core::conformation::Atom Class Reference

#include <Atom.hh>

Inheritance diagram for core::conformation::Atom:

Public Member Functions
	Atom ()
	Default constructor. 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 ()=default
	destructor More...
void	show (std::ostream &output) const
	Generate string representation of conformation::Atom for debugging purposes. More...
void	show () const
	Generate string representation of conformation::Atom to std::cout for debugging purposes. 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_
ShortSize	type_
ShortSize	mm_type_

Detailed Description

This atom class differs from the chameical::Atom, AtomType, and AtomTypeSet classes in that it only contains the information about the xyz coordinates. In the future, it might contain information about such things as B-factor. This information is generally initialized and set by conformation::Residue.

Note

chemical::Atoms are stored in chemical::ResidueType (within its ResidueGraph); conformation::Atoms are stored in conformation::Residue

Constructor & Destructor Documentation

Atom() [1/3]

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

inline

Default constructor.

Set atom type number to 0 and place the atom at the origin.

Atom() [2/3]

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

inline

constructor with an atom type number

Atom() [3/3]

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

~Atom()

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

virtualdefault

destructor

Member Function Documentation

mm_type() [1/2]

ShortSize core::conformation::Atom::mm_type ( ) const

inline

get the mm atom type number

References mm_type_.

Referenced by core::scoring::mm::mmtrie::MMEnergyTableAtom::mm_atom_type(), core::scoring::mm::mmtrie::MMEnergyTableAtom::operator<(), core::scoring::mm::mmtrie::MMEnergyTableAtom::operator==(), and core::scoring::mm::mmtrie::MMEnergyTableAtom::print().

mm_type() [2/2]

void core::conformation::Atom::mm_type ( ShortSize const  mm_type_in )

inline

set the mm atom type number

References mm_type_.

Referenced by core::scoring::methods::MMLJEnergyInter::eval_atom_derivative(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_derivatives(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_energy_ext(), core::scoring::mm::mmtrie::MMEnergyTableAtom::operator<(), and core::scoring::mm::mmtrie::MMEnergyTableAtom::operator==().

show() [1/2]

void core::conformation::Atom::show

(

)

const

Generate string representation of conformation::Atom to std::cout for debugging purposes.

show() [2/2]

void core::conformation::Atom::show

(

std::ostream &

output

)

const

Generate string representation of conformation::Atom for debugging purposes.

References xyz_.

Referenced by core::conformation::operator<<(), and core::conformation::Residue::show().

type() [1/2]

ShortSize core::conformation::Atom::type ( ) const

inline

Returns the AtomType number.

References type_.

Referenced by core::scoring::etable::etrie::EtableAtom::atom_type(), core::scoring::etable::etrie::EtableAtom::operator<(), core::scoring::etable::etrie::EtableAtom::operator==(), and core::scoring::etable::etrie::EtableAtom::print().

type() [2/2]

void core::conformation::Atom::type ( ShortSize const  type_in )

inline

set the atom type number

References type_.

