SEAMM From SMILES plug-in
A SEAMM plug-in for creating structures from a SMILES string.
This plug-in accepts SMILES (Simplified Molecular-Input Line Entry System) string representing a structure, and creates the structure if the current system/conformation in SEAMM. It uses the implementation in Open Babel which has an extension for handling radicals.
Free software: BSD license
Documentation: https://from-smiles-step.readthedocs.io.
Features
Accepts with a SMILES string directly or from a variable.
The generated structure can optionally be optimized using one of several forcefields.
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 OAC-1547580 and CHE-2136142.
History
- 2025.5.14 – Bugfix: Add references for RDKit
Added citations when using RDKit instead of OpenBabel
- 2024.2.24 – Added isomeric SMILES to structure names and ability to discard structures
Added ability to ignore or discard a structure from e.g. optimization
Added isomeric SMILES to the possible names for systems and configurations
- 2024.10.31 – Bugfix: Issue recognizing chemical names
Fixed an issue where the chemical name was handled as SMILES, causing the code to crash.
- 2023.11.10 – Bugfix: New configurations created incorrectly
New configurations made from other systems could remove the atoms in those systems.
- 2023.11.9.1 – Removed using structure names when perceiving type
Using structure names is too dangerous to use by perceiving if text is a name of SMILES and there is no easy test for valid SMILES. So change to only using names if the user specifies names.
- 2023.11.9 – Improved structure handling, added from names
Switched to standard structure handling, which adds more options
Added getting structures from Pubchem using the chemical name.
2023.7.18 – Added support for InChI and InChIKeys
2021.2.10 (10 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.
2020.2.4 (4 February 2021)
Internal Changes
Corrected an issue in CI.
2021.2.3 (3 February 2021)
Internal Changes
Upgraded to be compatible with the improved version of the MolSystem classes for describing the molecular system.
2020.12.4 (4 December 2020)
Internal Changes
Moved the continuous integration (CI) to GitHub Actions from TravisCI.
Moved documentation from ReadTheDocs to GitHub Pages and integrated with the rest of the SEAMM documentation.
2020.11.2 (2 November 2020)
Moved to the new command-line argument handling.
2020.9.24.1 (24 September 2020)
Fixed small bug with the title of the system when generated from SMILES.
2020.9.24 (24 September 2020)
Updated to work with the new MolSystem classes describing the molecular system.
0.9 (15 April 2020)
Internal changes for compatibility.
0.7.0 (17 December 2019)
Internal changes cleaning the code.
0.1.0 (20 January 2018)
First release on PyPI.
1 maintainer
Metadata
1 maintainer
Release files for from-smiles-step 2025.5.14
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| File | Size | Uploaded | Provenance | |
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| from_smiles_step-2025.5.14.tar.gz | 37.9 kB | Without provenance | Details |
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| from_smiles_step-2025.5.14-py2.py3-none-any.whl | Python 2, Python 3 | none | any | Details |
Total release size: 49.7 kB
Release files / from_smiles_step-2025.5.14.tar.gz
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