For one small molecule, the number should be not so many, if path length set
to be less than 3 or 4.
I am only familiar with the python bindings of OB. Where should I add a
code to print the paths out?
Thanks,
Er
2009/10/5 Noel O'Boyle <baoille...@gmail.com>
> They are not stored. If you think about it, there are almost an
> infinite number of such paths. A depth-first search is carried out for
> all atoms of the molecule. This generates the paths. If you look at
> the code maybe you could add a cout statement to print them out or
> something.
>
> - Noel
>
> 2009/10/5 erlangener <erlange...@gmail.com>:
> > 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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