May 26, 2018

Collection of cheminformatics and machine-learning software

Open source toolkit for cheminformatics.


  • 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

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