From: Rajarshi G. <raj...@gm...> - 2012-02-12 02:19:43
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Can anybody point me to code that will render a 2D depiction and highlight a substructure? I've looked at code from Nina ( https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ambit2-all/ambit2-rendering/src/main/java/ambit2/rendering/CompoundImageTools.java) but it looks like uses SelectAtomGenerator - which does not seem to occur in the 1.4.7 jar file. Does anybody know where it is? -- Rajarshi Guha NIH Chemical Genomics Center |
From: Nina J. <jel...@gm...> - 2012-02-12 08:24:44
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Rajarshi, It is in the cdk-jchempaint.jar (v 18 in my code) , and (just checked) is also in the latest release http://sourceforge.net/projects/cdk/files/CDK-JChemPaint/25/ . Regards, Nina On 12 February 2012 04:19, Rajarshi Guha <raj...@gm...> wrote: > Can anybody point me to code that will render a 2D depiction and highlight > a substructure? I've looked at code from Nina ( > https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ambit2-all/ambit2-rendering/src/main/java/ambit2/rendering/CompoundImageTools.java) > but it looks like uses SelectAtomGenerator - which does not seem to occur > in the 1.4.7 jar file. Does anybody know where it is? > > -- > Rajarshi Guha > NIH Chemical Genomics Center > > > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > > |
From: Rajarshi G. <raj...@gm...> - 2012-02-12 14:44:18
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Does htis mean, that if I want to show highlighted substructures in a CDK-based app, I need to include the JChempaint jar file? Should the renderers be part of the CDK? On Sun, Feb 12, 2012 at 3:24 AM, Nina Jeliazkova <jel...@gm...>wrote: > Rajarshi, > > It is in the cdk-jchempaint.jar (v 18 in my code) , and (just checked) is > also in the latest release > http://sourceforge.net/projects/cdk/files/CDK-JChemPaint/25/ . > > Regards, > Nina > > > On 12 February 2012 04:19, Rajarshi Guha <raj...@gm...> wrote: > >> Can anybody point me to code that will render a 2D depiction and >> highlight a substructure? I've looked at code from Nina ( >> https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ambit2-all/ambit2-rendering/src/main/java/ambit2/rendering/CompoundImageTools.java) >> but it looks like uses SelectAtomGenerator - which does not seem to >> occur in the 1.4.7 jar file. Does anybody know where it is? >> >> -- >> Rajarshi Guha >> NIH Chemical Genomics Center >> >> >> >> ------------------------------------------------------------------------------ >> Virtualization & Cloud Management Using Capacity Planning >> Cloud computing makes use of virtualization - but cloud computing >> also focuses on allowing computing to be delivered as a service. >> http://www.accelacomm.com/jaw/sfnl/114/51521223/ >> _______________________________________________ >> Cdk-devel mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-devel >> >> > -- Rajarshi Guha NIH Chemical Genomics Center |
From: Egon W. <ego...@gm...> - 2012-02-12 14:54:41
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On Sun, Feb 12, 2012 at 3:44 PM, Rajarshi Guha <raj...@gm...> wrote: > Does htis mean, that if I want to show highlighted substructures in a > CDK-based app, I need to include the JChempaint jar file? Should the > renderers be part of the CDK? CDK-JChemPaint != JChemPaint The former is the patch with all the new rendering and controller code; JChemPaint is the working applet / application based on a fork of those patches (with some patches that still need backporting). I have been working on getting renderextra in a submitable state, adding missing unit testing, JavaDoc, etc. But got some deadlines first, before I can spend more time on that... (anyone and all, ping me if you like to help with cleaning up the code!) https://github.com/egonw/groovy-jcp Nina, Rajarshi, I have had on my todo list for a long time to write up a Groovy JChemPaint example for structure highlighting, but not organized enough here at UM... in about a week I have a week off... Meanwhile, patches for groovy-jcp are welcome :) Otherwise, I also want to write tutorial for drawing radicals and lone pairs, for which there exists code already too... Egon -- Dr E.L. Willighagen Postdoctoral Researcher Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |