Hi Dave,
On Thu, Sep 25, 2014 at 9:53 AM, Dave Wood <[email protected]> wrote:
> 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.
>
I wouldn't really recommend using the functionality in the FingerprintMols
module. It probably should be deprecated. It is much safer (and not much
more difficult) to call the fingerprint functions directly.
Here's what's going on: The function FingerprintMols.FingerprintsFromMols()
uses FingerprintMols.FingerprintMol() internally. This sets fingerprint
options using the class FingerprintMols.FingerprinterDetails, which
includes a default value for the tgtDensity argument of 0.3. Setting
tgtDensity with the RDKit fingerprint can results in the fingerprinter
folding the fingerprint to achieve a particular target density of on bits:
In [6]: m = Chem.MolFromSmiles("CCCCNC(=O)[C@@H]1CCCN(C(=O)CCC(C)C)C1")
In [7]: Chem.RDKFingerprint(m).GetNumBits()
Out[7]: 2048
In [8]: Chem.RDKFingerprint(m,tgtDensity=0.3).GetNumBits()
Out[8]: 512
This explains the differences you are seeing.
-greg
> 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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