basic atom type More...

#include <AtomType.hh>

Collaboration diagram for core::chemical::AtomType:

Public Member Functions
	AtomType (std::string const &name_in, std::string const element_in)
	Construct a new atom type with its name and element. More...

	AtomType (AtomType const &src)

void	print (std::ostream &out) const

Real	lk_lambda () const
	Lazaridis and Karplus solvation parameter – lambda. More...

Real	lk_dgfree () const
	Lazaridis and Karplus solvation parameter – dgfree. More...

Real	lk_volume () const
	Lazaridis and Karplus solvation parameter – volume. More...

Real	lj_radius () const
	Lennard-Jones 6-12 potential parameter – atom radius. More...

Real	lj_wdepth () const
	Lennard-Jones 6-12 potential parameter – well depth. More...

bool	is_acceptor () const
	whether atom is a hydrogen bond acceptor More...

bool	is_donor () const
	whether atom is a hydrogen bond donor More...

bool	is_polar_hydrogen () const
	whether atom is a polar hydrogen atom More...

bool	is_hydrogen () const
	whether atom is a hydrogen atom More...

bool	is_heavyatom () const
	whether atom is a heavy atom More...

bool	is_virtual () const
	is atom type virtual? More...

bool	is_h2o () const
	whether atom is a water More...

bool	is_aromatic () const
	whether atom is aromatic More...

bool	atom_has_orbital () const
	atom has an orbital attached More...

bool	is_haro () const
	is the H atom aromatic? More...

void	set_parameter (std::string const &param, Real const setting)
	set LJ and LK solvation parameter for this atom type More...

void	set_property (std::string const &property, bool const setting)
	set relevant properties for this atom type hh More...

Hybridization const &	hybridization () const
	retrieve an atom's hybridization status. More...

void	clear_properties ()
	set all standard properties to false, set hybridization to UNKNOWN_HYBRID, and clear extra properties More...

void	add_property (std::string const &property)
	set standard property to true, or set the specified hybridization More...

utility::vector1< std::string >	get_all_properties () const

std::string	element () const
	returns the one- or two-letter element type More...

std::string	atom_type_name () const

Real	extra_parameter (Size const index) const
	return an additional, non-hardcoded property More...

void	set_extra_parameter (Size const index, Real const setting)
	return an additional, non-hardcoded property More...

void	set_all_extra_parameters (utility::vector1< Real > const &extra_parameters)
	all the extra parameters at once More...

std::string const &	name () const

Private Attributes
std::string const	name_

std::string const	element_

Real	lj_radius_

Real	lj_wdepth_

Real	lk_lambda_

Real	lk_volume_

Real	lk_dgfree_

utility::vector1< Real >	extra_parameters_

bool	is_acceptor_

bool	is_donor_

bool	is_polar_hydrogen_

bool	is_h2o_

bool	is_aromatic_

bool	atom_has_orbitals_

bool	atom_is_virtual_

Hybridization	hybridization_

Friends
std::ostream &	operator<< (std::ostream &out, const AtomType &atom_type)

Detailed Description

basic atom type

name, element, certain properties and parameters

Definition at line 64 of file AtomType.hh.

Constructor & Destructor Documentation

core::chemical::AtomType::AtomType	(	std::string const &	name_in,
		std::string const	element_in
	)

inline

Construct a new atom type with its name and element.

All its properties are unset by default.

Definition at line 72 of file AtomType.hh.

core::chemical::AtomType::AtomType ( AtomType const & src)

inline

Definition at line 85 of file AtomType.hh.

Member Function Documentation

void core::chemical::AtomType::add_property ( std::string const & property)

set standard property to true, or set the specified hybridization

Definition at line 194 of file AtomType.cc.

References atom_has_orbitals_, atom_is_virtual_, hybridization_, is_acceptor_, is_aromatic_, is_donor_, is_h2o_, is_polar_hydrogen_, name(), core::chemical::RING_HYBRID, core::chemical::SP2_HYBRID, and core::chemical::SP3_HYBRID.

Referenced by core::chemical::AtomTypeSet::read_atom_type_properties_table().

bool core::chemical::AtomType::atom_has_orbital ( ) const

inline

atom has an orbital attached

Definition at line 196 of file AtomType.hh.

References atom_has_orbitals_.

Referenced by core::io::pdb::dump_pdb_residue(), get_all_properties(), print(), and core::chemical::ResidueType::update_derived_data().

std::string core::chemical::AtomType::atom_type_name ( ) const

inline

Definition at line 253 of file AtomType.hh.

