peleffy.solvent.OPLSOBC

class peleffy.solvent.OPLSOBC(topologies)

It defines a template generator for OBC compatible with the OPLS2005 force field implemented in PELE.

__init__(topologies)

Initializes an OPLSOBC object.

Parameters

topologies (a Topology object or list[Topology object]) – The molecular topology representation to write as a Impact template

Examples

Generate the solvent parameters of a molecule

>>> from peleffy.topology import Molecule

>>> molecule = Molecule('molecule.pdb')

>>> from peleffy.forcefield import OPLS2005ForceField

>>> opls2005 = OPLS2005ForceField()
>>> parameters = opls2005.parameterize(molecule)

>>> from peleffy.topology import Topology

>>> topology = Topology(molecule, parameters)

>>> from peleffy.solvent import OPLSOBC

>>> solvent = OPLSOBC(topology)
>>> solvent.to_file('OBC_parameters.txt')

to_file(path)

Writes this OPLS2005CompatibleSolvent object to a file compatible with PELE.

Parameters

path (str) – Path to save the output file to

Attributes

name	The name of the solvent.
radii	A list of the dicts of radii of the parameterized molecules.
scales	A list of the dicts of scales of the parameterized molecules.
topologies	The peleffy’s Topology.