core::id::AtomID Class Reference

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

#include <AtomID.hh>

Collaboration diagram for core::id::AtomID:

Public Member Functions
	AtomID ()
	Default constructor. More...
	AtomID (AtomID const &src)
	Copy constructor. More...
	AtomID (Size const atomno_in, Size const rsd_in)
	Property constructor. 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...

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.

Definition at line 42 of file AtomID.hh.

Constructor & Destructor Documentation

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

inline

Default constructor.

Definition at line 49 of file AtomID.hh.

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

inline

Copy constructor.

Definition at line 56 of file AtomID.hh.

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

inline

Property constructor.

Definition at line 63 of file AtomID.hh.

Member Function Documentation

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

inline

Returns the AtomID atom number.

Definition at line 85 of file AtomID.hh.

References atomno_.

Referenced by core::pack::scmin::AtomTreeSCMinMinimizerMap::add_atom(), protocols::simple_moves::ConstrainToIdealMover::add_bond_angle_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_constraint(), protocols::enzdes::EnzdesConstraintReporter::add_constrained_nonligand_atom(), core::conformation::Conformation::append_residue_by_bond(), protocols::backrub::BackrubMover::apply(), core::pack::scmin::CartSCMinMinimizerMap::atom(), core::pack::scmin::AtomTreeSCMinMinimizerMap::atom(), 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::symmetry::atom_tree_get_atompairE_deriv(), core::optimization::atom_tree_get_atompairE_deriv(), core::id::DOF_ID::atomno(), core::scoring::methods::atoms_interact(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Conformation::bonded_neighbor_all_res(), protocols::toolbox::AllowInsert::calculate_atom_id_map(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), protocols::backrub::connected_mainchain_atomids(), core::pose::copy_dofs(), core::conformation::Conformation::debug_residue_torsions(), core::scoring::NeighborList::declare_atom_neighbor_1sided(), core::scoring::NeighborList::declare_atoms_neighbors(), core::scoring::constraints::AtomPairConstraint::dist(), core::scoring::methods::Fa_MbsolvEnergy::eval_atom_derivative(), core::scoring::rna::RNA_LJ_BaseEnergy::eval_atom_derivative(), core::scoring::methods::Fa_MbenvEnergy::eval_atom_derivative(), core::scoring::rna::RG_Energy_RNA::eval_atom_derivative(), core::scoring::packing::SurfVolEnergy::eval_atom_derivative(), core::scoring::packing::SurfEnergy::eval_atom_derivative(), core::scoring::packing::HolesEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::packing::HolesEnergyRes::eval_atom_derivative(), core::scoring::hackaro::HackAroEnergy::eval_atom_derivative(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::LK_CosThetaEnergy::eval_atom_derivative(), core::scoring::rna::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::scoring::methods::HybridVDW_Energy::eval_atom_derivative(), core::scoring::methods::DNA_BaseEnergy::eval_atom_derivative(), core::scoring::methods::VDW_Energy::eval_atom_derivative(), core::scoring::rna::RNA_DataBackboneEnergy::eval_atom_derivative(), core::scoring::rna::RNA_VDW_Energy::eval_atom_derivative(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::eval_atom_derivative(), core::scoring::methods::CustomAtomPairEnergy::eval_atom_derivative(), core::scoring::geometric_solvation::GeometricSolEnergy::eval_atom_derivative(), core::scoring::hackelec::HackElecEnergyAroAll::eval_atom_derivative(), core::scoring::hackelec::HackElecEnergyAroAro::eval_atom_derivative(), core::scoring::hackelec::RNAHackElecEnergy::eval_atom_derivative(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::eval_atom_derivative_intra_RNA(), core::scoring::geometric_solvation::GeometricSolEnergy::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::ContextIndependentGeometricSolEnergy::eval_atom_energy(), core::scoring::rna::RNA_LJ_BaseEnergy::eval_atom_energy(), core::scoring::geometric_solvation::GeometricSolEnergy::eval_atom_energy(), protocols::cartesian::MolecularDynamics::findCartomAtom(), core::pack::scmin::CartSCMinMinimizerMap::get_atom_index(), core::conformation::Conformation::get_torsion_angle_atom_ids(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::scoring::disulfides::FullatomDisulfideEnergy::old_eval_atom_derivative(), core::id::operator<<(), protocols::branch_angle::BranchAngleOptimizer::optimize_angles(), protocols::branch_angle::BranchAngleOptimizer::overall_params(), protocols::branch_angle::BranchAngleOptimizer::param1(), protocols::branch_angle::BranchAngleOptimizer::param2(), core::scoring::NeighborList::prepare_for_scoring(), core::scoring::rna::RNA_TorsionPotential::print_torsion_info(), core::scoring::constraints::AngleConstraint::read_def(), core::scoring::constraints::DihedralPairConstraint::read_def(), core::scoring::constraints::DistancePairConstraint::read_def(), core::scoring::constraints::DihedralConstraint::read_def(), core::scoring::constraints::CoordinateConstraint::read_def(), core::scoring::constraints::NamedAtomPairConstraint::read_def(), core::scoring::constraints::AtomPairConstraint::read_def(), core::scoring::constraints::LocalCoordinateConstraint::remap_resid(), core::scoring::constraints::DihedralPairConstraint::remap_resid(), core::scoring::constraints::DistancePairConstraint::remap_resid(), core::scoring::constraints::DihedralConstraint::remap_resid(), core::scoring::constraints::CoordinateConstraint::remap_resid(), core::scoring::constraints::AngleConstraint::remap_resid(), core::scoring::constraints::AtomPairConstraint::remap_resid(), core::kinematics::AtomTree::replace_residue_subtree(), core::conformation::symmetry::SymmetricConformation::set_bond_angle(), core::conformation::symmetry::SymmetricConformation::set_bond_length(), core::conformation::symmetry::SymmetricConformation::set_torsion_angle(), core::scoring::rna::RNA_TorsionPotential::Should_score_torsion(), core::scoring::constraints::CoordinateConstraint::show(), core::scoring::constraints::LocalCoordinateConstraint::show(), core::scoring::constraints::AtomPairConstraint::show(), core::scoring::constraints::DistancePairConstraint::show_violations(), core::scoring::constraints::DihedralPairConstraint::show_violations(), core::scoring::constraints::DihedralConstraint::show_violations(), core::scoring::constraints::CoordinateConstraint::show_violations(), core::scoring::constraints::AngleConstraint::show_violations(), core::scoring::constraints::AtomPairConstraint::show_violations(), core::scoring::constraints::LocalCoordinateConstraint::show_violations(), protocols::noesy_assign::store_distmap_with_namedatoms(), core::scoring::NeighborList::update_from_wide_nblist(), protocols::simple_moves::ConstrainToIdealMover::vary_bond_geometry(), protocols::viewer::visit_atomtree_node(), and core::pose::MiniPose::xyz().

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

inline

Definition at line 89 of file AtomID.hh.

References atomno_.

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

inline

Returns the AtomID residue number.

Definition at line 76 of file AtomID.hh.

References rsd_.

Referenced by protocols::simple_moves::ConstrainToIdealMover::add_bond_angle_constraint(), protocols::simple_moves::ConstrainToIdealMover::add_bond_constraint(), protocols::enzdes::EnzdesConstraintReporter::add_constrained_nonligand_atom(), core::scoring::constraints::MultiConstraint::add_individual_constraint(), protocols::simple_moves::AddCavitiesMover::add_suckers(), protocols::backrub::BackrubMover::apply(), core::pack::scmin::CartSCMinMinimizerMap::atom(), core::pack::scmin::AtomTreeSCMinMinimizerMap::atom(), 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::symmetry::atom_tree_get_atompairE_deriv(), core::optimization::atom_tree_get_atompairE_deriv(), core::scoring::methods::atoms_interact(), core::conformation::Conformation::backbone_torsion_angle_atoms(), core::conformation::Conformation::bonded_neighbor_all_res(), protocols::toolbox::AllowInsert::calculate_atom_id_map(), protocols::simple_moves::ConstrainToIdealMover::check_if_really_connected(), core::scoring::rna::RNA_TorsionPotential::check_intra_residue(), core::scoring::packstat::LeeRichards::compute(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), protocols::backrub::connected_mainchain_atomids(), core::pose::copy_dofs(), 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::constraints::AtomPairConstraint::dist(), core::scoring::constraints::AtomPairConstraint::effective_sequence_separation(), core::scoring::methods::Fa_MbsolvEnergy::eval_atom_derivative(), core::scoring::rna::RNA_LJ_BaseEnergy::eval_atom_derivative(), core::scoring::methods::Fa_MbenvEnergy::eval_atom_derivative(), core::scoring::rna::RG_Energy_RNA::eval_atom_derivative(), core::scoring::packing::SurfVolEnergy::eval_atom_derivative(), core::scoring::packing::SurfEnergy::eval_atom_derivative(), core::scoring::packing::HolesEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::packing::HolesEnergyRes::eval_atom_derivative(), core::scoring::hackaro::HackAroEnergy::eval_atom_derivative(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::LK_CosThetaEnergy::eval_atom_derivative(), core::scoring::rna::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::scoring::methods::HybridVDW_Energy::eval_atom_derivative(), core::scoring::methods::DNA_BaseEnergy::eval_atom_derivative(), core::scoring::methods::VDW_Energy::eval_atom_derivative(), core::scoring::rna::RNA_DataBackboneEnergy::eval_atom_derivative(), core::scoring::rna::RNA_VDW_Energy::eval_atom_derivative(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::eval_atom_derivative(), core::scoring::methods::CustomAtomPairEnergy::eval_atom_derivative(), core::scoring::geometric_solvation::GeometricSolEnergy::eval_atom_derivative(), core::scoring::hackelec::HackElecEnergyAroAll::eval_atom_derivative(), core::scoring::hackelec::HackElecEnergyAroAro::eval_atom_derivative(), core::scoring::hackelec::RNAHackElecEnergy::eval_atom_derivative(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::eval_atom_derivative_intra_RNA(), core::scoring::geometric_solvation::GeometricSolEnergy::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::ContextIndependentGeometricSolEnergy::eval_atom_energy(), core::scoring::rna::RNA_LJ_BaseEnergy::eval_atom_energy(), core::scoring::geometric_solvation::GeometricSolEnergy::eval_atom_energy(), core::scoring::symmetry::SymmetricScoreFunction::eval_dof_derivative(), core::scoring::ScoreFunction::eval_dof_derivative(), protocols::swa::rna::StepWiseRNA_Minimizer::Figure_out_moving_residues(), protocols::swa::Figure_out_moving_residues(), protocols::cartesian::MolecularDynamics::findCartomAtom(), protocols::topology_broker::fix_internal_coords_of_siblings(), core::pack::scmin::CartSCMinMinimizerMap::get_atom_index(), core::conformation::Conformation::get_torsion_angle_atom_ids(), protocols::simple_moves::ConstrainToIdealMover::i_want_this_atom_to_move(), core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup(), core::kinematics::ResidueCoordinateChangeList::mark_residue_moved(), core::scoring::disulfides::FullatomDisulfideEnergy::old_eval_atom_derivative(), core::id::operator<<(), protocols::branch_angle::BranchAngleOptimizer::optimize_angles(), protocols::branch_angle::BranchAngleOptimizer::overall_params(), protocols::branch_angle::BranchAngleOptimizer::param1(), protocols::branch_angle::BranchAngleOptimizer::param2(), core::scoring::NeighborList::prepare_for_scoring(), core::scoring::rna::RNA_TorsionPotential::print_torsion_info(), core::scoring::constraints::LocalCoordinateConstraint::remap_resid(), core::scoring::constraints::DistancePairConstraint::remap_resid(), core::scoring::constraints::DihedralPairConstraint::remap_resid(), core::scoring::constraints::DihedralConstraint::remap_resid(), core::scoring::constraints::CoordinateConstraint::remap_resid(), core::scoring::constraints::AngleConstraint::remap_resid(), core::scoring::constraints::AtomPairConstraint::remap_resid(), core::scoring::constraints::AngleConstraint::remapped_clone(), core::scoring::constraints::CoordinateConstraint::remapped_clone(), core::scoring::constraints::AtomPairConstraint::remapped_clone(), core::scoring::constraints::BackboneStubConstraint::remapped_clone(), core::scoring::constraints::LocalCoordinateConstraint::remapped_clone(), core::scoring::constraints::NamedAtomPairConstraint::remapped_clone(), core::scoring::constraints::DistancePairConstraint::remapped_clone(), core::scoring::constraints::DihedralPairConstraint::remapped_clone(), core::scoring::constraints::DihedralConstraint::remapped_clone(), core::kinematics::AtomTree::replace_residue_subtree(), core::id::DOF_ID::rsd(), core::conformation::symmetry::SymmetricConformation::set_bond_angle(), core::conformation::symmetry::SymmetricConformation::set_bond_length(), core::conformation::symmetry::SymmetricConformation::set_torsion_angle(), core::conformation::symmetry::SymmetricConformation::set_xyz(), core::scoring::rna::RNA_TorsionPotential::Should_score_torsion(), core::scoring::constraints::CoordinateConstraint::show(), core::scoring::constraints::LocalCoordinateConstraint::show(), core::scoring::constraints::AtomPairConstraint::show(), core::scoring::constraints::DihedralPairConstraint::show_violations(), core::scoring::constraints::DistancePairConstraint::show_violations(), core::scoring::constraints::DihedralConstraint::show_violations(), core::scoring::constraints::CoordinateConstraint::show_violations(), core::scoring::constraints::AngleConstraint::show_violations(), core::scoring::constraints::AtomPairConstraint::show_violations(), core::scoring::constraints::LocalCoordinateConstraint::show_violations(), protocols::noesy_assign::store_distmap_with_namedatoms(), core::scoring::NeighborList::update_from_wide_nblist(), protocols::simple_moves::ConstrainToIdealMover::vary_bond_geometry(), protocols::viewer::visit_atomtree_node(), and core::pose::MiniPose::xyz().