References name_.

Referenced by core::scoring::FACTSResidueInfo::modify_volume(), protocols::motifs::Motif::Motif(), and core::chemical::ResidueDatabaseIO::report_residue_type_atom().

void core::chemical::AtomType::clear_properties ( )

set all standard properties to false, set hybridization to UNKNOWN_HYBRID, and clear extra properties

Definition at line 181 of file AtomType.cc.

References atom_has_orbitals_, atom_is_virtual_, extra_parameters_, hybridization_, is_acceptor_, is_aromatic_, is_donor_, is_h2o_, is_polar_hydrogen_, and core::chemical::UNKNOWN_HYBRID.

std::string core::chemical::AtomType::element ( ) const

inline

returns the one- or two-letter element type

Definition at line 247 of file AtomType.hh.

References element_.

Referenced by core::scoring::calc_per_atom_sasa(), core::scoring::calc_per_res_hydrophobic_sasa(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::calculate_alt_state_hpatch_score(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), core::pack::interaction_graph::RotamerDotsRadiusData::get_NACCESS_SASA_radii_with_expanded_polars(), protocols::match::initialize_atomtype_2_probe_radius_map(), protocols::toolbox::match_enzdes_util::LigandConformer::initialize_from_residue(), protocols::match::downstream::LigandConformerBuilder::initialize_from_residue(), protocols::match::downstream::RigidLigandBuilder::initialize_from_residue(), core::chemical::orbitals::AssignOrbitals::make_orbital_type_name(), print(), protocols::swa::rna::print_atom_info(), protocols::swa::rna::print_individual_atom_info(), core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::set_rotamer(), core::pack::interaction_graph::HPatchNode< V, E, G >::set_rotamers(), core::chemical::AtomTypeDatabaseIO::write_atom_type_table(), protocols::match::output::ResidueKinemageWriter::write_rsd_coords(), and core::conformation::ResidueKinWriter::write_rsd_coords().

Real core::chemical::AtomType::extra_parameter ( Size const index) const

inline

return an additional, non-hardcoded property

Definition at line 260 of file AtomType.hh.

References extra_parameters_.

Referenced by core::chemical::AtomTypeSet::get_default_parameter(), core::scoring::GenBornResidueInfo::initialize(), core::scoring::FACTSResidueInfo::initialize_parameters(), and core::chemical::AtomTypeDatabaseIO::write_atom_type_extra_parameters_table().

utility::vector1< std::string > core::chemical::AtomType::get_all_properties ( ) const

Definition at line 224 of file AtomType.cc.

References atom_has_orbital(), hybridization(), is_acceptor(), is_aromatic(), is_donor(), is_h2o(), is_polar_hydrogen(), is_virtual(), name(), core::chemical::RING_HYBRID, core::chemical::SP2_HYBRID, core::chemical::SP3_HYBRID, and core::chemical::UNKNOWN_HYBRID.

Referenced by core::chemical::AtomTypeDatabaseIO::write_atom_type_properties_table().

Hybridization const& core::chemical::AtomType::hybridization ( ) const

inline

retrieve an atom's hybridization status.

Definition at line 226 of file AtomType.hh.

References hybridization_.

Referenced by core::scoring::methods::apply_lk_ball_fraction_weight_for_hbonds(), core::pack::rotamer_set::build_acceptor_acceptor_waters(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::scoring::hbonds::create_acc_orientation_vector(), core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::get_acceptor_base_atm_xyz(), core::scoring::geometric_solvation::GeometricSolEnergy::get_acceptor_base_atm_xyz(), get_all_properties(), core::scoring::rna::RNA_Mg_Energy::get_cos_theta(), core::scoring::hbonds::get_hb_acc_chem_type(), print(), and core::scoring::methods::setup_water_builders_for_residue_type().

bool core::chemical::AtomType::is_acceptor ( ) const

inline

whether atom is a hydrogen bond acceptor

Definition at line 143 of file AtomType.hh.

References is_acceptor_.

Referenced by core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), get_all_properties(), core::scoring::etable::Etable::precalc_etable_coefficients(), print(), protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), core::scoring::methods::LK_hack::residue_pair_energy(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), and core::chemical::ResidueType::update_derived_data().

bool core::chemical::AtomType::is_aromatic ( ) const

inline

whether atom is aromatic

Definition at line 189 of file AtomType.hh.

References is_aromatic_.

