This repo contains associated code for the paper MolSkill: Implicit molecular scoring via chemists in the loop.
We recommend that you make a fresh conda environment (currently we only support Python 3.9 Linux builds) and install the provided conda package for convenience:
conda install molskill -c msr-ai4science -c conda-forgeAdditionally, you can also use the provided environment.yml file for manual installation.
A CUDA-enabled GPU is not required for usage, but strongly recommended for speed if you plan on scoring a large amount of compounds.
This work mainly exposes the MolSkillScorer class under the molskill.scorer module. We interface with RDKit to provide predictions accordingly. The user only has to provide a list of molecular strings that they wish to score.
from molskill.scorer import MolSkillScorer
smiles_strs = ["CCO", "O=C(Oc1ccccc1C(=O)O)C"]
scorer = MolSkillScorer()
scores = scorer.score(smiles_strs)We provide and use by default a pre-trained model on all the data that was collected during the original study. If a user wants to train custom models, please check the train.py script also included under this repository.
If you find this work or parts thereof useful, please consider citing the following BibTeX entry:
@article{choung2023
...
}
This project welcomes contributions and suggestions. Most contributions require you to agree to a Contributor License Agreement (CLA) declaring that you have the right to, and actually do, grant us the rights to use your contribution. For details, visit https://cla.opensource.microsoft.com.
When you submit a pull request, a CLA bot will automatically determine whether you need to provide a CLA and decorate the PR appropriately (e.g., status check, comment). Simply follow the instructions provided by the bot. You will only need to do this once across all repos using our CLA.
This project has adopted the Microsoft Open Source Code of Conduct. For more information see the Code of Conduct FAQ or contact [email protected] with any additional questions or comments.
This project may contain trademarks or logos for projects, products, or services. Authorized use of Microsoft trademarks or logos is subject to and must follow Microsoft's Trademark & Brand Guidelines. Use of Microsoft trademarks or logos in modified versions of this project must not cause confusion or imply Microsoft sponsorship.Any use of third-party trademarks or logos are subject to those third-party's policies.