IMP::atom::CHARMMPatch Class Reference

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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 to identify the residue which will be patched.

Inheritance diagram for IMP::atom::CHARMMPatch:

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Public Member Functions
void	add_deleted_atom (std::string name)
void	apply (CHARMMResidueTopology &res1, CHARMMResidueTopology &res2) const
	Apply the patch to the given pair of residues.
void	apply (CHARMMResidueTopology &res) const
	Apply the patch to the residue, modifying its topology accordingly.
	CHARMMPatch (std::string type)

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Member Function Documentation

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.

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).

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

• charmm_topology.h
• atom/__init__.py