Referenced by get_all_properties(), core::scoring::rna::RNA_FullAtomStackingEnergy::is_aro(), and print().

bool core::chemical::AtomType::is_donor ( ) const

inline

whether atom is a hydrogen bond donor

Definition at line 150 of file AtomType.hh.

References is_donor_.

Referenced by protocols::qsar::scoring_grid::HbaGrid::atom_score(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), get_all_properties(), core::scoring::etable::Etable::precalc_etable_coefficients(), print(), protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::qsar::scoring_grid::HbdGrid::refresh(), core::scoring::methods::LK_hack::residue_pair_energy(), and protocols::qsar::scoring_grid::HbaGrid::score().

bool core::chemical::AtomType::is_h2o ( ) const

inline

whether atom is a water

Definition at line 182 of file AtomType.hh.

References is_h2o_.

Referenced by core::scoring::calc_atom_masks(), get_all_properties(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::WaterAdductHBondPotential::h2o_hbond_score_1way(), core::scoring::etable::Etable::precalc_etable_coefficients(), print(), and core::scoring::methods::WaterAdductIntraEnergy::residue_energy().

bool core::chemical::AtomType::is_haro ( ) const

inline

is the H atom aromatic?

Definition at line 202 of file AtomType.hh.

References name_.

Referenced by core::chemical::ResidueType::update_derived_data().

bool core::chemical::AtomType::is_heavyatom ( ) const

inline

whether atom is a heavy atom

Definition at line 172 of file AtomType.hh.

References element_.

Referenced by core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), core::scoring::saxs::FastSAXSEnergy::eval_atom_derivative(), core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::scoring::electron_density::PattersonCorrEnergy::eval_atom_derivative(), core::scoring::electron_density::ElecDensEnergy::eval_atom_derivative(), core::scoring::electron_density::FastDensEnergy::eval_atom_derivative(), core::conformation::Conformation::fill_missing_atoms(), core::scoring::packing::PoseBalls::PoseBalls(), and core::import_pose::atom_tree_diffs::rms_error_with_noise().

bool core::chemical::AtomType::is_hydrogen ( ) const

inline

whether atom is a hydrogen atom

Definition at line 164 of file AtomType.hh.

References element_.

Referenced by core::scoring::automorphic_rmsd(), core::scoring::calc_per_res_hydrophobic_sasa(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf_without_ff(), protocols::ligand_docking::frac_atoms_within(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::packing::PoseBallsLite::PoseBallsLite(), core::scoring::saxs::SAXSEnergy::rehash_form_factors(), core::conformation::setup_links(), and core::chemical::ResidueType::update_derived_data().

bool core::chemical::AtomType::is_polar_hydrogen ( ) const

inline

whether atom is a polar hydrogen atom

Definition at line 157 of file AtomType.hh.

References is_polar_hydrogen_.

Referenced by core::pack::rotamer_set::build_moving_O_bridge_waters(), core::scoring::calc_per_atom_sasa(), get_all_properties(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::packing::PoseBallsLite::PoseBallsLite(), core::scoring::etable::Etable::precalc_etable_coefficients(), print(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), and core::chemical::ResidueType::update_derived_data().

bool core::chemical::AtomType::is_virtual ( ) const

is atom type virtual?

Definition at line 98 of file AtomType.cc.

References atom_is_virtual_, and name_.

Referenced by core::io::pdb::FileData::append_residue(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), get_all_properties(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), core::conformation::Residue::is_virtual(), and core::scoring::methods::MMBondLengthEnergy::residue_pair_energy().

Real core::chemical::AtomType::lj_radius ( ) const

inline

Lennard-Jones 6-12 potential parameter – atom radius.

Definition at line 128 of file AtomType.hh.

References lj_radius_.

Referenced by protocols::qsar::scoring_grid::VdwGrid::atom_score(), protocols::swa::rna::fast_full_atom_VDW_repulsion_screen(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::chemical::AtomTypeSet::get_default_parameter(), protocols::sic_dock::SICFast::init(), protocols::match::initialize_atomtype_2_probe_radius_map(), core::scoring::packstat::LeeRichards::LeeRichards(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::packing::PoseBallsLite::PoseBallsLite(), print(), protocols::qsar::scoring_grid::VdwGrid::refresh(), core::scoring::methods::GaussianOverlapEnergy::residue_pair_energy(), protocols::qsar::scoring_grid::VdwGrid::score(), core::scoring::methods::LK_BallEnergy::setup_d2_bounds(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::update_VDW_screen_bin(), and core::chemical::AtomTypeDatabaseIO::write_atom_type_table().

