API

openpharmmdflow.from_cif(path: str | PathLike) → openff.toolkit.Molecule

Convert a Crystallographic Information File (CIF) to an OpenFF Toolkit Molecule.

Parameters

pathstr or os.PathLike

The path to the CIF file.

Returns

openff.toolkit.Molecule

An OpenFF Toolkit Molecule object representing the molecular structure.

Raises

RuntimeError

If the required external tool ‘apptainer’ is not found.

Notes

This function utilizes the ‘codcif2sdf’ external tool inside an apptainer image to convert a CIF file to a Structure Data File (SDF), and then reads the SDF file into an OpenFF Toolkit Molecule object. Bond order is guessed.

Examples

>>> from openpharmmdflow import from_cif
>>> molecule = from_cif("/path/to/example.cif")
>>> molecule.visualize()