import/export multiple mol files at once

User 1b14b56d14

06-03-2015 13:23:59


I was looking for a way to import multiple .mol files into a new data 
and structure entity, all at once. I have a folder with hundreds of 
single mol files, and i would like to import them all at once, so 
hundreds of rows should be created. Is that possible? And also the 
other way around, when a sdf file has been created, how do you export 
hundreds of coumpounds in the sdf file at once to single mol files?

Thanks for your help,
Cheers, Geert (Using Instant Jchem v 

ChemAxon e49cf225c6

06-03-2015 13:48:31


I'd suggest to use molconverter (you can find it in your ChemAxon installation folder):

To merge multiple mol files from a directory:

molconvert  mol -o output.mol *.mol

To split structure into files:

 molconvert  mol -m -o output.mol input.mol

It will produce files named output1.mol output2.mol, ...

Also I move this topic to the Instant JChem section, hopefully they can suggest other solutions.

User 1b14b56d14

06-03-2015 13:59:28

Hi, thanks for the reply.


the molconvert.bat does not run on my computer, i see the command box appearing but dissapearing as fast, so it wont load it

how should i run this molconvert.bat?


I have little experience with these kind of commands :)


cheers, geert

ChemAxon e49cf225c6

06-03-2015 14:15:43

Try to open up a command prompt by typing "cmd" into your Windows start menu. (Alternatively you can find at manually in C:\windows\system32\cmd.exe).

Navigate to your installation folder where molconvert.bat is located with the cd command.  On my system it's something like this:

cd "\Program Files (x86)\ChemAxon\MarvinBeans\bin"

 After that you can start typing those molconvert commands. Don't forget to use absolute paths for your files, e.g.:

molconvert mol -o c:\files\output\output.mol c:\files\*.mol 

I hope that helps. Maybe the IJC team can provide a more convenient solution.