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Molconverter in the Marvin Beans package from ChemAxon


To convert a file named input_file into another file output_file enter the command

molconvert xxxxx input_file -o output_file

where you should replace xxxxx by the strings corresponding to the chemical formats desired for the output file (the format of the input file is automatically perceived). Examples of formats are

mol – MDL Molfile

smiles – SMILES

inchi – InChI

name – IUPAC name

For example, to convert file propan1ol.mol in the MDL Molfile format into SMILES you should use the command

molconvert smiles propan1ol.mol -o propan1ol.smi

A full list of possible formats is in ChemAxon web site.

Depending on your installation of Marvin Beans you may need to include the full path to the molconvert program (e.g. C:\Programs\ChemAxon\MarvinBeans\bin\molconvert). Don’t forget that if you are not at the directory of input_file and output_file, you should include the full path leading to these files.

Useful options of molconvert are the addition or removing of hydrogen atoms. To add hydrogen atoms to the output structure include “:H” after the specification of the file format. To delete hydrogen atoms use “:-H” instead.

For example, to convert file propan1ol.mol into file propan1olH.mol, both in the MDL Molfile format but the second with H atoms, use the command

molconvert mol:H propan1ol.mol -o propan1olH.mol




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Webmaster: Vasco Bonifácio

last update: 06.02.2010