core::id::AtomID Class Reference

Atom identifier class. Defined by the atom number and the residue number. More...

#include <AtomID.hh>

Public Member Functions
constexpr	AtomID ()
	Default constructor. More...
	AtomID (AtomID const &)=default
	Copy constructor. More...
AtomID &	operator= (AtomID const &)=default
	Assignment operator. More...
	AtomID (Size const atomno_in, Size const rsd_in)
	Property constructor. More...
void	set (core::Size atomno_in, core::Size rsd_in)
	Set the value of atom and residue. More...
Size	rsd () const
	Returns the AtomID residue number. More...
Size &	rsd ()
Size	atomno () const
	Returns the AtomID atom number. More...
Size &	atomno ()
bool	valid () const
	Returns true if the AtomID is valid. More...
utility::json_spirit::Value	serialize () const
	serialize an AtomID to a json_spirit object More...
void	deserialize (utility::json_spirit::mObject data)
	deserialize a json_spirit object to an AtomID More...

Static Public Member Functions
static constexpr AtomID	BOGUS_ATOM_ID ()
static constexpr AtomID	CHAINBREAK_BOGUS_ATOM_ID ()

Private Attributes
Size	atomno_
	Atom number within the Residue. More...
Size	rsd_
	Residue number within the complex. More...

Friends
std::ostream &	operator<< (std::ostream &os, AtomID const &a)
	stream << AtomID More...
bool	operator== (AtomID const &a, AtomID const &b)
	a and b are the same atom More...
bool	operator!= (AtomID const &a, AtomID const &b)
	a and b are different atom More...
bool	operator< (AtomID const &a, AtomID const &b)
	a is LOWER than b (e.g., first by smaller residue index number then by smaller atom index number) More...

Detailed Description

Atom identifier class. Defined by the atom number and the residue number.

Constructor & Destructor Documentation

AtomID() [1/3]

constexpr core::id::AtomID::AtomID ( )

inlineconstexpr

Default constructor.

Referenced by BOGUS_ATOM_ID(), and CHAINBREAK_BOGUS_ATOM_ID().

AtomID() [2/3]

core::id::AtomID::AtomID ( AtomID const &  )

inlinedefault

Copy constructor.

AtomID() [3/3]

core::id::AtomID::AtomID ( Size const  atomno_in, Size const  rsd_in  )

inline

Property constructor.

Member Function Documentation

atomno() [1/2]

Size& core::id::AtomID::atomno ( )

inline

References atomno_.

atomno() [2/2]

Size core::id::AtomID::atomno ( ) const

inline

Returns the AtomID atom number.

References atomno_.

Referenced by protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_amide_bond_cyclic_constraints(), core::pack::scmin::AtomTreeSCMinMinimizerMap::add_atom(), protocols::simple_moves::ConstrainToIdealMover::add_bond_angle_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_dihedral_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_length_constraint(), protocols::enzdes::EnzdesConstraintReporter::add_constrained_nonligand_atom(), protocols::metal_interface::AddZincSiteConstraints::add_constraints(), protocols::stepwise::modeler::align::StepWisePoseAligner::add_coordinate_constraints_from_map(), protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), core::conformation::Conformation::append_residue_by_bond(), protocols::symmetry::SetupNCSMover::apply(), protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), protocols::backrub::BackrubMover::apply(), core::pack::scmin::AtomTreeSCMinMinimizerMap::atom(), core::pack::scmin::CartSCMinMinimizerMap::atom(), protocols::hbnet::HBNet::atom_hbonds_to_bridging_water(), core::pose::atom_id_to_named_atom_id(), core::conformation::atom_id_to_named_atom_id(), core::scoring::hbonds::HBond::atom_is_acceptor(), core::scoring::hbonds::HBond::atom_is_donorH(), core::pose::MiniPose::atom_name(), core::optimization::atom_tree_get_atompairE_deriv(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::conformation::Conformation::atom_tree_torsion(), core::id::DOF_ID::atomno(), core::conformation::Conformation::atoms_are_bonded(), core::scoring::methods::atoms_interact(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Conformation::backbone_torsion_angle_atoms_meta_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_oligourea(), core::conformation::Conformation::backbone_torsion_angle_atoms_ortho_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_para_aramid(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::backtrack(), core::conformation::Conformation::bonded_neighbor_all_res(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_acc_nbr_residue_check(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_donor_nbr_residue_check(), core::pose::toolbox::AtomID_Mapper::calculate_atom_id_map(), core::optimization::cart_numerical_derivative_check(), core::optimization::cartesian_collect_atompairE_deriv(), core::import_pose::RNA_JumpMover::check_forward_backward(), protocols::stepwise::modeler::align::StepWisePoseAligner::check_matching_atom_names(), protocols::simple_filters::SimpleHbondsToAtomFilter::compute(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_burial(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), protocols::ligand_docking::ComputeLigandRDF::compute_rdf(), protocols::backrub::connected_mainchain_atomids(), protocols::sic_dock::ConstraintSetScore::ConstraintSetScore(), protocols::cyclic_peptide::crosslinker::correct_thioether_virtuals(), protocols::constraint_generator::DistanceConstraintGenerator::create_constraint(), protocols::constraint_generator::CoordinateConstraintGenerator::create_coordinate_constraint(), protocols::cartesian::MolecularDynamics::createDihedral(), protocols::md::CartesianMD::cst_on_pose_dynamic(), core::conformation::Conformation::debug_residue_torsions(), core::scoring::NeighborList::declare_atom_neighbor_1sided(), core::scoring::NeighborList::declare_atoms_neighbors(), core::scoring::MultipoleElecPotential::determine_polarization_groups(), core::select::util::determine_whether_point_is_buried(), protocols::electron_density::BfactorMultifunc::dfunc(), protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc(), core::pack::scmin::CartSCMinMultifunc::dfunc(), core::scoring::constraints::AtomPairConstraint::dist(), core::scoring::constraints::AtomToAxisConstraint::dist(), protocols::md::CartesianMD::do_initialize(), core::energy_methods::FaMPEnvSmoothEnergy::eval_atom_derivative(), protocols::membrane::scoring::FaWaterToBilayerEnergy::eval_atom_derivative(), core::energy_methods::HolesEnergy::eval_atom_derivative(), core::energy_methods::SurfEnergy::eval_atom_derivative(), core::energy_methods::SurfVolEnergy::eval_atom_derivative(), core::scoring::packing::HolesEnergyRes::eval_atom_derivative(), core::energy_methods::EnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::NPDHBondEnergy::eval_atom_derivative(), core::energy_methods::CustomAtomPairEnergy::eval_atom_derivative(), core::energy_methods::DNA_BaseEnergy::eval_atom_derivative(), core::energy_methods::FA_ElecEnergyAroAll::eval_atom_derivative(), core::energy_methods::FA_ElecEnergyAroAro::eval_atom_derivative(), core::energy_methods::RG_Energy_RNA::eval_atom_derivative(), core::energy_methods::RNA_FA_ElecEnergy::eval_atom_derivative(), core::energy_methods::StackElecEnergy::eval_atom_derivative(), core::energy_methods::HackAroEnergy::eval_atom_derivative(), core::energy_methods::HybridVDW_Energy::eval_atom_derivative(), core::energy_methods::RNA_DataBackboneEnergy::eval_atom_derivative(), core::energy_methods::RNA_VDW_Energy::eval_atom_derivative(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergy::eval_atom_derivative(), core::scoring::vdwaals::VDW_Energy::eval_atom_derivative(), core::energy_methods::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::energy_methods::Fa_MbenvEnergy::eval_atom_derivative(), core::energy_methods::FaMPEnvEnergy::eval_atom_derivative(), core::energy_methods::ChemicalShiftAnisotropyEnergy::eval_atom_derivative(), core::energy_methods::DipolarCouplingEnergy::eval_atom_derivative(), core::energy_methods::Fa_MbsolvEnergy::eval_atom_derivative(), core::energy_methods::FaMPSolvEnergy::eval_atom_derivative(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative(), core::energy_methods::ResidualDipolarCouplingEnergy::eval_atom_derivative(), core::energy_methods::RNA_LJ_BaseEnergy::eval_atom_derivative(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative_intra_RNA(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