basic atom type More...

#include <AtomType.hh>

Public Member Functions
	AtomType ()

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

	AtomType (AtomType const &)=default

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_repulsive () const
	is atom type repulsive (REPL, REPLS, HREPS) 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
	Get the name of this AtomType. Note that this is NOT the same as the atom name that is written out to PDB. You want pose.residue(i).atom_name(j) for that. More...

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...

void	name (std::string const &setting)

std::string const &	name () const
	Get the name of this AtomType. Note that this is NOT the same as the atom name that is written out to PDB. You want pose.residue(i).atom_name(j) for that. More...

Private Attributes
std::string	name_

std::string	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_

bool	atom_is_repulsive_

Hybridization	hybridization_

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

Detailed Description

basic atom type

name, element, certain properties and parameters

Constructor & Destructor Documentation

core::chemical::AtomType::AtomType ( )

inline

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

inline

Construct a new atom type with its name and element.

All its properties are unset by default.

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

default

Member Function Documentation

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

set standard property to true, or set the specified hybridization

References atom_has_orbitals_, atom_is_repulsive_, 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

References atom_has_orbitals_.

Referenced by get_all_properties(), and print().

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

inline

Get the name of this AtomType. Note that this is NOT the same as the atom name that is written out to PDB. You want pose.residue(i).atom_name(j) for that.

References name_.

Referenced by core::chemical::AutomorphismIterator::can_pair(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), core::scoring::facts::FACTSRsdTypeInfo::initialize_intrascale(), core::scoring::facts::FACTSRsdTypeInfo::initialize_parameters(), protocols::vardist_solaccess::VarSolDistSasaCalculator::initialize_sasa_arrays(), protocols::motifs::Motif::Motif(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), 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

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

References element_.

Referenced by core::scoring::calc_per_atom_sasa(), core::scoring::calc_per_res_hydrophobic_sasa(), core::scoring::sasa::SasaCalc::calc_per_res_sasas(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::calculate(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::calculate_alt_state_hpatch_score(), core::scoring::SplitUnfoldedTwoBodyPotential::calculate_residue_emap(), core::chemical::sdf::MolWriter::compose_atoms(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), core::pack::interaction_graph::SurfacePotential::compute_pose_hpatch_score(), protocols::constraint_generator::HydrogenBondConstraintGenerator::compute_valid_atoms(), protocols::motif_grafting::movers::MotifGraftMover::count_clashes_between_two_poses(), protocols::hbnet::HBNet::estimate_saturation(), protocols::metal_interface::find_closest_atom(), core::util::find_metalbinding_atoms_for_complex(), core::conformation::carbohydrates::get_linkage_position_of_saccharide_residue(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore(), protocols::match::initialize_atomtype_2_probe_radius_map(), protocols::toolbox::match_enzdes_util::LigandConformer::initialize_from_residue(), protocols::match::downstream::RigidLigandBuilder::initialize_from_residue(), protocols::match::downstream::LigandConformerBuilder::initialize_from_residue(), protocols::vardist_solaccess::VarSolDistSasaCalculator::initialize_sasa_arrays(), core::chemical::orbitals::AssignOrbitals::make_orbital_type_name(), protocols::stepwise::modeler::rna::phosphate_base_phosphate_square_deviation(), print(), protocols::stepwise::modeler::rna::print_atom_info(), protocols::stepwise::modeler::rna::print_individual_atom_info(), protocols::simple_moves::PeriodicBoxMover::report_thermodynamics(), core::pack::interaction_graph::RotamerDotsRadiusData::RotamerDotsRadiusData(), core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::set_rotamer(), core::pack::interaction_graph::HPatchNode< V, E, G >::set_rotamers(), protocols::simple_moves::PeriodicBoxMover::setup_pose(), protocols::buns::BuriedUnsatisfiedPolarsCalculator2::sulphur_bond_check(), core::chemical::AtomTypeDatabaseIO::write_atom_type_table(), core::chemical::ResidueTypeKinWriter::write_restype(), 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

References extra_parameters_.

Referenced by core::scoring::power_diagram::PowerDiagram::construct_from_pose(), core::chemical::AtomTypeSet::get_default_parameter(), core::scoring::MultipoleElecPotential::get_single_rotamer_effective_radii(), core::scoring::GenBornResidueInfo::initialize(), core::scoring::facts::FACTSRsdTypeInfo::initialize_parameters(), protocols::vardist_solaccess::VarSolDistSasaCalculator::initialize_sasa_arrays(), core::scoring::power_diagram::PowerDiagram::make_new_sphere(), core::scoring::lkball::LKBallDatabase::setup_atom_weights(), and core::chemical::AtomTypeDatabaseIO::write_atom_type_extra_parameters_table().