Referenced by protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::scoring::etable::Etable::analytic_etable_derivatives(), core::scoring::etable::Etable::analytic_etable_evaluation(), core::scoring::etable::Etable::analytic_lk_derivatives(), core::scoring::etable::Etable::analytic_lk_energy(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), core::scoring::etable::TableLookupEvaluator::atom_pair_energy(), core::scoring::etable::TableLookupEvaluator::atom_pair_lk_energy_and_deriv_v(), core::scoring::etable::TableLookupEvaluator::atom_pair_lk_energy_and_deriv_v_efficient(), protocols::qsar::scoring_grid::SolvationMetaGrid::atom_score(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), protocols::sewing::hashing::LigandBindingResPlacer::best_rotamer_for_residue(), protocols::match::bump_grid_to_enclose_pose(), protocols::match::bump_grid_to_enclose_residue(), protocols::match::bump_grid_to_enclose_residue_backbone(), core::scoring::atomic_depth::AtomicDepth::calcdepth(), core::energy_methods::LK_hack::calculate_derivatives_for_residue_pair(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies(), core::scoring::lkball::LK_BallEnergy::calculate_lk_ball_atom_energies_cp(), core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue(), core::scoring::lkball::LK_BallEnergy::calculate_lk_desolvation_of_single_atom_by_residue_no_count_pair(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_don_orientation_vector(), core::scoring::hbonds::create_rotamer_descriptor(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::energy_methods::Fa_MbsolvEnergy::dsolvationE(), core::energy_methods::FaMPSolvEnergy::dsolvationE(), core::energy_methods::SuckerEnergy::eval_atom_derivative(), core::energy_methods::Fa_MbenvEnergy::eval_atom_derivative(), core::energy_methods::FaMPEnvEnergy::eval_atom_derivative(), core::energy_methods::Fa_MbsolvEnergy::eval_dE_dR_over_r(), core::energy_methods::FaMPSolvEnergy::eval_dE_dR_over_r(), core::energy_methods::LK_hack::eval_dE_dR_over_r(), core::scoring::etable::TableLookupEvaluator::eval_dE_dR_over_r(), core::scoring::lkball::LK_BallEnergy::eval_desolvation_derivs_no_count_pair(), core::energy_methods::Fa_MbenvEnergy::eval_fa_mbenv(), core::energy_methods::FaMPEnvEnergy::eval_fa_mbenv(), core::energy_methods::RNA_LJ_BaseEnergy::eval_lj(), core::energy_methods::Fa_MbsolvEnergy::eval_lk(), core::energy_methods::FaMPSolvEnergy::eval_lk(), protocols::ligand_docking::ga_ligand_dock::GridScorer::fast_eval_etable_split_fasol(), protocols::match::fill_grid_with_backbone_heavyatom_spheres(), protocols::match::fill_grid_with_residue_heavyatom_spheres(), protocols::match::fill_grid_with_residue_spheres(), core::scoring::lkball::LK_DomeEnergy::fill_occlusions_1way(), core::scoring::atomic_depth::AtomicDepth::fillatom(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(), core::pack::interaction_graph::RotamerDots::get_atom_radius(), protocols::simple_moves::AddCavitiesMover::get_closest_heavy_atom(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_grid_all_atomtypes(), protocols::ligand_docking::ga_ligand_dock::GridScorer::get_grid_atomtypes(), protocols::cryst::getMW(), core::scoring::lkball::lkbtrie::LKBTrieEvaluator::heavyatom_heavyatom_energy(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::initialize_bg_bg_atom_atom_overlaps(), protocols::match::downstream::LigandConformerBuilder::initialize_from_residue(), protocols::match::downstream::RigidLigandBuilder::initialize_from_residue(), core::scoring::elec::electrie::ElecAtom::operator<(), core::scoring::etable::etrie::EtableAtom::operator<(), core::scoring::lkball::lkbtrie::LKBAtom::operator<(), core::scoring::elec::electrie::ElecAtom::operator==(), core::scoring::etable::etrie::EtableAtom::operator==(), core::scoring::lkball::lkbtrie::LKBAtom::operator==(), core::pack::interaction_graph::InvRotamerDots::overlap_exposed(), core::scoring::etable::TableLookupEvaluator::pair_energy_H(), core::energy_methods::LK_hack::residue_pair_energy(), core::energy_methods::SuckerEnergy::residue_pair_energy(), protocols::qsar::scoring_grid::SolvationMetaGrid::score(), core::energy_methods::Fa_MbsolvEnergy::solv_deriv(), core::energy_methods::FaMPSolvEnergy::solv_deriv(), core::energy_methods::Fa_MbsolvEnergy::solvationE(), core::energy_methods::FaMPSolvEnergy::solvationE(), core::scoring::lkball::LK_BallEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way(), and core::pack::interaction_graph::InvRotamerDots::write_circle_intersection_mask_to_kinemage().

xyz() [1/2]

Vector const& core::conformation::Atom::xyz ( ) const

inline

Returns the atom coordinates as an xyzVector.

