read-structure-step 2022.5.23

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

SEAMM Read Structure Plug-in

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.

• Free software: BSD license

• Documentation: https://molssi-seamm.github.io/read_structure_step/index.html

• Code: https://github.com/molssi-seamm/read_structure_step

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

History

2021.2.12 (12 February 2021)

• Updated the README file to give a better description.

• Updated the short description in setup.py to work with the new installer.

• Added keywords for better searchability.

2021.2.4 (4 February 2021)

• Updated for compatibility with the new system classes in MolSystem 2021.2.2 release.

2020.12.5 (5 December 2020)

• Internal: switching CI from TravisCI to GitHub Actions, and in the process moving documentation from ReadTheDocs to GitHub Pages where it is consolidated with the main SEAMM documentation.

2020.8.1 (1 August 2020)

• Removed leftover debug print statements.

0.9 (15 April 2020)

• General bug fixing and code cleanup.

• Part of release of all modules.

0.7.1 (23 November 2019)

• First release on PyPI.