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()).

Definition at line 332 of file charmm_topology.h.

Public Member Functions
	CHARMMIdealResidueTopology (std::string type)

	CHARMMIdealResidueTopology (ResidueType type)

std::string	get_default_first_patch () const

std::string	get_default_last_patch () const

virtual std::string	get_type_name () const

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

void	remove_atom (std::string name)
	Remove the named atom. More...

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
virtual void	clear_caches ()

CheckLevel	get_check_level () const

LogLevel	get_log_level () const

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)

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)
	Construct an object with the given name. More...

virtual void	do_destroy ()

Protected Attributes inherited from IMP::atom::CHARMMResidueTopologyBase
CHARMMAngles	angles_

base::Vector< CHARMMAtomTopology >	atoms_

CHARMMBonds	bonds_

CHARMMDihedrals	dihedrals_

CHARMMDihedrals	impropers_

CHARMMInternalCoordinates	internal_coordinates_

Member Function Documentation

virtual ::IMP::base::VersionInfo IMP::atom::CHARMMIdealResidueTopology::get_version_info ( ) const

virtual

Get information about the module and version of the object.

Reimplemented from IMP::atom::CHARMMResidueTopologyBase.

Reimplemented in IMP::atom::CHARMMResidueTopology.

Definition at line 355 of file charmm_topology.h.

void IMP::atom::CHARMMIdealResidueTopology::remove_atom ( std::string name )

Remove the named atom.

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

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

charmm_topology.h

Detailed Description

Public Member Functions

Additional Inherited Members

Member Function Documentation