Real core::chemical::AtomType::lj_wdepth ( ) const

inline

Lennard-Jones 6-12 potential parameter – well depth.

Definition at line 135 of file AtomType.hh.

References lj_wdepth_.

Referenced by protocols::toolbox::pose_metric_calculators::fast_clash_check(), protocols::forge::remodel::fast_clash_check(), core::chemical::AtomTypeSet::get_default_parameter(), print(), and core::chemical::AtomTypeDatabaseIO::write_atom_type_table().

Real core::chemical::AtomType::lk_dgfree ( ) const

inline

Lazaridis and Karplus solvation parameter – dgfree.

Definition at line 114 of file AtomType.hh.

References lk_dgfree_.

Referenced by core::chemical::AtomTypeSet::get_default_parameter(), print(), and core::chemical::AtomTypeDatabaseIO::write_atom_type_table().

Real core::chemical::AtomType::lk_lambda ( ) const

inline

Lazaridis and Karplus solvation parameter – lambda.

Definition at line 107 of file AtomType.hh.

References lk_lambda_.

Referenced by core::chemical::AtomTypeSet::get_default_parameter(), print(), and core::chemical::AtomTypeDatabaseIO::write_atom_type_table().

Real core::chemical::AtomType::lk_volume ( ) const

inline

Lazaridis and Karplus solvation parameter – volume.

Definition at line 121 of file AtomType.hh.

References lk_volume_.

Referenced by core::chemical::AtomTypeSet::get_default_parameter(), print(), and core::chemical::AtomTypeDatabaseIO::write_atom_type_table().

std::string const& core::chemical::AtomType::name ( ) const

inline

Definition at line 278 of file AtomType.hh.

void core::chemical::AtomType::print ( std::ostream & out) const

Definition at line 56 of file AtomType.cc.

References atom_has_orbital(), element(), extra_parameters_, hybridization(), is_acceptor(), is_aromatic(), is_donor(), is_h2o(), is_polar_hydrogen(), lj_radius(), lj_wdepth(), lk_dgfree(), lk_lambda(), lk_volume(), name(), core::chemical::RING_HYBRID, core::chemical::SP2_HYBRID, core::chemical::SP3_HYBRID, and core::chemical::UNKNOWN_HYBRID.

Referenced by core::chemical::operator<<().

void core::chemical::AtomType::set_all_extra_parameters ( utility::vector1< Real > const & extra_parameters)

all the extra parameters at once

Definition at line 246 of file AtomType.cc.

References extra_parameters_.

void core::chemical::AtomType::set_extra_parameter	(	Size const	index,
		Real const	setting
	)

inline

return an additional, non-hardcoded property

Definition at line 267 of file AtomType.hh.

References extra_parameters_.

Referenced by core::chemical::AtomTypeSet::read_atom_type_extra_parameters_table().

void core::chemical::AtomType::set_parameter	(	std::string const &	param,
		Real const	setting
	)

set LJ and LK solvation parameter for this atom type

currently parameters are "LJ_RADIUS","LJ_WDEPTH","LK_VOLUME", "LK_DGFREE","LK_LAMBDA".It will abort if the parameter name is not recoganized. Supplemented by membrane specific solvation parameters: "MEMB_LK_DGFREE","MEMB_LK_DGREFCE","LK_DGREFCE". These are the header files in atom_properties.txt

Definition at line 114 of file AtomType.cc.

References lj_radius_, lj_wdepth_, lk_dgfree_, lk_lambda_, and lk_volume_.

Referenced by core::chemical::AtomTypeSet::create_atom_type_from_database(), and core::chemical::AtomTypeSet::read_file().

void core::chemical::AtomType::set_property	(	std::string const &	property,
		bool const	setting
	)

set relevant properties for this atom type hh

set relevant properties for this atom type

currently properties are "ACCEPTOR","DONOR","POLAR_HYDROGEN", "H2O", and hybridization types including "SP2_HYBRID", "SP3_HYBRID" and "RING_HYBRID". It will abort if the property name is not recoganized. To add properties, edit atom_properties.txt and add your property to the last column then add code here that will read the property.

Definition at line 150 of file AtomType.cc.

References atom_has_orbitals_, atom_is_virtual_, hybridization_, is_acceptor_, is_aromatic_, is_donor_, is_h2o_, is_polar_hydrogen_, core::chemical::RING_HYBRID, core::chemical::SP2_HYBRID, and core::chemical::SP3_HYBRID.