scikit-learn classes for molecule transformation
Project description
scikit-mol
Scikit-Learn classes for molecular vectorization using RDKit
The intended usage is to be able to add molecular vectorization directly into scikit-learn pipelines, so that the final model directly predict on RDKit molecules or SMILES strings
As example with the needed scikit-learn and -mol imports and RDKit mol objects in the mol_list_train and _test lists:
pipe = Pipeline([('mol_transformer', MorganTransformer()), ('Regressor', Ridge())])
pipe.fit(mol_list_train, y_train)
pipe.score(mol_list_test, y_test)
pipe.predict([Chem.MolFromSmiles('c1ccccc1C(=O)C')])
>>> array([4.93858815])
The scikit-learn compatibility should also make it easier to include the fingerprinting step in hyperparameter tuning with scikit-learns utilities
The first draft for the project was created at the RDKIT UGM 2022 hackathon 2022-October-14
Implemented
- Transformer Classes
- SmilesToMol
- Desc2DTransformer
- MACCSTransformer
- RDKitFPTransformer
- AtomPairFingerprintTransformer
- TopologicalTorsionFingerprintTransformer
- MorganTransformer
- Utilities
- CheckSmilesSanitazion
Installation
Users can install latest tagged release from pip
pip install scikit-mol
Bleeding edge
pip install git+https://github.com:EBjerrum/scikit-mol.git
Developers
git clone git@github.com:EBjerrum/scikit-mol.git
pip install -e .
Documentation
None yet, but there are some # %% delimted examples in the notebooks directory that have some demonstrations
BUGS
Probably still
TODO
- Make standardizer less 'chatty'
- Unit test coverage of classes
- Make further example notebooks
- Standalone usage (not in pipeline)
- Advanced pipelining
- Hyperparameter optimization via external optimizer e.g. https://scikit-optimize.github.io/stable/
Ideas
- LINGOS transformer
Contributers:
- Esben Bjerrum, esben@cheminformania.com
- Carmen Esposito https://github.com/cespos
- Son Ha, sonha@uni-mainz.de
- Oh-hyeon Choung, ohhyeon.choung@gmail.com
- Andreas Poehlmann, https://github.com/ap--
- Ya Chen, https://github.com/anya-chen
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for scikit_mol-0.0.1-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 3bae9cf06728b8c3f54131aedf26ca75d63ccc8033e3136a1f5222b7d6632ed3 |
|
MD5 | 088ea3df31f26221adbc78f460dceb3d |
|
BLAKE2b-256 | 533d108796f4a35664f594fd69fe194d661d1c590f608b60c13764877520b07d |