IMP::atom::CHARMMPatch Class Reference

A CHARMM patch residue. More...

#include <IMP/atom/charmm_topology.h>

Inheritance diagram for IMP::atom::CHARMMPatch:

Public Member Functions
	CHARMMPatch (std::string type)
	Construct a new, empty patch residue. More...
void	add_removed_atom (std::string name)
void	apply (CHARMMResidueTopology *res) const
	Apply the patch to the residue, modifying its topology accordingly. More...
void	apply (CHARMMResidueTopology *res1, CHARMMResidueTopology *res2) const
	Apply the patch to the given pair of residues. More...
virtual void	do_show (std::ostream &out) const
unsigned int	get_number_of_removed_atoms () const
std::string	get_removed_atom (unsigned int i) const
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 ()
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. 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)

Related Functions
(Note that these are not member functions.)
typedef IMP::base::Vector < IMP::base::WeakPointer < CHARMMPatch > >	CHARMMPatchesTemp
Related Functions inherited from IMP::atom::CHARMMResidueTopologyBase
typedef IMP::base::Vector < IMP::base::WeakPointer < CHARMMResidueTopologyBase > >	CHARMMResidueTopologyBasesTemp
Related Functions inherited from IMP::base::Object
typedef IMP::base::Vector < IMP::base::WeakPointer < Object > >	ObjectsTemp

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

Detailed Description

Patch residues are similar to regular residues, except that they are used to modify an existing residue. Any atoms they contain replace or add to those in the residue; they can also remove atoms. Atom names are as for regular residues, except for patches that affect two residues (e.g. DISU, LINK) in which each atom contains a 1 or 2 prefix (plus an optional colon) to identify the residue which will be patched; for example, both 1:CA and 1CA identify the CA atom in the first residue.

Definition at line 373 of file charmm_topology.h.

Constructor & Destructor Documentation

IMP::atom::CHARMMPatch::CHARMMPatch

(

std::string

type

)

To get an existing patch, use CHARMMParameters::get_patch() instead.

Definition at line 379 of file charmm_topology.h.

Member Function Documentation

void IMP::atom::CHARMMPatch::apply

(

CHARMMResidueTopology *

res

)

const

Note

Most CHARMM patches are designed to be applied in isolation; it is usually an error to try to apply two different patches to the same residue. Thus, by default IMP prohibits this. To allow an already-patched residue to be re-patched, first call CHARMMResidueTopology::set_patched(false).

void IMP::atom::CHARMMPatch::apply	(	CHARMMResidueTopology *	res1,
		CHARMMResidueTopology *	res2
	)		const

This can only be used for special two-residue patches, such as DISU or LINK. In a two-residue patch, each atom has a 1: or 2: prefix to identify the residue it refers to.

Exceptions

ValueException

if the patch is not a two-residue patch.

Friends And Related Function Documentation

typedef IMP::base::Vector<IMP::base::WeakPointer< CHARMMPatch > > CHARMMPatchesTemp

related

Pass a set of objects.

Definition at line 413 of file charmm_topology.h.

---

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

• charmm_topology.h