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read-structure-step
Readme
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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.
Example +++++++
.. code:: python
import read_structure_step seamm_structure = read_structure_step.read("spc.xyz")
This package was created with Cookiecutter_ and the molssi-seamm/cookiecutter-seamm-plugin
_ project template.
.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _molssi-seamm/cookiecutter-seamm-plugin
: https://github.com/molssi-seamm/cookiecutter-seamm-plugin
Developed by the Molecular Sciences Software Institute (MolSSI_),
which receives funding from the National Science Foundation
_ under
award ACI-1547580
.. _MolSSI: https://www.molssi.org
.. _National Science Foundation
: https://www.nsf.gov
2023.11.16 -- Bugfix: titles in SDF files
2023.11.5 -- Added writers for CIF and mmCIF.
2023.11.2 -- Initial changes to structure handling
2023.8.30 -- Support for spacegroup symmetry
2023.7.28 -- Implemented ranges for reading XYZ and SDF files.
2023.7.27.1 -- Removed debug printing.
2023.7.27 -- Support for .gz and .bz2 files, and multi-structure .xyz files
2023.7.6 -- Bugfixes
2023.1.30 -- Fixed issue#43, duplicate systems or configuration created
2023.1.24 -- Added handler for XYZ files and added properties
Added a custom handler for XYZ files to cope with some of the variant formats.
Supports files with no atom count on the first line
Supports the variant used in the Minnesota Solubility database, which has 3 header lines.
Add capability to store properties into the database for formats such as MOPAC and SDF that can handle properties. Also can output the properties when writing the files.
Fixed bugs if the system name or configuration name is not a string, but rather a number.
2022.10.28 -- Fixed bug reading cif and mmcif files
There was a bug that caused a crash when reading cif and mmcif files, and potentially some other formats. It has been fixed throughout.
The standard error for properties were missing a commma in the property name. The comma is standard elsewhere in SEAMM so add it here: ', stderr'
2022.10.26 -- Handling OpenBabel error messages for MOPAC .mop files Hiding messages about errors Kekulizing structures, which doesn't seem to be a serious issue, and printing any other messages as warnings.
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.
FAQs
A SEAMM plug-in to read common formats in computational chemistry
We found that read-structure-step demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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