Detailed Description

Storage and access to force field.

Definition at line 19 of file ForceFieldParameters.h.

Public Member Functions
void	add_bonds (Hierarchy mhd) const
	add bonds to the structure defined in the hierarchy More...

void	add_radii (Hierarchy mhd, double scale=1.0, FloatKey radius_key=FloatKey("radius")) const
	Add or replace radii in the structure defined in the hierarchy. More...

void	add_well_depths (Hierarchy mhd) const
	Add LennardJones well depths to the structure. More...

Float	get_epsilon (Atom atom) const
	get epsilon for non bonded vdW More...

Float	get_radius (Atom atom) const
	get radius More...

Public Member Functions inherited from IMP::base::Object
virtual void	clear_caches ()

CheckLevel	get_check_level () const

LogLevel	get_log_level () const

virtual VersionInfo	get_version_info () const
	Get information about the module and version of the object. More...

void	set_check_level (CheckLevel l)

void	set_log_level (LogLevel l)
	Set the logging level used in this object. More...

void	set_was_used (bool tf) const

void	show (std::ostream &out=std::cout) const

const std::string &	get_name () const

void	set_name (std::string name)

virtual std::string	get_type_name () const

Protected Types
typedef std::map< AtomType, ChargePair >	AtomTypeMap

typedef std::pair< std::string, double >	ChargePair

Protected Member Functions
void	add_bonds (Residue rd) const

void	add_bonds (Residue rd1, Residue rd2) const

Float	get_epsilon (const String &force_field_atom_type) const

virtual String	get_force_field_atom_type (Atom atom) const

Float	get_radius (const String &force_field_atom_type) const

Protected Member Functions inherited from IMP::base::Object
	Object (std::string name)
	Construct an object with the given name. More...

virtual void	do_destroy ()

Protected Attributes
std::map< ResidueType, AtomTypeMap >	atom_res_type_2_force_field_atom_type_

std::map< String, FloatPair >	force_field_2_vdW_

std::map< ResidueType, base::Vector< Bond > >	residue_bonds_

Member Function Documentation

void IMP::atom::ForceFieldParameters::add_bonds ( Hierarchy mhd ) const

add bonds to the structure defined in the hierarchy

void IMP::atom::ForceFieldParameters::add_radii	(	Hierarchy	mhd,
		double	scale = `1.0`,
		FloatKey	radius_key = `FloatKey("radius")`
	)		const

Add or replace radii in the structure defined in the hierarchy.

Each radius is scaled by the given scale.

void IMP::atom::ForceFieldParameters::add_well_depths ( Hierarchy mhd ) const

Add LennardJones well depths to the structure.

Float IMP::atom::ForceFieldParameters::get_epsilon ( Atom atom ) const

get epsilon for non bonded vdW

Float IMP::atom::ForceFieldParameters::get_radius ( Atom atom ) const

get radius

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