============================
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.
* 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
+++++++
.. code:: python
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.
.. _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
=======
History
=======
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.
Raw data
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The public interface\n consists of a single function.\n- Automatic file type recognition.\n- OpenBabel as an engine to parse formats, but other engines can be\n easily implemented.\n- Easily extensible to new formats.\n- Current support for PDB, Mol2 and XYZ files.\n\nExample\n+++++++\n\n.. code:: python\n\n import read_structure_step\n seamm_structure = read_structure_step.read(\"spc.xyz\")\n\nAcknowledgements\n----------------\n\nThis package was created with Cookiecutter_ and the `molssi-seamm/cookiecutter-seamm-plugin`_ project template.\n\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`molssi-seamm/cookiecutter-seamm-plugin`: https://github.com/molssi-seamm/cookiecutter-seamm-plugin\n\nDeveloped by the Molecular Sciences Software Institute (MolSSI_),\nwhich receives funding from the `National Science Foundation`_ under\naward ACI-1547580\n\n.. _MolSSI: https://www.molssi.org\n.. _`National Science Foundation`: https://www.nsf.gov\n\n\n=======\nHistory\n=======\n2023.11.16 -- Bugfix: titles in SDF files\n * Crashed reading some SDF files write by SEAMM due to the system and configuration\n names encoded in the title having multiple slashes (/).\n\n2023.11.5 -- Added writers for CIF and mmCIF.\n\n2023.11.2 -- Initial changes to structure handling\n * Moving towards the standard structure handling that has developed across SEAMM.\n \n2023.8.30 -- Support for spacegroup symmetry\n\n2023.7.28 -- Implemented ranges for reading XYZ and SDF files.\n\n2023.7.27.1 -- Removed debug printing.\n\n2023.7.27 -- Support for .gz and .bz2 files, and multi-structure .xyz files\n * Handle .gz and .bz2 files for .sdf and .xyz extensions.\n * Handle multi-structure XYZ files with a blank line between records.\n \n2023.7.6 -- Bugfixes\n * Fixed output of number of structures written to SDF files, which was off by 1.\n * Cleaned up the output for the write-structure step\n \n2023.1.30 -- Fixed issue#43, duplicate systems or configuration created\n\n * Reading a single structure from e.g. a .sdf file created a second system or\n configuration, depending on the stucture control options.\n\n2023.1.24 -- Added handler for XYZ files and added properties\n\n * Added a custom handler for XYZ files to cope with some of the variant formats.\n\n * Supports files with no atom count on the first line\n\n * Supports the variant used in the Minnesota Solubility database, which has 3 header\n lines.\n\n * Add capability to store properties into the database for formats such as MOPAC and\n SDF that can handle properties. 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