MolConverter

Overview

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.

• 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

• 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