basic chemical atom More...

#include <Atom.hh>

Collaboration diagram for core::chemical::Atom:

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, Real const charge, Vector const ideal_xyz, AtomICoor const icoor)

	Atom (Atom const &src)

void	print (std::ostream &out) const

std::string const &	name () const

std::string const &	mm_name () const

Size const &	atom_type_index () const

Size const &	mm_atom_type_index () const

Real const &	charge () const

Vector const &	ideal_xyz () const

AtomICoor const &	icoor () const

AtomICoor &	icoor ()

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	charge (Real const &charge)

void	ideal_xyz (Vector const &ideal_xyz)

void	icoor (AtomICoor const &icoor)

Private Attributes
std::string	name_

std::string	mm_name_

Size	atom_type_index_

Size	mm_atom_type_index_
	MM atom-type index. More...

Real	charge_

Vector	ideal_xyz_

AtomICoor	icoor_

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

Detailed Description

basic chemical atom

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

Definition at line 51 of file Atom.hh.

Constructor & Destructor Documentation

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

inline

Construct a new atom type with its name and element.

All its properties are unset by default.

Definition at line 59 of file Atom.hh.

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,
		Real const	charge,
		Vector const	ideal_xyz,
		AtomICoor const	icoor
	)

inline

Definition at line 69 of file Atom.hh.

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

inline

Definition at line 90 of file Atom.hh.

Member Function Documentation

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

inline

Definition at line 112 of file Atom.hh.

References atom_type_index_.

Referenced by protocols::match::bump_grid_to_enclose_pose(), print(), and core::conformation::Residue::Residue().

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

inline

Definition at line 123 of file Atom.hh.

References atom_type_index(), and atom_type_index_.

Referenced by atom_type_index().

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

inline

Definition at line 114 of file Atom.hh.

References charge_.

Referenced by core::chemical::SetAtomicCharge::apply(), core::conformation::Residue::atomic_charge(), core::scoring::PQR::PQR(), print(), core::chemical::ResidueDatabaseIO::report_residue_type_atom(), core::scoring::PoissonBoltzmannPotential::write_pqr(), and core::chemical::write_topology_file().

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

inline

Definition at line 125 of file Atom.hh.

References charge(), and charge_.

Referenced by charge().

AtomICoor const& core::chemical::Atom::icoor ( ) const

inline

Definition at line 116 of file Atom.hh.

References icoor_.

AtomICoor& core::chemical::Atom::icoor ( )

inline

Definition at line 118 of file Atom.hh.

References icoor_.

void core::chemical::Atom::icoor ( AtomICoor const & icoor)

inline

Definition at line 127 of file Atom.hh.

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

inline

Definition at line 115 of file Atom.hh.

References ideal_xyz_.

Referenced by core::chemical::ResidueType::calculate_icoor(), core::chemical::ResidueType::debug_dump_icoor(), core::scoring::mm::MMBondAngleResidueTypeParam::init(), protocols::match::upstream::UpstreamResTypeGeometry::initialize_from_residue_type(), core::conformation::Residue::Residue(), and core::chemical::ICoorAtomID::xyz().

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

inline

Definition at line 126 of file Atom.hh.

References ideal_xyz(), and ideal_xyz_.

Referenced by ideal_xyz().

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

inline

Definition at line 113 of file Atom.hh.

References mm_atom_type_index_.

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

inline

Definition at line 124 of file Atom.hh.

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

Definition at line 111 of file Atom.hh.

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

Definition at line 122 of file Atom.hh.

References mm_name_, and name().

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

inline

Definition at line 109 of file Atom.hh.

References name_.

Referenced by mm_name(), and print().

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

inline

Definition at line 120 of file Atom.hh.

References name(), and name_.

Referenced by name().

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

Definition at line 48 of file Atom.cc.

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

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

Friends And Related Function Documentation

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

friend

Definition at line 63 of file Atom.cc.

Member Data Documentation

Size core::chemical::Atom::atom_type_index_

private

Definition at line 140 of file Atom.hh.

Referenced by atom_type_index().

Real core::chemical::Atom::charge_

private

Definition at line 143 of file Atom.hh.

Referenced by charge().

AtomICoor core::chemical::Atom::icoor_

private

Definition at line 145 of file Atom.hh.

Referenced by icoor().

Vector core::chemical::Atom::ideal_xyz_

private

Definition at line 144 of file Atom.hh.

Referenced by ideal_xyz().

Size core::chemical::Atom::mm_atom_type_index_

private

MM atom-type index.

Definition at line 142 of file Atom.hh.

Referenced by mm_atom_type_index().

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

private

Definition at line 137 of file Atom.hh.

Referenced by mm_name().

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

private

Definition at line 127 of file Atom.hh.

Referenced by name().

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

src/core/chemical/Atom.hh
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