From: Egon W. <eg...@sc...> - 2002-08-23 11:43:08
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Hi all, for the IUPAC name generator I am in need of off the shell structures... Templates that is... I am going to make a template dir containing structures of many kinds in the future... Does it make sense to make this package cdk.templates, or should I make it cdk.iupac.templates? Egon |
From: Christoph S. <ste...@ic...> - 2002-08-23 13:17:45
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Egon Willighagen wrote: > Hi all, > > for the IUPAC name generator I am in need of off the shell structures... > Templates that is... I am going to make a template dir containing structures > of many kinds in the future... > > Does it make sense to make this package cdk.templates, or should I make > it cdk.iupac.templates? How will these templates be coded? Hard coded in by small MoleculeFactory-like code fragements, or will in a chemical file format? The first version might be faster. In any case, we might need templates/fragments in more than one place. Maybe org.openscience.cdk.templates.iupac? Cheers, Chris -- Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf) MPI of Chemical Ecology, Winzerlaer Str. 10, Beutenberg Campus, 07745 Jena, Germany Tel: +49(0)3641 571263 - Fax: +49(0)3641 571202 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |
From: Egon W. <eg...@sc...> - 2002-08-23 14:22:17
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On Friday 23 August 2002 15:17, Christoph Steinbeck wrote: > Egon Willighagen wrote: > > for the IUPAC name generator I am in need of off the shell structures... > > Templates that is... I am going to make a template dir containing > > structures of many kinds in the future... > > > > Does it make sense to make this package cdk.templates, or should I make > > it cdk.iupac.templates? > > How will these templates be coded? Hard coded in by small > MoleculeFactory-like code fragements, or will in a chemical file format? > The first version might be faster. Yes, I was planning to do that hard coded... like you did for some tests... > In any case, we might need templates/fragments in more than one place. > Maybe org.openscience.cdk.templates.iupac? Does that make sense? There is not much specific IUPAC about that, other than that it is used for the iupac generator, and probably a future IUPAC parser too... I would say, either cdk.templates then... I will be using subdires, like ringsystems, aminoacids, etc... Egon |
From: Christoph S. <ste...@ic...> - 2002-08-23 16:52:52
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Egon Willighagen wrote: > On Friday 23 August 2002 15:17, Christoph Steinbeck wrote: > >>Egon Willighagen wrote: >> >>>for the IUPAC name generator I am in need of off the shell structures... >>>Templates that is... I am going to make a template dir containing >>>structures of many kinds in the future... >>> >>>Does it make sense to make this package cdk.templates, or should I make >>>it cdk.iupac.templates? >> >>How will these templates be coded? Hard coded in by small >>MoleculeFactory-like code fragements, or will in a chemical file format? >>The first version might be faster. > > > Yes, I was planning to do that hard coded... like you did for some tests... > > >>In any case, we might need templates/fragments in more than one place. >>Maybe org.openscience.cdk.templates.iupac? > > > Does that make sense? There is not much specific IUPAC about that, other > than that it is used for the iupac generator, and probably a future IUPAC > parser too... I would say, either cdk.templates then... I will be using > subdires, like ringsystems, aminoacids, etc... I thought it would make sense to distinguish between templates that are used (only) for specific purposes. The fragments used in CASE systems might be different from those used for the IUPAC generator. There might, of course, be overlap. But I see that this is disputable. I guess you have to hardcode those fragments which are relevant for the name generator in the naming code anyway. I think in the end both ways have their pros and cons. Cheers, Chris |
From: Egon W. <eg...@sc...> - 2002-08-23 20:25:58
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On Friday 23 August 2002 18:52, Christoph Steinbeck wrote: > Egon Willighagen wrote: > > On Friday 23 August 2002 15:17, Christoph Steinbeck wrote: > >>Egon Willighagen wrote: > >>>for the IUPAC name generator I am in need of off the shell structures... > >>>Templates that is... I am going to make a template dir containing > >>>structures of many kinds in the future... > >>> > >>>Does it make sense to make this package cdk.templates, or should I make > >>>it cdk.iupac.templates? > >> > >>How will these templates be coded? Hard coded in by small > >>MoleculeFactory-like code fragements, or will in a chemical file format? > >>The first version might be faster. > > > > Yes, I was planning to do that hard coded... like you did for some > > tests... > > > >>In any case, we might need templates/fragments in more than one place. > >>Maybe org.openscience.cdk.templates.iupac? > > > > Does that make sense? There is not much specific IUPAC about that, other > > than that it is used for the iupac generator, and probably a future IUPAC > > parser too... I would say, either cdk.templates then... I will be using > > subdires, like ringsystems, aminoacids, etc... > > I thought it would make sense to distinguish between templates that are > used (only) for specific purposes. The fragments used in CASE systems > might be different from those used for the IUPAC generator. There might, > of course, be overlap. I have not yet coded any fragment generation code, but those fragments will probably include actual fragments with open valencies... like for example a naphtyl group... of course, most such fragments will only have 1 valancy... Do I understand correctly that CASE fragment are much smaller? More like functional group like sizes? > But I see that this is disputable. Maybe not ;) /me just want to understand the reasoning behind the dir layout that is going to be used... (I really hate moving files around in cvs). > I guess you have to hardcode those fragments which are relevant for the > name generator in the naming code anyway. I was also thinking of using those fragments in toolbars for JCP... were you can quickly pick a fragment to add to your drawn structure... these would be the same templates as used in the IUPAC generator... that is the reason why I would prefer not to use the cdk.template.iupac name, but something like cdk.template.rings ... > I think in the end both ways have their pros and cons. Ofcourse, that's why I posted my question... Egon |
From: Christoph S. <ste...@ic...> - 2002-08-24 11:03:41
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Egon Willighagen wrote: > Do I understand correctly that CASE fragment are much smaller? More like > functional group like sizes? Yes, but some fragments might well reach the size of the regular small ring fragments (benzene ring, pyrole ring, etc.). We can often derive good-list fragments like benzene rings from the spectroscopic data. > I was also thinking of using those fragments in toolbars for JCP... Right, I did not think of this. Very reasonable idea. So, generally I think that an org.openscience.cdk.templates package makes sense. Whether we need a structure underneath.... I gues, yes. Maybe grouped by compound classes and other general concepts (rings, etc.) Cheers, Chris -- Dr. Christoph Steinbeck (http://www.ice.mpg.de/departments/ChemInf) MPI of Chemical Ecology, Winzerlaer Str. 10, Beutenberg Campus, 07745 Jena, Germany Tel: +49(0)3641 571263 - Fax: +49(0)3641 571202 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |