SEAMM Read Structure Plug-in

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A SEAMM plug-in to read common formats in computational chemistry

The current version uses Open Babel as an engine to parse various formats such as PDB, Mol2 or XYZ and transform them into the SEAMM structure format for further use in SEAMM flowcharts.

Features

  • Emphasis in ease-of-use and simplicity. The public interface consists of a single function.

  • Automatic file type recognition.

  • OpenBabel as an engine to parse formats, but other engines can be easily implemented.

  • Easily extensible to new formats.

  • Current support for PDB, Mol2 and XYZ files.

Example

import read_structure_step
seamm_structure = read_structure_step.read("spc.xyz")

Acknowledgements

This package was created with Cookiecutter and the molssi-seamm/cookiecutter-seamm-plugin project template.

Developed by the Molecular Sciences Software Institute (MolSSI), which receives funding from the National Science Foundation under award ACI-1547580

Development Team

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