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[![Release](https://img.shields.io/github/release/martimunicoy/peleffy.svg?include_prereleases)](https://github.com/martimunicoy/peleffy/releases/) |\n| :------ | :------- |\n| **Status** | [![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/martimunicoy/peleffy.svg?logo=lgtm\u0026logoWidth=18)](https://lgtm.com/projects/g/martimunicoy/peleffy/context:python) [![Test](https://github.com/martimunicoy/peleffy/workflows/Test/badge.svg)](https://github.com/martimunicoy/peleffy/actions?query=workflow%3ATest) [![codecov](https://codecov.io/gh/martimunicoy/peleffy/branch/master/graph/badge.svg)](https://codecov.io/gh/martimunicoy/peleffy) |\n| **Installation** | [![Conda](https://img.shields.io/conda/v/martimunicoy/peleffy.svg)](https://anaconda.org/martimunicoy/peleffy) [![PyPI](https://img.shields.io/pypi/v/peleffy)](https://pypi.org/project/peleffy/) |\n\n# PELE Force Field Yielder\n\n\u003cp align=\"left\"\u003e\n  \u003cimg src=\"docs/figures/logo.png\" width=\"350\" title=\"peleffy logo\", alt=\"peleffy logo\"\u003e\n\u003c/p\u003e\n\nThe `peleffy` (PELE Force Field Yielder) is a Python package that builds [PELE](https://pele.bsc.es/pele.wt)-compatible force field templates. The current supported force fields are:\n- Any force field from the [Open Force Field toolkit](https://github.com/openforcefield/openforcefield).\n- OPLS2005.\n- A combination of them.\n\n## Documentation\nThe documentation for the `peleffy` package is available at [GitHub Pages](https://martimunicoy.github.io/peleffy).\n\n## Main features\n\n### Small molecules parameterization\nIt 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.\n\n```python\nfrom peleffy.topology import Molecule\nfrom peleffy.forcefield import OpenForceField\n\nmolecule = Molecule('path_to_pdb_file.pdb')\nopenff = OpenForceField('openff_unconstrained-1.3.0.offxml')\n\nparameters = openff.parameterize(molecule)\n```\n\n### Template generation\nA 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.\n\n```python\nfrom peleffy.topology import Topology\nfrom peleffy.template import Impact\n\ntopology = Topology(molecule, parameters)\n\nimpact_template = Impact(topology)\nimpact_template.to_file('ligand_parameters.txt')\n```\n\nA template with the OBC parameters for the implicit solvent of PELE can also be generated.\n```python\nfrom peleffy.solvent import OBC2\n\nobc2_solvent = OBC2(topology)\nobc2_solvent.to_file('ligand_obc.txt')\n```\n\nIt can also generate the rotamer library file for the side chain exploration of PELE.\n```python\nfrom peleffy.topology import RotamerLibrary\n\nrotamer_library = RotamerLibrary(molecule)\nrotamer_library.to_file('ligand_rotamers.txt')\n```\n\n### User-friendly CLI\nAll the commands above can be run with a single CLI directive.\n```bash\npython -m peleffy.main path_to_pdb_file.pdb -f 'openff_unconstrained-1.3.0.offxml' --with_solvent\n```\n\n## Contributors\nFor a full list of contributors, see the [GitHub Contributors page](https://github.com/martimunicoy/peleffy/graphs/contributors).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmartimunicoy%2Fpeleffy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmartimunicoy%2Fpeleffy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmartimunicoy%2Fpeleffy/lists"}