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
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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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leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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