Thanks Noel! Let me restate my problem and make it more clear with an
example.
I have three building blocks, which are
<A>: C1C=CCC2=CSC=C12
[image: Inline image 1]
<B>:C1C=CCC2=COC=C12
[image: Inline image 2]
<C>: C1=CC2=C(C=C1)C=CC=C2
[image: Inline image 3]
Here I got a target molecule only with its SMILES
"C1C=C2C(C=CC3=COC=C23)C2=CSC=C12".
To figure out how this target molecule was built.
I ran my program of substructure searching with SMARTS strings .
<A>: [#6]~1~[#6]~[#6]~[#6]~[#6]~2~[#6]~1~[#6]~s~[#6]~2
<B>: [#6]~1~[#6]~[#6]~[#6]~[#6]~2~[#6]~1~[#6]~o~[#6]~2
<C>: [#6]~1~[#6]~[#6]~[#6]~[#6]~2~[#6]~1~[#6]~[#6]~[#6]~[#6]~2
I got the result that it contains " A=1, B=1, C=1". But. I only want the
least number of building blocks that would make the whole target molecule.
In this case, according to the graph shown below, the result should be " A=
1, B = 1, C = 0", i.e. I only need A and B to make the above target
molecule.
As it can be seen in the graph (shown below) of target molecule, it is
apparent that it was built by A and B.
So I am wondering how I can get the correct composition and further, the
sequence of the building blocks of the target molecule by using SMARTS
string of the building blocks.
It's just a simplified instance of my real problem.
My real target molecules are built by 3~5 out of 30 building blocks.
The building blocks can be linked or fused together.
Thanks for your patience.
Best,
Ching-Yen
On Tue, Mar 10, 2015 at 5:04 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
> I think you need to think about solving your original problem in a
> different way. If you can post an example of the sort of molecule you
> are talking about and what the solution you would like to see, then
> maybe you will get some useful suggestions from this list.
>
> - Noel
>
> On 6 March 2015 at 03:44, Ching Yen Shih <ching...@buffalo.edu> wrote:
> > Hi all,
> >
> > I want to identify the sequence of substructures(building blocks) in the
> > target molecules. I already know which building blocks are in the target
> > molecules. The building blocks might be linked or fused. So, I am
> wondering
> > if there is a notation for fused bond. Say, I have a SMARTS string for
> > benzene, is it possible I just add a notation between two benzene strings
> > and use it for searching naphthalene?
> > Or any other suggestion for this case about identifying the sequence?
> >
> > Thanks for your attention and time.
> >
> > Best,
> > Ching-Yen
> >
> >
> >
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