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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.
The documentation for the peleffy package is available at GitHub Pages.
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)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')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_solventFor a full list of contributors, see the GitHub Contributors page.