cinemol

Direct-to-SVG small molecule drawer.

https://github.com/moltools/cinemol

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 4 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
○
Academic email domains
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (14.8%) to scientific vocabulary

Keywords

molecular-drawing scalable-vector-graphics three-dimensional-structure visualization

Last synced: 6 months ago · JSON representation ·

Repository

Direct-to-SVG small molecule drawer.

Basic Info

Host: GitHub
Owner: moltools
License: mit
Language: Python
Default Branch: main
Homepage: https://moltools.bioinformatics.nl/cinemol
Size: 13.9 MB

Statistics

Stars: 27
Watchers: 3
Forks: 3
Open Issues: 0
Releases: 0

Topics

molecular-drawing scalable-vector-graphics three-dimensional-structure visualization

Created over 3 years ago · Last pushed about 1 year ago

Metadata Files

Readme Contributing License Code of conduct Citation

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:

shell 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:

shell 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:

shell pip install cinemol

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

shell 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: ```bash 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: ```shell tox ``` Additionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/MolTools/CineMol/actions?query=workflow%3ATests). ### 📖 Building the Documentation The documentation can be built locally using the following: ```shell 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`](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`](docs/source/conf.py). The documentation can be deployed to [ReadTheDocs](https://readthedocs.io) using [this guide](https://docs.readthedocs.io/en/stable/intro/import-guide.html). The [`.readthedocs.yml`](.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](https://docs.readthedocs.io/en/stable/pull-requests.html). ### 📦 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: ```shell tox -e finish ``` This script does the following: 1. Uses [Bump2Version](https://github.com/c4urself/bump2version) to switch the version number in the `setup.cfg`, `src/cinemol/version.py`, and [`docs/source/conf.py`](docs/source/conf.py) to not have the `-dev` suffix 2. Packages the code in both a tar archive and a wheel using [`build`](https://github.com/pypa/build) 3. Uploads to PyPI using [`twine`](https://github.com/pypa/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.

Owner

Name: MolTools
Login: moltools
Kind: organization
Email: david.meijer@wur.nl
Location: Netherlands

Website: https://moltools.nl/
Repositories: 1
Profile: https://github.com/moltools

A set of software tools for dealing with natural product molecules.

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
title: "CineMol: a programmatically accessible direct-to-SVG 3D small molecule drawer"
authors:
  - family-names: "Meijer"
    given-names: "David"
  - family-names: "Medema"
    given-names: "Marnix H"
  - family-names: "van der Hooft"
    given-names: "Justin JJ"
date-released: 2024-05-23
version: 1.0.2
identifiers:
  - type: doi
    value: 10.1186/s13321-024-00851-y

GitHub Events

Total

Issues event: 1
Watch event: 4
Delete event: 1
Issue comment event: 2
Push event: 1
Pull request event: 2

Last Year

Issues event: 1
Watch event: 4
Delete event: 1
Issue comment event: 2
Push event: 1
Pull request event: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 1
Total pull requests: 1
Average time to close issues: 7 months
Average time to close pull requests: 24 days
Total issue authors: 1
Total pull request authors: 1
Average comments per issue: 7.0
Average comments per pull request: 0.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: 24 days
Issue authors: 0
Pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 0.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

iribirii (1)
trikaloudis (1)
svandenhaute (1)

Pull Request Authors

davidmeijer (6)

Top Labels

Issue Labels

bug (2) question (1)

Pull Request Labels

bug (1)

Packages

Total packages: 1
Total downloads:
- pypi 51 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 5
Total maintainers: 1

pypi.org: cinemol

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

Homepage: https://github.com/moltools/CineMol
Documentation: https://cinemol.readthedocs.io
License: MIT
Latest release: 1.0.2
published about 1 year ago

Versions: 5
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 51 Last month

Rankings

Dependent packages count: 9.4%

Average: 35.8%

Dependent repos count: 62.3%

Maintainers (1)

davidmeijer