multiple files

Hello,





I would like to convert my mol files to another format with one command





it is possible in babel:





babel -imol *.mol -osmi -m,





where "-m" means separated files.





However, babel does not recognise Chemaxon's mol format in some cases, e.g. when a group is inserted in the structure.





Is it possible to do this kind of conversion with molconvert? I need to keep the name of the files.





Thanks,


Zsolt

You can convert multiple files into one file (e.g. SD file) by molconverter script:

Code:

molconvert sdf *.mol > mols.sdf

To convert multiple mol files into separate files (in another format) is a bit complicated.


I can recommend two ways:


1. Call molconvert for each molecule and write batch file or a script to do automatize it. The capability of Unix shell scripts are very flexible and writing a simple script is very easy

Code:

#!/bin/sh # Unix shell script to convert all mol files in the current directory to smiles. FILES=`ls *.mol` for f in $FILES do     echo "Convert $f to smiles format: $f.smiles"     ./scripts/molconvert smiles $f > $f.smiles done

2. Write a custom Java application by using the MolConverter API





Meanwhile, I've found a suitable custom application for your request.


Originally, I wrote this example application to export compounds to separate image files. Iinstead of "jpeg" format, give the the required output format (e.g. "smiles"). convert mol files into image as a batch program