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core::conformation::Atom Class Reference

A simple object with atom's position and its chemical type. More...

#include <Atom.hh>

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Public Member Functions

 Atom ()
 default constructor and set atom type number to 0 and place the atom at the origin More...
 
 Atom (ShortSize const type_in, ShortSize const mm_type_in)
 constructor with an atom type number More...
 
 Atom (Vector const &xyz_in, ShortSize const type_in, ShortSize const mm_type_in)
 constructor with xyz and an atom type number More...
 
virtual ~Atom ()
 destructor More...
 
void type (ShortSize const type_in)
 set the atom type number More...
 
ShortSize type () const
 Returns the AtomType number. More...
 
void mm_type (ShortSize const mm_type_in)
 set the mm atom type number More...
 
ShortSize mm_type () const
 get the mm atom type number More...
 
Vector const & xyz () const
 Returns the atom coordinates as an xyzVector. More...
 
void xyz (Vector const &xyz_in)
 Sets the atom coordinates using an xyzVector. More...
 

Private Attributes

Vector xyz_
 position More...
 
ShortSize type_
 rosetta atom_type More...
 
ShortSize mm_type_
 mm_atom_type More...
 

Detailed Description

A simple object with atom's position and its chemical type.

Constructor & Destructor Documentation

core::conformation::Atom::Atom ( )
inline

default constructor and set atom type number to 0 and place the atom at the origin

core::conformation::Atom::Atom ( ShortSize const  type_in,
ShortSize const  mm_type_in 
)
inline

constructor with an atom type number

core::conformation::Atom::Atom ( Vector const &  xyz_in,
ShortSize const  type_in,
ShortSize const  mm_type_in 
)
inline

constructor with xyz and an atom type number

virtual core::conformation::Atom::~Atom ( )
inlinevirtual

destructor

Member Function Documentation

void core::conformation::Atom::mm_type ( ShortSize const  mm_type_in)
inline
ShortSize core::conformation::Atom::mm_type ( ) const
inline
void core::conformation::Atom::type ( ShortSize const  type_in)
inline

set the atom type number

References type_.

Referenced by core::scoring::etable::Etable::analytic_etable_derivatives(), core::scoring::etable::Etable::analytic_etable_evaluation(), core::scoring::methods::apply_lk_ball_fraction_weight_for_hbonds(), core::scoring::etable::TableLookupEvaluator::atom_pair_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::atom_pair_energy_(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), protocols::match::bump_grid_to_enclose_pose(), protocols::match::bump_grid_to_enclose_residue(), protocols::match::bump_grid_to_enclose_residue_backbone(), core::scoring::methods::LK_BallEnergy::calculate_lk_ball_atom_energies(), core::scoring::methods::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue(), core::scoring::methods::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_rotamer_descriptor(), protocols::pockets::PocketGrid::DARC_autoexpanding_pocket_eval(), protocols::pockets::PocketGrid::DARC_pocket_eval(), core::scoring::methods::SuckerEnergy::eval_atom_derivative(), core::scoring::methods::LK_hack::eval_dE_dR_over_r(), core::scoring::methods::Fa_MbsolvEnergy::eval_dE_dR_over_r(), core::scoring::etable::TableLookupEvaluator::eval_dE_dR_over_r(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_dE_dR_over_r_(), core::scoring::methods::LK_BallEnergy::eval_desolvation_derivs_no_count_pair(), core::scoring::methods::Fa_MbenvEnergy::eval_fa_mbenv(), core::scoring::rna::RNA_LJ_BaseEnergy::eval_lj(), core::scoring::methods::Fa_MbsolvEnergy::eval_lk(), protocols::match::fill_grid_with_backbone_heavyatom_spheres(), protocols::match::fill_grid_with_residue_heavyatom_spheres(), protocols::match::fill_grid_with_residue_spheres(), core::coarse::CoarseEtable::get_eID(), protocols::match::downstream::LigandConformerBuilder::initialize_from_residue(), protocols::match::downstream::RigidLigandBuilder::initialize_from_residue(), core::scoring::etable::BaseEtableEnergy< Derived >::memb_atom_pair_energy_(), core::scoring::etable::BaseEtableEnergy< Derived >::memb_eval_dE_dR_over_r_(), core::scoring::etable::etrie::EtableAtom::operator<(), core::scoring::hackelec::ElecAtom::operator<(), core::conformation::operator<<(), core::scoring::etable::etrie::EtableAtom::operator==(), core::scoring::hackelec::ElecAtom::operator==(), core::pack::interaction_graph::InvRotamerDots::overlap_exposed(), core::scoring::etable::TableLookupEvaluator::pair_energy_H(), core::scoring::etable::BaseEtableEnergy< Derived >::pair_energy_H_(), protocols::pockets::PocketGrid::recenter(), core::scoring::methods::LK_hack::residue_pair_energy(), core::scoring::methods::LK_BallEnergy::residue_pair_energy(), and core::scoring::methods::LK_BallEnergy::sum_contributions_for_atom_pair_one_way().