References xyz_.

Referenced by protocols::buns::BuriedUnsatisfiedPolarsCalculator2::acc_geom_check(), protocols::metal_interface::AddZincSiteConstraints::add_constraints(), protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::splice::Splice::add_dihedral_constraints(), protocols::splice::SpliceManager::add_dihedral_constraints(), protocols::legacy_sewing::Assembly::add_loop_segment(), core::energy_methods::add_to_individual_sol_energies(), core::pose::addVirtualResAsRoot(), protocols::loop_grower::SheetSampler::alignPerfectCA(), protocols::loop_grower::SheetSampler::alignStrand(), protocols::pockets::PocketGrid::alter_espGrid_with_bound_ligand(), core::scoring::etable::Etable::analytic_etable_derivatives(), core::scoring::etable::Etable::analytic_etable_evaluation(), core::scoring::etable::Etable::analytic_lk_derivatives(), core::scoring::etable::Etable::analytic_lk_energy(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::loop_grower::FragmentExtension::apply(), protocols::membrane::AqueousPoreFinder::apply(), protocols::protein_interface_design::movers::SpinMover::apply(), protocols::rbsegment_relax::IdealizeHelicesMover::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::rigid::RollMover::apply(), protocols::rigid::RotateJumpAxisMover::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::simple_moves::MissingDensityToJumpMover::apply(), protocols::simple_moves::Tumble::apply(), protocols::rbsegment_relax::FragInsertAndAlignMover::apply(), protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), protocols::simple_filters::SheetFilter::apply(), protocols::task_operations::InteractingRotamerExplosion::apply(), protocols::contact_map::ContactMap::apply(), protocols::hybridization::CartesianHybridize::apply_frag(), protocols::hybridization::CartesianSampler::apply_fragcsts(), protocols::hybridization::CartesianHybridize::apply_frame(), protocols::seeded_abinitio::SegmentHybridizer::apply_frame(), protocols::pockets::PlaidFingerprint::apply_rotation_offset_to_pose_(), core::conformation::Residue::apply_transform_downstream(), core::energy_methods::ResidualDipolarCouplingEnergy_Rohl::assemble_datamatrix(), protocols::match::downstream::LigandConformerBuilder::assign_conformer_group_to_residue(), protocols::pockets::ElectrostaticpotentialGrid::assign_esp_for_protein_grid_points(), core::scoring::orbitals::OrbitalsScore::assign_haro_derivs_one_way(), core::scoring::orbitals::OrbitalsScore::assign_hpol_derivs_one_way(), core::energy_methods::ProQ_Energy::atom_feature(), protocols::qsar::scoring_grid::SolvationMetaGrid::atom_score(), core::conformation::membrane::MembraneInfo::atom_z_position(), core::scoring::hbonds::HBondEnergy::atomistic_pair_energy(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), protocols::design_opt::Supercharge::AvNAPSA_values(), protocols::idealize::basic_idealize(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), protocols::sewing::hashing::LigandBindingResPlacer::best_rotamer_for_residue(), protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::boltzman(), core::conformation::Residue::build_orbital_xyz(), protocols::peptide_deriver::PeptideDeriverFilter::build_receptor_peptide_pose(), core::conformation::build_residue_tree(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_acc_nbr_residue_check(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_donor_nbr_residue_check(), core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_delta_internal_coordinates(), protocols::features::strand_assembly::cal_dis_angle_to_find_sheet(), core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_distance_squared(), protocols::features::strand_assembly::cal_min_avg_dis_between_two_sheets_by_cen_res(), protocols::features::strand_assembly::cal_min_dis_between_two_sheets_by_all_res(), protocols::features::strand_assembly::cal_shortest_dis_between_facing_aro_in_sw(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), core::scoring::calc_atom_masks(), protocols::membrane::calc_helix_axis(), core::select::