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

WWW: http://www.rdkit.org/