu_downstream(), get_atoms_lys(), get_atoms_lys_downstream(), get_atoms_met(), get_atoms_met_downstream(), get_atoms_phe(), get_atoms_phe_downstream(), get_atoms_pro(), get_atoms_pro_downstream(), get_atoms_ser(), get_atoms_ser_downstream(), get_atoms_thr(), get_atoms_thr_downstream(), get_atoms_trp(), get_atoms_trp_downstream(), get_atoms_tyr(), get_atoms_tyr_downstream(), get_atoms_val(), get_atoms_val_downstream(), get_cterminal_peptide_bond_reference_frame_atomids(), and get_nterminal_peptide_bond_reference_frame_atomids().

get_atoms_ala() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_ala	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_ala() [2/2]

AIDs core::pose::motif::get_atoms_ala	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids().

get_atoms_ala_downstream() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_ala_downstream	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_ala_downstream() [2/2]

AIDs core::pose::motif::get_atoms_ala_downstream	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids_with_downstream().

get_atoms_arg() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_arg	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_arg() [2/2]

AIDs core::pose::motif::get_atoms_arg	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids().

get_atoms_arg_downstream() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_arg_downstream	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_arg_downstream() [2/2]

AIDs core::pose::motif::get_atoms_arg_downstream	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids_with_downstream().

get_atoms_asn() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_asn	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_asn() [2/2]

AIDs core::pose::motif::get_atoms_asn	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids().

get_atoms_asn_downstream() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_asn_downstream	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_asn_downstream() [2/2]

AIDs core::pose::motif::get_atoms_asn_downstream	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids_with_downstream().

get_atoms_asp() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_asp	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_asp() [2/2]

AIDs core::pose::motif::get_atoms_asp	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids().

get_atoms_asp_downstream() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_asp_downstream	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_asp_downstream() [2/2]

AIDs core::pose::motif::get_atoms_asp_downstream	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids_with_downstream().

get_atoms_cys() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_cys	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_cys() [2/2]

AIDs core::pose::motif::get_atoms_cys	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids().

get_atoms_cys_downstream() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_cys_downstream	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_cys_downstream() [2/2]

AIDs core::pose::motif::get_atoms_cys_downstream	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids_with_downstream().

get_atoms_gln() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_gln	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_gln() [2/2]

AIDs core::pose::motif::get_atoms_gln	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids().

get_atoms_gln_downstream() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_gln_downstream	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_gln_downstream() [2/2]

AIDs core::pose::motif::get_atoms_gln_downstream	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids_with_downstream().

get_atoms_glu() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_glu	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_glu() [2/2]

AIDs core::pose::motif::get_atoms_glu	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids().

get_atoms_glu_downstream() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_glu_downstream	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_glu_downstream() [2/2]

AIDs core::pose::motif::get_atoms_glu_downstream	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids_with_downstream().

get_atoms_gly() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_gly	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_gly() [2/2]

AIDs core::pose::motif::get_atoms_gly	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids().

get_atoms_gly_downstream() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_gly_downstream	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_gly_downstream() [2/2]

AIDs core::pose::motif::get_atoms_gly_downstream	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids_with_downstream().

get_atoms_his() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_his	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_his() [2/2]

AIDs core::pose::motif::get_atoms_his	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids().

get_atoms_his_downstream() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_his_downstream	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_his_downstream() [2/2]

AIDs core::pose::motif::get_atoms_his_downstream	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids_with_downstream().

get_atoms_ile() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_ile	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_ile() [2/2]

AIDs core::pose::motif::get_atoms_ile	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids().

get_atoms_ile_downstream() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_ile_downstream	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_ile_downstream() [2/2]

AIDs core::pose::motif::get_atoms_ile_downstream	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids_with_downstream().

get_atoms_leu() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_leu	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_leu() [2/2]

AIDs core::pose::motif::get_atoms_leu	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids().

