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.
Birch On Oct 16, 2012, at 2:34 PM, Rajarshi Guha <[email protected]> wrote: > Do you need to note the attachment points? > > On Tue, Oct 16, 2012 at 1:37 PM, J Birch <[email protected]> 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. >> >> Thanks! >> Birch >> On Oct 16, 2012, at 1:32 PM, Rajarshi Guha <[email protected]> wrote: >> >>> What do you mean output format? A format to support the matches? >>> >>> On Tue, Oct 16, 2012 at 1:27 PM, J Birch <[email protected]> wrote: >>>> Is there any known SMART output format for CDK? >>>> >>>> Thanks! >>>> Birch >>>> >>>> ------------------------------------------------------------------------------ >>>> Don't let slow site performance ruin your business. Deploy New Relic APM >>>> Deploy New Relic app performance management and know exactly >>>> what is happening inside your Ruby, Python, PHP, Java, and .NET app >>>> Try New Relic at no cost today and get our sweet Data Nerd shirt too! >>>> http://p.sf.net/sfu/newrelic-dev2dev >>>> _______________________________________________ >>>> Cdk-user mailing list >>>> [email protected] >>>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>> >>> >>> >>> -- >>> Rajarshi Guha | http://blog.rguha.net >>> NIH Center for Advancing Translational Science >> > > > > -- > Rajarshi Guha | http://blog.rguha.net > NIH Center for Advancing Translational Science ------------------------------------------------------------------------------ Don't let slow site performance ruin your business. Deploy New Relic APM Deploy New Relic app performance management and know exactly what is happening inside your Ruby, Python, PHP, Java, and .NET app Try New Relic at no cost today and get our sweet Data Nerd shirt too! http://p.sf.net/sfu/newrelic-dev2dev _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
