Hi Jean-Marc,
tempfn.close() should allow you to delete the file.
A better alternative would be using using
with temp file.TemporaryFile as tempfn
...
As the file will be automatically closed and deleted for you as soon as it goes
out of scope at the end of the context manager block.
Cheers,
p.
> On 29 Mar 2020, at 13:44, Jean-Marc Nuzillard <jm.nuzill...@univ-reims.fr>
> wrote:
>
> Dear all,
>
> The following code:
> ______________________________________
> from rdkit import Chem
> import os
> import tempfile
>
> # create temp .sdf file with a benzene molecule inside
> m1 = Chem.MolFromSmiles('c1ccccc1')
> m1.SetProp('_Name', 'benzene')
> tempfn = tempfile.mktemp('.sdf')
> writer = Chem.SDWriter(tempfn)
> writer.write(m1)
> writer.close()
>
> # read the molecule from temp .sdf file and print compound name
> reader = Chem.SDMolSupplier(tempfn)
> m2 = reader[0]
> print(m2.GetProp('_Name'))
>
> # unlik temp file
> os.unlink(tempfn)
> ______________________________________
>
> running it in windows gives:
>
> benzene
> Traceback (most recent call last):
> File "rdclose.py", line 21, in <module>
> os.unlink(tempfn)
> PermissionError: [WinError 32] The process cannot access the file because it
> is being used by another process:
> 'C:\\Users\\jmn\\AppData\\Local\\Temp\\tmpojn1j4nb.sdf'
>
> I suspect the reason is that reader file is not closed.
> Trying reader.close() results in a message saying that reader has no close()
> method.
>
> Thank you in advance for helping me to get rid of the temp file.
>
> Take care,
>
> Jean-Marc Nuzillard
>
> --
> Jean-Marc Nuzillard
> Directeur de Recherches au CNRS
>
> Institut de Chimie Moléculaire de Reims
> CNRS UMR 7312
> Moulin de la Housse
> CPCBAI, Bâtiment 18
> BP 1039
> 51687 REIMS Cedex 2
> France
>
> Tel : 03 26 91 82 10
> Fax : 03 26 91 31 66
> http://www.univ-reims.fr/icmr
> http://eos.univ-reims.fr/LSD/CSNteam.html
>
> http://www.univ-reims.fr/LSD/
> http://www.univ-reims.fr/LSD/JmnSoft/
>
>
>
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