get_atoms_leu_downstream() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_leu_downstream	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_leu_downstream() [2/2]

AIDs core::pose::motif::get_atoms_leu_downstream	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids_with_downstream().

get_atoms_lys() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_lys	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_lys() [2/2]

AIDs core::pose::motif::get_atoms_lys	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids().

get_atoms_lys_downstream() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_lys_downstream	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_lys_downstream() [2/2]

AIDs core::pose::motif::get_atoms_lys_downstream	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids_with_downstream().

get_atoms_met() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_met	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_met() [2/2]

AIDs core::pose::motif::get_atoms_met	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids().

get_atoms_met_downstream() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_met_downstream	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_met_downstream() [2/2]

AIDs core::pose::motif::get_atoms_met_downstream	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids_with_downstream().

get_atoms_phe() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_phe	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_phe() [2/2]

AIDs core::pose::motif::get_atoms_phe	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids().

get_atoms_phe_downstream() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_phe_downstream	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_phe_downstream() [2/2]

AIDs core::pose::motif::get_atoms_phe_downstream	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids_with_downstream().

get_atoms_pro() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_pro	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_pro() [2/2]

AIDs core::pose::motif::get_atoms_pro	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids().

get_atoms_pro_downstream() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_pro_downstream	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_pro_downstream() [2/2]

AIDs core::pose::motif::get_atoms_pro_downstream	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids_with_downstream().

get_atoms_ser() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_ser	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_ser() [2/2]

AIDs core::pose::motif::get_atoms_ser	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids().

get_atoms_ser_downstream() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_ser_downstream	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_ser_downstream() [2/2]

AIDs core::pose::motif::get_atoms_ser_downstream	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids_with_downstream().

get_atoms_thr() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_thr	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_thr() [2/2]

AIDs core::pose::motif::get_atoms_thr	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids().

get_atoms_thr_downstream() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_thr_downstream	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_thr_downstream() [2/2]

AIDs core::pose::motif::get_atoms_thr_downstream	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids_with_downstream().

get_atoms_trp() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_trp	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_trp() [2/2]

AIDs core::pose::motif::get_atoms_trp	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids().

get_atoms_trp_downstream() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_trp_downstream	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_trp_downstream() [2/2]

AIDs core::pose::motif::get_atoms_trp_downstream	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids_with_downstream().

get_atoms_tyr() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_tyr	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_tyr() [2/2]

AIDs core::pose::motif::get_atoms_tyr	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids().

get_atoms_tyr_downstream() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_tyr_downstream	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_tyr_downstream() [2/2]

AIDs core::pose::motif::get_atoms_tyr_downstream	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids_with_downstream().

get_atoms_val() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_val	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_val() [2/2]

AIDs core::pose::motif::get_atoms_val	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids().

get_atoms_val_downstream() [1/2]

utility::vector1<core::id::AtomID> core::pose::motif::get_atoms_val_downstream	(	Pose const &	pose,
		core::Size const &	ir
	)

get_atoms_val_downstream() [2/2]

AIDs core::pose::motif::get_atoms_val_downstream	(	PoseCR	p,
		SizeCR	i
	)

References get_AIDs().

Referenced by get_sidechain_reference_frame_atomids_with_downstream().

get_backbone_reference_frame() [1/4]

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
	)

get_backbone_reference_frame() [2/4]

Xform core::pose::motif::get_backbone_reference_frame	(	Pose const &	p,
		numeric::Size const &	i
	)

References a(), get_backbone_reference_frame(), core::conformation::Residue::is_protein(), core::pose::Pose::residue(), and core::pose::Pose::size().

get_backbone_reference_frame() [3/4]

numeric::xyzTransform<core::Real> core::pose::motif::get_backbone_reference_frame	(	Pose const &	pose,
		core::Size const &	ir
	)

get_backbone_reference_frame() [4/4]

Xform core::pose::motif::get_backbone_reference_frame	(	xyzVector< Real > const &	N,
		xyzVector< Real > const &	CA,
		xyzVector< Real > const &	C
	)

References core::chemical::element::C, protocols::frag_picker::CA, protocols::frag_picker::CEN, and core::chemical::element::N.