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

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

Referenced by protocols::hbnet::HBNet::find_unsats(), and core::chemical::AtomTypeDatabaseIO::write_atom_type_properties_table().

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

inline

retrieve an atom's hybridization status.

References hybridization_.

Referenced by core::pack::rotamer_set::build_acceptor_acceptor_waters(), protocols::simple_moves::ExplicitWaterMover::build_backbone_rotamer_clouds(), core::pack::rotamer_set::build_donor_acceptor_waters(), core::pack::rotamer_set::build_sew_waters_to_acceptor(), core::scoring::hbonds::create_acc_orientation_vector(), core::energy_methods::MgEnergy::eval_mg_interaction(), core::scoring::PointWaterPotential::eval_pointwater_derivs(), core::scoring::PointWaterPotential::eval_pointwater_score(), get_all_properties(), core::scoring::magnesium::get_cos_theta(), core::scoring::hbonds::get_hb_acc_chem_type(), print(), and core::scoring::lkball::setup_water_builders_for_residue_type().

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

inline

whether atom is a hydrogen bond acceptor

References is_acceptor_.

Referenced by core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), protocols::hbnet::UnsatSelector::apply(), core::scoring::elec::GroupElec::build_groupinfo(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), protocols::hydrate::calculate_water_overcoordinated_hb_correction(), protocols::hbnet::UnsatSelector::compute(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), core::energy_methods::LK_PolarNonPolarEnergy::eval_residue_pair_derivatives(), protocols::hbnet::HBNet::find_unsats(), protocols::magnesium::MgWaterHydrogenPacker::find_water_neighbor_vecs(), get_all_properties(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_hbond(), protocols::magnesium::MgHydrater::hydrate_magnesium_with_orbital_frame(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), protocols::ligand_docking::rdf::RDFBinaryHbondFunction::operator()(), core::scoring::etable::MembEtable::precalc_etable_coefficients(), core::scoring::etable::Etable::precalc_etable_coefficients(), print(), protocols::simple_pose_metric_calculators::NumberHBondsCalculator::recompute(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), core::energy_methods::LK_hack::residue_pair_energy(), core::energy_methods::LK_PolarNonPolarEnergy::residue_pair_energy_ext(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), and core::scoring::lkball::LKBallDatabase::setup_atom_weights().

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

inline

whether atom is aromatic

References is_aromatic_.

Referenced by get_all_properties(), print(), and core::energy_methods::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way().

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

inline

whether atom is a hydrogen bond donor

References is_donor_.

Referenced by core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), protocols::qsar::scoring_grid::HbaGrid::atom_score(), core::scoring::elec::GroupElec::build_groupinfo(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::energy_methods::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), core::energy_methods::LK_PolarNonPolarEnergy::eval_residue_pair_derivatives(), protocols::hbnet::HBNet::find_unsats(), get_all_properties(), core::energy_methods::LK_PolarNonPolarEnergy::get_residue_pair_energy_one_way(), protocols::magnesium::MgHydrater::hydrate_magnesium_with_orbital_frame(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), protocols::ligand_docking::rdf::RDFBinaryHbondFunction::operator()(), core::scoring::etable::MembEtable::precalc_etable_coefficients(), core::scoring::etable::Etable::precalc_etable_coefficients(), print(), protocols::simple_pose_metric_calculators::NumberHBondsCalculator::recompute(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::qsar::scoring_grid::HbdGrid::refresh(), core::energy_methods::LK_hack::residue_pair_energy(), core::energy_methods::LK_PolarNonPolarEnergy::residue_pair_energy_ext(), protocols::qsar::scoring_grid::HbaGrid::score(), and core::scoring::lkball::LKBallDatabase::setup_atom_weights().

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

inline

whether atom is a water

References is_h2o_.

Referenced by core::scoring::sasa::LeGrandSasa::calc_atom_masks(), 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::energy_methods::WaterAdductIntraEnergy::residue_energy().

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

inline

is the H atom aromatic?

References name_.

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

inline

whether atom is a heavy atom

References element_.