util::calc_sc_neighbors(), core::scoring::atomic_depth::AtomicDepth::calcdepth(), protocols::docking::EllipsoidalRandomizationMover::calculate_axes(), protocols::features::strand_assembly::calculate_dihedral_w_4_resnums(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), protocols::pockets::PlaidFingerprint::calculate_ligand_CoM(), protocols::pmut_scan::PointMutScanDriver::calculate_neighbor_table(), protocols::docking::EllipsoidalRandomizationMover::calculate_plane_axes(), protocols::pockets::NonPlaidFingerprint::calculate_protein_CoM(), core::energy_methods::FiberDiffractionEnergyDens::calculate_rho_fast2(), protocols::scoring::methods::pcs::PCS_Energy::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3::calculate_scores_and_tensors_from_pose_and_PCS_data(), protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4::calculate_scores_and_tensors_from_pose_and_PCS_data(), core::energy_methods::ProQ_Energy::calculateZ(), core::select::util::cbeta_vector(), protocols::cyclic_peptide::FlipChiralityMover::center_mass(), protocols::hybridization::FoldTreeHybridize::center_of_mass(), protocols::pose_length_moves::InsertResMover::center_of_mass(), protocols::simple_moves::Tumble::center_of_mass(), protocols::geometry::center_of_mass(), core::pose::center_of_mass(), protocols::hybridization::FragmentBiasAssigner::chainbreak(), protocols::loop_grower::LoopGrower::check_coordinates(), protocols::rbsegment_relax::ConfChangeMover::check_gaps(), core::scoring::MembranePotential::check_spanning(), protocols::features::strand_assembly::StrandBundleFeatures::check_strand_too_closeness(), protocols::features::strand_assembly::check_strand_too_closeness(), protocols::features::strand_assembly::check_whether_sheets_are_connected_with_near_bb_atoms(), protocols::features::strand_assembly::check_whether_sw_is_not_connected_with_continuous_atoms(), protocols::fldsgn::filters::HelixBendFilter::compute(), protocols::simple_filters::AngleToVector::compute(), protocols::simple_filters::AtomicDistanceFilter::compute(), protocols::fldsgn::filters::InterlockingAromaFilter::compute(), core::scoring::CenRotEnvPairPotential::compute_centroid_environment(), core::scoring::SmoothEnvPairPotential::compute_centroid_environment(), core::scoring::ChemicalShiftAnisotropy::compute_csascore(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), core::scoring::CenRotEnvPairPotential::compute_dcentroid_environment(), core::scoring::SmoothEnvPairPotential::compute_dcentroid_environment(), core::scoring::DipolarCoupling::compute_dcscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::MembranePotential::compute_membrane_embedding(), core::scoring::electron_density::ElectronDensity::compute_symm_rotations(), protocols::relax::RangeRelaxMover::constrain_to_reference(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::abinitio::copy_side_chains(), core::conformation::membrane::MembraneGeometry::corrected_xyz(), protocols::motif_grafting::movers::MotifGraftMover::count_clashes_between_two_poses(), core::energy_methods::ProQ_Energy::crd(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_don_orientation_vector(), protocols::floppy_tail::create_extra_output(), protocols::legacy_sewing::create_model_from_pose(), core::scoring::hbonds::create_rotamer_descriptor(), protocols::cryst::crystRMS(), core::pack::rotamer_set::debug_dump_rotamers(), core::conformation::Conformation::debug_residue_torsions(), core::conformation::Conformation::detect_bonds(), core::conformation::Conformation::detect_disulfides(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), protocols::features::strand_assembly::determine_core_heading_surface_heading_by_distance(), protocols::features::strand_assembly::determine_heading_direction_by_vector(), protocols::electron_density::BfactorMultifunc::dfunc(), core::scoring::disulfides::DisulfideMatchingPotential::disulfide_RT(), core::energy_methods::LinearChainbreakEnergy::do_score_dev(), core::energy_methods::LinearChainbreakEnergy::do_score_ovp(