core::chemical::MMAtomType Class Reference

Basic MM atom type. More...

#include <MMAtomType.hh>

Public Member Functions
	MMAtomType (std::string const &name_in)
	Construct a new MMAtomType with its name. More...
std::string const &	name () const
	Return the name of the MMAtomType. More...
Real	lj_radius () const
	Return the LJ radius of the atom type. More...
Real	lj_radius_sq () const
	Return the squared LJ radius of the atom type. More...
Real	lj_wdepth () const
	Return the LJ well depth of the atom type. More...
Real	lj_three_bond_radius () const
	Return the LJ radius for use when atoms types are seperated by 3 bonds. More...
Real	lj_three_bond_radius_sq () const
	Return the squaredLJ radius for use when atoms types are seperated by 3 bonds. More...
Real	lj_three_bond_wdepth () const
	Return the LJ well depth for use when atoms types are seperated by 3 bonds. More...
void	set_parameter (std::string const &param, Real const setting)
	set LJ and LK solvation parameter for this atom type More...

Private Attributes
std::string const	name_
	name of the mm atom type More...
Real	lj_radius_
	Lennard-Jones parameters. More...
Real	lj_radius_sq_
Real	lj_wdepth_
Real	lj_three_bond_radius_
Real	lj_three_bond_radius_sq_
Real	lj_three_bond_wdepth_

Detailed Description

Basic MM atom type.

Simple class for holding the name and the LJ properties of a Charmm molecular mechanics atom type. Borrows heavily and functions similarly to the rosetta atom type class, AtomType

Constructor & Destructor Documentation

core::chemical::MMAtomType::MMAtomType ( std::string const &  name_in )

inline

Construct a new MMAtomType with its name.

Member Function Documentation

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

inline

Return the LJ radius of the atom type.

References lj_radius_.

Real core::chemical::MMAtomType::lj_radius_sq ( ) const

inline

Return the squared LJ radius of the atom type.

References lj_radius_sq_.

Real core::chemical::MMAtomType::lj_three_bond_radius ( ) const

inline

Return the LJ radius for use when atoms types are seperated by 3 bonds.

References lj_three_bond_radius_.

Real core::chemical::MMAtomType::lj_three_bond_radius_sq ( ) const

inline

Return the squaredLJ radius for use when atoms types are seperated by 3 bonds.

References lj_three_bond_radius_sq_.

Real core::chemical::MMAtomType::lj_three_bond_wdepth ( ) const

inline

Return the LJ well depth for use when atoms types are seperated by 3 bonds.

References lj_three_bond_wdepth_.

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

inline

Return the LJ well depth of the atom type.

References lj_wdepth_.

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

inline

Return the name of the MMAtomType.

References name_.

Referenced by core::chemical::ResidueType::print_bondangles(), core::chemical::ResidueTypeKinWriter::write_restype(), and core::chemical::write_topology_file().

void core::chemical::MMAtomType::set_parameter	(	std::string const &	param,
		Real const	setting
	)

set LJ and LK solvation parameter for this atom type

References lj_radius_, lj_radius_sq_, lj_three_bond_radius_, lj_three_bond_radius_sq_, lj_three_bond_wdepth_, and lj_wdepth_.

Member Data Documentation

Real core::chemical::MMAtomType::lj_radius_

private

Lennard-Jones parameters.

Referenced by lj_radius(), and set_parameter().

Real core::chemical::MMAtomType::lj_radius_sq_

private

Referenced by lj_radius_sq(), and set_parameter().

Real core::chemical::MMAtomType::lj_three_bond_radius_

private

Referenced by lj_three_bond_radius(), and set_parameter().

Real core::chemical::MMAtomType::lj_three_bond_radius_sq_

private

Referenced by lj_three_bond_radius_sq(), and set_parameter().

Real core::chemical::MMAtomType::lj_three_bond_wdepth_

private

Referenced by lj_three_bond_wdepth(), and set_parameter().

Real core::chemical::MMAtomType::lj_wdepth_

private

Referenced by lj_wdepth(), and set_parameter().

std::string const core::chemical::MMAtomType::name_

private

name of the mm atom type

Referenced by name().

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

• src/core/chemical/MMAtomType.hh
• src/core/chemical/MMAtomType.cc