core::id::AtomID Class Reference

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

#include <AtomID.hh>

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.

Constructor & Destructor Documentation

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

inline

Default constructor.

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

inline

Copy constructor.

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

inline

Property constructor.

Member Function Documentation

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

inline

Returns the AtomID atom number.

References atomno_.

Referenced by core::pack::scmin::AtomTreeSCMinMinimizerMap::add_atom(), core::conformation::Conformation::append_residue_by_bond(), 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::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::bonded_neighbor_all_res(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), 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::membrane::FaMPSolvEnergy::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::membrane::FaMPEnvEnergy::eval_atom_derivative(), core::scoring::rna::RNA_VDW_Energy::eval_atom_derivative(), core::scoring::methods::HybridVDW_Energy::eval_atom_derivative(), core::scoring::membrane::FaMPEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::DNA_BaseEnergy::eval_atom_derivative(), core::scoring::rna::data::RNA_DataBackboneEnergy::eval_atom_derivative(), core::scoring::rna::StackElecEnergy::eval_atom_derivative(), core::scoring::rna::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::scoring::methods::CustomAtomPairEnergy::eval_atom_derivative(), core::scoring::vdwaals::VDW_Energy::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergyAroAll::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergyAroAro::eval_atom_derivative(), core::scoring::methods::LK_PolarNonPolarEnergy::eval_atom_derivative(), core::scoring::elec::RNA_FA_ElecEnergy::eval_atom_derivative(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergy::eval_atom_derivative(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base(), core::scoring::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::scoring::rna::RNA_LJ_BaseEnergy::eval_atom_energy(), core::pose::copydofs::CopyDofs::figure_out_dofs(), 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(), core::pose::rna::is_torsion_valid(), core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup(), core::scoring::methods::IdealParametersDatabase::lookup_torsion_legacy(), core::scoring::disulfides::FullatomDisulfideEnergy::old_eval_atom_derivative(), core::id::operator<<(), core::scoring::NeighborList::prepare_for_scoring(), core::pose::rna::print_torsion_info(), core::scoring::constraints::AngleConstraint::read_def(), core::scoring::constraints::DistancePairConstraint::read_def(), core::scoring::constraints::DihedralPairConstraint::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::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::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::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::AngleConstraint::show_violations(), core::scoring::constraints::CoordinateConstraint::show_violations(), core::scoring::constraints::AtomPairConstraint::show_violations(), core::scoring::constraints::LocalCoordinateConstraint::show_violations(), core::scoring::NeighborList::update_from_wide_nblist(), core::conformation::Conformation::update_residue_torsions(), and core::pose::MiniPose::xyz().

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

inline

References atomno_.

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

inline

Returns the AtomID residue number.

References rsd_.

Referenced by core::scoring::constraints::MultiConstraint::add_individual_constraint(), 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::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::bonded_neighbor_all_res(), core::scoring::rna::RNA_TorsionPotential::check_intra_residue(), core::scoring::packstat::LeeRichards::compute(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), 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::hackaro::HackAroEnergy::eval_atom_derivative(), core::scoring::membrane::FaMPSolvEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::packing::HolesEnergyRes::eval_atom_derivative(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::membrane::FaMPEnvEnergy::eval_atom_derivative(), core::scoring::rna::RNA_VDW_Energy::eval_atom_derivative(), core::scoring::methods::HybridVDW_Energy::eval_atom_derivative(), core::scoring::membrane::FaMPEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::DNA_BaseEnergy::eval_atom_derivative(), core::scoring::rna::data::RNA_DataBackboneEnergy::eval_atom_derivative(), core::scoring::rna::StackElecEnergy::eval_atom_derivative(), core::scoring::rna::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::scoring::methods::CustomAtomPairEnergy::eval_atom_derivative(), core::scoring::vdwaals::VDW_Energy::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergyAroAll::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergyAroAro::eval_atom_derivative(), core::scoring::methods::LK_PolarNonPolarEnergy::eval_atom_derivative(), core::scoring::elec::RNA_FA_ElecEnergy::eval_atom_derivative(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergy::eval_atom_derivative(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base(), core::scoring::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::scoring::rna::RNA_LJ_BaseEnergy::eval_atom_energy(), core::scoring::symmetry::SymmetricScoreFunction::eval_dof_derivative(), core::scoring::ScoreFunction::eval_dof_derivative(), core::pose::copydofs::CopyDofs::figure_out_dofs(), 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(), core::pose::rna::is_torsion_valid(), core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup(), core::kinematics::ResidueCoordinateChangeList::mark_residue_moved(), core::scoring::disulfides::FullatomDisulfideEnergy::old_eval_atom_derivative(), core::id::operator<<(), core::scoring::NeighborList::prepare_for_scoring(), core::pose::rna::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::BackboneStubLinearConstraint::remapped_clone(), core::scoring::constraints::LocalCoordinateConstraint::remapped_clone(), core::scoring::constraints::NamedAtomPairConstraint::remapped_clone(), core::scoring::constraints::BackboneStubConstraint::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::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::AngleConstraint::show_violations(), core::scoring::constraints::CoordinateConstraint::show_violations(), core::scoring::constraints::AtomPairConstraint::show_violations(), core::scoring::constraints::LocalCoordinateConstraint::show_violations(), core::scoring::NeighborList::update_from_wide_nblist(), core::conformation::Conformation::update_residue_torsions(), and core::pose::MiniPose::xyz().

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

inline

References rsd_.

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 core::scoring::constraints::LocalCoordinateConstraint::LocalCoordinateConstraint(), core::scoring::constraints::Obsolet_NamedAtomPairConstraint::mapto(), 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::DistancePairConstraint::remapped_clone(), core::scoring::constraints::DihedralPairConstraint::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(), 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

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)

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

friend

stream << AtomID

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

friend

a and b are the same atom

Member Data Documentation

Size core::id::AtomID::atomno_

private

Atom number within the Residue.

Referenced by atomno(), and valid().

Size core::id::AtomID::rsd_

private

Residue number within the complex.

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