Package: read-structure-step
SEAMM Read Structure Plug-inA SEAMM plug-in to read common formats in computational chemistryThe 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 licenseDocumentation:https://molssi-seamm.github.io/read_structure_step/index.htmlCode:https://github.com/molssi-seamm/read_structure_stepFeaturesEmphasis 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.Exampleimportread_structure_stepseamm_structure=read_structure_step.read("spc.xyz")AcknowledgementsThis package was created withCookiecutterand themolssi-seamm/cookiecutter-seamm-pluginproject template.Developed by the Molecular Sciences Software Institute (MolSSI),
which receives funding from theNational Science Foundationunder
award ACI-1547580History2023.11.16 – Bugfix: titles in SDF filesCrashed 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 handlingMoving towards the standard structure handling that has developed across SEAMM.2023.8.30 – Support for spacegroup symmetry2023.7.28 – 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 filesHandle .gz and .bz2 files for .sdf and .xyz extensions.Handle multi-structure XYZ files with a blank line between records.2023.7.6 – BugfixesFixed output of number of structures written to SDF files, which was off by 1.Cleaned up the output for the write-structure step2023.1.30 – Fixed issue#43, duplicate systems or configuration createdReading 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 propertiesAdded a custom handler for XYZ files to cope with some of the variant formats.Supports files with no atom count on the first lineSupports 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 filesThere 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 filesHiding 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.