Referenced by protocols::pose_sewing::calculate_motif_score_bt_residues(), protocols::simple_filters::MotifScoreFilter::compute(), core::energy_methods::CenPairMotifDegreeEnergy::finalize_total_energy(), core::energy_methods::CenPairMotifEnergy::finalize_total_energy(), get_backbone_reference_frame(), core::scoring::motif::get_residue_pair_xform(), protocols::simple_filters::SSElementMotifContactFilter::get_SSelements_in_contact(), core::energy_methods::SSElementMotifContactEnergy::get_SSelements_in_contact(), protocols::sewing::scoring::MotifScorer::get_stub(), protocols::legacy_sewing::scoring::LegacyMotifScorer::get_stub(), protocols::legacy_sewing::scoring::LegacyPartnerMotifScorer::interface_motif_score(), protocols::sewing::scoring::PartnerMotifScorer::interface_motif_score(), protocols::sewing::scoring::SubsetPartnerMotifScorer::interface_motif_score(), protocols::pose_sewing::filters::CoreScorer::report_sm(), core::energy_methods::MotifDockEnergy::residue_pair_energy(), and core::scoring::motif::set_residue_pair_xform().

get_backbone_reference_frame_atomids()

utility::vector1< core::id::AtomID > core::pose::motif::get_backbone_reference_frame_atomids	(	Pose const &	pose,
		core::Size const &	ir
	)

References core::conformation::Residue::aa(), core::chemical::aa_gly, core::id::AtomID::BOGUS_ATOM_ID(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by core::scoring::motif::align_motif_pose_super().

get_backbone_reference_frame_atomids_with_downstream()

utility::vector1< core::id::AtomID > core::pose::motif::get_backbone_reference_frame_atomids_with_downstream	(	Pose const &	pose,
		core::Size const &	ir
	)

References core::chemical::ResidueType::atom_is_backbone(), core::chemical::ResidueType::atom_is_hydrogen(), core::chemical::ResidueType::atom_is_polar_hydrogen(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by core::scoring::motif::get_motif_atom_mask().

get_cterminal_peptide_bond_reference_frame() [1/4]

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
	)

get_cterminal_peptide_bond_reference_frame() [2/4]

Xform core::pose::motif::get_cterminal_peptide_bond_reference_frame	(	Pose const &	p,
		numeric::Size const &	i
	)

References a(), get_cterminal_peptide_bond_reference_frame(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_upper_terminus(), and core::pose::Pose::residue().

get_cterminal_peptide_bond_reference_frame() [3/4]

numeric::xyzTransform<core::Real> core::pose::motif::get_cterminal_peptide_bond_reference_frame	(	Pose const &	pose,
		core::Size const &	ir
	)

get_cterminal_peptide_bond_reference_frame() [4/4]

Xform core::pose::motif::get_cterminal_peptide_bond_reference_frame	(	xyzVector< Real > const &	O,
		xyzVector< Real > const &	C,
		xyzVector< Real > const &	CA
	)

References core::chemical::element::C, protocols::frag_picker::CA, and core::chemical::element::O.

