chemical-helper

A set of Python script to handle interconversion of chemical strctures

• Github repository: https://github.com/commons-research/chemical-helper/
• Documentation https://commons-research.github.io/chemical-helper/

Getting started with your project

First, create a repository on GitHub with the same name as this project, and then run the following commands:

git init -b main
git add .
git commit -m "init commit"
git remote add origin [email protected]:commons-research/chemical-helper.git
git push -u origin main

Finally, install the environment and the pre-commit hooks with

make install

You are now ready to start development on your project! The CI/CD pipeline will be triggered when you open a pull request, merge to main, or when you create a new release.

To finalize the set-up for publishing to PyPi or Artifactory, see here. For activating the automatic documentation with MkDocs, see here. To enable the code coverage reports, see here.

Releasing a new version

• Create an API Token on Pypi.
• Add the API Token to your projects secrets with the name PYPI_TOKEN by visiting this page.
• Create a new release on Github.
• Create a new tag in the form *.*.*.

For more details, see here.

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Repository initiated with fpgmaas/cookiecutter-poetry.

To check if a SMILES string is canonical:

poetry run python -m chemical_helper.cli is-canonical --smiles "[input_smiles_string]"

For converting any SMILES to canonical SMILES:

poetry run python -m chemical_helper.cli to-canonical-smiles --smiles "[input_smiles_string]"

Replace [input_smiles_string] with your SMILES string.

For example:

poetry run python -m chemical_helper.cli to-canonical-smiles --smiles "CCCCCCCCCCCCCCCCCC(=O)OCC(CO[C@H]1C([C@H]([C@H](C(CS(=O)(=O)[O-])O1)O)O)O)OC(=O)CCCCCCCCCCCCCCCCC"

And for converting canonical SMILES to InChI:

poetry run python -m chemical_helper.cli to-inchi --cansmiles "[canonical_smiles_string]"

Replace [canonical_smiles_string] with your canonical SMILES string.

For example:

poetry run python -m chemical_helper.cli to-inchi --cansmiles "CCCCCCCCCCCCCCCCCC(=O)OCC(CO[C@H]1C([C@H]([C@H](C(CS(=O)(=O)[O-])O1)O)O)O)OC(=O)CCCCCCCCCCCCCCCCC"