read-structure-step 2025.5.14

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

2025.5.14 – Standardized citations to OpenBabel

• Internal change which should not affect users.

2025.3.4 – Improved handling of system names in SDF files

• Switched to new handling of system and configuration names as properties in SDF files, rather than encoded in the title. This avoids problems with special characters in name, for example when using SMILES as the name.

2025.1.15 – Added ability to write using an arbitrary list of structures.

2025.1.3.1 – Bugfix: Issue with reading XYZ files

• If the XYZ file had the charge and spin multiplicity encoded in the comment line, and the spin multiplicity came before the charge, the spin multiplicity was not correctly set. This fixes that issue.

2025.1.3 – Enhancements to SDF and XYZ files

• Added more keywords to the header of XYZ files to allow for more flexibility in reading them. Specifically ‘title’, ‘model’, and ‘name’, which can be used to name the system and/or configuration.

• When reading SDF files, ‘keep current name’ will use the encoded system name in SDF files written by SEAMM, if it exists.

• Fixed minor issue writing SDF files where the ‘configurations’ widget was displayed when writing the current configuration. The widget is now correctly hidden.

2024.12.29 – Bugfix: Issue with reusing systems matching SDF files.

• The logic was faulty, so if the first structure in an SDF file was a configuration of an existing system, it was not added to the system correctly.

2024.12.7 – Minor update due to changes in molsystem

• The molsystem was updated to improve the handling of properties. This required changes in this module to match the new molsystem.

2024.11.29 – Added chemical formula as option for system/configuration names

2024.11.13 – Bugfix: Issues with the names of properties

• Fixed syntax of the properties pulled out from MOPAC encoded parameterization inputs.

2024.11.3 – Bugfix: MOPAC files with references in comments

• Fixed a bug that caused a crash when reading MOPAC files with references in the comments.

• Updated the MOPAC reader to the new approach for running MOPAC in the cases that it is needed: Z-matrices and mixed inputs that OpenBabel can’t handle.

2024.8.23 – Enhancements to directory handling

• Changed the handling of paths to make them relative to the directory that the step is running in. In a loop, for instance, files are relative to the iteration directory.

• When reading files, allow the syntax ‘job://<job number>/…’ to read files from another job. If the job number is omitted, so the prefix is ‘job:///…’, the top directory of the current job is used.

2024.7.28 – Added new names for systems and configurations

• Made the naming of systems and configurations consistent with the standard parameters for them in the GUI.

• Removed all “from file” options, replacing them with “title”, which means the title from the file, if it exists, or the filename if it doesn’t.

2023.11.16 – Bugfix: titles in SDF files

• Crashed reading some SDF files write by SEAMM due to the system and configuration names encoded in the title having multiple slashes (/).

2023.11.5 – Added writers for CIF and mmCIF.

2023.11.2 – Initial changes to structure handling

• Moving towards the standard structure handling that has developed across SEAMM.

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

• Handle .gz and .bz2 files for .sdf and .xyz extensions.

• Handle multi-structure XYZ files with a blank line between records.

2023.7.6 – Bugfixes

• Fixed output of number of structures written to SDF files, which was off by 1.

• Cleaned up the output for the write-structure step

2023.1.30 – Fixed issue#43, duplicate systems or configuration created

• Reading a single structure from e.g. a .sdf file created a second system or configuration, depending on the stucture control options.

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: ‘<prop>, 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.