Hi All,
I have been generating explicit bit strings of RDKit fingerprints and was
surprised by this result. Is this the expected behaviour? From the
documentation it looks like the default length should be 2048.
Interestingly if I call the RDKFingerprint method directly the lengths are
all the expected 2048.
In [1]: smi1 = "CCCCNC(=O)[C@@H]1CCCN(C(=O)CCC(C)C)C1"
In [2]: smi2 = "COC(=O)c1cccc(CN2C(=O)N[C@@](C)(c3ccc4c(c3)OCCO4)C2=O)c1"
In [3]: smi3 = "CN(C)[C@@H](Cc1ccccc1)C(=O)NNC(=O)c1ccccc1O"
In [4]: from rdkit import Chem
In [5]: mols = [("mol1", Chem.MolFromSmiles(smi1)), ("mol2",
Chem.MolFromSmiles(smi2)), ("mol3", Chem.MolFromSmiles(smi3))]
In [6]: from rdkit.Chem.Fingerprints import FingerprintMols
*In [7]: print [ len(fp[1].ToBitString()) for fp in
FingerprintMols.FingerprintsFromMols(mols) ][512, 2048, 1024]*
In [8]: from rdkit.Chem.rdmolops import RDKFingerprint
In [9]: print [ len(RDKFingerprint(mol[1]).ToBitString()) for mol in mols ]
[2048, 2048, 2048]
I can use the RDKFingerprint method as a solution, but I thought it was
worth mentioning.
Dave
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