basic chemical atom More...

#include <Atom.hh>

Public Member Functions
	Atom ()
	Construct a new atom type with its name and element. More...

	Atom (std::string const &name_in, std::string const mm_name, Size const atom_type_index, Size const mm_atom_type_index, ElementCOP element, Real const charge, Vector const ideal_xyz)
	Construct a new atom with the type it is, the mm type, and the name. More...

	Atom (Atom const &src)

	~Atom ()

void	print (std::ostream &out) const

bool	operator== (Atom const &atom) const

Atom &	operator= (Atom const &atom)

std::string const &	name () const

std::string const &	mm_name () const

Size const &	atom_type_index () const

Size const &	mm_atom_type_index () const

ElementCOP	element_type () const

gasteiger::GasteigerAtomTypeDataCOP	gasteiger_atom_type () const

int const &	formal_charge () const

Real const &	charge () const

Vector const &	ideal_xyz () const

utility::vector1< Size > const &	bonded_orbitals () const

utility::vector1< Size > &	bonded_orbitals ()

bool	heavyatom_has_polar_hydrogens () const

bool	is_acceptor () const

bool	is_polar_hydrogen () const

bool	is_hydrogen () const

bool	is_haro () const

bool	is_virtual () const

bool	has_orbitals () const

void	name (std::string const &name)

void	mm_name (std::string const &name)

void	atom_type_index (Size const &atom_type_index)

void	mm_atom_type_index (Size const &mm_atom_type_index)

void	gasteiger_atom_type (core::chemical::gasteiger::GasteigerAtomTypeDataCOP gasteiger_atom_type)

void	formal_charge (int charge)

void	charge (Real const &charge)

void	ideal_xyz (Vector const &ideal_xyz)

void	heavyatom_has_polar_hydrogens (bool heavyatom_has_polar_hydrogens)

void	is_polar_hydrogen (bool polar)

void	is_hydrogen (bool hydrogen)

void	is_haro (bool haro)

void	is_acceptor (bool acceptor)

void	is_virtual (bool is_virtual)

void	has_orbitals (bool orbitals)

bool	is_fake () const
	Return true if this represents a fake/mock atom. (Real atoms have elements that exist on the periodic table.) More...

Private Attributes
std::string	name_

std::string	mm_name_

Size	atom_type_index_

Size	mm_atom_type_index_

ElementCOP	element_

gasteiger::GasteigerAtomTypeDataCOP	gasteiger_atom_type_
	Gasteiger atom-type. More...

int	formal_charge_
	The formal (integral) charge on the atom. More...

Real	charge_

Vector	ideal_xyz_

bool	heavyatom_has_polar_hydrogens_

bool	is_acceptor_

bool	is_polar_hydrogen_

bool	is_hydrogen_

bool	is_haro_

bool	is_virtual_

bool	has_orbitals_

utility::vector1< Size >	bonded_orbitals_

Friends
std::ostream &	operator<< (std::ostream &out, Atom const &atom)

Detailed Description

basic chemical atom

name, element, certain properties and parameters from .params file

Constructor & Destructor Documentation

core::chemical::Atom::Atom ( )

Construct a new atom type with its name and element.

All its properties are unset by default.

core::chemical::Atom::Atom	(	std::string const &	name_in,
		std::string const	mm_name,
		Size const	atom_type_index,
		Size const	mm_atom_type_index,
		ElementCOP	element,
		Real const	charge,
		Vector const	ideal_xyz
	)

Construct a new atom with the type it is, the mm type, and the name.

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

core::chemical::Atom::~Atom ( )

Member Function Documentation

Size const& core::chemical::Atom::atom_type_index ( ) const

inline

References atom_type_index_.

Referenced by core::chemical::HeavyAtomWithPolarHydrogensFilter::operator()(), core::chemical::HeavyAtomWithHydrogensFilter::operator()(), print(), core::conformation::Residue::Residue(), core::chemical::ResidueType::retype_atoms(), core::chemical::retype_get_element(), and core::chemical::ResidueType::set_atom_type().

void core::chemical::Atom::atom_type_index ( Size const & atom_type_index )

inline

References atom_type_index(), and atom_type_index_.

Referenced by atom_type_index().

utility::vector1<Size> const& core::chemical::Atom::bonded_orbitals ( ) const

inline

References bonded_orbitals_.

utility::vector1<Size>& core::chemical::Atom::bonded_orbitals ( )

inline

References bonded_orbitals_.

Real const& core::chemical::Atom::charge ( ) const

inline

References charge_.