_backbone_backbone(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_base_backbone(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_repulsive(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_atom_energy(), core::energy_methods::RNA_LJ_BaseEnergy::eval_atom_energy(), core::energy_methods::DNA_DihedralEnergy::eval_residue_pair_derivatives(), protocols::metal_interface::AddZincSiteConstraints::evaluate_constraints(), core::pose::copydofs::CopyDofs::figure_out_dofs(), core::conformation::Conformation::fill_missing_atoms(), core::util::find_metalbinding_atoms_helper(), protocols::hbnet::HBNet::find_unsats(), protocols::cartesian::MolecularDynamics::findCartomAtom(), protocols::abinitio::abscript::fix_internal_coords_of_siblings(), protocols::topology_broker::fix_internal_coords_of_siblings(), protocols::loops::fix_with_coord_cst(), protocols::topology_broker::CoordConstraintClaimer::generate_constraints(), core::pack::scmin::CartSCMinMinimizerMap::get_atom_index(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), core::conformation::Conformation::get_torsion_angle_atom_ids(), protocols::helical_bundle_predict::HBPHelix::get_torsions_for_helix(), protocols::magnesium::MgHydrater::hydrate_magnesium_in_pose(), protocols::magnesium::MgHydrater::hydrate_magnesium_with_orbital_frame(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), protocols::rna::movers::ErraserMinimizerMover::i_want_this_atom_to_move(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::pose::is_atom_axial_or_equatorial_to_ring(), core::pose::rna::is_torsion_valid(), core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup(), core::energy_methods::IdealParametersDatabase::lookup_torsion_legacy(), protocols::electron_density::BfactorMultifunc::multivec2poseBfacts(), protocols::cryst::ReportGradientsMover::normalization(), core::energy_methods::FullatomDisulfideEnergy::old_eval_atom_derivative(), protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction::operator()(), protocols::sic_dock::AtomIDHashFunction::operator()(), protocols::branch_angle::BranchAngleOptimizer::optimize_angles(), protocols::metal_interface::AddZincSiteConstraints::output_constraints_file(), protocols::branch_angle::BranchAngleOptimizer::overall_params(), protocols::branch_angle::BranchAngleOptimizer::param1(), protocols::branch_angle::BranchAngleOptimizer::param2(), core::scoring::per_res_rms_at_corresponding_atoms_no_super(), protocols::electron_density::BfactorMultifunc::poseBfacts2multivec(), core::scoring::NeighborList::prepare_for_scoring(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::print_atom_info(), protocols::stepwise::modeler::rna::print_torsion_info(), core::pose::rna::print_torsion_info(), protocols::hbnet::HBNet::quick_and_dirty_heavy_atom_is_unsat(), core::scoring::constraints::CoordinateConstraint::read_def(), core::scoring::constraints::AngleConstraint::read_def(), core::scoring::constraints::AtomPairConstraint::read_def(), core::scoring::constraints::DihedralConstraint::read_def(), core::scoring::constraints::DihedralPairConstraint::read_def(), core::scoring::constraints::DistancePairConstraint::read_def(), core::scoring::constraints::NamedAngleConstraint::read_def(), core::scoring::constraints::NamedDihedralConstraint::read_def(), core::scoring::constraints::AngleConstraint::remap_resid(), core::scoring::constraints::AtomPairConstraint::remap_resid(), core::scoring::constraints::CoordinateConstraint::remap_resid(), core::scoring::constraints::DihedralConstraint::remap_resid(), core::scoring::constraints::DihedralPairConstraint::remap_resid(), core::scoring::constraints::DistancePairConstraint::remap_resid(), core::scoring::constraints::LocalCoordinateConstraint::remap_resid(), core::kinematics::AtomTree::replace_residue_subtree(), serialize(), core::conformation::symmetry::SymmetricConformation::set_bond_angle(), core::conformation::symmetry::SymmetricConformation::set_bond_length(), core::scoring::nmr::NMRGridSearch::set_grid_search_center(), core::conformation::symmetry::MirrorSymmetricConformation::set_torsion_angle(), core::conformation::symmetry::SymmetricConformation::set_torsion_angle(), protocols::cyclic_peptide::crosslinker::set_up_thioether_constraints(), protocols::md::Rattle::setup_constraint(), core::scoring::constraints::AtomPairConstraint::show(), core::scoring::constraints::AtomToAxisConstraint::show(), core::scoring::constraints::CoordinateConstraint::show(), core::scoring::constraints::LocalCoordinateConstraint::show(), core::scoring::constraints::AngleConstraint::show_violations(), core::scoring::constraints::AtomPairConstraint::show_violations(), core::scoring::constraints::CoordinateConstraint::show_violations(), core::scoring::constraints::DihedralConstraint::show_violations(), core::scoring::constraints::DihedralPairConstraint::show_violations(), core::scoring::constraints::DistancePairConstraint::show_violations(), core::scoring::constraints::LocalCoordinateConstraint::show_violations(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::single_bunsat_thorough_check(), protocols::noesy_assign::store_distmap_with_namedatoms(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::three_body_approximate_buried_unsat_calculation(), core::kinematics::AtomTree::torsion_angle_dof_id(), core::import_pose::libraries::RNA_ChunkLibrary::update_atom_level_domain_map(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf(), core::scoring::NeighborList::update_from_wide_nblist(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligand_conf(), protocols::magnesium::update_mg_hoh_fold_tree(), protocols::backrub::BackrubSidechainMover::update_segments(), protocols::simple_moves::ConstrainToIdealMover::vary_bond_geometry(), protocols::metal_interface::AddZincSiteConstraints::view_constraints_in_pymol(), protocols::viewer::visit_atomtree_node(), and core::pose::MiniPose::xyz().

