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core::chemical::AtomType Class Reference

basic atom type More...

#include <AtomType.hh>

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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< Realextra_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

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.

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

Member Function Documentation

void core::chemical::AtomType::add_property ( std::string const &  property)
bool core::chemical::AtomType::atom_has_orbital ( ) const
inline
std::string core::chemical::AtomType::atom_type_name ( ) const
inline
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
Real core::chemical::AtomType::extra_parameter ( Size const  index) const
inline
utility::vector1< std::string > core::chemical::AtomType::get_all_properties ( ) const
Hybridization const& core::chemical::AtomType::hybridization ( ) const
inline
bool core::chemical::AtomType::is_acceptor ( ) const
inline
bool core::chemical::AtomType::is_aromatic ( ) const
inline
bool core::chemical::AtomType::is_donor ( ) const
inline
bool core::chemical::AtomType::is_h2o ( ) const
inline
bool core::chemical::AtomType::is_haro ( ) const
inline

is the H atom aromatic?

References name_.

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

bool core::chemical::AtomType::is_heavyatom ( ) const
inline
bool core::chemical::AtomType::is_hydrogen ( ) const
inline
bool core::chemical::AtomType::is_polar_hydrogen ( ) const
inline
bool core::chemical::AtomType::is_virtual ( ) const
Real core::chemical::AtomType::lj_radius ( ) const
inline
Real core::chemical::AtomType::lj_wdepth ( ) const
inline
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().

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

Referenced by add_property(), core::scoring::hackelec::atom_is_aro(), core::scoring::hackelec::atom_is_aro2(), protocols::swa::rna::base_atoms_square_deviation(), core::scoring::calc_per_atom_sasa(), protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf(), core::scoring::orbitals::OrbitalsAssigned::cp_function(), core::chemical::AtomTypeSet::create_atom_type_from_database(), protocols::toolbox::match_enzdes_util::EnzCstTemplateRes::determine_atom_inds_for_restype(), protocols::swa::rna::fast_full_atom_VDW_repulsion_screen(), get_all_properties(), core::scoring::rna::RNA_Mg_Energy::get_cos_theta(), core::scoring::orbitals::OrbitalsAssigned::get_hydrogens(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::get_matching_res_in_VDW_rep_screen_pose(), core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::get_mg_potential_costheta_gaussian_parameter(), core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::get_mg_potential_costheta_indirect_gaussian_parameter(), core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::get_mg_potential_gaussian_parameter(), core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::get_mg_potential_indirect_gaussian_parameter(), core::scoring::rna::get_rna_base_centroid(), protocols::swa::rna::get_surrounding_O2star_hydrogen(), protocols::match::initialize_atomtype_2_probe_radius_map(), protocols::toolbox::match_enzdes_util::LigandConformer::initialize_from_residue(), protocols::features::HBondFeatures::insert_site_row(), protocols::swa::rna::Is_virtual_base(), protocols::swa::rna::phosphate_base_phosphate_square_deviation(), protocols::swa::rna::phosphate_square_deviation(), core::scoring::packing::PoseBalls::PoseBalls(), core::scoring::etable::Etable::precalc_etable_coefficients(), print(), protocols::swa::rna::print_atom_info(), core::chemical::ResidueType::print_bondangles(), core::chemical::ResidueType::print_dihedrals(), protocols::swa::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::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), core::scoring::saxs::SAXSEnergy::rehash_form_factors(), 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::scoring::rna::RNA_Mg_Energy::residue_pair_energy_one_way(), protocols::features::OrbitalsFeatures::set_OrbH_features_data(), core::scoring::methods::LK_BallEnergy::setup_d2_bounds(), protocols::swa::rna::setup_suite_atom_id_map(), protocols::swa::rna::suite_square_deviation(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::update_VDW_screen_bin(), protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener::VDW_rep_screen(), core::chemical::AtomTypeDatabaseIO::write_atom_type_extra_parameters_table(), core::chemical::AtomTypeDatabaseIO::write_atom_type_properties_table(), core::chemical::AtomTypeDatabaseIO::write_atom_type_table(), and core::chemical::write_topology_file().

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 recoganized. 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_.

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.

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.

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

Friends And Related Function Documentation

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

Member Data Documentation

bool core::chemical::AtomType::atom_has_orbitals_
private
bool core::chemical::AtomType::atom_is_virtual_
private
std::string const core::chemical::AtomType::element_
private

Referenced by element(), is_heavyatom(), and is_hydrogen().

utility::vector1< Real > core::chemical::AtomType::extra_parameters_
private
Hybridization core::chemical::AtomType::hybridization_
private
bool core::chemical::AtomType::is_acceptor_
private
bool core::chemical::AtomType::is_aromatic_
private
bool core::chemical::AtomType::is_donor_
private
bool core::chemical::AtomType::is_h2o_
private
bool core::chemical::AtomType::is_polar_hydrogen_
private
Real core::chemical::AtomType::lj_radius_
private

Referenced by lj_radius(), and set_parameter().

Real core::chemical::AtomType::lj_wdepth_
private

Referenced by lj_wdepth(), and set_parameter().

Real core::chemical::AtomType::lk_dgfree_
private

Referenced by lk_dgfree(), and set_parameter().

Real core::chemical::AtomType::lk_lambda_
private

Referenced by lk_lambda(), and set_parameter().

Real core::chemical::AtomType::lk_volume_
private

Referenced by lk_volume(), and set_parameter().

std::string const core::chemical::AtomType::name_
private

Referenced by atom_type_name(), is_haro(), and is_virtual().


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