Referenced by core::chemical::SetAtomicCharge::apply(), core::chemical::SetAtomType::apply(), core::conformation::Residue::atomic_charge(), core::scoring::sasa::SasaCalc::calc_per_res_sasas(), formal_charge(), core::scoring::PQR::PQR(), print(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::scoring::PoissonBoltzmannPotential::write_pqr(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::write_topology_file().

void core::chemical::Atom::charge ( Real const & charge )

inline

References charge(), and charge_.

Referenced by charge().

ElementCOP core::chemical::Atom::element_type ( ) const

inline

References element_.

int const& core::chemical::Atom::formal_charge ( ) const

inline

References formal_charge_.

Referenced by core::chemical::write_topology_file().

void core::chemical::Atom::formal_charge ( int charge )

inline

References charge(), and formal_charge_.

gasteiger::GasteigerAtomTypeDataCOP core::chemical::Atom::gasteiger_atom_type ( ) const

References gasteiger_atom_type_.

Referenced by core::chemical::gasteiger::assign_gasteiger_atom_types(), gasteiger_atom_type(), print(), and core::chemical::ResidueType::set_gasteiger_atom_type().

void core::chemical::Atom::gasteiger_atom_type ( core::chemical::gasteiger::GasteigerAtomTypeDataCOP gasteiger_atom_type )

References gasteiger_atom_type(), and gasteiger_atom_type_.

bool core::chemical::Atom::has_orbitals ( ) const

inline

References has_orbitals_.

Referenced by core::chemical::ResidueType::set_atom_type(), and core::chemical::ResidueType::update_derived_data().

void core::chemical::Atom::has_orbitals ( bool orbitals )

inline

References has_orbitals_.

bool core::chemical::Atom::heavyatom_has_polar_hydrogens ( ) const

inline

References heavyatom_has_polar_hydrogens_.

void core::chemical::Atom::heavyatom_has_polar_hydrogens ( bool heavyatom_has_polar_hydrogens )

inline

References heavyatom_has_polar_hydrogens(), and heavyatom_has_polar_hydrogens_.

Referenced by heavyatom_has_polar_hydrogens().

Vector const& core::chemical::Atom::ideal_xyz ( ) const

inline

References ideal_xyz_.

Referenced by core::chemical::ResidueType::calculate_icoor(), core::io::pdb::check_and_correct_sister_atom_based_on_chirality(), core::io::pdb::check_and_correct_sister_atom_based_on_outgroup(), core::chemical::ResidueType::debug_dump_icoor(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), core::conformation::Residue::Residue(), core::chemical::ResidueType::set_ideal_xyz(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::ICoorAtomID::xyz().

void core::chemical::Atom::ideal_xyz ( Vector const & ideal_xyz )

inline

References ideal_xyz(), and ideal_xyz_.

Referenced by ideal_xyz().

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

inline

References is_acceptor_.

Referenced by core::chemical::ResidueType::set_atom_type(), and core::chemical::ResidueType::update_derived_data().

void core::chemical::Atom::is_acceptor ( bool acceptor )

inline

References is_acceptor_.

bool core::chemical::Atom::is_fake ( ) const

Return true if this represents a fake/mock atom. (Real atoms have elements that exist on the periodic table.)

References element_, is_virtual_, name(), and core::chemical::TR.

Referenced by core::chemical::gasteiger::assign_gasteiger_atom_types().

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

inline

References is_haro_.

Referenced by core::chemical::ResidueType::set_atom_type(), and core::chemical::ResidueType::update_derived_data().

void core::chemical::Atom::is_haro ( bool haro )

inline

References is_haro_.

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

inline

References is_hydrogen_.

Referenced by core::chemical::ResidueType::set_atom_type(), and core::chemical::ResidueType::update_derived_data().

void core::chemical::Atom::is_hydrogen ( bool hydrogen )

inline

References is_hydrogen_.

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

inline

References is_polar_hydrogen_.

Referenced by core::chemical::ResidueType::set_atom_type(), and core::chemical::ResidueType::update_derived_data().

void core::chemical::Atom::is_polar_hydrogen ( bool polar )

inline

References is_polar_hydrogen_.

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

inline

References is_virtual_.

Referenced by core::chemical::SetAtomType::apply(), core::chemical::ResidueType::set_atom_type(), and core::chemical::ResidueType::update_derived_data().

void core::chemical::Atom::is_virtual ( bool is_virtual )

inline

References is_virtual(), and is_virtual_.

Referenced by is_virtual().

Size const& core::chemical::Atom::mm_atom_type_index ( ) const

inline

References mm_atom_type_index_.

void core::chemical::Atom::mm_atom_type_index ( Size const & mm_atom_type_index )

inline

References mm_atom_type_index(), and mm_atom_type_index_.

