MolConverter
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.
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
Resources
Guides
Documentation
Release Information
Training & Examples
Support & FAQ
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