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Specified grid spacing for ShapeTanimotoDistance is ignored. #4364

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greglandrum opened this issue Jul 27, 2021 Discussed in #4363 · 0 comments
Closed

Specified grid spacing for ShapeTanimotoDistance is ignored. #4364

greglandrum opened this issue Jul 27, 2021 Discussed in #4363 · 0 comments
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@greglandrum
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Discussed in #4363

Originally posted by ljmartin July 27, 2021
Hi all,
Looking for some help interpreting the usage of ShapeTanimotoDist. I'd like to see the effect of finer grid spacing. Changing the gridSpacing parameter apparently doesn't change the results:

from rdkit import Chem
from rdkit.Chem.rdShapeHelpers import ShapeTanimotoDist

testmol = Chem.MolFromSmiles('CCCC')
testmolH = Chem.AddHs(testmol)
AllChem.EmbedMultipleConfs(testmolH, 2)

print('change grid spacing:')
for gs in [0.0001, 0.001, 0.01, 0.1, 1]:
    print(ShapeTanimotoDist(testmolH, testmolH, 0,1,gridSpacing=gs))

which returns:

change grid spacing
0.4034090909090909
0.4034090909090909
0.4034090909090909
0.4034090909090909
0.4034090909090909

Am I missing something? Thanks!
Lewis

@greglandrum greglandrum added this to the 2021_03_5 milestone Jul 27, 2021
greglandrum added a commit to greglandrum/rdkit that referenced this issue Jul 27, 2021
greglandrum added a commit that referenced this issue Aug 24, 2021
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