cinemol 1.0.1

CineMol is a tool for drawing small molecule configurations directly to SVG.

CineMol

CineMol is a direct-to-SVG small molecule drawer. Read more about CineMol in our publication.

You can try out CineMol online here.

💪 Getting Started

The cinemol command line tool is automatically installed. It can be used from the shell with the --help flag to show all subcommands:

python3 -m cinemol --help

The cinemol command line tool can be used to convert 3D molecular structures to SVG images. The following example converts a penicillin G conformer to a spacefilling SVG image:

python3 -m cinemol examples/data/penicillin_G.sdf examples/svgs/cartoon_spacefilling.svg -s spacefilling -l cartoon -r 100 -sc 10.0 -hs

This command will generate the following SVG image:

CineMol can also be used as a Python package. You can find examples in the examples folder.

Find more information in the documentation.

🚀 Installation

The most recent release can be installed from PyPI with:

pip install cinemol

The most recent code and data can be installed directly from GitHub with:

pip install git+https://github.com/MolTools/CineMol.git

👐 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.

👋 Attribution

⚖️ License

The code in this package is licensed under the MIT License.

📖 Citation

If you use CineMol in your research, please cite our pre-print.

🍪 Cookiecutter

This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.

🛠️ For Developers

See developer instructions

The final section of the README is for if you want to get involved by making a code contribution.

Development Installation

To install in development mode, use the following:

git clone git+https://github.com/MolTools/CineMol.git
cd CineMol
pip install -e .

🥼 Testing

After cloning the repository and installing tox with pip install tox, the unit tests in the tests/ folder can be run reproducibly with:

tox

Additionally, these tests are automatically re-run with each commit in a GitHub Action.

📖 Building the Documentation

The documentation can be built locally using the following:

git clone git+https://github.com/MolTools/CineMol.git
cd CineMol
tox -e docs
open docs/build/html/index.html

The documentation automatically installs the package as well as the docs extra specified in the setup.cfg. sphinx plugins like texext can be added there. Additionally, they need to be added to the extensions list in docs/source/conf.py.

The documentation can be deployed to ReadTheDocs using this guide. The .readthedocs.yml YAML file contains all the configuration you'll need. You can also set up continuous integration on GitHub to check not only that Sphinx can build the documentation in an isolated environment (i.e., with tox -e docs-test) but also that ReadTheDocs can build it too.

📦 Making a Release

After installing the package in development mode and installing tox with pip install tox, the commands for making a new release are contained within the finish environment in tox.ini. Run the following from the shell:

tox -e finish

This script does the following:

1. Uses Bump2Version to switch the version number in the setup.cfg, src/cinemol/version.py, and docs/source/conf.py to not have the -dev suffix
2. Packages the code in both a tar archive and a wheel using build
3. Uploads to PyPI using twine. Be sure to have a .pypirc file configured to avoid the need for manual input at this step
4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can use tox -e bumpversion -- minor after.