interconverts between industry standard file formats

MolConverter is a command line program in Marvin Beans and JChem that converts between various file types. Operating in batch mode users can specify various documents, molecule files, graphic and compression/encoding formats. When handling chemical structures users can specify how to handle chemical features relevant to molecule file formats.

Product Type:component
Interfaces:CLIAPI ( Java )

Technical overview

Rich functionality

  • Structure files supported: MOL, SDF, RXN, RDF (V2000/V3000), SMILES, MRV, CML, PDB, SMARTS, InChI, IUPAC name, etc.
  • SMARTS/SMIRKS (recursive supported)
  • Output graphic formats (JPG, PNG, BMP, POV, SVG, PDF)
  • Non chemical data such as SDF fields can be converted

Chemically aware

  • Calculate 2D/3D coordinates
  • Filtering by fields (SDF import)
  • Remove explicit H atoms
  • Valence checking
  • Remove small fragments / keep the largest
  • Extensive 3D cleaning options

Command line tool

Running the MolConverter from command line


Release Information
Training & Examples
Support & FAQ

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