Referenced by get_cterminal_peptide_bond_reference_frame(), get_peptide_bond_reference_frame(), core::scoring::motif::get_residue_pair_xform(), and core::scoring::motif::set_residue_pair_xform().

get_cterminal_peptide_bond_reference_frame_atomids() [1/2]

AIDs core::pose::motif::get_cterminal_peptide_bond_reference_frame_atomids	(	Pose const &	p,
		numeric::Size const &	i,
		bool	extra
	)

References core::conformation::Residue::atom_index(), get_AIDs(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_upper_terminus(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by core::scoring::motif::align_motif_pose_super(), core::scoring::motif::get_motif_atom_mask(), and get_peptide_bond_reference_frame_atomids().

get_cterminal_peptide_bond_reference_frame_atomids() [2/2]

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
	)

get_frame_ala() [1/2]

numeric::xyzTransform<core::Real> core::pose::motif::get_frame_ala	(	Pose const &	pose,
		core::Size const &	ir
	)

get_frame_ala() [2/2]

Xform core::pose::motif::get_frame_ala	(	PoseCR	p,
		SizeCR	i
	)

References a(), core::conformation::Residue::aa(), core::chemical::aa_ala, and core::pose::Pose::residue().

Referenced by get_sidechain_reference_frame().

get_frame_arg() [1/2]

numeric::xyzTransform<core::Real> core::pose::motif::get_frame_arg	(	Pose const &	pose,
		core::Size const &	ir
	)

get_frame_arg() [2/2]

Xform core::pose::motif::get_frame_arg	(	PoseCR	p,
		SizeCR	i
	)

References a(), core::conformation::Residue::aa(), core::chemical::aa_arg, and core::pose::Pose::residue().

Referenced by get_sidechain_reference_frame().

get_frame_asn() [1/2]

numeric::xyzTransform<core::Real> core::pose::motif::get_frame_asn	(	Pose const &	pose,
		core::Size const &	ir
	)

get_frame_asn() [2/2]

Xform core::pose::motif::get_frame_asn	(	PoseCR	p,
		SizeCR	i
	)

References a(), core::conformation::Residue::aa(), core::chemical::aa_asn, and core::pose::Pose::residue().

Referenced by get_sidechain_reference_frame().

get_frame_asp() [1/2]

numeric::xyzTransform<core::Real> core::pose::motif::get_frame_asp	(	Pose const &	pose,
		core::Size const &	ir
	)

get_frame_asp() [2/2]

Xform core::pose::motif::get_frame_asp	(	PoseCR	p,
		SizeCR	i
	)

References a(), core::conformation::Residue::aa(), core::chemical::aa_asp, get_frame_vee(), and core::pose::Pose::residue().

Referenced by get_sidechain_reference_frame().

get_frame_cys() [1/2]

numeric::xyzTransform<core::Real> core::pose::motif::get_frame_cys	(	Pose const &	pose,
		core::Size const &	ir
	)

get_frame_cys() [2/2]

Xform core::pose::motif::get_frame_cys	(	PoseCR	p,
		SizeCR	i
	)

References a(), core::conformation::Residue::aa(), core::chemical::aa_cys, and core::pose::Pose::residue().

Referenced by get_sidechain_reference_frame().

get_frame_gln() [1/2]

numeric::xyzTransform<core::Real> core::pose::motif::get_frame_gln	(	Pose const &	pose,
		core::Size const &	ir
	)

get_frame_gln() [2/2]

Xform core::pose::motif::get_frame_gln	(	PoseCR	p,
		SizeCR	i
	)

References a(), core::conformation::Residue::aa(), core::chemical::aa_gln, and core::pose::Pose::residue().

Referenced by get_sidechain_reference_frame().

get_frame_glu() [1/2]

numeric::xyzTransform<core::Real> core::pose::motif::get_frame_glu	(	Pose const &	pose,
		core::Size const &	ir
	)

get_frame_glu() [2/2]

Xform core::pose::motif::get_frame_glu	(	PoseCR	p,
		SizeCR	i
	)

References a(), core::conformation::Residue::aa(), core::chemical::aa_glu, get_frame_vee(), and core::pose::Pose::residue().

Referenced by get_sidechain_reference_frame().

get_frame_gly() [1/2]

numeric::xyzTransform<core::Real> core::pose::motif::get_frame_gly	(	Pose const &	pose,
		core::Size const &	ir
	)

get_frame_gly() [2/2]

Xform core::pose::motif::get_frame_gly	(	PoseCR	p,
		SizeCR	i
	)

References a(), core::conformation::Residue::aa(), core::chemical::aa_gly, and core::pose::Pose::residue().

