Detailed Description

The topology of a single residue in a model.

Each CHARMMResidueTopology object can represent an 'unknown' residue (containing no atoms or bonds) or is a copy of an existing CHARMMIdealResidueTopology. Optionally, patches can be applied to residues (see CHARMMPatch::apply()) to add N- or C-termini, disulfide bridges, sidechain modifications, etc.

Inheritance diagram for IMP::atom::CHARMMResidueTopology:

List of all members.

Public Member Functions
	CHARMMResidueTopology (ResidueType type)
	Create an empty topology, containing no atoms or bonds.
	CHARMMResidueTopology (CHARMMIdealResidueTopology *ideal)
	Construct residue topology as a copy of an existing topology.
bool	get_patched () const
void	set_patched (bool patched)
Public Member Functions inherited from IMP::atom::CHARMMIdealResidueTopology
	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 CHARMMResidueTopology *	get_from (IMP::base::Object *o)

Constructor & Destructor Documentation

IMP::atom::CHARMMResidueTopology::CHARMMResidueTopology ( ResidueType type )

Create an empty topology, containing no atoms or bonds.

IMP::atom::CHARMMResidueTopology::CHARMMResidueTopology ( CHARMMIdealResidueTopology * ideal )

Construct residue topology as a copy of an existing topology.

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

charmm_topology.h

Detailed Description

Public Member Functions

Static Public Member Functions

Constructor & Destructor Documentation