BOGUS_ATOM_ID()

static constexpr AtomID core::id::AtomID::BOGUS_ATOM_ID ( )

inlinestaticconstexpr

References AtomID().

Referenced by protocols::loops::addScoresForLoopParts(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::align_and_calculate_rmsd(), protocols::hybridization::HybridizeProtocol::align_by_domain(), protocols::helical_bundle::align_mainchain_atoms(), protocols::helical_bundle::align_mainchain_atoms_of_residue_range(), core::scoring::motif::align_motif_pose_NCAC_super(), core::scoring::motif::align_motif_pose_super(), core::import_pose::libraries::RNA_ChunkLibrary::align_to_chunk(), protocols::antibody_legacy::Antibody::align_to_native(), protocols::antibody::align_to_native(), protocols::helical_bundle_predict::HelicalBundlePredictApplication::align_to_native_pose(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::align_with_offset(), protocols::helical_bundle::FitSimpleHelix::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), core::chemical::ICoorAtomID::atom_id(), protocols::symmetric_docking::SymDockProtocol::calc_Irms(), core::scoring::calpha_superimpose_pose(), core::sequence::calpha_superimpose_with_mapping(), protocols::antibody::cdr_backbone_rmsds(), protocols::electron_density::DockPDBIntoDensityMover::compare_and_align_poses(), core::pose::convert_from_std_map(), protocols::stepwise::modeler::rna::create_alignment_id_map_legacy(), protocols::helical_bundle::FitSimpleHelixMultiFunc::dfunc(), core::conformation::Conformation::fill_missing_atoms(), protocols::simple_moves::RepeatPropagationMover::generate_overlap(), protocols::pose_creation::MergePDBMover::generate_overlaps(), core::pose::motif::get_AIDs(), core::pose::motif::get_backbone_reference_frame_atomids(), protocols::hybridization::InsertChunkMover::get_local_sequence_mapping(), core::conformation::get_residue_connections(), protocols::loops::loop_rmsd_with_superimpose_core(), protocols::pose_creation::MergePDBatOverlapMover::merge_poses(), protocols::tcr::orient_tcr_chain(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), core::conformation::Residue::resolve_partial_atom_id(), protocols::hybridization::DomainAssembly::run(), protocols::simple_moves::SuperimposeMover::superimpose(), protocols::fldsgn::MatchResidues::superimpose_comb(), protocols::grafting::superimpose_overhangs_heavy(), core::scoring::superimpose_polymer_heavyatoms(), protocols::fibril::superimpose_pose_on_subset_bb(), protocols::toolbox::pose_manipulation::superimpose_pose_on_subset_CA(), protocols::hybridization::FoldTreeHybridize::superimpose_strand_pairings_to_templates(), protocols::simple_moves::SuperimposeMover::superimposebb(), protocols::docking::ConformerSwitchMover::switch_conformer(), protocols::hybridization::TMalign_poses(), protocols::hybridization::update_atom_map(), and core::chemical::ICoorAtomID::xyz().

CHAINBREAK_BOGUS_ATOM_ID()

static constexpr AtomID core::id::AtomID::CHAINBREAK_BOGUS_ATOM_ID ( )

inlinestaticconstexpr

References AtomID().

deserialize()

void core::id::AtomID::deserialize ( utility::json_spirit::mObject  data )

inline

deserialize a json_spirit object to an AtomID

References atomno_, and rsd_.

