chem-caption
Science Score: 44.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.8%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: lamalab-org
- License: mit
- Language: Python
- Default Branch: main
- Size: 2.25 MB
Statistics
- Stars: 4
- Watchers: 1
- Forks: 1
- Open Issues: 19
- Releases: 1
Metadata Files
README.md
ChemCaption
Caption molecules and materials for pretraining for neural networks.
💪 Getting Started
ChemCaption is a tool designed to generate prompts for molecular features to train neural networks.
Here is a quick example of one of the featurizers designed to count the number of elements in a molecule.
```python from chemcaption.presets import ORGANIC from chemcaption.molecules import SMILESMolecule from chemcaption.featurize.composition import ElementCountFeaturizer
Molecule we want to featurize
molecule = SMILESMolecule("C1(Br)=CC=CC=C1Br")
We can eather specify the symbol or the full name
elcountname = ElementCountFeaturizer(['carbon', 'hydrogen', 'oxygen', 'bromine'])
Featurize the molecule
prompt = elcountname.text_featurize(molecule=molecule) ```
The generate prompt has the following QA pair.
text
Question: What are the atom counts of Carbon, Hydrogen, Hidrogen, and Bromine of the molecule with SMILES Brc1ccccc1Br?
Answer: 6, 4, 0, and 2
For more details and all other available featurizers please visit the documentation.
🚀 Installation
The most recent release can be installed from PyPI with:
bash
pip install chemcaption
The most recent code and data can be installed directly from GitHub with:
bash
pip install git+https://github.com/lamalab-org/chem-caption
Some of the ChemCaption featurizers are dependent on morfeus and might require additional dependencies to be installed. You can see all the optional dependencies for morfeus-ml here
👐 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.
🍪 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/lamalab-org/chem-caption $ cd chem-caption $ pip install -e . ``` ### 🥼 Testing After cloning the repository and installing `nox` with `pip install nox`, the unit tests in the `tests/` folder can be run reproducibly with: ```shell $ nox ``` Additionally, these tests are automatically re-run with each commit in a [GitHub Action](https://github.com/kjappelbaum/chem-caption/actions?query=workflow%3ATests). ### 📖 Building the Documentation The documentation can be built locally using the following: ```shell $ git clone git+https://github.com/lamalab-org/chem-caption $ cd chem-caption $ nox --session 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). ### 📦 Making a Release After installing the package in development mode and installing `nox` with `pip install nox`, the commands for making a new release are contained within the `finish` environment in `noxfile.py`. Run the following from the shell: ```shell $ nox --session finish ``` This script does the following: 1. Uses [Bump2Version](https://github.com/c4urself/bump2version) to switch the version number in the `setup.cfg`, `src/chemcaption/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 `nox -e bumpversion -- minor` after.Owner
- Name: Laboratory for AI for Materials
- Login: lamalab-org
- Kind: organization
- Repositories: 1
- Profile: https://github.com/lamalab-org
Research group led by Kevin Maik Jablonka
Citation (CITATION.cff)
cff-version: 1.0.2 message: "If you use this software, please cite it as below." title: "chemcaption" authors: - name: "Benedict Oshomah Emoekabu" - name: "Kevin Maik Jablonka " version: 0.0.1-dev doi: url: "https://github.com/kjappelbaum/chem-caption"
GitHub Events
Total
- Issues event: 4
- Watch event: 2
- Issue comment event: 11
- Push event: 20
- Pull request review event: 5
- Pull request review comment event: 22
- Pull request event: 7
- Create event: 5
Last Year
- Issues event: 4
- Watch event: 2
- Issue comment event: 11
- Push event: 20
- Pull request review event: 5
- Pull request review comment event: 22
- Pull request event: 7
- Create event: 5
Issues and Pull Requests
Last synced: over 1 year ago
All Time
- Total issues: 80
- Total pull requests: 43
- Average time to close issues: about 2 months
- Average time to close pull requests: 15 days
- Total issue authors: 2
- Total pull request authors: 2
- Average comments per issue: 1.3
- Average comments per pull request: 1.49
- Merged pull requests: 35
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- kjappelbaum (73)
- Arkhymadhe (6)
- AdrianM0 (1)
Pull Request Authors
- Arkhymadhe (35)
- kjappelbaum (8)
- Stoick01 (4)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/checkout v2 composite
- actions/setup-python v2 composite
- codecov/codecov-action v1 composite