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core::chemical::AtomType Class Reference

basic atom type More...

#include <AtomType.hh>

Collaboration diagram for core::chemical::AtomType:
Collaboration graph

List of all members.

Public Member Functions

 AtomType (std::string const &name_in, std::string const element_in)
 Construct a new atom type with its name and element.
 AtomType (AtomType const &src)
void print (std::ostream &out) const
Real lk_lambda () const
 Lazaridis and Karplus solvation parameter -- lambda.
Real lk_dgfree () const
 Lazaridis and Karplus solvation parameter -- dgfree.
Real lk_volume () const
 Lazaridis and Karplus solvation parameter -- volume.
Real lj_radius () const
 Lennard-Jones 6-12 potential parameter -- atom radius.
Real lj_wdepth () const
 Lennard-Jones 6-12 potential parameter -- well depth.
bool is_acceptor () const
 whether atom is a hydrogen bond acceptor
bool is_donor () const
 whether atom is a hydrogen bond donor
bool is_polar_hydrogen () const
 whether atom is a polar hydrogen atom
bool is_hydrogen () const
 whether atom is a hydrogen atom
bool is_heavyatom () const
 whether atom is a heavy atom
bool is_virtual () const
 is atom type virtual?
bool is_h2o () const
 whether atom is a water
bool is_aromatic () const
 whether atom is aromatic
bool atom_has_orbital () const
 atom has an orbital attached
bool is_haro () const
 is the H atom aromatic?
void set_parameter (std::string const &param, Real const setting)
 set LJ and LK solvation parameter for this atom type
void set_property (std::string const &property, bool const setting)
 set relevant properties for this atom type hh
Hybridization const & hybridization () const
 retrieve an atom's hybridization status.
void clear_properties ()
 set all standard properties to false, set hybridization to UNKNOWN_HYBRID, and clear extra properties
void add_property (std::string const &property)
 set standard property to true, or set the specified hybridization
utility::vector1< std::string > get_all_properties () const
std::string element () const
 returns the one- or two-letter element type
std::string atom_type_name () const
Real extra_parameter (Size const index) const
 return an additional, non-hardcoded property
void set_extra_parameter (Size const index, Real const setting)
 return an additional, non-hardcoded property
void set_all_extra_parameters (utility::vector1< Real > const &extra_parameters)
 all the extra parameters at once
std::string const & name () const


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)

set standard property to true, or set the specified hybridization

References name(), core::chemical::RING_HYBRID, core::chemical::SP2_HYBRID, and core::chemical::SP3_HYBRID.

bool core::chemical::AtomType::atom_has_orbital ( ) const [inline]

atom has an orbital attached

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

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 core::chemical::UNKNOWN_HYBRID.

std::string core::chemical::AtomType::element ( ) const [inline]
Real core::chemical::AtomType::extra_parameter ( Size const  index) const [inline]

return an additional, non-hardcoded property

Referenced by core::scoring::GenBornResidueInfo::initialize().

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]

whether atom is aromatic

Referenced by get_all_properties(), and print().

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?

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]

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

Referenced by protocols::toolbox::pose_metric_calculators::fast_clash_check(), and print().

Real core::chemical::AtomType::lk_dgfree ( ) const [inline]

Lazaridis and Karplus solvation parameter -- dgfree.

Referenced by print().

Real core::chemical::AtomType::lk_lambda ( ) const [inline]

Lazaridis and Karplus solvation parameter -- lambda.

Referenced by print().

Real core::chemical::AtomType::lk_volume ( ) const [inline]

Lazaridis and Karplus solvation parameter -- volume.

Referenced by print().

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(), 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::orbitals::OrbitalsAssigned::get_hydrogens(), 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(), 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::viewer::print_node(), protocols::match::output::print_node(), core::conformation::print_node(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute(), core::scoring::saxs::SAXSEnergy::rehash_form_factors(), 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(), 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

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

return an additional, non-hardcoded property

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

Referenced by 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 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]

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