Referenced by core::scoring::nmr::pcs::PCSSingle::deserialize(), core::scoring::nmr::pre::PRESingle::deserialize(), and core::scoring::nmr::rdc::RDCSingle::deserialize().

operator=()

AtomID& core::id::AtomID::operator= ( AtomID const &  )

inlinedefault

Assignment operator.

rsd() [1/2]

Size& core::id::AtomID::rsd ( )

inline

References rsd_.

rsd() [2/2]

Size core::id::AtomID::rsd ( ) const

inline

Returns the AtomID residue number.

References rsd_.

Referenced by protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::add_amide_bond_cyclic_constraints(), protocols::simple_moves::ConstrainToIdealMover::add_bond_angle_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_dihedral_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_length_constraint(), protocols::enzdes::EnzdesConstraintReporter::add_constrained_nonligand_atom(), protocols::metal_interface::AddZincSiteConstraints::add_constraints(), protocols::stepwise::modeler::align::StepWisePoseAligner::add_coordinate_constraints_from_map(), core::scoring::constraints::MultiConstraint::add_individual_constraint(), protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), protocols::simple_moves::AddCavitiesMover::add_suckers(), core::scoring::MultipoleElecPotential::align_residue_multipole_axes(), protocols::backrub::BackrubSidechainMover::apply(), protocols::constraint_generator::CoordinateConstraintGenerator::apply(), protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), protocols::backrub::BackrubMover::apply(), protocols::environment::EnvMover::apply(), core::pack::scmin::AtomTreeSCMinMinimizerMap::atom(), core::pack::scmin::CartSCMinMinimizerMap::atom(), protocols::hbnet::HBNet::atom_hbonds_to_bridging_water(), core::pose::atom_id_to_named_atom_id(), core::conformation::atom_id_to_named_atom_id(), core::scoring::hbonds::HBond::atom_is_acceptor(), core::scoring::hbonds::HBond::atom_is_donorH(), core::pose::MiniPose::atom_name(), core::optimization::atom_tree_get_atompairE_deriv(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::conformation::Conformation::atom_tree_torsion(), core::conformation::Conformation::atoms_are_bonded(), core::scoring::methods::atoms_interact(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Conformation::backbone_torsion_angle_atoms_meta_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_oligourea(), core::conformation::Conformation::backbone_torsion_angle_atoms_ortho_aramid(), core::conformation::Conformation::backbone_torsion_angle_atoms_para_aramid(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::backtrack(), protocols::environment::bond_angles(), protocols::environment::bond_lengths(), core::conformation::Conformation::bonded_neighbor_all_res(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_acc_nbr_residue_check(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_donor_nbr_residue_check(), core::pose::toolbox::AtomID_Mapper::calculate_atom_id_map(), core::optimization::cart_numerical_derivative_check(), core::optimization::cartesian_collect_atompairE_deriv(), core::import_pose::RNA_JumpMover::check_forward_backward(), protocols::simple_moves::ConstrainToIdealMover::check_if_really_connected(), core::scoring::rna::RNA_TorsionPotential::check_intra_residue(), protocols::stepwise::modeler::align::StepWisePoseAligner::check_matching_atom_names(), protocols::simple_filters::SimpleHbondsToAtomFilter::compute(), core::scoring::packstat::LeeRichards::compute(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), protocols::ligand_docking::ComputeLigandRDF::compute_rdf(), protocols::backrub::connected_mainchain_atomids(), protocols::sic_dock::ConstraintSetScore::ConstraintSetScore(), protocols::cartesian::MolecularDynamics::createDihedral(), protocols::md::CartesianMD::cst_on_pose_dynamic(), core::conformation::Conformation::debug_residue_torsions(), core::scoring::NeighborList::declare_atom_neighbor_1sided(), core::scoring::NeighborList::declare_atoms_neighbors(), core::scoring::constraints::ConstraintSet::deprecated_eval_atom_derivative(), core::scoring::constraints::ConstraintSet::deprecated_eval_atom_derivative_for_residue_pairs(), core::scoring::MultipoleElecPotential::determine_polarization_groups(), protocols::electron_density::BfactorMultifunc::dfunc(), protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc(), core::pack::scmin::CartSCMinMultifunc::dfunc(), core::scoring::constraints::AtomPairConstraint::dist(), core::scoring::constraints::AtomToAxisConstraint::dist(), protocols::md::CartesianMD::do_initialize(), protocols::ligand_docking::ga_ligand_dock::GridScorer::dof_derivative(), core::scoring::constraints::AtomPairConstraint::effective_sequence_separation(), core::energy_methods::FaMPEnvSmoothEnergy::eval_atom_derivative(), protocols::membrane::scoring::FaWaterToBilayerEnergy::eval_atom_derivative(), core::energy_methods::HolesEnergy::eval_atom_derivative(), core::energy_methods::MPSpanAngleEnergy::eval_atom_derivative(), core::energy_methods::MPSpanInsertionEnergy::eval_atom_derivative(), core::energy_methods::SurfEnergy::eval_atom_derivative(), core::energy_methods::SurfVolEnergy::eval_atom_derivative(), core::scoring::packing::HolesEnergyRes::eval_atom_derivative(), core::energy_methods::MPHelicalityEnergy::eval_atom_derivative(), core::energy_methods::MPResidueLipophilicityEnergy::eval_atom_derivative(), core::energy_methods::EnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::energy_methods::NPDHBondEnergy::eval_atom_derivative(), core::energy_methods::CustomAtomPairEnergy::eval_atom_derivative(), core::energy_methods::DNA_BaseEnergy::eval_atom_derivative(), core::energy_methods::FA_ElecEnergyAroAll::eval_atom_derivative(), core::energy_methods::FA_ElecEnergyAroAro::eval_atom_derivative(), core::energy_methods::RG_Energy_RNA::eval_atom_derivative(), core::energy_methods::RNA_FA_ElecEnergy::eval_atom_derivative(), core::energy_methods::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::energy_methods::StackElecEnergy::eval_atom_derivative(), core::energy_methods::HackAroEnergy::eval_atom_derivative(), core::energy_methods::HybridVDW_Energy::eval_atom_derivative(), core::energy_methods::RNA_DataBackboneEnergy::eval_atom_derivative(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::eval_atom_derivative(), core::energy_methods::RNA_VDW_Energy::eval_atom_derivative(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergy::eval_atom_derivative(), core::scoring::vdwaals::VDW_Energy::eval_atom_derivative(), core::energy_methods::Fa_MbenvEnergy::eval_atom_derivative(), core::energy_methods::FaMPEnvEnergy::eval_atom_derivative(), core::energy_methods::ChemicalShiftAnisotropyEnergy::eval_atom_derivative(), core::energy_methods::DipolarCouplingEnergy::eval_atom_derivative(), core::energy_methods::Fa_MbsolvEnergy::eval_atom_derivative(), core::energy_methods::FaMPSolvEnergy::eval_atom_derivative(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative(), core::energy_methods::ResidualDipolarCouplingEnergy::eval_atom_derivative(), core::energy_methods::RNA_LJ_BaseEnergy::eval_atom_derivative(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base(), core::energy_methods::LK_PolarNonPolarEnergy::eval_atom_derivative_intra_RNA(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_backbone_backbone(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_base_backbone(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_repulsive(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_atom_energy(), core::energy_methods::RNA_LJ_BaseEnergy::eval_atom_energy(), core::scoring::ScoreFunction::eval_dof_derivative(), protocols::metal_interface::AddZincSiteConstraints::evaluate_constraints(), protocols::environment::EXCN_Env_Security_Exception::EXCN_Env_Security_Exception(), core::pose::copydofs::CopyDofs::figure_out_dofs(), core::util::find_metalbinding_atoms_helper(), protocols::hbnet::HBNet::find_unsats(), protocols::cartesian::MolecularDynamics::findCartomAtom(), protocols::abinitio::abscript::fix_internal_coords_of_siblings(), protocols::topology_broker::fix_internal_coords_of_siblings(), core::pack::scmin::CartSCMinMinimizerMap::get_atom_index(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_deriv_for_chemical_shift(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), core::conformation::Conformation::get_torsion_angle_atom_ids(), protocols::helical_bundle_predict::HBPHelix::get_torsions_for_helix(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_conect_records_for_atom(), protocols::magnesium::MgHydrater::hydrate_magnesium_in_pose(), protocols::magnesium::MgHydrater::hydrate_magnesium_with_orbital_frame(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), protocols::rna::movers::ErraserMinimizerMover::i_want_this_atom_to_move(), protocols::kinematic_closure::ClosureProblem::ids_span_cut(), protocols::simple_moves::DOFHistogramRecorder::insert_dofs_by_residue(), core::pose::is_atom_axial_or_equatorial_to_ring(), core::conformation::Conformation::is_bonded(), core::pose::rna::is_torsion_valid(), core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup(), core::kinematics::ResidueCoordinateChangeList::mark_residue_moved(), protocols::electron_density::BfactorMultifunc::multivec2poseBfacts(), protocols::cryst::ReportGradientsMover::normalization(), core::energy_methods::FullatomDisulfideEnergy::old_eval_atom_derivative(), protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction::operator()(), protocols::sic_dock::AtomIDHashFunction::operator()(), protocols::branch_angle::BranchAngleOptimizer::optimize_angles(), protocols::metal_interface::AddZincSiteConstraints::output_constraints_file(), protocols::branch_angle::BranchAngleOptimizer::overall_params(), protocols::branch_angle::BranchAngleOptimizer::param1(), protocols::branch_angle::BranchAngleOptimizer::param2(), core::scoring::per_res_rms_at_corresponding_atoms_no_super(), protocols::electron_density::BfactorMultifunc::poseBfacts2multivec(), core::scoring::NeighborList::prepare_for_scoring(), protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::print_atom_info(), protocols::stepwise::modeler::rna::print_torsion_info(), core::pose::rna::print_torsion_info(), protocols::hbnet::HBNet::quick_and_dirty_heavy_atom_is_unsat(), core::scoring::constraints::AngleConstraint::remap_resid(), core::scoring::constraints::AtomPairConstraint::remap_resid(), core::scoring::constraints::CoordinateConstraint::remap_resid(), core::scoring::constraints::DihedralConstraint::remap_resid(), core::scoring::constraints::DihedralPairConstraint::remap_resid(), core::scoring::constraints::DistancePairConstraint::remap_resid(), core::scoring::constraints::LocalCoordinateConstraint::remap_resid(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::remapped_clone(), core::scoring::constraints::AngleConstraint::remapped_clone(), core::scoring::constraints::AtomPairConstraint::remapped_clone(), core::scoring::constraints::AtomToAxisConstraint::remapped_clone(), core::scoring::constraints::BackboneStubConstraint::remapped_clone(), core::scoring::constraints::BackboneStubLinearConstraint::remapped_clone(), core::scoring::constraints::CoordinateConstraint::remapped_clone(), core::scoring::constraints::DihedralConstraint::remapped_clone(), core::scoring::constraints::DihedralPairConstraint::remapped_clone(), core::scoring::constraints::DistancePairConstraint::remapped_clone(), core::scoring::constraints::LocalCoordinateConstraint::remapped_clone(), core::scoring::constraints::NamedAngleConstraint::remapped_clone(), core::scoring::constraints::NamedAtomPairConstraint::remapped_clone(), core::scoring::constraints::RTConstraint::remapped_clone(), core::kinematics::AtomTree::replace_residue_subtree(), core::id::DOF_ID::rsd(), serialize(), core::conformation::Conformation::set_bond_angle(), core::conformation::symmetry::SymmetricConformation::set_bond_angle(), core::conformation::Conformation::set_bond_length(), core::conformation::symmetry::SymmetricConformation::set_bond_length(), core::scoring::nmr::NMRGridSearch::set_grid_search_center(), core::conformation::Conformation::set_torsion_angle(), core::conformation::symmetry::MirrorSymmetricConformation::set_torsion_angle(), core::conformation::symmetry::SymmetricConformation::set_torsion_angle(), protocols::cyclic_peptide::crosslinker::set_up_thioether_constraints(), core::conformation::symmetry::SymmetricConformation::set_xyz(), protocols::md::Rattle::setup_constraint(), core::scoring::constraints::AtomPairConstraint::show(), core::scoring::constraints::AtomToAxisConstraint::show(), core::scoring::constraints::CoordinateConstraint::show(), core::scoring::constraints::LocalCoordinateConstraint::show(), core::scoring::constraints::AngleConstraint::show_violations(), core::scoring::constraints::AtomPairConstraint::show_violations(), core::scoring::constraints::CoordinateConstraint::show_violations(), core::scoring::constraints::DihedralConstraint::show_violations(), core::scoring::constraints::DihedralPairConstraint::show_violations(), core::scoring::constraints::DistancePairConstraint::show_violations(), core::scoring::constraints::LocalCoordinateConstraint::show_violations(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::single_bunsat_thorough_check(), protocols::noesy_assign::store_distmap_with_namedatoms(), core::scoring::hbonds::NPDHBondSet::sum_dEtot_dEhb_for_atom(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::three_body_approximate_buried_unsat_calculation(), core::kinematics::AtomTree::torsion_angle_dof_id(), core::kinematics::tree::Atom_::update_domain_map(), core::scoring::NeighborList::update_from_wide_nblist(), protocols::magnesium::update_mg_hoh_fold_tree(), protocols::backrub::BackrubSidechainMover::update_segments(), protocols::simple_moves::ConstrainToIdealMover::vary_bond_geometry(), protocols::metal_interface::AddZincSiteConstraints::view_constraints_in_pymol(), protocols::viewer::visit_atomtree_node(), and core::pose::MiniPose::xyz().

