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Espaloma Charge
Standalone charge assignment from Espaloma framework. https://doi.org/10.1039/D2SC02739A
Installation
$ pip install espaloma_charge
Examples
Option0: Assign charges to rdkit molecule.
>>> from rdkit import Chem; from espaloma_charge import charge
>>> molecule = Chem.MolFromSmiles("N#N")
>>> charge(molecule)
array([0., 0.], dtype=float32)
Assign charges to your favorite molecule in
Option1: Use with openff-toolkit
(installation required)
>>> from openff.toolkit.topology import Molecule
>>> from espaloma_charge.openff_wrapper import EspalomaChargeToolkitWrapper
>>> toolkit_registry = EspalomaChargeToolkitWrapper()
>>> molecule = Molecule.from_smiles("N#N")
>>> molecule.assign_partial_charges('espaloma-am1bcc', toolkit_registry=toolkit_registry)
>>> molecule.partial_charges
<Quantity([0. 0.], 'elementary_charge')>
Option2: Use as Command Line Interface to write antechamber
-compatible charges.
$ espaloma_charge -i in.mol2 -o in.crg
$ antechamber -fi mol2 -fo mol2 -i in.mol2 -o out.mol2 -c rc -cf in.crg
Reference
If you are using this little tool in your pipeline, please consider citing:
@Article{D2SC02739A,
author ="Wang, Yuanqing and Fass, Josh and Kaminow, Benjamin and Herr, John E. and Rufa, Dominic and Zhang, Ivy and Pulido, Iván and Henry, Mike and Bruce Macdonald, Hannah E. and Takaba, Kenichiro and Chodera, John D.",
title ="End-to-end differentiable construction of molecular mechanics force fields",
journal ="Chem. Sci.",
year ="2022",
volume ="13",
issue ="41",
pages ="12016-12033",
publisher ="The Royal Society of Chemistry",
doi ="10.1039/D2SC02739A",
url ="http://dx.doi.org/10.1039/D2SC02739A"}
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