peleffy.solvent.OBC2

class peleffy.solvent.OBC2(topologies)

Implementation of the OBC2 solvent.

__init__(topologies)

Initializes an OBC2 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 OpenForceField

>>> openff = OpenForceField('openff_unconstrained-1.2.1.offxml')
>>> parameters = openff.parameterize(molecule)

>>> from peleffy.topology import Topology

>>> topology = Topology(molecule, parameters)

>>> from peleffy.solvent import OBC2

>>> solvent = OBC2(topology)
>>> solvent.to_file('OBC_parameters.txt')

to_dict()

Returns this OpenFFCompatibleSolvent object as a dictionary.

Returns

data – A dictionary containing the data of this SolventWrapper object

Return type

dict

to_file(path)

Writes this OpenFFCompatibleSolvent object to a file.

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.
solute_dielectric	The solute dielectric value of this solvent object.
solvent_dielectric	The solvent dielectric value of this solvent object.
solvent_radius	The solvent radius value of this solvent object.
surface_area_penalty	The surface area penalty value of this solvent object.
topologies	The peleffy’s Topology.