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PELE Force Field Yielder

<p align="left"> <img src="docs/figures/logo.png" width="350" title="peleffy logo", alt="peleffy logo"> </p>

The peleffy (PELE Force Field Yielder) is a Python package that builds PELE-compatible force field templates. The current supported force fields are:

• Any force field from the Open Force Field toolkit.
• OPLS2005.
• A combination of them.

Documentation

The documentation for the peleffy package is available at GitHub Pages.

Main features

Small molecules parameterization

It can take a molecular structure from a PDB file or a SMILES tag and parameterize it with any of the supported force fields. The resulting parameters are stored in a dictionary-like object that can be easily manipulated.

from peleffy.topology import Molecule
from peleffy.forcefield import OpenForceField

molecule = Molecule('path_to_pdb_file.pdb')
openff = OpenForceField('openff_unconstrained-1.3.0.offxml')

parameters = openff.parameterize(molecule)

Template generation

A peleffy's molecular representation can be employed, along with its parameters, to build a Topology file. A Topology file is a wrapper of topological elements that can be written as an Impact template file, compatible with PELE.

from peleffy.topology import Topology
from peleffy.template import Impact

topology = Topology(molecule, parameters)

impact_template = Impact(topology)
impact_template.to_file('ligand_parameters.txt')

A template with the OBC parameters for the implicit solvent of PELE can also be generated.

from peleffy.solvent import OBC2

obc2_solvent = OBC2(topology)
obc2_solvent.to_file('ligand_obc.txt')

It can also generate the rotamer library file for the side chain exploration of PELE.

from peleffy.topology import RotamerLibrary

rotamer_library = RotamerLibrary(molecule)
rotamer_library.to_file('ligand_rotamers.txt')

User-friendly CLI

All the commands above can be run with a single CLI directive.

python -m peleffy.main path_to_pdb_file.pdb -f 'openff_unconstrained-1.3.0.offxml' --with_solvent

Contributors

For a full list of contributors, see the GitHub Contributors page.