Rosetta 3.4
Public Member Functions
core::conformation::Atom Class Reference

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

#include <Atom.hh>

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List of all members.

Public Member Functions

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

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 ( ) [inline, virtual]

destructor


Member Function Documentation

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

set the atom type number

Referenced by core::scoring::methods::apply_lk_ball_fraction_weight_for_hbonds(), 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(), core::scoring::methods::SuckerEnergy::eval_atom_derivative(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_dE_dR_over_r_(), core::scoring::methods::LK_BallEnergy::eval_desolvation_derivs_no_count_pair(), protocols::match::fill_grid_with_backbone_heavyatom_spheres(), protocols::match::fill_grid_with_residue_heavyatom_spheres(), protocols::match::fill_grid_with_residue_spheres(), protocols::match::downstream::RigidLigandBuilder::initialize_from_residue(), protocols::match::downstream::LigandConformerBuilder::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::hackelec::ElecAtom::operator<(), core::scoring::etable::etrie::EtableAtom::operator<(), core::conformation::operator<<(), core::scoring::hackelec::ElecAtom::operator==(), core::scoring::etable::etrie::EtableAtom::operator==(), 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().

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

Sets the atom coordinates using an xyzVector.

Vector const& core::conformation::Atom::xyz ( ) const [inline]

Returns the atom coordinates as an xyzVector.

Referenced by core::scoring::geometric_solvation::add_to_individual_sol_energies(), protocols::simple_filters::SheetFilter::apply(), protocols::rigid::RotateJumpAxisMover::apply(), protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::rbsegment_relax::FragInsertAndAlignMover::apply(), protocols::protein_interface_design::movers::SpinMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::hybridize::CartesianHybridize::apply(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::comparative_modeling::hybridize::CartesianHybridize::apply_frag(), protocols::comparative_modeling::hybridize::CartesianHybridize::apply_frame(), 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::scoring::methods::pcs::PCS_Energy::calculate_scores_and_tensors_from_pose_and_PCS_data(), core::pack::task::operation::util::cbeta_vector(), protocols::comparative_modeling::hybridize::FoldTreeHybridize::center_of_mass(), protocols::features::helixAssembly::HelixBundleFeatures::checkHelixContacts(), 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(), protocols::abinitio::copy_side_chains(), core::scoring::orbitals::OrbitalsAssigned::cp_function(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::hbonds::create_don_orientation_vector(), 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::Conformation::detect_disulfides(), protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::methods::SuckerEnergy::eval_atom_derivative(), core::scoring::methods::MMLJEnergyIntra::eval_atom_derivative(), core::scoring::methods::MMLJEnergyInter::eval_atom_derivative(), core::scoring::methods::LinearChainbreakEnergy::eval_atom_derivative(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensCenEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::etable::CoarseEtableEnergy::eval_dE_dR_over_r_(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_dE_dR_over_r_(), core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::methods::CartesianBondedEnergy::eval_intrares_energy(), core::scoring::methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CenHBEnergy::eval_residue_pair_derivatives(), protocols::electron_density::fast2DRotAlignPose(), protocols::electron_density::fastTransAlignPose(), core::io::silent::BinaryRNASilentStruct::fill_struct(), core::io::silent::BinaryProteinSilentStruct::fill_struct(), protocols::electron_density::findLoopFromDensity(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), core::scoring::orbitals::OrbitalsAssigned::get_hydrogens(), core::scoring::orbitals::OrbitalsAssigned::get_lp_xyz(), protocols::comparative_modeling::hybridize::InsertChunkMover::get_superposition_transformation(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), 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(), 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(), protocols::topology_broker::RigidChunkClaimer::initialize_dofs(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), core::scoring::etable::BaseEtableEnergy< Derived >::interpolate_bins(), 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::mm::mmtrie::MMEnergyTableAtom::operator<(), core::scoring::hackelec::ElecAtom::operator<(), core::scoring::etable::etrie::EtableAtom::operator<(), core::conformation::operator<<(), core::scoring::mm::mmtrie::MMEnergyTableAtom::operator==(), core::scoring::hackelec::ElecAtom::operator==(), core::scoring::etable::etrie::EtableAtom::operator==(), core::conformation::Residue::orient_onto_residue(), 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_(), protocols::pockets::PlaidFingerprint::PlaidFingerprint(), core::scoring::mm::mmtrie::MMEnergyTableAtom::print(), core::scoring::hackelec::ElecAtom::print(), core::scoring::etable::etrie::EtableAtom::print(), protocols::viewer::print_node(), protocols::pockets::PocketGrid::recenter(), protocols::features::helixAssembly::HelixBundleFeatures::report_features(), protocols::features::OrbitalsFeatures::report_haro_orbital_interactions(), protocols::features::OrbitalsFeatures::report_hpol_orbital_interactions(), protocols::geometry::residue_center_of_mass(), core::conformation::symmetry::residue_center_of_mass(), core::scoring::methods::MembraneEnvSmoothEnergy::residue_energy(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::methods::BurialEnergy::residue_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::MembraneCenPairEnergy::residue_pair_energy(), core::scoring::methods::LK_hack::residue_pair_energy(), core::scoring::methods::CenPairEnergy::residue_pair_energy(), core::scoring::methods::CartesianBondedEnergy::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::pack::task::operation::util::select_coord_for_residue(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), protocols::features::OrbitalsFeatures::set_OrbOrb_features_data(), core::conformation::Residue::set_xyz(), protocols::flexpep_docking::FlexPepDockingFlags::setDefaultAnchors(), core::scoring::saxs::FastSAXSEnergy::setup_for_derivatives(), core::scoring::methods::MembraneEnvSmoothEnergy::setup_for_derivatives(), core::scoring::methods::EnvSmoothEnergy::setup_for_derivatives(), core::scoring::saxs::FastSAXSEnergy::setup_for_scoring(), protocols::pockets::NonPlaidFingerprint::setup_from_EggshellGrid(), 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::conformation::Residue::xyz(), and core::chemical::ICoorAtomID::xyz().


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