Referenced by mm_atom_type_index().

std::string const& core::chemical::Atom::mm_name ( ) const

inline

References mm_name_.

Referenced by core::scoring::methods::MMTorsionEnergy::eval_intrares_energy(), core::scoring::methods::MMBondLengthEnergy::eval_intrares_energy(), core::scoring::methods::MMBondAngleEnergy::eval_intrares_energy(), core::conformation::Residue::mm_atom_name(), print(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::scoring::methods::MMTorsionEnergy::residue_pair_energy(), core::scoring::methods::MMBondLengthEnergy::residue_pair_energy(), and core::scoring::methods::MMBondAngleEnergy::residue_pair_energy().

void core::chemical::Atom::mm_name ( std::string const & name )

inline

References mm_name_, and name().

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

inline

References name_.

Referenced by is_fake(), mm_name(), print(), core::chemical::ResidueType::ResidueType(), core::chemical::ResidueType::show_all_atom_names(), and core::chemical::ResidueTypeKinWriter::write_restype().

void core::chemical::Atom::name ( std::string const & name )

inline

References name(), and name_.

Referenced by name().

Atom & core::chemical::Atom::operator= ( Atom const & atom )

References atom_type_index_, bonded_orbitals_, charge_, element_, formal_charge_, gasteiger_atom_type_, has_orbitals_, heavyatom_has_polar_hydrogens_, ideal_xyz_, is_acceptor_, is_haro_, is_hydrogen_, is_polar_hydrogen_, is_virtual_, mm_atom_type_index_, mm_name_, and name_.

bool core::chemical::Atom::operator== ( Atom const & atom ) const

inline

References atom_type_index_, bonded_orbitals_, charge_, element_, formal_charge_, gasteiger_atom_type_, has_orbitals_, heavyatom_has_polar_hydrogens_, ideal_xyz_, is_acceptor_, is_haro_, is_hydrogen_, is_polar_hydrogen_, is_virtual_, mm_atom_type_index_, mm_name_, and name_.

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

References atom_type_index(), charge(), gasteiger_atom_type(), mm_atom_type_index(), mm_name(), and name().

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

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	out,
		Atom const &	atom
	)

friend

Member Data Documentation

Size core::chemical::Atom::atom_type_index_

private

Referenced by atom_type_index(), operator=(), and operator==().

utility::vector1<Size> core::chemical::Atom::bonded_orbitals_

private

Referenced by bonded_orbitals(), operator=(), and operator==().

Real core::chemical::Atom::charge_

private

Referenced by charge(), operator=(), and operator==().

ElementCOP core::chemical::Atom::element_

private

Referenced by element_type(), is_fake(), operator=(), and operator==().

int core::chemical::Atom::formal_charge_

private

The formal (integral) charge on the atom.

Referenced by formal_charge(), operator=(), and operator==().

gasteiger::GasteigerAtomTypeDataCOP core::chemical::Atom::gasteiger_atom_type_

private

Gasteiger atom-type.

Referenced by gasteiger_atom_type(), operator=(), and operator==().

bool core::chemical::Atom::has_orbitals_

private

Referenced by has_orbitals(), operator=(), and operator==().

bool core::chemical::Atom::heavyatom_has_polar_hydrogens_

private

Referenced by heavyatom_has_polar_hydrogens(), operator=(), and operator==().

Vector core::chemical::Atom::ideal_xyz_

private

Referenced by ideal_xyz(), operator=(), and operator==().

bool core::chemical::Atom::is_acceptor_

private

Referenced by is_acceptor(), operator=(), and operator==().

bool core::chemical::Atom::is_haro_

private

Referenced by is_haro(), operator=(), and operator==().

bool core::chemical::Atom::is_hydrogen_

private

Referenced by is_hydrogen(), operator=(), and operator==().

bool core::chemical::Atom::is_polar_hydrogen_

private

Referenced by is_polar_hydrogen(), operator=(), and operator==().

bool core::chemical::Atom::is_virtual_

private

Referenced by is_fake(), is_virtual(), operator=(), and operator==().

Size core::chemical::Atom::mm_atom_type_index_

private

Referenced by mm_atom_type_index(), operator=(), and operator==().

std::string core::chemical::Atom::mm_name_

private

Referenced by mm_name(), operator=(), and operator==().

std::string core::chemical::Atom::name_

private

Referenced by name(), operator=(), and operator==().

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

symlinks/rosetta/src/core/chemical/Atom.hh
symlinks/rosetta/src/core/chemical/Atom.cc

Public Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation