Greg,

    I need to be able to use SMARTS patterns to identify substructures in 
molecules
that can be aromatic, and I need to be able to handle cases where there can be
differences in the way that the molecule was entered or drawn by a user.


    For example, consider the following alkenyl-substituted pyridine, there
are two possible Kekule structures


    m1 = 'C=CC1=NC=CC=C1'
    m2 = 'C=CC1N=CC=CC1'


    Now consider two SMARTS


    pattern1 = '[C]=[C]-[C]={C]

    pattern2 = '[C]=[C]-[C]=[N]'



    I need to be able to detect the existence of each pattern in the molecule



    If m1 is the only available generated Kekule structure, then pattern2 will 
be recognized.

    If m2 is the only available generated Kekule  structure, then pattern1 will 
be recognized.



    Hence, I am getting different answers for the same input molecule just 
because

it was drawn in different Kekule structures.


    Regards,

    Jim Metz



    





-----Original Message-----
From: Greg Landrum <greg.land...@gmail.com>
To: James T. Metz <jamestm...@aol.com>
Cc: RDKit Discuss <rdkit-discuss@lists.sourceforge.net>
Sent: Mon, Sep 11, 2017 10:31 am
Subject: Re: [Rdkit-discuss] how to output multiple Kekule structures



Hi Jim,


The code currently has no way to enumerate Kekule structures. I don't recall 
this coming up in the past and, to be honest, it doesn't seem all that 
generally useful. 


Perhaps there's an alternate way to solve the problem; what are you trying to 
do?


-greg





On Mon, Sep 11, 2017 at 5:04 PM, James T. Metz via Rdkit-discuss 
<rdkit-discuss@lists.sourceforge.net> wrote:

Hello,


    Suppose I read in an aromatic SMILES e.g., for benzene



    c1ccccc1



    I would like to generate the major canonical resonance forms

and save the results as two separate molecules.  Essentially
I am trying to generate


    m1 = 'C1=CC=CC-C1'

    m2 = 'C1C=CC=CC1'



    Can this be done in RDkit?  I have found a KEKULE_ALL 

option in the detailed documentation which seems to be what I
am trying to do, but I don't understand how this option is to be used,
or the proper syntax.


    If it is necessary to somehow renumber the atoms and re-generate

Kekule structures, that is OK.  Thank you.


    Regards,

    Jim Metz














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