Referenced by get_sidechain_reference_frame().

get_frame_his() [1/2]

numeric::xyzTransform<core::Real> core::pose::motif::get_frame_his	(	Pose const &	pose,
		core::Size const &	ir
	)

get_frame_his() [2/2]

Xform core::pose::motif::get_frame_his	(	PoseCR	p,
		SizeCR	i
	)

References a(), core::conformation::Residue::aa(), core::chemical::aa_his, protocols::frag_picker::CEN, and core::pose::Pose::residue().

Referenced by get_sidechain_reference_frame().

get_frame_ile() [1/2]

numeric::xyzTransform<core::Real> core::pose::motif::get_frame_ile	(	Pose const &	pose,
		core::Size const &	ir
	)

get_frame_ile() [2/2]

Xform core::pose::motif::get_frame_ile	(	PoseCR	p,
		SizeCR	i
	)

References a(), core::conformation::Residue::aa(), core::chemical::aa_ile, and core::pose::Pose::residue().

Referenced by get_sidechain_reference_frame().

get_frame_leu() [1/2]

numeric::xyzTransform<core::Real> core::pose::motif::get_frame_leu	(	Pose const &	pose,
		core::Size const &	ir
	)

get_frame_leu() [2/2]

Xform core::pose::motif::get_frame_leu	(	PoseCR	p,
		SizeCR	i
	)

References a(), core::conformation::Residue::aa(), core::chemical::aa_leu, get_frame_vee(), and core::pose::Pose::residue().

Referenced by get_sidechain_reference_frame().

get_frame_lys() [1/2]

numeric::xyzTransform<core::Real> core::pose::motif::get_frame_lys	(	Pose const &	pose,
		core::Size const &	ir
	)

get_frame_lys() [2/2]

Xform core::pose::motif::get_frame_lys	(	PoseCR	p,
		SizeCR	i
	)

References a(), core::conformation::Residue::aa(), core::chemical::aa_lys, and core::pose::Pose::residue().

Referenced by get_sidechain_reference_frame().

get_frame_met() [1/2]

numeric::xyzTransform<core::Real> core::pose::motif::get_frame_met	(	Pose const &	pose,
		core::Size const &	ir
	)

get_frame_met() [2/2]

Xform core::pose::motif::get_frame_met	(	PoseCR	p,
		SizeCR	i
	)

References a(), core::conformation::Residue::aa(), core::chemical::aa_met, and core::pose::Pose::residue().

Referenced by get_sidechain_reference_frame().

get_frame_phe() [1/2]

numeric::xyzTransform<core::Real> core::pose::motif::get_frame_phe	(	Pose const &	pose,
		core::Size const &	ir
	)

get_frame_phe() [2/2]

Xform core::pose::motif::get_frame_phe	(	PoseCR	p,
		SizeCR	i
	)

References a(), core::conformation::Residue::aa(), core::chemical::aa_phe, protocols::frag_picker::CEN, and core::pose::Pose::residue().

Referenced by get_sidechain_reference_frame().

get_frame_pro() [1/2]

numeric::xyzTransform<core::Real> core::pose::motif::get_frame_pro	(	Pose const &	pose,
		core::Size const &	ir
	)

get_frame_pro() [2/2]

Xform core::pose::motif::get_frame_pro	(	PoseCR	p,
		SizeCR	i
	)

References a(), core::conformation::Residue::aa(), core::chemical::aa_pro, and core::pose::Pose::residue().

Referenced by get_sidechain_reference_frame().

get_frame_ser() [1/2]

numeric::xyzTransform<core::Real> core::pose::motif::get_frame_ser	(	Pose const &	pose,
		core::Size const &	ir
	)

get_frame_ser() [2/2]

Xform core::pose::motif::get_frame_ser	(	PoseCR	p,
		SizeCR	i
	)

References a(), core::conformation::Residue::aa(), core::chemical::aa_ser, and core::pose::Pose::residue().

