Detailed Description

A CHARMM patch residue.

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 372 of file charmm_topology.h.

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...

unsigned int	get_number_of_removed_atoms () const

std::string	get_removed_atom (unsigned int i) 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...

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_

Constructor & Destructor Documentation

IMP::atom::CHARMMPatch::CHARMMPatch ( std::string type )

Construct a new, empty patch residue.

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

Apply the patch to the residue, modifying its topology accordingly.

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

Apply the patch to the given pair of residues.

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.

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

virtual

Get information about the module and version of the object.

Reimplemented from IMP::atom::CHARMMResidueTopologyBase.

Definition at line 410 of file charmm_topology.h.

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

charmm_topology.h

Detailed Description

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation