From: Miguel R. C. <mig...@un...> - 2006-04-06 13:15:18
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Hi all, I would like to know if there is already implemented in cdk a class which looks for all resonance structures from a determinate molecule. If it isn't yet I will try to implemented it. Cheers, Miquel - - - Miguel Rojas Cherto Junior Research Group for Applied Bioinformatics (http://almost.cubic.uni-koeln.de/jrg) Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Zülpicher Str. 47 50674 Cologne Tel: +49(0)221-470-7428 / +49(0)221-2913909 Fax: +49 (0) 221-470-7786 |
From: peter murray-r. <pm...@ca...> - 2006-04-06 13:43:54
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At 14:18 06/04/2006, Miguel Rojas Cherto wrote: >Hi all, > >I would like to know if there is already=20 >implemented in cdk a class which looks for all=20 >resonance structures from a determinate molecule. >If it isn't yet I will try to implemented it. That would be very useful - it is a necessary=20 part of adding multiple bonds and charges when=20 there are only atoms and connections. I think the=20 current CDK does not always add all the double=20 bonds. (I also had to do this for JUMBO - I think=20 it needs a full backtracking algorithm). There are some problems: - do you allow indefinite separation of charge? - what happens if you cannot create a system without unpaired electrons. you will also need to control very large=20 structures which can have zillions of resonance structures. P. >Cheers, >Miquel > >- - - >Miguel Rojas Cherto >Junior Research Group for Applied Bioinformatics=20 >(<http://almost.cubic.uni-koeln.de/jrg>http://almost.cubic.uni-koeln.de/jrg= ) >Cologne University BioInformatics Center=20 >(<http://www.cubic.uni-koeln.de>http://www.cubic.uni-koeln.de) >Z=FClpicher Str. 47 >50674 Cologne >Tel: +49(0)221-470-7428 / +49(0)221-2913909 >Fax: +49 (0) 221-470-7786 Peter Murray-Rust Unilever Centre for Molecular Sciences Informatics University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK +44-1223-763069=20 |
From: Christoph S. <c.s...@un...> - 2006-04-06 17:13:44
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Miguel Rojas Cherto wrote: > Hi all, >=20 > I would like to know if there is already implemented in cdk a class=20 > which looks for all resonance structures from a determinate molecule. > If it isn't yet I will try to implemented it. In addition to Peter's thoughtful comments: No, there is no such class. The only thing that comes close to what you want is the SaturationChecker= , I=20 think, which tries to insert bond orders such that at least one valid str= ucture=20 is formed, and not even that is working in all cases. The following manuscripts might provide some ideas: http://pubs.acs.org/cgi-bin/article.cgi/jcisd8/2005/45/i05/pdf/ci049645z.= pdf In http://pubs.acs.org/cgi-bin/article.cgi/jcisd8/2005/45/i02/pdf/ci049915d.= pdf Labute mentions an algorithm called "Maximum weighted matching algorithm"= to=20 assign bond orders to PI systems. Dunno if this helps. I'm not pointing you to the completely unreadable article=20 http://pubs.acs.org/cgi-bin/article.cgi/jcisd8/1996/36/i03/pdf/ci950174d.= pdf :-) Cheers, Chris --=20 Priv. Doz. Dr. Christoph Steinbeck (c.s...@un...) Head of the Research Group for Molecular Informatics Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.d= e) Z=FClpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |
From: <ten...@gm...> - 2006-04-07 08:07:41
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hi, only in a very rough manner, as a pi system detection descriptor, see QSAR package. Here I search for pi systems, but I do not enumerate them. Your problem is also related to the Tautomer generation (enumertion). As Peter has pointed out, for some molecules there can be a lot of solutions. To store them all as a CDK molecule is maybe not possible. best regards Christian > --- Ursprüngliche Nachricht --- > Von: Miguel Rojas Cherto <mig...@un...> > An: cdk...@li... > Betreff: [Cdk-devel] resonance structures > Datum: Thu, 06 Apr 2006 15:18:57 +0200 > > Hi all, > > I would like to know if there is already implemented in cdk a class > which looks for all resonance structures from a determinate molecule. > If it isn't yet I will try to implemented it. > > Cheers, > Miquel > > - - - > Miguel Rojas Cherto > Junior Research Group for Applied Bioinformatics > (http://almost.cubic.uni-koeln.de/jrg) > Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) > Zülpicher Str. 47 > 50674 Cologne > Tel: +49(0)221-470-7428 / +49(0)221-2913909 > Fax: +49 (0) 221-470-7786 > -- "Feel free" - 10 GB Mailbox, 100 FreeSMS/Monat ... Jetzt GMX TopMail testen: http://www.gmx.net/de/go/topmail |