MolConverter
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 document, molecule file, graphic and compression/encoding formats. When handling chemical structures users can specify how to handle chemical features relevant to molecule file formats.
Rich functionality
- Strucutre files supported: MOL, SDF, RXN, RDF (V2000/V3000), SMILES, MRV, CML, PDB
- SMARTS/SMIRKS (recursive supported)
- Outputs graphic formats (JPG, PNG, BMP, POV, SVG, EPS, 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
