Hi Jessica,
On Tue, Jun 21, 2016 at 2:16 PM, Jessica Krause <jessica.kra...@tu-bs.de>
wrote:
>
> I am using RDKit for a while now. My focus is the transformation of
molecules in simplified reduced forms. With the help of SMARTS I specify
> molecular substructures and pattern to transform these parts into
> pseudoatoms. Afterwards I would like to get the maximum common
> substructures out of the reduced graphs. These is done to compare
> molecules and their MCS in small datasets of molecules.
>
> SMILES string:
>
> CCC(C)C(C(=O)O)N Isoleucin reduced form:
> [Zn][Zn][Zn]([Zn])[Zn]([Nb])[Mo]
>
> CC(C)CC(C(=O)O)N Leucin reduced form:
> [Zn][Zn]([Zn])[Zn][Zn]([Nb])[Mo]
>
>
> I would like to know how to group together Zn-Zn-Zn- ... as a single
> -Zn- atom in the reduced graph. Because these linker atoms (Zn) are only
> carbon atoms which can be compressed together. The number of the linkers
> doesn't play a role in the reduced form and gives false results by
> comparing the reduced graphs one below the other when they have a
> different length of carbon atoms next to each other.
>
This is a fun problem and I think I have some ideas of how it might be
solved. To be sure I get at least close to correct, could you please tell
me what answers you would expect as output for the two examples above?
Best,
-greg
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