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

inline

Definition at line 80 of file AtomID.hh.

References rsd_.

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

inline

Returns true if the AtomID is valid.

Note

must return false for BOGUS_ATOM_ID

Definition at line 95 of file AtomID.hh.

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::AngleConstraint::remapped_clone(), core::scoring::constraints::CoordinateConstraint::remapped_clone(), core::scoring::constraints::AtomPairConstraint::remapped_clone(), core::scoring::constraints::AmbiguousNMRDistanceConstraint::remapped_clone(), core::scoring::constraints::LocalCoordinateConstraint::remapped_clone(), core::scoring::constraints::NamedAtomPairConstraint::remapped_clone(), core::scoring::constraints::DihedralPairConstraint::remapped_clone(), core::scoring::constraints::DistancePairConstraint::remapped_clone(), core::scoring::constraints::DihedralConstraint::remapped_clone(), core::kinematics::AtomTree::replace_residue_subtree(), core::scoring::constraints::NamedAtomPairConstraint::setup_for_scoring(), core::pose::stub_id_to_named_stub_id(), core::conformation::stub_id_to_named_stub_id(), protocols::hybridization::update_atom_map(), core::id::DOF_ID::valid(), and core::id::StubID::valid().

Friends And Related Function Documentation

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

friend

a and b are different atom

Definition at line 118 of file AtomID.hh.

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)

Definition at line 127 of file AtomID.hh.

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

friend

stream << AtomID

Definition at line 50 of file AtomID.cc.

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

friend

a and b are the same atom

Definition at line 109 of file AtomID.hh.

Member Data Documentation

Size core::id::AtomID::atomno_

private

Atom number within the Residue.

Definition at line 140 of file AtomID.hh.

Referenced by atomno(), and valid().

Size core::id::AtomID::rsd_

private

Residue number within the complex.

Definition at line 143 of file AtomID.hh.

Referenced by rsd(), and valid().

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

• src/core/id/AtomID.hh