Re: [Rdkit-discuss] Dask + Rdkit Use Cases

[Oren Herschander]

Yes! Thanks Francois :) Pat is the one who introduced me to your wonderful
group. Big fan.



Oren Herschander

*Information** Forager*

Scale Dask Without the Fuss: https://coiled.io/


On Wed, Jan 26, 2022 at 1:41 AM Francois Berenger  wrote:

> On 25/01/2022 01:57, Oren Herschander wrote:
> > Hi Everyone,
> > I'm working on a research project about how Dask and other python
> > tools for distributed/parallel computing are used in Life Sciences.
> >
> > I'm on the lookout for use cases, stories, and overall thoughts that
> > combine rdkit or other similar software with Dask. Emails are great,
> > but if you have the time for a quick conversation those are a lot of
> > fun too! :)
>
> In case you don't already know, Patrick Walters gave a try at dask to
> parallelize some python chemoinformatics and tells all about it here:
>
>
> https://patwalters.github.io/practicalcheminformatics/jupyter/dask/parallel/2021/03/28/dask-cheminformatics.html
>
> > Thank you so much! I really appreciate the help!
> >
> > Cheers,
> > Oren
> >
> >  [1]
> >
> > Oren Herschander
> >
> > _Information__ Forager @ _https://coiled.io/
> >
> >
> >
> > Links:
> > --
> > [1] https://coiled.io
> > ___
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> > Rdkit-discuss@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
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Re: [Rdkit-discuss] problem with latest bulds?

[Tim Dudgeon]

And to clarify, the build completes OK. It's just that the Python
bindings don't work.

On Wed, Jan 26, 2022 at 2:42 PM Tim Dudgeon  wrote:

> Yes, it sounds similar, but I'm not applying that fix (though on the
> Release_2021_09_4 tag I do also see that same problem).
> I'm just doing a plain vanilla build from the code on master branch.
>
> On Wed, Jan 26, 2022 at 2:30 PM Paolo Tosco 
> wrote:
>
>> Hi Tim,
>>
>> there was a similar report a few days ago, caused by a sed command
>> overwriting its input and resulting in no output:
>>
>> Cannot import Draw · Issue #4904 · rdkit/rdkit (github.com)
>> 
>>
>> Could it be you are experiencing the same issue? Current ,master builds
>> fine for me too.
>>
>> Cheers,
>> p.
>>
>> On Wed, Jan 26, 2022 at 2:58 PM Tim Dudgeon 
>> wrote:
>>
>>> I'm building RDKit from the latest code on the master branch.
>>> The build is fine, but the python bindings seem broken:
>>>
>>> >>> from rdkit import Chem
>>> Traceback (most recent call last):
>>>   File "", line 1, in 
>>>   File "/data/github/rdkit/rdkit/rdkit/__init__.py", line 6, in 
>>> from . import rdBase
>>> ImportError: cannot import name 'rdBase' from partially initialized
>>> module 'rdkit' (most likely due to a circular import)
>>> (/data/github/rdkit/rdkit/rdkit/__init__.py)
>>>
>>> Are others seeing this too?
>>>
>>> Tim
>>> ___
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>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>
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Re: [Rdkit-discuss] problem with latest bulds?

[Tim Dudgeon]

Yes, it sounds similar, but I'm not applying that fix (though on the
Release_2021_09_4 tag I do also see that same problem).
I'm just doing a plain vanilla build from the code on master branch.

On Wed, Jan 26, 2022 at 2:30 PM Paolo Tosco 
wrote:

> Hi Tim,
>
> there was a similar report a few days ago, caused by a sed command
> overwriting its input and resulting in no output:
>
> Cannot import Draw · Issue #4904 · rdkit/rdkit (github.com)
> 
>
> Could it be you are experiencing the same issue? Current ,master builds
> fine for me too.
>
> Cheers,
> p.
>
> On Wed, Jan 26, 2022 at 2:58 PM Tim Dudgeon  wrote:
>
>> I'm building RDKit from the latest code on the master branch.
>> The build is fine, but the python bindings seem broken:
>>
>> >>> from rdkit import Chem
>> Traceback (most recent call last):
>>   File "", line 1, in 
>>   File "/data/github/rdkit/rdkit/rdkit/__init__.py", line 6, in 
>> from . import rdBase
>> ImportError: cannot import name 'rdBase' from partially initialized
>> module 'rdkit' (most likely due to a circular import)
>> (/data/github/rdkit/rdkit/rdkit/__init__.py)
>>
>> Are others seeing this too?
>>
>> Tim
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>>
>
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Re: [Rdkit-discuss] problem with latest bulds?

[Paolo Tosco]

Hi Tim,

there was a similar report a few days ago, caused by a sed command
overwriting its input and resulting in no output:

Cannot import Draw · Issue #4904 · rdkit/rdkit (github.com)


Could it be you are experiencing the same issue? Current ,master builds
fine for me too.

Cheers,
p.

On Wed, Jan 26, 2022 at 2:58 PM Tim Dudgeon  wrote:

> I'm building RDKit from the latest code on the master branch.
> The build is fine, but the python bindings seem broken:
>
> >>> from rdkit import Chem
> Traceback (most recent call last):
>   File "", line 1, in 
>   File "/data/github/rdkit/rdkit/rdkit/__init__.py", line 6, in 
> from . import rdBase
> ImportError: cannot import name 'rdBase' from partially initialized module
> 'rdkit' (most likely due to a circular import)
> (/data/github/rdkit/rdkit/rdkit/__init__.py)
>
> Are others seeing this too?
>
> Tim
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Re: [Rdkit-discuss] problem with latest bulds?

[David Cosgrove]

Hi Tim,
I built from master a couple of hours ago on a Ubuntu 20 system without
problems.
Dave

On Wed, 26 Jan 2022 at 13:58, Tim Dudgeon  wrote:

> I'm building RDKit from the latest code on the master branch.
> The build is fine, but the python bindings seem broken:
>
> >>> from rdkit import Chem
> Traceback (most recent call last):
>   File "", line 1, in 
>   File "/data/github/rdkit/rdkit/rdkit/__init__.py", line 6, in 
> from . import rdBase
> ImportError: cannot import name 'rdBase' from partially initialized module
> 'rdkit' (most likely due to a circular import)
> (/data/github/rdkit/rdkit/rdkit/__init__.py)
>
> Are others seeing this too?
>
> Tim
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-- 
David Cosgrove
Freelance computational chemistry and chemoinformatics developer
http://cozchemix.co.uk
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[Rdkit-discuss] problem with latest bulds?

[Tim Dudgeon]

I'm building RDKit from the latest code on the master branch.
The build is fine, but the python bindings seem broken:

>>> from rdkit import Chem
Traceback (most recent call last):
  File "", line 1, in 
  File "/data/github/rdkit/rdkit/rdkit/__init__.py", line 6, in 
from . import rdBase
ImportError: cannot import name 'rdBase' from partially initialized module
'rdkit' (most likely due to a circular import)
(/data/github/rdkit/rdkit/rdkit/__init__.py)

Are others seeing this too?

Tim
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