RDKit Introduction
RDKit is an open-source toolkit for cheminformatics, based on operations on 2D and 3D molecular compounds. It leverages machine learning methods for compound descriptor generation, fingerprint generation, compound structure similarity calculation, and 2D/3D molecular visualization. It is a highly practical library bridging chemistry and machine learning. It can interconvert various chemical file formats such as mol2, mol, SMILES, sdf, and display them in 2D or 3D for developers.
Examples Include
- Reading and writing molecules
- Image generation & saving
- Feature extraction & molecular similarity computation — three calculation methods are demonstrated
Running Example — SimpleSmilesExample
After running successfully, the command line should display the following:
[INFO ] - smi1: c1ccccc1 [INFO ] - smi2: c1ccccn1 [INFO ] - AllBitSimilarity: 0.98681640625 [INFO ] - CosineSimilarity: 0.4147806778921701 [INFO ] - DiceSimilarity: 0.5454545454545454
Save molecule image:
