Thanks Geoff,
In FP3, the molecular fingerprint is calculated using a predefined smarts
patterns, which can then be matched by the fingerprint bits.
However, if FP2, the fingerprint is calculated based on hashing the
fragments with length=1-7. Here is my problem, the hashed bits can not
matched back to the fragments. There is also not (I did not find) file
storing these fragments. So, my question here is how to get the fragments
with length equal to 1 ~7, such as C-C, C=C, C#C, CCC,,,,.
Yes, after we get the fragment bits, we can use the XOR to get the fragment
difference.
Thanks,
Er
2009/10/1 Geoffrey Hutchison <ge...@geoffhutchison.net>
> Anyone knows how to get the fragments (not the bit fingerprints)
>> before the fingerprint hashing?
>>
>
> I do not know of a direct way in the code, although the fingerprints are
> simply a set of SMARTS patterns. You could parse the file and then match the
> SMARTS against your molecules.
>
> Further, how to get the fragment difference of two molecules?
>>
>
> I'm not sure what you mean. Do you want the difference between the two bit
> fingerprints? You'd take the exclusive or (XOR) of the two bitvectors. That
> will give you the bits which are in one but not both.
>
> Does that help?
>
> -Geoff
>
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