Hi Ed
Thank you very much for pointing to that issue. You are right, due to the
new release the code has changed a bit.
I have added some further chemical reaction functionality (see GitHub
https://github.com/rdkit/rdkit/commit/8aac978f1b4f6088d8bb3c86aff138763d014c00)
and thereby accidentally introduced also a memory leak in the RunReactants
code :(.
A commit fixing that bug will be provided this afternoon on GitHub.
Additionally, a patched version of RDKit will be released soon.
Thanks again and best,
Nadine
2014-12-01 20:08 GMT+01:00 Edward Pyzer-Knapp <[email protected]>:
> Hi RDKitters
>
> I am experiencing a slightly strange issue when doing a large number of
> SMARTS reactions.
>
> If I do the reaction inside a loop, as the index of the loop gets larger,
> I see python grabbing more and more memory from the OS
>
> Min Example:
>
> rxn = ReactionFromSmarts(""[*:1][Cl:3].[*:2][Cl:4]>>[*:1][*:2]") # This
> links two molecules together at the position marked with Cl atoms
>
> #Assuming I have a function that returns two random relevant smiles,
> gen_random_smiles()
>
> for i in range(0, 1000):
> smiles1, smiles2 = gen_random_smiles()
> mol1 = MolFromSmiles(smiles1)
> mol2 = MolFromSmiles(smiles2)
> prods = rxn.RunReactants((mol1, mol2))
> yield prods
>
> Will result in a steadily climbing memory usage. This persists if I alter
> the code to force garbage collection. I do not remember this happening in
> earlier versions of RDKit, has anything changed that would alter this
> behaviour? Or do I perhaps have some rose tinted specs on and this is just
> python memory fragmentation?
>
> Ed Pyzer-Knapp
>
>
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