Hi Alsa,
In the line where you save the file, you need to specify a selection,
otherwise, everything will be saved
Look at http://www.pymolwiki.org/index.php/Save#PYMOL_API
So instead of
cmd.save(filenameN + '.mol')
you want something like
cmd.save(filenameN + '.mol', filename)
I haven't tested this myself though.
Hope this helps
Folmer
2015-06-06 11:53 GMT+02:00 AE <alsalisb...@yahoo.com>:
> Good day,
>
> I have several thousands of files, which I upload using the loop:
>
> myDir = ‘/dirWithFiles'
> for filename in os.listdir(myDir):
> cmd.load (filename)
> filenameN = os.path.splitext(filename)[0]
> cmd.save(filenameN + '.mol')
> cmd.disable(filename)
>
> I am trying to save them one by one in a different (.mol) format. However,
> the files are saved together, i.e.: first file opened contains only
> molecule from the first file; second: first + second; third: first + second
> + third etc. But I want firstFile.readableFormat to be converted into
> firstFile.mol, secondFile.readableFormat - secondFile.mol etc, without any
> addition of other files. How can I do that?
>
> Thank you,
>
> Best Regards,
>
> Alsa
>
> Sorry I have sent it already, accidentally forgot to finish the question
> in subject(
>
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Folmer Fredslund
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