rdkit

Collection of cheminformatics and machine-learning software

Open source toolkit for cheminformatics. Features: * Input/Output: SMILES/SMARTS, SDF, TDT, SLN 1, Corina mol2 1, PDB, sequence notation, FASTA (peptides only), HELM (peptides only) * Substructure searching * Canonical SMILES * Chirality support (i.e. R/S or E/Z labeling) * Chemical transformations (e.g. remove matching substructures) * Chemical reactions * Molecular serialization (e.g. mol <-> text) * 2D depiction, including constrained depiction * Fingerprinting: Daylight-like, atom pairs, topological torsions, Morgan algorithm, "MACCS keys", extended reduced graphs, etc. * Similarity/diversity picking * Gasteiger-Marsili charges * Bemis and Murcko scaffold determination * Salt stripping * Functional-group filters