serialize()

utility::json_spirit::Value core::id::AtomID::serialize ( ) const

inline

serialize an AtomID to a json_spirit object

References atomno(), atomno_, rsd(), and rsd_.

set()

void core::id::AtomID::set	(	core::Size	atomno_in,
		core::Size	rsd_in
	)

Set the value of atom and residue.

References atomno_, and rsd_.

valid()

bool core::id::AtomID::valid ( ) const

inline

Returns true if the AtomID is valid.

Note

must return false for BOGUS_ATOM_ID

References atomno_, and rsd_.

Referenced by protocols::simple_filters::JumpEvaluator::apply(), protocols::hybridization::atom_map_valid_size(), protocols::hybridization::get_superposition_transformation(), core::scoring::constraints::LocalCoordinateConstraint::LocalCoordinateConstraint(), core::scoring::constraints::Obsolet_NamedAtomPairConstraint::mapto(), protocols::hybridization::natom_aligned(), core::scoring::constraints::LocalCoordinateConstraint::read_def(), core::scoring::constraints::AtomPairConstraint::read_def(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::remap_resid(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::remapped_clone(), core::scoring::constraints::AngleConstraint::remapped_clone(), core::scoring::constraints::AtomPairConstraint::remapped_clone(), core::scoring::constraints::CoordinateConstraint::remapped_clone(), core::scoring::constraints::DihedralConstraint::remapped_clone(), core::scoring::constraints::DihedralPairConstraint::remapped_clone(), core::scoring::constraints::DistancePairConstraint::remapped_clone(), core::scoring::constraints::LocalCoordinateConstraint::remapped_clone(), core::scoring::constraints::NamedAngleConstraint::remapped_clone(), core::scoring::constraints::NamedAtomPairConstraint::remapped_clone(), core::scoring::constraints::NamedDihedralConstraint::remapped_clone(), core::scoring::constraints::RTConstraint::remapped_clone(), core::kinematics::AtomTree::replace_residue_subtree(), core::scoring::nmr::NMRGridSearch::set_grid_search_center(), core::scoring::constraints::FabConstraint::setup_csts(), core::scoring::constraints::SiteConstraint::setup_csts(), core::scoring::constraints::SiteConstraintResidues::setup_csts(), core::conformation::stub_id_to_named_stub_id(), core::pose::stub_id_to_named_stub_id(), protocols::hybridization::update_atom_map(), core::id::StubID::valid(), and core::id::DOF_ID::valid().

Friends And Related Function Documentation

operator!=

bool operator!= ( AtomID const &  a, AtomID const &  b  )

friend

a and b are different atom

operator<

bool operator< ( AtomID const &  a, AtomID const &  b  )

friend

a is LOWER than b (e.g., first by smaller residue index number then by smaller atom index number)

operator<<

std::ostream& operator<< ( std::ostream &  os, AtomID const &  a  )

friend

stream << AtomID

operator==

bool operator== ( AtomID const &  a, AtomID const &  b  )

friend

a and b are the same atom

Member Data Documentation

atomno_

Size core::id::AtomID::atomno_

private

Atom number within the Residue.

Referenced by atomno(), deserialize(), serialize(), set(), and valid().

rsd_

Size core::id::AtomID::rsd_

private

Residue number within the complex.

Referenced by deserialize(), rsd(), serialize(), set(), and valid().

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The documentation for this class was generated from the following files:

• src/core/id/AtomID.hh
• src/core/id/AtomID.cc