from-smiles-step 2025.5.14

A SEAMM plug-in for creating structures from a SMILES string.

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.