Referenced by core::import_pose::atom_tree_diffs::dump_atom_tree_diff(), core::energy_methods::FastSAXSEnergy::eval_atom_derivative(), core::energy_methods::FiberDiffractionEnergy::eval_atom_derivative(), core::energy_methods::ElecDensAllAtomCenEnergy::eval_atom_derivative(), core::energy_methods::ElecDensEnergy::eval_atom_derivative(), core::energy_methods::ElecDensAtomwiseEnergy::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

References element_.

Referenced by protocols::simple_moves::chiral::ChiralMover::apply(), 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(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand(), core::chemical::HeavyAtomWithHydrogensFilter::operator()(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::packing::PoseBallsLite::PoseBallsLite(), core::energy_methods::SAXSEnergy::rehash_form_factors(), core::scoring::residue_rmsd_nosuper(), core::scoring::residue_rmsd_super(), and core::conformation::setup_links().

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

inline

whether atom is a polar hydrogen atom

References is_polar_hydrogen_.

Referenced by core::pack::rotamer_set::build_moving_O_bridge_waters(), core::pack::rotamer_set::build_single_edge_waters(), core::scoring::calc_per_atom_sasa(), core::scoring::sasa::LeGrandSasa::calculate(), protocols::hbnet::UnsatSelector::compute(), get_all_properties(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_bb_hbond(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::has_hbond(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore(), protocols::task_operations::CrystalContactsOperation::is_crystal_contact(), core::chemical::HeavyAtomWithPolarHydrogensFilter::operator()(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::packing::PoseBallsLite::PoseBallsLite(), core::scoring::etable::Etable::precalc_etable_coefficients(), print(), and protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score().

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

inline

is atom type repulsive (REPL, REPLS, HREPS)

References atom_is_repulsive_.

Referenced by get_all_properties(), core::chemical::rna::get_rna_base_centroid(), and core::conformation::Residue::is_repulsive().

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

inline

is atom type virtual?

References atom_is_virtual_, and name_.

Referenced by core::io::pose_to_sfr::PoseToStructFileRepConverter::add_atom_to_sfr(), core::io::pose_to_sfr::PoseToStructFileRepConverter::append_atom_info_to_sfr(), core::energy_methods::ProQ_Energy::atom13_0(), core::scoring::atomic_depth::AtomicDepth::boundbox(), core::scoring::atomic_depth::AtomicDepth::boundingatom(), core::scoring::sasa::LeGrandSasa::calc_atom_masks(), core::simple_metrics::per_residue_metrics::PerResidueClashMetric::calculate(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::methods::MMBondLengthEnergy::eval_atom_derivative(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::scoring::atomic_depth::AtomicDepth::fillvoxels(), core::energy_methods::D2H_SA_Energy::finalize_total_energy(), get_all_properties(), core::scoring::inline_intraresidue_atom_pair_energy(), core::scoring::inline_residue_atom_pair_energy(), core::conformation::Residue::is_virtual(), core::scoring::PQR::PQR(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), and core::chemical::MutableResidueType::set_atom_type().

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

inline

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

There are two functionally identical versions of the Lennard-Jones potential:

E ~ 4eps(sigma1/d)^12 - (sigma1/d)^6 and and E ~ eps(sigma2/d)^12 - 2*(sigma2/d)^6

where sigma1 and sigma2 represent two different interpretations of the radius. eps represents the depth of the potential well. Sigma1 represents the distance between the two atoms where the Lennard-Jones energy is 0, i.e. where a collision is just forming/resolving. Sigma2 represents the distance between the two atoms where the derivative of the Lennard-Jones energy is 0, i.e. the minimum of the well depth.

In rosetta, we mean sigma2 when we talk about radii, but PyMOL usually sets the radii to sigma1. If you see two atoms overlapping using the Rosetta radii, they're not necessarily in collision. They are just not at their minimum value.

The distances are related as sigma2 = 2^(1.0/6)*sigma1; sigma2 ~= 1.22*sigma1

References lj_radius_.

