Re: [Rdkit-discuss] Error writing gzipped sdf

[Paolo T. <pao...@gm...>]

Hi Steve,

sorry, my bad. Use "wt+".

p.


On 02/09/2018 15:26, Sharky El Sharko wrote:
>
> 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 <sha...@gm... 
>> <mailto:sha...@gm...>> 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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>