Referenced by get_sidechain_reference_frame().

get_frame_thr() [1/2]

numeric::xyzTransform<core::Real> core::pose::motif::get_frame_thr	(	Pose const &	pose,
		core::Size const &	ir
	)

get_frame_thr() [2/2]

Xform core::pose::motif::get_frame_thr	(	PoseCR	p,
		SizeCR	i
	)

References a(), core::conformation::Residue::aa(), core::chemical::aa_thr, and core::pose::Pose::residue().

Referenced by get_sidechain_reference_frame().

get_frame_trp() [1/2]

numeric::xyzTransform<core::Real> core::pose::motif::get_frame_trp	(	Pose const &	pose,
		core::Size const &	ir
	)

get_frame_trp() [2/2]

Xform core::pose::motif::get_frame_trp	(	PoseCR	p,
		SizeCR	i
	)

References a(), core::conformation::Residue::aa(), core::chemical::aa_trp, protocols::frag_picker::CEN, and core::pose::Pose::residue().

Referenced by get_sidechain_reference_frame().

get_frame_tyr() [1/2]

numeric::xyzTransform<core::Real> core::pose::motif::get_frame_tyr	(	Pose const &	pose,
		core::Size const &	ir
	)

get_frame_tyr() [2/2]

Xform core::pose::motif::get_frame_tyr	(	PoseCR	p,
		SizeCR	i
	)

References a(), core::conformation::Residue::aa(), core::chemical::aa_tyr, protocols::frag_picker::CEN, and core::pose::Pose::residue().

Referenced by get_sidechain_reference_frame().

get_frame_val() [1/2]

numeric::xyzTransform<core::Real> core::pose::motif::get_frame_val	(	Pose const &	pose,
		core::Size const &	ir
	)

get_frame_val() [2/2]

Xform core::pose::motif::get_frame_val	(	PoseCR	p,
		SizeCR	i
	)

References a(), core::conformation::Residue::aa(), core::chemical::aa_val, get_frame_vee(), and core::pose::Pose::residue().

Referenced by get_sidechain_reference_frame().

get_frame_vee()

Xform core::pose::motif::get_frame_vee	(	Vec const &	a,
		Vec const &	b,
		Vec const &	c
	)

References a(), protocols::match::upstream::b, and protocols::frag_picker::CEN.

Referenced by get_frame_asp(), get_frame_glu(), get_frame_leu(), and get_frame_val().

get_nterminal_peptide_bond_reference_frame() [1/4]

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
	)

get_nterminal_peptide_bond_reference_frame() [2/4]

Xform core::pose::motif::get_nterminal_peptide_bond_reference_frame	(	Pose const &	p,
		numeric::Size const &	i
	)

References a(), core::conformation::Residue::aa(), core::chemical::aa_pro, get_nterminal_peptide_bond_reference_frame(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_protein(), and core::pose::Pose::residue().

get_nterminal_peptide_bond_reference_frame() [3/4]

numeric::xyzTransform<core::Real> core::pose::motif::get_nterminal_peptide_bond_reference_frame	(	Pose const &	pose,
		core::Size const &	ir
	)

get_nterminal_peptide_bond_reference_frame() [4/4]

Xform core::pose::motif::get_nterminal_peptide_bond_reference_frame	(	xyzVector< Real > const &	H,
		xyzVector< Real > const &	N,
		xyzVector< Real > const &	CA
	)

References protocols::frag_picker::CA, core::chemical::element::H, and core::chemical::element::N.

