The only thing I am missing in the current solution is handling branches correctly. I have the atom list, and the bond list, but when an atom is connected to two other atoms via two bonds, I need to correctly identify one of those connections as a branch wrapping it with parenthesis.
On Oct 16, 2012, at 2:34 PM, Rajarshi Guha <rajarshi.guha@...> wrote:
> Do you need to note the attachment points?
> On Tue, Oct 16, 2012 at 1:37 PM, J Birch <birchsport@...> wrote:
>> We have an algorithm right now that fragments a molecule, and the task is to convert the fragments into valid SMARTS format (i.e 'ccC(N)C') where that represents a single fragment. I don't believe the smalls representation is the same. Am I incorrect in that assumption? We do use the smiles format of the entire molecule in this, but we use Daylight to overlay the fragment which needs to be in SMARTS. I am just trying to avoid using our home-grown solution if one already exists.
>> On Oct 16, 2012, at 1:32 PM, Rajarshi Guha <rajarshi.guha@...> wrote:
>>> What do you mean output format? A format to support the matches?
>>> On Tue, Oct 16, 2012 at 1:27 PM, J Birch <birchsport@...> wrote:
>>>> Is there any known SMART output format for CDK?
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> NIH Center for Advancing Translational Science