An introduction to scikit-chem¶

scikit-chem is a high level cheminformatics library built on rdkit that aims to integrate with the Scientific Python Stack by promoting interoperativity with libraries such as pandas and scikit-learn, and emulating similar patterns and APIs as found in those libraries.

Some notable features include:

• Pythonic core API

• Consistent, declarative interfaces for many cheminformatics tasks, including:

  • Reading file formats
  • Chemical standardization
  • Conformer generation
  • Filtering
  • Feature calculation
  • Pipelining

• A simple interface for chemical datasets

• Structure visualization

• Interactivity in Jupyter Notebooks

scikit-chem should be thought of as a simple complement to the excellent rdkit - scikit-chem objects are subclasses of rdkit objects, and as such, the two libraries can usually be used together easily when the advanced functionality of rdkit is required.