Hi Christos,
thanks for pointing out the pickle issue and the solution using
PropertyMol. After reading the documentation this should definitely solve
the problem.
Best,
Michael
Michael Reutlinger, PhD
Scientist, Molecular Design and Chemical Biology
Roche Pharma Research and Early Development
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On Mon, Feb 2, 2015 at 11:17 AM, Christos Kannas <[email protected]>
wrote:
> Hi Michael,
>
> The problem occurs because child processes return their results using
> pickle, and the ordinary rdkit molecule object when is being pickled it
> looses information.
> A solution that I use is to convert the molecule objects to PropertyMol
> objects, which retain their properties.
>
> Best,
>
> Christos
>
> Christos Kannas
>
> Researcher
> Ph.D Student
>
> Mob (UK): +44 (0) 7447700937
> Mob (Cyprus): +357 99530608
>
> [image: View Christos Kannas's profile on LinkedIn]
> <http://cy.linkedin.com/in/christoskannas>
>
> On 2 February 2015 at 09:03, Reutlinger, Michael <
> [email protected]> wrote:
>
>> Hi all,
>>
>> I am currently trying to parallelize part of a script using RDKIT and
>> concurrent.futures. The function that is executed in parallel returns
>> processed molecules as RDKIT Mol objects.
>>
>> Without parallelization everything is fine and the Mol objects keep all
>> the properties that they had before the processing. When using
>> concurrent.futures, the returned molecules lose all properties and seem to
>> be created from scratch maybe with unknown side-effects.
>>
>> I am wondering if anyone experienced the same issue and knows how to
>> circumvent this. I attached a ipython notebook with a small script
>> demonstrating the issue.
>>
>> Best,
>> Michael
>>
>>
>>
>>
>> Example Code:
>>
>> from concurrent import futures
>> from rdkit import Chem
>> from rdkit.Chem import AllChem
>> from rdkit.Chem.Draw import IPythonConsole
>>
>> def process(mol):
>> if not "Name" in mol.GetPropNames():
>> print "Processing: Name missing"
>> mol.SetProp("Processed","True")
>> return mol
>>
>> mol = Chem.MolFromSmiles("N[C@@H](C)C(=O)O")
>> mol.SetProp("Name","Alanine")
>>
>> with futures.ProcessPoolExecutor(max_workers=1) as pool:
>> future = pool.submit(process, mol)
>> molOut = future.result()
>> if "Name" not in molOut.GetPropNames():
>> print "Result: Name missing"
>> if "Processed" not in molOut.GetPropNames():
>> print "Result: Processed missing"
>>
>>
>>
>>
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