Hi Park,
I didn't quite understand your original question.
Here's how to calculate the Tanimoto coefficient, which is defined as the
intersection of two sets/the union of two sets.
>>> import pybel
>>> molA = pybel.readstring("smi", "CO")
>>> molB = pybel.readstring("smi", "CCO")
>>> fps = [mol.calcfp() for mol in [molA, molB]]
>>> print fps[0].bits
[516]
>>> print fps[1].bits
[516, 532, 671]
>>> union = set(fps[0].bits) | set(fps[1].bits)
>>> print union
set([532, 516, 671])
>>> intersection = set(fps[0].bits) & set(fps[1].bits)
>>> print intersection
set([516])
>>> print len(intersection) / float(len(union))
0.333333333333
>>>
The Tanimoto coefficient is 0.3333.
- Noel
On 18 May 2012 03:20, Park Hyerin <parkh...@gmail.com> wrote:
>
> I guessed "_openbabel.so" has tanimoto formula and calculates it, but I
> cannot see inside of "_openbabel.so".
> Can I get the code of tanimoto calculate function?
>
> From that... I want to calculate substructure coefficient.
>
> I'll be thank full for your help and kindness ;)
>
>
> Park.
>
>
>
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