parmed.topologyobjects.NonbondedException

class parmed.topologyobjects.NonbondedException(atom1, atom2, type=None)

The AMOEBA force field has complex exclusion and exception rules (referred to as “adjustments” in the Amber-converted files). This class stores per-particle exceptions.

Parameters

atom1Atom

One of the atoms in the exclusion pair

atom2Atom

The other atom in the exclusion pair

typeNonbondedExceptionType

The nonbonded exception type that describes how the various nonbonded interactions between these two atoms should work

Notes

NonbondedException objects “contain” two atoms and will return True when used with the binary in operator

__init__(atom1, atom2, type=None)

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

Methods

__init__(atom1, atom2[, type])

Initialize self.