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

Project description

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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.

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

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.

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