AE,
you need to delete the loaded file before loading another. cmd.save will save
ALL objects in the buffer by default as you have experienced yourself. Also
your handling of the filename is slightly off, since pymol strips the extender
upon loading, i.e. "test01.pdb" becomes "test01" object. You have two choices
here, either you can retain all files in the buffer (not sure if this is your
intention) or use Pymol as a file converter (you could use BABEL for that as
well, might work better ?!). This is how I would write the code (untested
however):
cmd.reinitialize()
myDir = ‘/dirWithFiles'
for filename in os.listdir(myDir):
cmd.load (filename)
obj_name = os.path.splitext(filename)[0]
filenameN = obj_name + '.mol'
cmd.save(filename, obj_name)
cmd.delete(obj_name) # comment out this line of you want to keep all
files in the buffer
-----Original Message-----
From: AE [mailto:[email protected]]
Sent: Saturday, June 06, 2015 5:54 AM
To: [email protected]
Subject: Re: [PyMOL] How to forbid merging of files?
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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