Thanks again Paolo for your help with fixing this issue on my machine.
Best,
Alexis
On Thu, 9 Sept 2021 at 11:45, Paolo Tosco <paolo.tosco.m...@gmail.com>
wrote:
> Just to close the loop on this topic if someone runs into the same issue:
>
> the problem was caused by RDBASE being set to
> %CONDA_PREFIX%\Lib\site-packages\rdkit.
>
> As a consequence, the RDConfig.py script would not use the correctly
> configured paths set in RDPaths.py, but rather set the RDDataDir path to
> %RDBASE%\Data, which is incorrect for the directory layout of a Windows
> conda distribution.
> Therefore, the FragmentDescriptors.csv was not being found and all
> fragment descriptors were missing,
>
> Unsetting the RDBASE environment variable fixed the problem.
>
> Cheers,
> Paolo
>
> On Wed, Sep 8, 2021 at 5:40 PM Paolo Tosco <paolo.tosco.m...@gmail.com>
> wrote:
>
>> Hi Alexis,
>>
>> I did some more investigation. The fragment descriptors are parsed from a
>> CSV file located in RDConfig.RDDataDir:
>> On my machine I see this:
>>
>> >>> import os
>> >>> from rdkit.Chem import Fragments
>> >>> len([f for f in dir(Fragments) if f.startswith("fr_")])
>> 85
>> >>> from rdkit import RDConfig
>> >>> fragment_descriptors_csv = os.path.join(RDConfig.RDDataDir,
>> 'FragmentDescriptors.csv')
>> >>> os.path.exists(fragment_descriptors_csv)
>> True
>> >>> with open(fragment_descriptors_csv) as hnd:
>> ... print(len([line for line in hnd if (not line.startswith("#")) and
>> len(line.split('\t')) >= 3]))
>> ...
>> 86
>>
>> The 86/85 discrepancy is caused by the fact that the fr_sulfone entry in
>> the CSV file is duplicate.
>>
>> If the CSV file existed and were empty no fragment descriptors would be
>> available.
>> Similarly, if the file did not exist (maybe because RDConfig.RDDataDir
>> is misconfigured), no fragment descriptors would be available and no
>> warning would be printed, as in _LoadPatterns() (rdkit/Chem/Fragments.py/) an
>> IOError exception will just be ignored.
>>
>> I hope the above helps troubleshooting.
>>
>> Cheers,
>> p.
>>
>> On Wed, Sep 8, 2021 at 2:50 PM Alexis Parenty <
>> alexis.parenty.h...@gmail.com> wrote:
>>
>>> Hi Paolo,
>>> Thanks a lot for your response. I am going to try rdkit 2021.03.5 right
>>> now...
>>>
>>> I have checked where I have installed the previous built: I did use
>>> conda-forge on both platforms:
>>>
>>> [image: image.png]
>>>
>>> Weird...
>>>
>>> best,
>>>
>>> Alexis
>>>
>>>
>>>
>>> On Wed, 8 Sept 2021 at 14:04, Paolo Tosco <paolo.tosco.m...@gmail.com>
>>> wrote:
>>>
>>>> Hi Alexis,
>>>>
>>>> I have just installed rdkit 2021.03.5 from the conda-forge channel on
>>>> a Windows machine and 208 descriptors are indeed available.
>>>>
>>>> >>> import sys
>>>> >>> sys.platform
>>>> 'win32'
>>>> >>> import rdkit
>>>> >>> rdkit.__version__
>>>> '2021.03.5'
>>>> >>> from rdkit.Chem import Descriptors
>>>> >>> len(Descriptors._descList)
>>>> 208
>>>>
>>>> The number of available descriptors depends on how RDKit is built.
>>>> My guess is that the RDKit installation that you have on Windows does
>>>> not come from the conda-forge channel and was built differently from
>>>> the one you have installed on Linux.
>>>>
>>>> Cheers,
>>>> p.
>>>>
>>>> On Wed, Sep 8, 2021 at 11:30 AM Alexis Parenty <
>>>> alexis.parenty.h...@gmail.com> wrote:
>>>>
>>>>> Hi everyone,
>>>>>
>>>>> I have noticed some inconsistencies with the list of rdkit chemical
>>>>> descriptor available between my Windows machine and my Linux machine.
>>>>> I am running the same rdkit version on both platforms (2021.03.1) on
>>>>> the same 3.9 python version.
>>>>>
>>>>> running the following from windows:
>>>>>
>>>>>
>>>>> print(len(Descriptors._descList))
>>>>> for each_descriptor in Descriptors._descList:
>>>>> print(each_descriptor[0])
>>>>>
>>>>>
>>>>> ==> 123
>>>>> and no fragment descriptors ("fr_xxx")
>>>>>
>>>>> running the same from linux:
>>>>> ==> 208
>>>>> (same descriptors as on Windows + all the descriptors from the
>>>>> Chem.Fragments module)
>>>>>
>>>>>
>>>>> Could the fragment descriptors available on Linux be added to the list
>>>>> of available fragments on Windows so that the ML models stay cross
>>>>> platform
>>>>> compatible?
>>>>>
>>>>> Many thanks and regards,
>>>>>
>>>>> Alexis
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Rdkit-discuss mailing list
>>>>> Rdkit-discuss@lists.sourceforge.net
>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>>
>>>> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
