Hi Paolo,
I'm afraid I get the same error with 'wb+'.
S
On 02/09/18 15:24, Paolo Tosco wrote:
Hi Steve,
Try replacing “w+” with “wb+” to open the file as a binary stream.
Cheers,
p.
On 2 Sep 2018, at 16:13, Sharky El Sharko <[email protected]
<mailto:[email protected]>> wrote:
Hi,
Please can someone tell me why I am getting an error writing a
gzipped sdf, and how to fix it. I am running python 3.6.5 with the
latest RDKit (2018.03.3), and the following code:
#!/usr/bin/env python
import gzip
from rdkit import Chem
outfZ = gzip.open('out02.sdf.gz', 'w+')
writer = Chem.SDWriter(outfZ)
m1 = Chem.MolFromSmiles('Cc1ccccc1')
m2 = Chem.MolFromSmiles('Nc1ccccc1')
list_of_mols = [m1, m2]
for mol in list_of_mols:
writer.write(mol)
writer.close()
outfZ.close()
gives the following error:
Traceback (most recent call last):
File "./exampleGzip02.py", line 12, in <module>
writer.write(mol)
File "/xxx/yyy/miniconda2/envs/my-rdkit-env/lib/python3.6/gzip.py",
line 260, in write
data = memoryview(data)
TypeError: memoryview: a bytes-like object is required, not 'str'
I tried a few ways to wrestle the mol into a binary format, but
without success. Can anyone enlighten me, please.
Thanks very much.
Kind regards,
Steve
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