## Re: [Cdk-devel] Difference in bond between undefined and undefined ?

 Re: [Cdk-devel] Difference in bond between undefined and undefined ? From: Stefan Kuhn - 2003-03-17 07:51:21 ```Am Saturday 15 March 2003 09:06 schrieben Sie: > At 15:20 14/03/2003 +0100, Stefan Kuhn wrote: > >Hi developers, > >I just made the MDLWriter to write chiralities and I discovered that t= here > >seems to be no difference between the ordinary bond and the undefined > >chiraltiy, i. e. the swung dash (or no value for this, to put it anoth= er > >way). Did I oversee it or is it not there ? Should we have a value for > >undefined=3Dswung dash in CDKConstants (and use it) ? > >Cheers > >Stefan > > MDL has a value of 4 =3D Either. It depends how you interpret "either".= (I am > not sure what you mean by "swung bond"). I'm actually talking about the 4 in MDL, represented by what I would call= a=20 swung dash in graphical representations. Currently in the CDK 4 and 0 in = MDL=20 both get read as 0=3DUNDEFINED. As a first measure I would suggest to int= roduce=20 a separate value for both (which doesn't mean that a more elaborate conce= pt=20 wouldn't be fine). The only problem with this is that UNDEFINED would mor= e=20 fit to MDL 4 (and MDL 0 would be NONE or so), but it might be that people= =20 already use the CDK and rely on UNDEFINED meaning 4. Any solution ? Stefan > > This is a difficult area and is discussed at length recently in: > > http://www.angelfire.com/sc3/iupacstructures/ > > I would encourage CDK to use an abstraction based on these discussions = as > the starting point. My opinion is that chirality should be based on at= oms > rather than bonds as the latter (a) require 2D coordinates and (b) are > often very poorly represent ed in diagrams. There is a problem for > *publishers* who have to manage graphical representations but this is n= ot > the main emphasis of CDK. > > Best > > P. > > >-- > >Stefan Kuhn M. A. > >Cologne University BioInformatics Center (http://www.cubic.uni-koeln.d= e) > >Z=C3=83=C2=BClpicher Str. 47, 50674 Cologne > >Tel: +49(0)221-470-7428 Fax: +49 (0) 221-470-5092 > > > > > > > >------------------------------------------------------- > >This SF.net email is sponsored by:Crypto Challenge is now open! > >Get cracking and register here for some mind boggling fun and > >the chance of winning an Apple iPod: > >http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en > >_______________________________________________ > >Cdk-devel mailing list > >Cdk-devel@... > >https://lists.sourceforge.net/lists/listinfo/cdk-devel --=20 Stefan Kuhn M. A. Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Z=C3=BClpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7428 Fax: +49 (0) 221-470-5092 ```

 Re: [Cdk-devel] Difference in bond between undefined and undefined ? From: Stefan Kuhn - 2003-03-17 07:51:21 ```Am Saturday 15 March 2003 09:06 schrieben Sie: > At 15:20 14/03/2003 +0100, Stefan Kuhn wrote: > >Hi developers, > >I just made the MDLWriter to write chiralities and I discovered that t= here > >seems to be no difference between the ordinary bond and the undefined > >chiraltiy, i. e. the swung dash (or no value for this, to put it anoth= er > >way). Did I oversee it or is it not there ? Should we have a value for > >undefined=3Dswung dash in CDKConstants (and use it) ? > >Cheers > >Stefan > > MDL has a value of 4 =3D Either. It depends how you interpret "either".= (I am > not sure what you mean by "swung bond"). I'm actually talking about the 4 in MDL, represented by what I would call= a=20 swung dash in graphical representations. Currently in the CDK 4 and 0 in = MDL=20 both get read as 0=3DUNDEFINED. As a first measure I would suggest to int= roduce=20 a separate value for both (which doesn't mean that a more elaborate conce= pt=20 wouldn't be fine). The only problem with this is that UNDEFINED would mor= e=20 fit to MDL 4 (and MDL 0 would be NONE or so), but it might be that people= =20 already use the CDK and rely on UNDEFINED meaning 4. Any solution ? Stefan > > This is a difficult area and is discussed at length recently in: > > http://www.angelfire.com/sc3/iupacstructures/ > > I would encourage CDK to use an abstraction based on these discussions = as > the starting point. My opinion is that chirality should be based on at= oms > rather than bonds as the latter (a) require 2D coordinates and (b) are > often very poorly represent ed in diagrams. There is a problem for > *publishers* who have to manage graphical representations but this is n= ot > the main emphasis of CDK. > > Best > > P. > > >-- > >Stefan Kuhn M. A. > >Cologne University BioInformatics Center (http://www.cubic.uni-koeln.d= e) > >Z=C3=83=C2=BClpicher Str. 47, 50674 Cologne > >Tel: +49(0)221-470-7428 Fax: +49 (0) 221-470-5092 > > > > > > > >------------------------------------------------------- > >This SF.net email is sponsored by:Crypto Challenge is now open! > >Get cracking and register here for some mind boggling fun and > >the chance of winning an Apple iPod: > >http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0031en > >_______________________________________________ > >Cdk-devel mailing list > >Cdk-devel@... > >https://lists.sourceforge.net/lists/listinfo/cdk-devel --=20 Stefan Kuhn M. A. Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Z=C3=BClpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7428 Fax: +49 (0) 221-470-5092 ```
 Re: [Cdk-devel] Difference in bond between undefined and undefined ? From: - 2003-03-17 08:02:13 ```Citeren Stefan Kuhn : > Am Saturday 15 March 2003 09:06 schrieben Sie: > > At 15:20 14/03/2003 +0100, Stefan Kuhn wrote: > > >I just made the MDLWriter to write chiralities and I discovered that > there > > >seems to be no difference between the ordinary bond and the undefined > > >chiraltiy, i. e. the swung dash (or no value for this, to put it another > > >way). Did I oversee it or is it not there ? Should we have a value for > > >undefined=swung dash in CDKConstants (and use it) ? > > >Cheers > > >Stefan > > > > MDL has a value of 4 = Either. It depends how you interpret "either". (I > am > > not sure what you mean by "swung bond"). > > I'm actually talking about the 4 in MDL, represented by what I would call a > swung dash in graphical representations. Currently in the CDK 4 and 0 in MDL > both get read as 0=UNDEFINED. As a first measure I would suggest to introduce > a separate value for both (which doesn't mean that a more elaborate concept > wouldn't be fine). The only problem with this is that UNDEFINED would more > fit to MDL 4 (and MDL 0 would be NONE or so), but it might be that people > already use the CDK and rely on UNDEFINED meaning 4. Any solution ? I am not sure how others interpreted things, but I read CDK 0 as being MDL NONE, that is no bond stereo given... and now the undefined stero as in MDL 4, which is, I presume the wiggly bond... As far as I know, that one cannot be represented in CDK at this moment... I agree that we need the undefined represented too, so we need to come up with a nice scheme of constants to represent those... The Renderer2D now has code that makes it impossible to simply add UNDEFINED as CDK const = 4... Renumbering the constants is not really a problem, but we need to identity first the code where bond stereo info is used, with and without the use of the constants from CDKConstants... Egon ```