parmed.topologyobjects.Cmap

class parmed.topologyobjects.Cmap(atom1, atom2, atom3, atom4, atom5, type=None)

A coupled-torsion correction map term defined between 5 atoms connected by four covalent bonds. This is a coupled-torsion potential in which the torsions are consecutive.

Parameters

atom1Atom

An atom on one end of the valence coupled-torsion bonded to atom2

atom2Atom

An atom in the middle of the CMAP bonded to atoms 1 and 3

atom3Atom

An atom in the middle of the CMAP bonded to atoms 2 and 4

atom4Atom

An atom in the middle of the CMAP bonded to atoms 3 and 5

atom5Atom

An atom in the middle of the CMAP bonded to atom 4

typeCmapType

The CmapType object containing the parameter map for this term

Notes

A CMAP can contain bonds or atoms. A bond is contained if it exists between atoms 1 and 2, between atoms 2 and 3, between atoms 3 and 4, or between atoms 4 and 5.

Examples

>>> a1, a2, a3, a4, a5 = Atom(), Atom(), Atom(), Atom(), Atom()
>>> cmap = Cmap(a1, a2, a3, a4, a5)
>>> Bond(a1, a2) in cmap and Bond(a2, a3) in cmap
True
>>> Bond(a1, a3) in cmap
False

Methods

delete()	Deletes this Cmap from the atoms that make it up.
extended(atom1, atom2, atom3, atom4, atom5, …)	Alternative constructor for correction maps defined with 8 atoms (each torsion being separately specified).
same_atoms(thing)	A coupled-torsion is equivalent if the 5 atoms are in the same or reverse order Allow comparison with another type of cmap or with a sequence of 5 indexes

__init__(atom1, atom2, atom3, atom4, atom5, type=None)

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__(atom1, atom2, atom3, atom4, atom5)	Initialize self.
delete()	Deletes this Cmap from the atoms that make it up.
extended(atom1, atom2, atom3, atom4, atom5, …)	Alternative constructor for correction maps defined with 8 atoms (each torsion being separately specified).
same_atoms(thing)	A coupled-torsion is equivalent if the 5 atoms are in the same or reverse order Allow comparison with another type of cmap or with a sequence of 5 indexes