ShortSize core::conformation::Atom::type ( ) const
inline
Vector const& core::conformation::Atom::xyz ( ) const
inline

Returns the atom coordinates as an xyzVector.

References xyz_.

Referenced by core::scoring::geometric_solvation::add_to_individual_sol_energies(), core::scoring::etable::Etable::analytic_etable_derivatives(), core::scoring::etable::Etable::analytic_etable_evaluation(), protocols::protein_interface_design::movers::SpinMover::apply(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::simple_filters::SheetFilter::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::hybridization::CartesianHybridize::apply_frag(), protocols::seeded_abinitio::SegmentHybridizer::apply_frame(), protocols::seeded_abinitio::PlaceFragments::apply_frame(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::hybridization::CartesianHybridize::apply_frame(), protocols::pockets::PlaidFingerprint::apply_rotation_offset_to_pose_(), core::conformation::Residue::apply_transform_downstream(), core::scoring::orbitals::OrbitalsAssigned::aromatic_ring_center(), core::scoring::orbitals::OrbitalsScore::assign_haro_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::conformation::build_residue_tree(), protocols::features::helixAssembly::HelixBundleFeatures::calc_pc_and_com(), protocols::pockets::PlaidFingerprint::calculate_ligand_CoM(), protocols::pockets::NonPlaidFingerprint::calculate_protein_CoM(), protocols::scoring::methods::pcs::PCS_Energy::calculate_scores_and_tensors_from_pose_and_PCS_data(), core::pack::task::operation::util::cbeta_vector(), protocols::hybridization::FoldTreeHybridize::center_of_mass(), protocols::geometry::center_of_mass(), protocols::features::helixAssembly::HelixBundleFeatures::check_cap_distances(), protocols::features::strand_assembly::StrandBundleFeatures::check_sheet_dis_antiparallel(), protocols::features::strand_assembly::StrandBundleFeatures::check_sheet_dis_parallel(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), core::scoring::MembranePotential::compute_membrane_embedding(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::scoring::electron_density::ElectronDensity::compute_symm_rotations(), core::scoring::orbitals::OrbitalsAssigned::CoordinatesDihedral(), core::scoring::orbitals::OrbitalsAssigned::CoordinatesTetrahedral(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), core::scoring::orbitals::OrbitalsAssigned::cp_function(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_don_orientation_vector(), protocols::floppy_tail::create_extra_output(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::electron_density::ElectronDensity::dCCdx_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdx_res(), core::pack::rotamer_set::debug_dump_rotamers(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::Conformation::detect_disulfides(), core::scoring::methods::LinearChainbreakEnergy::do_score_dev(), core::scoring::methods::LinearChainbreakEnergy::do_score_ovp(), protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::methods::MMLJEnergyIntra::eval_atom_derivative(), core::scoring::methods::SuckerEnergy::eval_atom_derivative(), core::scoring::methods::MMLJEnergyInter::eval_atom_derivative(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::methods::LK_hack::eval_dE_dR_over_r(), core::scoring::methods::Fa_MbsolvEnergy::eval_dE_dR_over_r(), core::scoring::etable::AnalyticEtableEvaluator::eval_dE_dR_over_r(), core::scoring::etable::TableLookupEvaluator::eval_dE_dR_over_r(), core::scoring::etable::CoarseEtableEnergy::eval_dE_dR_over_r_(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_dE_dR_over_r_(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::scoring::methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CenHBEnergy::eval_residue_pair_derivatives(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), protocols::electron_density::fast2DRotAlignPose(), protocols::electron_density::fastTransAlignPose(), core::io::silent::BinaryRNASilentStruct::fill_struct(), core::io::silent::BinaryProteinSilentStruct::fill_struct(), protocols::features::strand_assembly::StrandBundleFeatures::find_antiparallel(), protocols::features::strand_assembly::StrandBundleFeatures::find_parallel(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::get_acceptor_base_atm_xyz(), core::scoring::geometric_solvation::GeometricSolEnergy::get_acceptor_base_atm_xyz(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergy::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::get_atom_atom_geometric_solvation_for_donor(), core::scoring::geometric_solvation::GeometricSolEnergy::get_atom_atom_geometric_solvation_for_donor(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::scoring::rna::RNA_Mg_Energy::get_cos_theta(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), protocols::pockets::DelphiElectrostatics::get_electrostatics_energy(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::get_fixed_pt(), core::scoring::orbitals::OrbitalsAssigned::get_hydrogens(), core::scoring::orbitals::OrbitalsAssigned::get_lp_xyz(), protocols::hybridization::get_superposition_transformation(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hackelec::HackElecEnergy::heavyatom_heavyatom_energy(), core::scoring::methods::MMLJEnergyInter::heavyatom_hydrogenatom_energy(), core::scoring::hackelec::HackElecEnergy::heavyatom_hydrogenatom_energy(), protocols::seeded_abinitio::SegmentHybridizer::hybridize(), core::scoring::methods::MMLJEnergyInter::hydrogenatom_heavyatom_energy(), core::scoring::hackelec::HackElecEnergy::hydrogenatom_heavyatom_energy(), core::scoring::methods::MMLJEnergyInter::hydrogenatom_hydrogenatom_energy(), core::scoring::hackelec::HackElecEnergy::hydrogenatom_hydrogenatom_energy(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), core::scoring::methods::EnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::scoring::methods::MembraneEnvSmoothEnergy::increment_f1_f2_for_atom_pair(), protocols::topology_broker::RigidChunkClaimer::initialize_dofs(), protocols::rbsegment_relax::FragInsertAndAlignMover::initialize_rb_fragments(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), core::scoring::etable::TableLookupEvaluator::interpolate_bins(), core::scoring::etable::BaseEtableEnergy< Derived >::interpolate_bins(), core::scoring::etable::Etable::interpolated_analytic_etable_evaluation(), protocols::simple_moves::BBConRotMover::make_move(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), core::scoring::electron_density::ElectronDensity::matchPoseToPatterson(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::matchResFast(), core::scoring::etable::BaseEtableEnergy< Derived >::memb_atom_pair_energy_(), core::scoring::etable::BaseEtableEnergy< Derived >::memb_eval_dE_dR_over_r_(), protocols::motifs::Motif::Motif(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::scoring::etable::etrie::EtableAtom::operator<(), core::scoring::hackelec::ElecAtom::operator<(), core::scoring::mm::mmtrie::MMEnergyTableAtom::operator<(), core::conformation::operator<<(), core::scoring::etable::etrie::EtableAtom::operator==(), core::scoring::mm::mmtrie::MMEnergyTableAtom::operator==(), core::scoring::hackelec::ElecAtom::operator==(), core::conformation::Residue::orient_onto_residue(), core::pack::interaction_graph::InvRotamerDots::overlap_exposed(), protocols::match::NumNeighborsMPM::passes_com_vector_criterion(), core::conformation::Residue::place(), protocols::motifs::Motif::place_atom_(), protocols::motifs::Motif::place_atoms_(), protocols::motifs::Motif::place_residue_(), core::scoring::etable::etrie::EtableAtom::print(), core::scoring::hackelec::ElecAtom::print(), core::scoring::mm::mmtrie::MMEnergyTableAtom::print(), protocols::viewer::print_node(), core::scoring::methods::PoissonBoltzmannEnergy::protein_position_equal_within(), core::conformation::symmetry::SymmetricConformation::recalculate_transforms(), protocols::pockets::PocketGrid::recenter(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::remove_invrots_clashing_with_parent_res(), protocols::features::SmotifFeatures::report_features(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_angles(), protocols::features::ProteinBondGeometryFeatures::report_intrares_lengths(), protocols::features::ProteinBondGeometryFeatures::report_intrares_torsions(), core::conformation::symmetry::residue_center_of_mass(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::residue_conformations_redundant(), core::scoring::methods::BurialEnergy::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::methods::MembraneEnvSmoothEnergy::residue_energy(), core::scoring::methods::MembraneCenPairEnergy::residue_pair_energy(), core::scoring::methods::CenPairEnergy::residue_pair_energy(), core::scoring::methods::SmoothCenPairEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::LK_hack::residue_pair_energy(), protocols::geometry::return_nearest_residue(), core::conformation::symmetry::return_nearest_residue(), protocols::pockets::PlaidFingerprint::rmsd(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), core::scoring::MembranePotential::score_normal_center(), core::pack::task::operation::util::select_coord_for_residue(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), protocols::scoring::methods::pcs2::GridSearchIteratorCA::set_vec(), core::conformation::Residue::set_xyz(), protocols::flexpep_docking::FlexPepDockingFlags::setDefaultAnchors(), core::scoring::saxs::FastSAXSEnergy::setup_for_derivatives(), core::scoring::methods::EnvSmoothEnergy::setup_for_derivatives(), core::scoring::methods::MembraneEnvSmoothEnergy::setup_for_derivatives(), core::scoring::saxs::FastSAXSEnergy::setup_for_scoring(), protocols::hybridization::DDomainParse::split(), protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(), core::scoring::MembranePotential::termini_penalty(), protocols::scoring::methods::pcs2::PcsDataCenter::update_X_Y_Z_all(), protocols::scoring::methods::pcs::PCS_data::update_X_Y_Z_all(), core::chemical::ICoorAtomID::xyz(), and core::conformation::Residue::xyz().

void core::conformation::Atom::xyz ( Vector const &  xyz_in)
inline

Sets the atom coordinates using an xyzVector.

References xyz_.

Member Data Documentation

ShortSize core::conformation::Atom::mm_type_
private

mm_atom_type

Referenced by mm_type().

ShortSize core::conformation::Atom::type_
private

rosetta atom_type

Referenced by type().

Vector core::conformation::Atom::xyz_
private

position

Referenced by xyz().


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