Hi RDKitters,
I might be being stupid here, but I'm trying to marry up the bitinfo from a
hashed fingerprint to the actual fingerprint and I can't seem to do it.
from rdkit import Chem, DataStructs
from rdkit.Chem import rdMolDescriptors as rdMD
info = {}
mol = Chem.MolFromSmiles('CCCCC')
print rdMD.GetHashedMorganFingerprint(mol, radius=2, nBits = 1024, bitInfo =
info).GetNonzeroElements()
print '\n',info
{33: 2, 294: 2, 591: 2, 80: 3, 887: 1, 794: 2, 381: 1}
{2246728737: ((0, 0), (4, 0)), 3542456614: ((0, 1), (4, 1)), 1685248591: ((1,
2), (3, 2)), 2245384272: ((1, 0), (2, 0), (3, 0)), 1510461303: ((2, 1),),
1173125914: ((1, 1), (3, 1)), 2738269565: ((2, 2),)}
The indices on the bitinfo appear to be the unhashed values. What I'd expect to
see it something similar to the bit vector version of this code
info = {}
mol = Chem.MolFromSmiles('CCCCC')
print list(rdMD.GetMorganFingerprintAsBitVect(mol, radius=2, nBits = 1024,
bitInfo = info).GetOnBits())
print '\n',info
[33, 80, 294, 381, 591, 794, 887]
{33: ((0, 0), (4, 0)), 294: ((0, 1), (4, 1)), 591: ((1, 2), (3, 2)), 80: ((1,
0), (2, 0), (3, 0)), 887: ((2, 1),), 794: ((1, 1), (3, 1)), 381: ((2, 2),)}
I think I might be going about something the wrong way here so I'll explain
what I'm doing. I'm using the output from GetHashedMorganFingerprint in machine
learning and from this I'm trying to generate some of Sereina's lovely
similarity maps. However I'm having issues hacking her code because of the
bitInfo vectors don't match my FP's.
Thanks in advance.
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
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