Referenced by core::scoring::sc::MolecularSurfaceCalculator::AddResidue(), protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_loop_bump_check(), protocols::qsar::scoring_grid::VdwGrid::atom_score(), protocols::rna::movers::bump_check(), core::pose::xyzStripeHashPose::extract_pose_balls(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::fast_full_atom_VDW_repulsion_screen(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_atom_neighbor_stuff(), core::util::find_metalbinding_atoms_helper(), core::energy_methods::OccludedHbondSolEnergy_onebody::get_atom_atom_occ_solvation(), core::energy_methods::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::simple_metrics::per_residue_metrics::PerResidueClashMetric::is_clashing(), core::pack::task::residue_selector::is_sc_bb_clash(), core::pack::task::residue_selector::is_sc_sc_clash(), core::scoring::packstat::LeeRichards::LeeRichards(), protocols::stepwise::modeler::rna::phosphate::PhosphateMover::pass_clash_check(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::packing::PoseBallsLite::PoseBallsLite(), core::scoring::PQR::PQR(), print(), protocols::qsar::scoring_grid::VdwGrid::refresh(), core::energy_methods::GaussianOverlapEnergy::residue_pair_energy(), protocols::qsar::scoring_grid::VdwGrid::score(), core::scoring::lkball::LK_BallEnergy::setup_d2_bounds(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::update_VDW_screen_bin(), core::scoring::epr_deer::EPRSpinLabel::weight(), core::chemical::AtomTypeDatabaseIO::write_atom_type_table(), and core::pose::xyzStripeHashPose::xyzStripeHashPose().

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

inline

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

References lj_wdepth_.

Referenced by protocols::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.

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.

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.

References lk_volume_.

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

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

inline

References name_.

Referenced by core::chemical::orbitals::AssignOrbitals::assign_only_pi_orbitals_to_atom(), core::energy_methods::atom_is_aro(), core::energy_methods::atom_is_aro2(), core::scoring::calc_per_atom_sasa(), core::scoring::sasa::LeGrandSasa::calculate(), core::scoring::SplitUnfoldedTwoBodyPotential::calculate_residue_emap(), core::chemical::sdf::MolWriter::compose_typeinfo(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf(), core::chemical::MutableResidueType::copy_atom_info(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::determine_atom_inds_for_restype(), protocols::hbnet::HBNet::estimate_saturation(), protocols::hbnet::HBNet::find_unsats(), protocols::magnesium::MgWaterHydrogenPacker::find_water_neighbor_vecs(), core::scoring::magnesium::get_cos_theta(), protocols::membrane::scoring::FaWaterToBilayerEnergy::get_menv_params_for_residue(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_costheta_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_costheta_indirect_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_gaussian_parameter(), core::scoring::magnesium::MgKnowledgeBasedPotential::get_mg_potential_indirect_gaussian_parameter(), core::chemical::rna::get_rna_base_centroid(), protocols::match::initialize_atomtype_2_probe_radius_map(), protocols::toolbox::match_enzdes_util::LigandConformer::initialize_from_residue(), protocols::features::HBondFeatures::insert_site_row(), protocols::stepwise::modeler::rna::is_virtual_base(), protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction::operator()(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::etable::Etable::precalc_etable_coefficients(), protocols::stepwise::modeler::rna::print_atom_info(), core::chemical::ResidueType::print_bondangles(), protocols::stepwise::modeler::rna::print_individual_atom_info(), protocols::match::output::print_node(), core::conformation::print_node(), protocols::viewer::print_node(), core::chemical::AtomTypeSet::read_atom_type_extra_parameters_table(), core::chemical::AtomTypeSet::read_atom_type_properties_table(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), core::energy_methods::SAXSEnergy::rehash_form_factors(), core::energy_methods::RNA_MgPointEnergy::residue_pair_energy_one_way(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), core::scoring::lkball::LKBallDatabase::setup_atom_weights(), core::scoring::lkball::LK_BallEnergy::setup_d2_bounds(), core::scoring::lkball::setup_water_builders_for_residue_type(), core::chemical::AtomTypeDatabaseIO::write_atom_type_extra_parameters_table(), core::chemical::AtomTypeDatabaseIO::write_atom_type_properties_table(), core::chemical::AtomTypeDatabaseIO::write_atom_type_table(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::write_topology_file().

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

inline

Get the name of this AtomType. Note that this is NOT the same as the atom name that is written out to PDB. You want pose.residue(i).atom_name(j) for that.

Referenced by add_property(), get_all_properties(), and print().

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

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

all the extra parameters at once

References extra_parameters_.

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

inline

return an additional, non-hardcoded property

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 Recognized. Supplemented by membrane specific solvation parameters: "MEMB_LK_DGFREE","MEMB_LK_DGREFCE","LK_DGREFCE". These are the header files in atom_properties.txt

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

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 recognized. To add properties, edit atom_properties.txt and add your property to the last column then add code here that will read the property.

References atom_has_orbitals_, atom_is_repulsive_, 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.