Dear all,
James' question about boost.thread dependencies reminded me that I seem to
have neglected to post anything about one of the useful additions to the
most recent RDKit release; I'll remedy that now.
I added multi-threading support for a few more time-consuming functions
that are embarrassingly parallel: conformation generation, force field
minimization of multiple-conformer molecules, and Open3D alignment of
multiple-conformer molecules.
Here's a quick demonstration of how this works.
Start by creating a basic molecule:
In [1]: from rdkit import Chem
In [2]: from rdkit.Chem import AllChem
In [3]: m = Chem.MolFromSmiles('Cc1cc(C(=O)NCC(=O)N)c(C)n1c2ccc(F)cc2') #
CHEMBL2113931
In [4]: mh = Chem.AddHs(m)
Time how long it takes to generate 50 conformers using one thread:
In [5]: %timeit AllChem.EmbedMultipleConfs(mh,50)
1 loops, best of 3: 260 ms per loop
And using 4 threads:
In [6]: %timeit AllChem.EmbedMultipleConfs(mh,50,numThreads=4)
10 loops, best of 3: 77.6 ms per loop
Nice speed up there.
Do a force-field minimization of all of those conformations with one thread:
In [7]: %timeit tm = Chem.Mol(mh);AllChem.UFFOptimizeMoleculeConfs(tm)
1 loops, best of 3: 1.11 s per loop
And using 4 threads:
In [8]: %timeit tm =
Chem.Mol(mh);AllChem.UFFOptimizeMoleculeConfs(tm,numThreads=4)
1 loops, best of 3: 288 ms per loop
Another good improvement.
Use the O3A code to align all the conformers to another molecule:
In [16]: m2 =
Chem.MolFromSmiles(r'Cc1cc(\C=C\2/SC(=Nc3ccccc3)NC2=O)c(C)n1c4ccccc4') #
CHEMBL599702
In [17]: m2h = Chem.AddHs(m2)
In [18]: AllChem.EmbedMolecule(m2h)
Out[18]: 0
In [19]: AllChem.UFFOptimizeMolecule(m2h)
Out[19]: 1
In [20]: refParams = AllChem.MMFFGetMoleculeProperties(m2h)
In [21]: prbParams = AllChem.MMFFGetMoleculeProperties(mh)
In [23]: %timeit
tm=Chem.Mol(mh);AllChem.GetO3AForProbeConfs(tm,m2h,prbPyMMFFMolProperties=prbParams,refPyMMFFMolProperties=refParams)
1 loops, best of 3: 1.13 s per loop
Do the same alignment with 4 threads:
In [24]: %timeit
tm=Chem.Mol(mh);AllChem.GetO3AForProbeConfs(tm,m2h,prbPyMMFFMolProperties=prbParams,refPyMMFFMolProperties=refParams,numThreads=4)
1 loops, best of 3: 304 ms per loop
I think this is a convenient (and very easy) way to take advantage of one
of the convenient features of modern compute hardware.
Best,
-greg
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