Rosetta Core  2014.35
Public Member Functions | Private Attributes | Friends | List of all members
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...
 
Sizersd ()
 
Size atomno () const
 Returns the AtomID atom number. More...
 
Sizeatomno ()
 
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

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().


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