Referenced by get_nterminal_peptide_bond_reference_frame(), get_peptide_bond_reference_frame(), core::scoring::motif::get_residue_pair_xform(), and core::scoring::motif::set_residue_pair_xform().

get_nterminal_peptide_bond_reference_frame_atomids() [1/2]

AIDs core::pose::motif::get_nterminal_peptide_bond_reference_frame_atomids	(	Pose const &	p,
		numeric::Size const &	i,
		bool	extra
	)

References core::conformation::Residue::aa(), core::chemical::aa_pro, core::conformation::Residue::atom_index(), get_AIDs(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_protein(), and core::pose::Pose::residue().

Referenced by core::scoring::motif::align_motif_pose_super(), core::scoring::motif::get_motif_atom_mask(), and get_peptide_bond_reference_frame_atomids().

get_nterminal_peptide_bond_reference_frame_atomids() [2/2]

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
	)

get_peptide_bond_reference_frame()

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

References get_cterminal_peptide_bond_reference_frame(), and get_nterminal_peptide_bond_reference_frame().

get_peptide_bond_reference_frame_atomids()

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

References get_cterminal_peptide_bond_reference_frame_atomids(), and get_nterminal_peptide_bond_reference_frame_atomids().

get_sidechain_reference_frame() [1/2]

Xform core::pose::motif::get_sidechain_reference_frame	(	Pose const &	p,
		numeric::Size const &	i
	)

References core::conformation::Residue::aa(), core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_cys, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_gly, core::chemical::aa_his, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_ser, core::chemical::aa_thr, core::chemical::aa_trp, core::chemical::aa_tyr, core::chemical::aa_val, 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::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by core::scoring::motif::get_residue_pair_xform(), and core::scoring::motif::set_residue_pair_xform().

get_sidechain_reference_frame() [2/2]

numeric::xyzTransform<core::Real> core::pose::motif::get_sidechain_reference_frame	(	Pose const &	pose,
		core::Size const &	ir
	)

get_sidechain_reference_frame_atomids()

utility::vector1< core::id::AtomID > core::pose::motif::get_sidechain_reference_frame_atomids	(	Pose const &	pose,
		core::Size const &	ir
	)

References core::conformation::Residue::aa(), core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_cys, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_gly, core::chemical::aa_his, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_ser, core::chemical::aa_thr, core::chemical::aa_trp, core::chemical::aa_tyr, core::chemical::aa_val, get_atoms_ala(), get_atoms_arg(), get_atoms_asn(), get_atoms_asp(), get_atoms_cys(), get_atoms_gln(), get_atoms_glu(), get_atoms_gly(), get_atoms_his(), get_atoms_ile(), get_atoms_leu(), get_atoms_lys(), get_atoms_met(), get_atoms_phe(), get_atoms_pro(), get_atoms_ser(), get_atoms_thr(), get_atoms_trp(), get_atoms_tyr(), get_atoms_val(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by core::scoring::motif::align_motif_pose_super(), and core::scoring::motif::get_motif_atom_mask().

get_sidechain_reference_frame_atomids_with_downstream()

utility::vector1< core::id::AtomID > core::pose::motif::get_sidechain_reference_frame_atomids_with_downstream	(	Pose const &	pose,
		core::Size const &	ir
	)

References core::conformation::Residue::aa(), core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_cys, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_gly, core::chemical::aa_his, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_ser, core::chemical::aa_thr, core::chemical::aa_trp, core::chemical::aa_tyr, core::chemical::aa_val, get_atoms_ala_downstream(), get_atoms_arg_downstream(), get_atoms_asn_downstream(), get_atoms_asp_downstream(), get_atoms_cys_downstream(), get_atoms_gln_downstream(), get_atoms_glu_downstream(), get_atoms_gly_downstream(), get_atoms_his_downstream(), get_atoms_ile_downstream(), get_atoms_leu_downstream(), get_atoms_lys_downstream(), get_atoms_met_downstream(), get_atoms_phe_downstream(), get_atoms_pro_downstream(), get_atoms_ser_downstream(), get_atoms_thr_downstream(), get_atoms_trp_downstream(), get_atoms_tyr_downstream(), get_atoms_val_downstream(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by core::scoring::motif::get_motif_atom_mask().