core::conformation::Atom Class Reference

#include <Atom.hh>

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 ()
	destructor More...
void	show (std::ostream &output=std::cout) const
	Generate string representation of conformation::Atom 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

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

inline

Default constructor.

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

set the mm atom type number

References mm_type_.

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

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().

void core::conformation::Atom::show

(

std::ostream &

output = std::cout

)

const

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

References numeric::xyzVector< class >::x(), xyz_, numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

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

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::etable::Etable::analytic_lk_derivatives(), core::scoring::etable::Etable::analytic_lk_energy(), 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_(), core::scoring::etable::TableLookupEvaluator::atom_pair_lk_energy_and_deriv_v(), core::scoring::etable::TableLookupEvaluator::atom_pair_lk_energy_and_deriv_v_efficient(), core::scoring::methods::LK_BallEnergy::calculate_lk_ball_atom_energies(), core::scoring::methods::LK_BallEnergy::calculate_lk_ball_atom_energies_cp(), 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::methods::LK_hack::eval_dE_dR_over_r(), core::scoring::methods::Fa_MbsolvEnergy::eval_dE_dR_over_r(), core::scoring::membrane::FaMPSolvEnergy::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::membrane::FaMPEnvEnergy::eval_fa_mbenv(), core::scoring::rna::RNA_LJ_BaseEnergy::eval_lj(), core::scoring::methods::Fa_MbsolvEnergy::eval_lk(), core::scoring::membrane::FaMPSolvEnergy::eval_lk(), core::coarse::CoarseEtable::get_eID(), 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::elec::ElecAtom::operator<(), core::scoring::etable::etrie::EtableAtom::operator==(), core::scoring::elec::ElecAtom::operator==(), core::pack::interaction_graph::InvRotamerDots::overlap_exposed(), core::scoring::etable::TableLookupEvaluator::pair_energy_H(), core::scoring::etable::BaseEtableEnergy< Derived >::pair_energy_H_(), core::scoring::methods::LK_hack::residue_pair_energy(), core::scoring::methods::LK_BallEnergy::residue_pair_energy(), and core::scoring::methods::LK_BallEnergy::sum_deriv_contributions_for_atom_pair_one_way().

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

inline

Returns the AtomType number.

References type_.

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

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(), core::scoring::etable::Etable::analytic_lk_derivatives(), core::scoring::etable::Etable::analytic_lk_energy(), 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::methods::ProQ_Energy::atom_feature(), core::conformation::membrane::MembraneInfo::atom_z_position(), core::scoring::orbitals::OrbitalsStatistics::bb_stats(), core::conformation::build_residue_tree(), core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_delta_internal_coordinates(), core::pack::dunbrack::cenrot::CentroidRotamerSampleData::cal_distance_squared(), core::scoring::methods::ProQ_Energy::calculateZ(), core::pack::task::operation::util::cbeta_vector(), core::membrane::geometry::center_of_mass(), core::pose::center_of_mass(), 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::methods::ProQ_Energy::crd(), 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_bonds(), core::scoring::methods::LinearChainbreakEnergy::do_score_dev(), core::scoring::methods::LinearChainbreakEnergy::do_score_ovp(), 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::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::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::membrane::FaMPSolvEnergy::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::CenRotEnvEnergy::eval_residue_derivatives(), core::pack::dunbrack::cenrot::CenRotDunEnergy::eval_residue_derivatives(), core::scoring::methods::SmoothCenPairEnergy::eval_residue_pair_derivatives(), core::scoring::methods::CenHBEnergy::eval_residue_pair_derivatives(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_orientation_score(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary::fill_rotamer_vector(), core::io::silent::BinarySilentStruct::fill_struct(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_acceptor_base_atm_xyz(), 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::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(), core::scoring::orbitals::OrbitalsAssigned::get_hydrogens(), core::scoring::orbitals::OrbitalsAssigned::get_lp_xyz(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::elec::FA_ElecEnergy::heavyatom_heavyatom_energy(), core::scoring::methods::MMLJEnergyInter::heavyatom_hydrogenatom_energy(), core::scoring::elec::FA_ElecEnergy::heavyatom_hydrogenatom_energy(), core::scoring::methods::MMLJEnergyInter::hydrogenatom_heavyatom_energy(), core::scoring::elec::FA_ElecEnergy::hydrogenatom_heavyatom_energy(), core::scoring::methods::MMLJEnergyInter::hydrogenatom_hydrogenatom_energy(), core::scoring::elec::FA_ElecEnergy::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(), core::scoring::methods::EnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::scoring::methods::MembraneEnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::scoring::membrane::FaMPEnvSmoothEnergy::increment_f1_f2_for_atom_pair(), core::scoring::etable::TableLookupEvaluator::interpolate_bins(), core::scoring::etable::BaseEtableEnergy< Derived >::interpolate_bins(), core::scoring::etable::Etable::interpolated_analytic_etable_evaluation(), core::scoring::methods::IdealParametersDatabase::lookup_bondangle_buildideal(), core::scoring::methods::IdealParametersDatabase::lookup_bondlength_buildideal(), 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_(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::scoring::etable::etrie::EtableAtom::operator<(), core::scoring::elec::ElecAtom::operator<(), core::scoring::mm::mmtrie::MMEnergyTableAtom::operator<(), core::scoring::etable::etrie::EtableAtom::operator==(), core::scoring::mm::mmtrie::MMEnergyTableAtom::operator==(), core::scoring::elec::ElecAtom::operator==(), core::conformation::Residue::orient_onto_residue(), core::conformation::Residue::orient_onto_residue_peptoid(), core::pack::interaction_graph::InvRotamerDots::overlap_exposed(), core::conformation::Residue::place(), core::scoring::etable::etrie::EtableAtom::print(), core::scoring::elec::ElecAtom::print(), core::scoring::mm::mmtrie::MMEnergyTableAtom::print(), core::scoring::methods::PoissonBoltzmannEnergy::protein_position_equal_within(), core::conformation::symmetry::SymmetricConformation::recalculate_transforms(), core::conformation::symmetry::residue_center_of_mass(), core::scoring::methods::EnvSmoothEnergy::residue_energy(), core::scoring::methods::MembraneEnvSmoothEnergy::residue_energy(), core::scoring::membrane::FaMPEnvSmoothEnergy::residue_energy(), core::scoring::methods::SmoothCenPairEnergy::residue_pair_energy(), core::scoring::methods::MembraneCenPairEnergy::residue_pair_energy(), core::scoring::methods::CenPairEnergy::residue_pair_energy(), core::scoring::methods::CenRotPairEnergy::residue_pair_energy(), core::scoring::membrane::MPPairEnergy::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(), core::conformation::membrane::MembraneInfo::residue_z_position(), core::membrane::geometry::return_nearest_residue(), core::conformation::symmetry::return_nearest_residue(), core::pose::return_nearest_residue(), core::scoring::orbitals::OrbitalsStatistics::sc_H_orbital(), core::scoring::MembranePotential::score_normal_center(), core::pack::task::operation::util::select_coord_for_residue(), core::conformation::Residue::set_xyz(), core::scoring::saxs::FastSAXSEnergy::setup_for_derivatives(), core::scoring::methods::EnvSmoothEnergy::setup_for_derivatives(), core::scoring::methods::MembraneEnvSmoothEnergy::setup_for_derivatives(), core::scoring::membrane::FaMPEnvSmoothEnergy::setup_for_derivatives(), core::scoring::saxs::FastSAXSEnergy::setup_for_scoring(), core::scoring::MembranePotential::termini_penalty(), 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

Referenced by mm_type().

ShortSize core::conformation::Atom::type_

private

Referenced by type().

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