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

• Descriptors
  • MolecularDescriptorTransformer

• Fingerprints
  • MorganFingerprintTransformer
  • MACCSKeysFingerprintTransformer
  • RDKitFingerprintTransformer
  • AtomPairFingerprintTransformer
  • TopologicalTorsionFingerprintTransformer
  • MHFingerprintTransformer
  • SECFingerprintTransformer
  • AvalonFingerprintTransformer

• Conversions
  • SmilesToMol

• Standardizer
  • Standardizer

• 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

Documentation

There are a collection of notebooks in the notebooks directory which demonstrates some different aspects and use cases

• Basic Usage and fingerprint transformers
• Descriptor transformer
• Pipelining with Scikit-Learn classes
• Molecular standardization
• Sanitizing SMILES input
• Integrated hyperparameter tuning of Scikit-Learn estimator and Scikit-Mol transformer
• Using parallel execution to speed up descriptor and fingerprint calculations
• Testing different fingerprints as part of the hyperparameter optimization

Contributing

There are more information about how to contribute to the project in CONTRIBUTION.md

BUGS

Probably still, please check issues at GitHub and report there

Contributers:

• Esben Jannik Bjerrum @ebjerrum, esbenbjerrum+scikit_mol@gmail.com
• Carmen Esposito @cespos
• Son Ha, sonha@uni-mainz.de
• Oh-hyeon Choung, ohhyeon.choung@gmail.com
• Andreas Poehlmann, @ap--
• Ya Chen, @anya-chen
• Rafał Bachorz @rafalbachorz
• Adrien Chaton @adrienchaton
• @VincentAlexanderScholz
• @RiesBen