IMP::atom::CHARMMIdealResidueTopology Class Reference

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Detailed Description

The ideal topology of a single residue.

These residue topologies can be constructed manually (by adding CHARMMAtomTopology objects with add_atom()). However, they are more commonly populated automatically by reading a CHARMM topology file (CHARMMParameters::get_residue_topology()).

Inheritance diagram for IMP::atom::CHARMMIdealResidueTopology:

List of all members.

Public Member Functions
	CHARMMIdealResidueTopology (std::string type)
	CHARMMIdealResidueTopology (ResidueType type)
std::string	get_default_first_patch () const
std::string	get_default_last_patch () const
void	remove_atom (std::string name)
	Remove the named atom.
void	set_default_first_patch (std::string patch)
void	set_default_last_patch (std::string patch)
Public Member Functions inherited from IMP::atom::CHARMMResidueTopologyBase
void	add_angle (const CHARMMAngle &bond)
void	add_atom (const CHARMMAtomTopology &atom)
void	add_bond (const CHARMMBond &bond)
void	add_dihedral (const CHARMMDihedral &bond)
void	add_improper (const CHARMMDihedral &bond)
void	add_internal_coordinate (const CHARMMInternalCoordinate &ic)
const CHARMMAngle &	get_angle (unsigned int index) const
const CHARMMAtomTopology &	get_atom (unsigned int i) const
const CHARMMAtomTopology &	get_atom (AtomType type) const
const CHARMMAtomTopology &	get_atom (std::string name) const
const CHARMMBond &	get_bond (unsigned int index) const
const CHARMMDihedral &	get_dihedral (unsigned int index) const
const CHARMMDihedral &	get_improper (unsigned int index) const
const CHARMMInternalCoordinate &	get_internal_coordinate (unsigned int index) const
unsigned int	get_number_of_angles () const
unsigned int	get_number_of_atoms () const
unsigned int	get_number_of_bonds () const
unsigned int	get_number_of_dihedrals () const
unsigned int	get_number_of_impropers () const
unsigned int	get_number_of_internal_coordinates () const
std::string	get_type () const
Public Member Functions inherited from IMP::base::Object
std::size_t	__hash__ () const
virtual std::string	get_type_name () const =0
	Return a string identifying the type of the object.
virtual IMP::base::VersionInfo	get_version_info () const =0
	Get information about the module and version of the object.
void	set_check_level (CheckLevel l)
void	set_log_level (LogLevel l)
	Set the logging level used in this object.
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)

Static Public Member Functions
static CHARMMIdealResidueTopology *	get_from (IMP::base::Object *o)

Additional Inherited Members
Protected Member Functions inherited from IMP::atom::CHARMMResidueTopologyBase
	CHARMMResidueTopologyBase (std::string type)
Protected Member Functions inherited from IMP::base::Object
	Object (std::string name)
Protected Attributes inherited from IMP::atom::CHARMMResidueTopologyBase
CHARMMAngles	angles_
base::Vector< CHARMMAtomTopology >	atoms_
CHARMMBonds	bonds_
CHARMMDihedrals	dihedrals_
CHARMMDihedrals	impropers_
CHARMMInternalCoordinates	internal_coordinates_

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Member Function Documentation

void IMP::atom::CHARMMIdealResidueTopology::remove_atom

(

std::string

name

)

Remove the named atom.

Any bonds/angles that involve this atom are also removed.

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

• charmm_topology.h