peleffy.template.Impact

class peleffy.template.Impact(topology, for_amber=False)

It is in charge of writing a Molecule object as a PELE’s Impact template.

__init__(topology, for_amber=False)

Initializes an Impact object.

Parameters

• topology (a peleffy.topology.Topology object) – The molecular topology representation to write as a Impact template

• for_amber (bool) – Whether to save an Impact file compatible with PELE’s Amber force field implementation or not. Default is False which will create an Impact file compatible with OPLS2005

Examples

Write the Impact template of a peleffy’s molecule

>>> from peleffy.topology import Molecule

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

>>> from peleffy.forcefield import OpenForceField

>>> openff = OpenForceField('openff_unconstrained-2.0.0.offxml')
>>> parameters = openff.parameterize(molecule)

>>> from peleffy.topology import Topology

>>> topology = Topology(molecule, parameters)

>>> from peleffy.template import Impact

>>> impact = Impact(topology)
>>> impact.to_file('molz')

Write the Impact template of a peleffy’s molecule compatible with PELE’s Amber forcefield implementation

>>> from peleffy.topology import Molecule

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

>>> from peleffy.forcefield import OpenForceField

>>> openff = OpenForceField('openff_unconstrained-2.0.0.offxml')
>>> parameters = openff.parameterize(molecule)

>>> from peleffy.topology import Topology

>>> topology = Topology(molecule, parameters)

>>> from peleffy.template import Impact

>>> impact = Impact(topology, for_amber=True)
>>> impact.to_file('molz')

classmethod from_file(impact_file)

It loads an Impact template object from a file.

Parameters

impact_file (str) – The path to the impact file

Returns

molecule – The resulting Molecule object

Return type

a peleffy.topology.Molecule object

to_file(path)

It writes the Impact template to a file.

Parameters

path (str) – Path to write to

Attributes

H_6R_OF_2
molecule	The peleffy’s Molecule.
topology	The peleffy’s Topology.