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::don_geom_check(), protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(), protocols::simple_ddg::ddG::duplicate_waters_across_jump(), protocols::pockets::EggshellGrid::EggshellGrid(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), protocols::metal_interface::MatchGrafter::ensure_proper_his_tautomers(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::energy_methods::NPDHBondEnergy::eval_atom_derivative(), core::energy_methods::SuckerEnergy::eval_atom_derivative(), core::energy_methods::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensEnergy::eval_atom_derivative(), core::scoring::methods::MMLJEnergyInter::eval_atom_derivative(), core::energy_methods::BranchEnergy::eval_atom_derivative(), core::energy_methods::ChainbreakEnergy::eval_atom_derivative(), core::energy_methods::LinearBranchEnergy::eval_atom_derivative(), core::energy_methods::LinearChainbreakEnergy::eval_atom_derivative(), core::energy_methods::Fa_MbsolvEnergy::eval_dE_dR_over_r(), core::energy_methods::FaMPSolvEnergy::eval_dE_dR_over_r(), core::energy_methods::LK_hack::eval_dE_dR_over_r(), core::scoring::etable::AnalyticEtableEvaluator::eval_dE_dR_over_r(), core::scoring::etable::TableLookupEvaluator::eval_dE_dR_over_r(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd1(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_angle_energies_two_from_rsd2(), core::energy_methods::CartesianBondedEnergy::eval_interresidue_bond_energy(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_derivatives(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_energy(), core::scoring::methods::MMLJEnergyIntra::eval_intrares_energy_ext(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), core::energy_methods::CenRotEnvEnergy::eval_residue_derivatives(), core::energy_methods::PointWaterEnergy::eval_residue_pair_derivatives(), core::energy_methods::FastDensEnergy::eval_residue_pair_derivatives(), core::energy_methods::CenHBEnergy::eval_residue_pair_derivatives(), core::energy_methods::CenRotPairEnergy::eval_residue_pair_derivatives(), core::energy_methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::energy_methods::CenHBEnergy::eval_residue_pair_derivatives_soft(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_score(), protocols::metal_interface::AddZincSiteConstraints::evaluate_constraints(), core::scoring::MembranePotential::evaluate_env(), core::scoring::SmoothEnvPairPotential::evaluate_env_and_cbeta_deriv(), protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(), core::energy_methods::PairEnergy::evaluate_rotamer_pair_energies(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), protocols::pockets::GenPharmacophore::extract_rna_rings_from_protein_rna_complex(), protocols::ligand_docking::ga_ligand_dock::GridScorer::fast_eval_etable_split_fasol(), protocols::pockets::DarcParticleSwarmMinimizer::fill_atom_arrays_for_electrostatics_(), core::io::silent::BinarySilentStruct::fill_struct(), core::scoring::atomic_depth::AtomicDepth::fillatom(), core::energy_methods::BranchEnergy::finalize_total_energy(), core::energy_methods::ChainbreakEnergy::finalize_total_energy(), core::energy_methods::LinearBranchEnergy::finalize_total_energy(), protocols::features::strand_assembly::StrandBundleFeatures::find_antiparallel(), protocols::simple_moves::ExplicitWaterMover::find_closest(), protocols::simple_filters::HelixHelixAngleFilter::find_closest_res(), core::scoring::fiber_diffraction::find_max_r(), core::scoring::fiber_diffraction::find_min_xyz(), protocols::loophash::FastGapMover::find_next_gap(), protocols::features::strand_assembly::StrandBundleFeatures::find_parallel(), protocols::features::strand_assembly::find_sheet(), protocols::rigid::RigidBodyTiltMover::find_tilt_center(), protocols::metal_interface::ZincSiteFinder::find_zinc_site(), protocols::electron_density::findLoopFromDensity(), protocols::membrane::geometry::EmbeddingDef::from_span(), protocols::membrane::geometry::EmbeddingDef::from_span_positive_z(), protocols::loop_grower::LoopGrower::GDThatonative(), protocols::sewing::hashing::Hasher::generate_key(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_acceptor_base_atm_xyz(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::get_anchors(), core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::energy_methods::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::energy_methods::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), protocols::features::strand_assembly::StrandBundleFeatures::get_avg_dis_CA_CA(), protocols::features::strand_assembly::get_avg_dis_CA_CA(), protocols::features::strand_assembly::get_avg_dis_strands(), protocols::rna::denovo::movers::RNA_HelixMover::get_backbone_centroid(), core::pose::get_center_of_mass(), protocols::features::strand_assembly::get_central_residues_in_each_of_two_edge_strands(), protocols::membrane::get_chain_and_z(), protocols::features::strand_assembly::get_closest_distance_between_strands(), core::scoring::magnesium::get_cos_theta(), core::scoring::disulfides::FullatomDisulfidePotential::get_disulfide_params(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), protocols::pockets::NonPlaidFingerprint::get_electrostatics_energy(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::get_fixed_pt(), protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms(), protocols::matdes::get_matching_subunits(), protocols::features::strand_assembly::StrandBundleFeatures::get_nearest_res_from_strand(), protocols::relax::LocalRelax::get_neighbor_graph(), protocols::electron_density::DockPDBIntoDensityMover::get_radius(), protocols::electron_density::get_radius(), protocols::electron_density::get_spectrum(), protocols::hybridization::get_superposition_transformation(), protocols::hybridization::CartesianSampler::get_transform(), protocols::simple_moves::BBConRotMover::get_VdRdPhi(), protocols::simple_moves::BBGaussianMover::get_VdRdPhi(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), protocols::loops::has_severe_pep_bond_geom_issues(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::methods::MMLJEnergyInter::heavyatom_heavyatom_energy(), core::scoring::lkball::lkbtrie::LKBTrieEvaluator::heavyatom_heavyatom_energy(), core::scoring::methods::MMLJEnergyInter::heavyatom_hydrogenatom_energy(), protocols::seeded_abinitio::SegmentHybridizer::hybridize(), core::scoring::methods::MMLJEnergyInter::hydrogenatom_heavyatom_energy(), core::scoring::methods::MMLJEnergyInter::hydrogenatom_hydrogenatom_energy(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::pockets::NonPlaidFingerprint::include_eggshell_points_based_on_known_ligand(), protocols::motifs::LigandMotifSearch::incorporate_motifs(), protocols::motifs::MotifSearch::incorporate_motifs(), core::energy_methods::EnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::energy_methods::MembraneEnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::energy_methods::FaMPEnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::scoring::MembranePotential::init_membrane_center_normal(), protocols::topology_broker::RigidChunkClaimer::initialize_dofs(), protocols::rbsegment_relax::FragInsertAndAlignMover::initialize_rb_fragments(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), protocols::features::HBondFeatures::insert_site_atoms_row(), core::scoring::etable::TableLookupEvaluator::interpolate_bins(), core::scoring::etable::Etable::interpolated_analytic_etable_evaluation(), core::pose::rna::is_rna_chainbreak(), protocols::features::strand_assembly::is_this_strand_at_edge(), core::pose::rna::is_tna_chainbreak(), protocols::features::strand_assembly::StrandBundleFeatures::judge_facing(), protocols::features::strand_assembly::judge_facing(), protocols::loops::loop_closure::ccd::load_coords_and_torsions(), protocols::loop_grower::LoopPartialSolution::LoopPartialSolution(), protocols::simple_moves::BBConRotMover::make_move(), protocols::pockets::ElectrostaticpotentialGrid::mark_protein_espGrid_points(), core::scoring::electron_density::ElectronDensity::matchAtomFast(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), core::scoring::electron_density::ElectronDensity::matchPose(), core::scoring::electron_density::ElectronDensity::matchPoseInPocket(), core::scoring::electron_density::ElectronDensity::matchRes(), core::scoring::electron_density::ElectronDensity::matchResFast(), protocols::motifs::Motif::Motif(), protocols::ligand_docking::ga_ligand_dock::atmInfo::nbr_atom(), core::scoring::nmr::NMRDummySpinlabelConformer::NMRDummySpinlabelConformer(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), protocols::electron_density::BfactorMultifunc::operator()(), core::scoring::elec::electrie::ElecAtom::operator<(), core::scoring::etable::etrie::EtableAtom::operator<(), core::scoring::lkball::lkbtrie::LKBAtom::operator<(), core::scoring::mm::mmtrie::MMEnergyTableAtom::operator<(), core::scoring::elec::electrie::ElecAtom::operator==(), core::scoring::etable::etrie::EtableAtom::operator==(), core::scoring::lkball::lkbtrie::LKBAtom::operator==(), core::scoring::mm::mmtrie::MMEnergyTableAtom::operator==(), core::conformation::Residue::orient_onto_residue(), core::conformation::Residue::orient_onto_residue_peptoid(), protocols::dna::PDBOutput::output_hbond_info(), core::pack::interaction_graph::InvRotamerDots::overlap_exposed(), protocols::hybridization::MRMover::pack_missing_sidechains(), protocols::match::NumNeighborsMPM::passes_com_vector_criterion(), protocols::ncbb::oop::pep_COM(), core::conformation::Residue::place(), protocols::motifs::Motif::place_atom_(), protocols::cryst::MakeLatticeMover::place_near_origin(), protocols::motifs::Motif::place_residue_helper(), protocols::electron_density::pose_spherical_samples(), core::scoring::PQR::PQR(), core::energy_methods::FA_GrpElecEnergy::precalc_context(), core::scoring::elec::electrie::ElecAtom::print(), core::scoring::etable::etrie::EtableAtom::print(), core::scoring::lkball::lkbtrie::LKBAtom::print(), core::scoring::mm::mmtrie::MMEnergyTableAtom::print(), protocols::viewer::print_node(), core::energy_methods::PoissonBoltzmannEnergy::protein_position_equal_within(), core::conformation::membrane::membrane_geometry::Bicelle::protein_slice_diameter_at_mem_cen(), core::conformation::membrane::membrane_geometry::Slab::r_alpha(), core::conformation::membrane::MembraneGeometry::r_alpha_p_z(), core::pose::radius_of_gyration(), protocols::sewing::hashing::ModelFileReader::read_model_file(), core::conformation::symmetry::SymmetricConformation::recalculate_transforms(), protocols::pockets::PocketGrid::recenter(), protocols::fldsgn::NcontactsCalculator::recompute(), protocols::toolbox::match_enzdes_util::InvrotTreeNode::remove_invrots_clashing_with_parent_res(), protocols::features::SaltBridgeFeatures::report_features(), protocols::features::ModelFeatures::report_features(), 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::energy_methods::EnvSmoothEnergy::residue_energy(), core::energy_methods::MembraneEnvSmoothEnergy::residue_energy(), core::energy_methods::BurialEnergy::residue_energy(), core::energy_methods::FaMPEnvSmoothEnergy::residue_energy(), core::energy_methods::CenPairEnergy::residue_pair_energy(), core::energy_methods::CenRotPairEnergy::residue_pair_energy(), core::energy_methods::MembraneCenPairEnergy::residue_pair_energy(), core::energy_methods::SmoothCenPairEnergy::residue_pair_energy(), core::energy_methods::CenHBEnergy::residue_pair_energy(), core::energy_methods::LK_hack::residue_pair_energy(), core::energy_methods::MPPairEnergy::residue_pair_energy(), core::energy_methods::PointWaterEnergy::residue_pair_energy(), core::scoring::methods::MMBondAngleEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), core::scoring::methods::MMLJEnergyInter::residue_pair_energy(), core::conformation::membrane::MembraneInfo::residue_z_position(), core::conformation::symmetry::return_nearest_residue(), core::pose::return_nearest_residue(), protocols::symmetry::SymmetrySlider::rg(), protocols::toolbox::pose_manipulation::rigid_body_move(), protocols::pockets::PlaidFingerprint::rmsd(), protocols::loop_grower::LoopGrower::RMStonative(), protocols::membrane::rsd_closest_to_chain_tm_com(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), protocols::qsar::scoring_grid::SolvationMetaGrid::score(), core::scoring::MembranePotential::score_normal_center(), protocols::features::strand_assembly::see_whether_sheet_is_antiparallel(), core::select::util::select_coord_for_residue(), protocols::hbnet::HBNet::set_constraints(), protocols::electron_density::DockPDBIntoDensityMover::set_nRsteps_from_pose(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), protocols::pockets::NonPlaidFingerprint::set_origin_from_residue(), protocols::design_opt::Supercharge::set_surface(), protocols::scoring::methods::pcs2::GridSearchIteratorCA::set_vec(), core::conformation::Residue::set_xyz(), protocols::flexpep_docking::FlexPepDockingFlags::setDefaultAnchors(), core::scoring::NeighborList::setup(), core::energy_methods::FaMPEnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::EnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::FastSAXSEnergy::setup_for_derivatives(), core::energy_methods::MembraneEnvSmoothEnergy::setup_for_derivatives(), core::energy_methods::FastSAXSEnergy::setup_for_scoring(), protocols::hybridization::setup_user_coordinate_constraints(), protocols::features::strand_assembly::StrandBundleFeatures::sheet_dis_by_terminals(), protocols::features::strand_assembly::StrandBundleFeatures::sheet_torsion(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::single_bunsat_thorough_check(), protocols::loop_grower::LoopPartialSolutionStore::skeleton_filter(), protocols::hybridization::DDomainParse::split(), protocols::rbsegment_relax::ConfChangeMover::stage2(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata(), core::util::switch_to_centroid_rot_set(), protocols::topology_broker::RigidChunkClaimer::switch_to_fullatom(), core::scoring::MembranePotential::termini_penalty(), protocols::sewing::requirements::ClashRequirement::test(), core::scoring::MembranePotential::tm_projection_penalty(), protocols::loop_grower::transform_to_closest_symmunit(), protocols::hybridization::MRMover::trim_target_pose(), core::scoring::nmr::pcs::PCSSingleSet::update_spin_coordinates(), core::scoring::nmr::pre::PREMultiSet::update_spin_coordinates(), core::scoring::nmr::rdc::RDCMultiSet::update_spin_coordinates(), protocols::scoring::methods::pcs::PCS_data::update_X_Y_Z_all(), protocols::scoring::methods::pcs2::PcsDataCenter::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs1::PCS_data_Ts1::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs2::PCS_data_Ts2::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs3::PCS_data_Ts3::update_X_Y_Z_all(), protocols::scoring::methods::pcsTs4::PCS_data_Ts4::update_X_Y_Z_all(), protocols::features::helixAssembly::HelixBundleFeatures::validate_bundle(), core::scoring::epr_deer::EPRSpinLabel::weight(), core::pack::interaction_graph::InvRotamerDots::write_circle_intersection_mask_to_kinemage(), protocols::features::strand_assembly::write_number_of_electrostatic_interactions_of_residues_to_files(), core::scoring::PoissonBoltzmannPotential::write_pqr(), protocols::features::strand_assembly::WriteToDB_ending_loop(), protocols::features::strand_assembly::WriteToDB_starting_loop(), core::scoring::elec::electrie::ElecAtom::xyz(), core::scoring::lkball::lkbtrie::LKBAtom::xyz(), core::chemical::ICoorAtomID::xyz(), and core::conformation::Residue::xyz().

xyz() [2/2]

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

inline

Sets the atom coordinates using an xyzVector.

References xyz_.

Member Data Documentation

mm_type_

ShortSize core::conformation::Atom::mm_type_

private

Referenced by mm_type().

type_

ShortSize core::conformation::Atom::type_

private

Referenced by type().

xyz_

Vector core::conformation::Atom::xyz_

private

Referenced by show(), and xyz().

---

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

• src/core/conformation/Atom.hh
• src/core/conformation/Atom.cc