Rosetta 3.4
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core::id::AtomID Class Reference

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

#include <AtomID.hh>

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List of all members.

Public Member Functions

 AtomID ()
 Default constructor.
 AtomID (AtomID const &src)
 Copy constructor.
 AtomID (Size const atomno_in, Size const rsd_in)
 Property constructor.
Size rsd () const
 Returns the AtomID residue number.
Sizersd ()
Size atomno () const
 Returns the AtomID atom number.
Sizeatomno ()
bool valid () const
 Returns true if the AtomID is valid.

Friends

std::ostream & operator<< (std::ostream &os, AtomID const &a)
 stream << AtomID
bool operator== (AtomID const &a, AtomID const &b)
 a and b are the same atom
bool operator!= (AtomID const &a, AtomID const &b)
 a and b are different atom
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)

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.

Referenced by core::pack::scmin::SCMinMinimizerMap::add_atom(), core::conformation::Conformation::append_residue_by_bond(), protocols::backrub::BackrubMover::apply(), core::pack::scmin::SCMinMinimizerMap::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::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::rna::RNA_VDW_Energy::eval_atom_derivative(), core::scoring::rna::RNA_LJ_BaseEnergy::eval_atom_derivative(), core::scoring::rna::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::scoring::rna::RNA_DataBackboneEnergy::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::HolesEnergyRes::eval_atom_derivative(), core::scoring::packing::HolesEnergy::eval_atom_derivative(), core::scoring::methods::VDW_Energy::eval_atom_derivative(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::HybridVDW_Energy::eval_atom_derivative(), core::scoring::methods::Fa_MbsolvEnergy::eval_atom_derivative(), core::scoring::methods::Fa_MbenvEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::DNA_BaseEnergy::eval_atom_derivative(), core::scoring::methods::CustomAtomPairEnergy::eval_atom_derivative(), core::scoring::hackelec::RNAHackElecEnergy::eval_atom_derivative(), core::scoring::hackelec::HackElecEnergyAroAro::eval_atom_derivative(), core::scoring::hackelec::HackElecEnergyAroAll::eval_atom_derivative(), core::scoring::hackaro::HackAroEnergy::eval_atom_derivative(), core::scoring::geometric_solvation::GeometricSolEnergy::eval_atom_derivative(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::eval_atom_derivative(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base(), core::scoring::geometric_solvation::GeometricSolEnergy::eval_atom_derivative_intra_RNA(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::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::rna::RNA_LJ_BaseEnergy::eval_atom_energy(), core::scoring::geometric_solvation::GeometricSolEnergy::eval_atom_energy(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::eval_atom_energy(), core::conformation::Conformation::get_torsion_angle_atom_ids(), core::scoring::methods::TorsionDatabase::lookup(), 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::constraints::NamedAtomPairConstraint::read_def(), core::scoring::constraints::DihedralPairConstraint::read_def(), core::scoring::constraints::DihedralConstraint::read_def(), core::scoring::constraints::CoordinateConstraint::read_def(), core::scoring::constraints::AtomPairConstraint::read_def(), core::scoring::constraints::AngleConstraint::read_def(), core::scoring::constraints::LocalCoordinateConstraint::remap_resid(), core::scoring::constraints::DihedralPairConstraint::remap_resid(), core::scoring::constraints::DihedralConstraint::remap_resid(), core::scoring::constraints::CoordinateConstraint::remap_resid(), core::scoring::constraints::AtomPairConstraint::remap_resid(), core::scoring::constraints::AngleConstraint::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::LocalCoordinateConstraint::show(), core::scoring::constraints::CoordinateConstraint::show(), core::scoring::constraints::AtomPairConstraint::show(), core::scoring::constraints::LocalCoordinateConstraint::show_violations(), core::scoring::constraints::DihedralPairConstraint::show_violations(), core::scoring::constraints::DihedralConstraint::show_violations(), core::scoring::constraints::CoordinateConstraint::show_violations(), core::scoring::constraints::AtomPairConstraint::show_violations(), core::scoring::constraints::AngleConstraint::show_violations(), protocols::viewer::visit_atomtree_node(), and core::pose::MiniPose::xyz().

Size& core::id::AtomID::atomno ( ) [inline]
Size& core::id::AtomID::rsd ( ) [inline]
Size core::id::AtomID::rsd ( ) const [inline]

Returns the AtomID residue number.

Referenced by core::scoring::constraints::MultiConstraint::add_individual_constraint(), protocols::simple_moves::AddCavitiesMover::add_suckers(), protocols::backrub::BackrubMover::apply(), core::pack::scmin::SCMinMinimizerMap::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::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::kinematics::AtomTree::delete_seqpos(), 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::rna::RNA_VDW_Energy::eval_atom_derivative(), core::scoring::rna::RNA_LJ_BaseEnergy::eval_atom_derivative(), core::scoring::rna::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::scoring::rna::RNA_DataBackboneEnergy::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::HolesEnergyRes::eval_atom_derivative(), core::scoring::packing::HolesEnergy::eval_atom_derivative(), core::scoring::methods::VDW_Energy::eval_atom_derivative(), core::scoring::methods::MembraneEnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::HybridVDW_Energy::eval_atom_derivative(), core::scoring::methods::Fa_MbsolvEnergy::eval_atom_derivative(), core::scoring::methods::Fa_MbenvEnergy::eval_atom_derivative(), core::scoring::methods::EnvSmoothEnergy::eval_atom_derivative(), core::scoring::methods::DNA_BaseEnergy::eval_atom_derivative(), core::scoring::methods::CustomAtomPairEnergy::eval_atom_derivative(), core::scoring::hackelec::RNAHackElecEnergy::eval_atom_derivative(), core::scoring::hackelec::HackElecEnergyAroAro::eval_atom_derivative(), core::scoring::hackelec::HackElecEnergyAroAll::eval_atom_derivative(), core::scoring::hackaro::HackAroEnergy::eval_atom_derivative(), core::scoring::geometric_solvation::GeometricSolEnergy::eval_atom_derivative(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::eval_atom_derivative(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base(), core::scoring::geometric_solvation::GeometricSolEnergy::eval_atom_derivative_intra_RNA(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::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::rna::RNA_LJ_BaseEnergy::eval_atom_energy(), core::scoring::geometric_solvation::GeometricSolEnergy::eval_atom_energy(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::eval_atom_energy(), protocols::swa::Figure_out_moving_residues(), protocols::topology_broker::fix_internal_coords_of_siblings(), core::conformation::Conformation::get_torsion_angle_atom_ids(), 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(), protocols::rna::print_internal_coords(), core::conformation::promote_sameresidue_child_of_jump_atom(), core::kinematics::AtomTree::promote_sameresidue_nonjump_child(), core::scoring::constraints::LocalCoordinateConstraint::remap_resid(), core::scoring::constraints::DihedralPairConstraint::remap_resid(), core::scoring::constraints::DihedralConstraint::remap_resid(), core::scoring::constraints::CoordinateConstraint::remap_resid(), core::scoring::constraints::AtomPairConstraint::remap_resid(), core::scoring::constraints::AngleConstraint::remap_resid(), core::scoring::constraints::NamedAtomPairConstraint::remapped_clone(), core::scoring::constraints::LocalCoordinateConstraint::remapped_clone(), core::scoring::constraints::DihedralPairConstraint::remapped_clone(), core::scoring::constraints::DihedralConstraint::remapped_clone(), core::scoring::constraints::CoordinateConstraint::remapped_clone(), core::scoring::constraints::BackboneStubConstraint::remapped_clone(), core::scoring::constraints::AtomPairConstraint::remapped_clone(), core::scoring::constraints::AngleConstraint::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::LocalCoordinateConstraint::show(), core::scoring::constraints::CoordinateConstraint::show(), core::scoring::constraints::AtomPairConstraint::show(), core::scoring::constraints::LocalCoordinateConstraint::show_violations(), core::scoring::constraints::DihedralPairConstraint::show_violations(), core::scoring::constraints::DihedralConstraint::show_violations(), core::scoring::constraints::CoordinateConstraint::show_violations(), core::scoring::constraints::AtomPairConstraint::show_violations(), core::scoring::constraints::AngleConstraint::show_violations(), protocols::viewer::visit_atomtree_node(), and core::pose::MiniPose::xyz().

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


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