After getting the paths of length 1-7, it is easy to get the difference. The
problem is how to get the paths of length 1-7. Where are the paths stored in
OB?
-Er
2009/10/5 Noel O'Boyle <baoille...@gmail.com>
> More than one fragment could hash to the same bit, so why not just do
> the analysis yourself by hand? Write some code to compare all paths of
> length 1-7 in the two molecules and see which are different.
>
> - Noel
>
> 2009/10/5 erlangener <erlange...@gmail.com>:
> > 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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