From: John M. <jo...@eb...> - 2013-11-22 11:01:37
|
Hi All, Does anyone know how to highlight atoms in different colours using the CDK renders? Stephan and I have been scratching our heads and really looks like it’s not possible. We have code for this in Knime but simply can’t believe it’s not in the main rendering code. I always thought the ColorHash was how it was done but this (see below) only works for bonds :/. Map<IChemObject,Color> highlight = Maps.newHashMap(); highlight.put(m.getAtom(0), Color.green); highlight.put(m.getAtom(1), Color.red); renderer.getRenderer2DModel().set(RendererModel.ColorHash.class, highlight); Cheers, J |
From: John M. <jo...@eb...> - 2013-11-22 11:03:12
|
I should add… without using JChemPaint! On 22 Nov 2013, at 11:01, John May <jo...@eb...> wrote: > Hi All, > > Does anyone know how to highlight atoms in different colours using the CDK renders? Stephan and I have been scratching our heads and really looks like it’s not possible. We have code for this in Knime but simply can’t believe it’s not in the main rendering code. > > I always thought the ColorHash was how it was done but this (see below) only works for bonds :/. > > Map<IChemObject,Color> highlight = Maps.newHashMap(); > highlight.put(m.getAtom(0), Color.green); > highlight.put(m.getAtom(1), Color.red); > renderer.getRenderer2DModel().set(RendererModel.ColorHash.class, highlight); > > Cheers, > J > > ------------------------------------------------------------------------------ > Shape the Mobile Experience: Free Subscription > Software experts and developers: Be at the forefront of tech innovation. > Intel(R) Software Adrenaline delivers strategic insight and game-changing > conversations that shape the rapidly evolving mobile landscape. Sign up now. > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk_______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel |
From: gilleain t. <gil...@gm...> - 2013-11-22 11:13:31
|
Hi, Do you mean the text of the atom labels should be different colors, or do you want colored circles underneath the atoms? I'm just switching workspaces to CDK, I'll check… gilleain On 11/22/13, John May <jo...@eb...> wrote: > I should add… without using JChemPaint! > > On 22 Nov 2013, at 11:01, John May <jo...@eb...> wrote: > >> Hi All, >> >> Does anyone know how to highlight atoms in different colours using the CDK >> renders? Stephan and I have been scratching our heads and really looks >> like it’s not possible. We have code for this in Knime but simply can’t >> believe it’s not in the main rendering code. >> >> I always thought the ColorHash was how it was done but this (see below) >> only works for bonds :/. >> >> Map<IChemObject,Color> highlight = Maps.newHashMap(); >> highlight.put(m.getAtom(0), Color.green); >> highlight.put(m.getAtom(1), Color.red); >> renderer.getRenderer2DModel().set(RendererModel.ColorHash.class, >> highlight); >> >> Cheers, >> J >> >> ------------------------------------------------------------------------------ >> Shape the Mobile Experience: Free Subscription >> Software experts and developers: Be at the forefront of tech innovation. >> Intel(R) Software Adrenaline delivers strategic insight and game-changing >> >> conversations that shape the rapidly evolving mobile landscape. Sign up >> now. >> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk_______________________________________________ >> Cdk-devel mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-devel > > |
From: Nina J. <jel...@gm...> - 2013-11-22 11:15:47
|
Hi John, On 22 November 2013 13:01, John May <jo...@eb...> wrote: > Hi All, > > Does anyone know how to highlight atoms in different colours using the CDK > renders? > Yes :) http://apps.ideaconsult.net:8080/ambit2/dataset/1736?model_uri=http://apps.ideaconsult.net:8080/ambit2/model/48 There are several ways, ambit code is at http://sourceforge.net/p/ambit/code/HEAD/tree/trunk/ambit2-all/ambit2-rendering/src/main/java/ambit2/rendering/CompoundImageTools.java Regards, Nina > Stephan and I have been scratching our heads and really looks like it’s > not possible. We have code for this in Knime but simply can’t believe it’s > not in the main rendering code. > > I always thought the ColorHash was how it was done but this (see below) > only works for bonds :/. > > Map<IChemObject,Color> highlight = Maps.newHashMap(); > highlight.put(m.getAtom(0), Color.green); > highlight.put(m.getAtom(1), Color.red); > renderer.getRenderer2DModel().set(RendererModel.ColorHash.class, > highlight); > > Cheers, > J > > > > ------------------------------------------------------------------------------ > Shape the Mobile Experience: Free Subscription > Software experts and developers: Be at the forefront of tech innovation. > Intel(R) Software Adrenaline delivers strategic insight and game-changing > conversations that shape the rapidly evolving mobile landscape. Sign up > now. > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > > |
From: gilleain t. <gil...@gm...> - 2013-11-22 11:24:26
|
Ah, Nina's code seems quite comprehensive, and looks like it will do all sorts of useful things here. However, the 'standard' way to do things (inherited from the old JCP code) was to use an instance of an IAtomColorer, eg: IAtomColorer atomColorer = new IAtomColorer() { … //implement this somehow BasicAtomGenerator atomGenerator = //etc atomGenerator.set(BasicAtomGenerator.AtomColorer.class, atomColorer); should work, I think? gilleain On 11/22/13, Nina Jeliazkova <jel...@gm...> wrote: > Hi John, > > > On 22 November 2013 13:01, John May <jo...@eb...> wrote: > >> Hi All, >> >> Does anyone know how to highlight atoms in different colours using the >> CDK >> renders? >> > > Yes :) > > http://apps.ideaconsult.net:8080/ambit2/dataset/1736?model_uri=http://apps.ideaconsult.net:8080/ambit2/model/48 > > There are several ways, ambit code is at > http://sourceforge.net/p/ambit/code/HEAD/tree/trunk/ambit2-all/ambit2-rendering/src/main/java/ambit2/rendering/CompoundImageTools.java > > > Regards, > Nina > > >> Stephan and I have been scratching our heads and really looks like it’s >> not possible. We have code for this in Knime but simply can’t believe >> it’s >> not in the main rendering code. >> >> I always thought the ColorHash was how it was done but this (see below) >> only works for bonds :/. >> >> Map<IChemObject,Color> highlight = Maps.newHashMap(); >> highlight.put(m.getAtom(0), Color.green); >> highlight.put(m.getAtom(1), Color.red); >> renderer.getRenderer2DModel().set(RendererModel.ColorHash.class, >> highlight); >> >> Cheers, >> J >> >> >> >> ------------------------------------------------------------------------------ >> Shape the Mobile Experience: Free Subscription >> Software experts and developers: Be at the forefront of tech innovation. >> Intel(R) Software Adrenaline delivers strategic insight and game-changing >> conversations that shape the rapidly evolving mobile landscape. Sign up >> now. >> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk >> _______________________________________________ >> Cdk-devel mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-devel >> >> > |
From: John M. <joh...@gm...> - 2013-11-22 11:35:18
|
Hi Gilleain, Nina Thanks for the examples. > Do you mean the text of the atom labels should be different colors, or > do you want colored circles underneath the atoms? Circles underneath like Nina linked to in Ambit. > There are several ways, I thought as much :-) > ambit code is at http://sourceforge.net/p/ambit/code/HEAD/tree/trunk/ambit2-all/ambit2-rendering/src/main/java/ambit2/rendering/CompoundImageTools.java Hmmm the SelectAtomGenerator… doesn’t exist in 1.4.x or master? > IAtomColorer atomColorer = new IAtomColorer() { … //implement this somehow > BasicAtomGenerator atomGenerator = //etc > atomGenerator.set(BasicAtomGenerator.AtomColorer.class, atomColorer); This colours the atom symbol / glyph, is there a non-extension way to do the highlight. Cheers, John On 22 Nov 2013, at 11:24, gilleain torrance <gil...@gm...> wrote: > Ah, Nina's code seems quite comprehensive, and looks like it will do > all sorts of useful things here. > > However, the 'standard' way to do things (inherited from the old JCP > code) was to use an instance of an IAtomColorer, eg: > > IAtomColorer atomColorer = new IAtomColorer() { … //implement this somehow > BasicAtomGenerator atomGenerator = //etc > atomGenerator.set(BasicAtomGenerator.AtomColorer.class, atomColorer); > > should work, I think? > > gilleain > > > > > On 11/22/13, Nina Jeliazkova <jel...@gm...> wrote: >> Hi John, >> >> >> On 22 November 2013 13:01, John May <jo...@eb...> wrote: >> >>> Hi All, >>> >>> Does anyone know how to highlight atoms in different colours using the >>> CDK >>> renders? >>> >> >> Yes :) >> >> http://apps.ideaconsult.net:8080/ambit2/dataset/1736?model_uri=http://apps.ideaconsult.net:8080/ambit2/model/48 >> >> There are several ways, ambit code is at >> http://sourceforge.net/p/ambit/code/HEAD/tree/trunk/ambit2-all/ambit2-rendering/src/main/java/ambit2/rendering/CompoundImageTools.java >> >> >> Regards, >> Nina >> >> >>> Stephan and I have been scratching our heads and really looks like it’s >>> not possible. We have code for this in Knime but simply can’t believe >>> it’s >>> not in the main rendering code. >>> >>> I always thought the ColorHash was how it was done but this (see below) >>> only works for bonds :/. >>> >>> Map<IChemObject,Color> highlight = Maps.newHashMap(); >>> highlight.put(m.getAtom(0), Color.green); >>> highlight.put(m.getAtom(1), Color.red); >>> renderer.getRenderer2DModel().set(RendererModel.ColorHash.class, >>> highlight); >>> >>> Cheers, >>> J >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Shape the Mobile Experience: Free Subscription >>> Software experts and developers: Be at the forefront of tech innovation. >>> Intel(R) Software Adrenaline delivers strategic insight and game-changing >>> conversations that shape the rapidly evolving mobile landscape. Sign up >>> now. >>> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk >>> _______________________________________________ >>> Cdk-devel mailing list >>> Cdk...@li... >>> https://lists.sourceforge.net/lists/listinfo/cdk-devel >>> >>> >> > > ------------------------------------------------------------------------------ > Shape the Mobile Experience: Free Subscription > Software experts and developers: Be at the forefront of tech innovation. > Intel(R) Software Adrenaline delivers strategic insight and game-changing > conversations that shape the rapidly evolving mobile landscape. Sign up now. > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel |
From: Nina J. <jel...@gm...> - 2013-11-22 11:45:28
|
Hi John, On 22 November 2013 13:35, John May <joh...@gm...> wrote: > Hi Gilleain, Nina > > Thanks for the examples. > > Do you mean the text of the atom labels should be different colors, or > > do you want colored circles underneath the atoms? > > > Circles underneath like Nina linked to in Ambit. > > There are several ways, > > > I thought as much :-) > > ambit code is at > http://sourceforge.net/p/ambit/code/HEAD/tree/trunk/ambit2-all/ambit2-rendering/src/main/java/ambit2/rendering/CompoundImageTools.java > > > > Hmmm the SelectAtomGenerator… doesn’t exist in 1.4.x or master? > > IAtomColorer atomColorer = new IAtomColorer() { … //implement this somehow > BasicAtomGenerator atomGenerator = //etc > atomGenerator.set(BasicAtomGenerator.AtomColorer.class, atomColorer); > > this version uses CDK 1.4.11 - CDK renderers only, not JChemPaint (JCP is a pain to have server side). The CDK renderer part might have changed in later version. > > This colours the atom symbol / glyph, is there a non-extension way to do > the highlight. > There is a custom MySelectAtomGenerator which does the highlighting based on atom property (in the demo link the three colors corresponds to ranks 1,2,3 as calculated by SmartCYP) . I think Bioclipse does the highlighting differently, may be someone from Bioclipse team could elaborate. Regards, Nina > > Cheers, > John > > On 22 Nov 2013, at 11:24, gilleain torrance <gil...@gm...> > wrote: > > Ah, Nina's code seems quite comprehensive, and looks like it will do > all sorts of useful things here. > > However, the 'standard' way to do things (inherited from the old JCP > code) was to use an instance of an IAtomColorer, eg: > > IAtomColorer atomColorer = new IAtomColorer() { … //implement this somehow > BasicAtomGenerator atomGenerator = //etc > atomGenerator.set(BasicAtomGenerator.AtomColorer.class, atomColorer); > > should work, I think? > > gilleain > > > > > On 11/22/13, Nina Jeliazkova <jel...@gm...> wrote: > > Hi John, > > > On 22 November 2013 13:01, John May <jo...@eb...> wrote: > > Hi All, > > Does anyone know how to highlight atoms in different colours using the > CDK > renders? > > > Yes :) > > > http://apps.ideaconsult.net:8080/ambit2/dataset/1736?model_uri=http://apps.ideaconsult.net:8080/ambit2/model/48 > > There are several ways, ambit code is at > > http://sourceforge.net/p/ambit/code/HEAD/tree/trunk/ambit2-all/ambit2-rendering/src/main/java/ambit2/rendering/CompoundImageTools.java > > > Regards, > Nina > > > Stephan and I have been scratching our heads and really looks like it’s > not possible. We have code for this in Knime but simply can’t believe > it’s > not in the main rendering code. > > I always thought the ColorHash was how it was done but this (see below) > only works for bonds :/. > > Map<IChemObject,Color> highlight = Maps.newHashMap(); > highlight.put(m.getAtom(0), Color.green); > highlight.put(m.getAtom(1), Color.red); > renderer.getRenderer2DModel().set(RendererModel.ColorHash.class, > highlight); > > Cheers, > J > > > > > ------------------------------------------------------------------------------ > Shape the Mobile Experience: Free Subscription > Software experts and developers: Be at the forefront of tech innovation. > Intel(R) Software Adrenaline delivers strategic insight and game-changing > conversations that shape the rapidly evolving mobile landscape. Sign up > now. > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > > > > > > ------------------------------------------------------------------------------ > Shape the Mobile Experience: Free Subscription > Software experts and developers: Be at the forefront of tech innovation. > Intel(R) Software Adrenaline delivers strategic insight and game-changing > conversations that shape the rapidly evolving mobile landscape. Sign up > now. > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > > > > > ------------------------------------------------------------------------------ > Shape the Mobile Experience: Free Subscription > Software experts and developers: Be at the forefront of tech innovation. > Intel(R) Software Adrenaline delivers strategic insight and game-changing > conversations that shape the rapidly evolving mobile landscape. Sign up > now. > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > > |
From: gilleain t. <gil...@gm...> - 2013-11-22 11:52:34
|
Hi, No, there's no standard way to do coloured shape highlights. I guess it would be more flexible if the 'compact elements' options (circle, square) could be solid/transparent and above/below the element symbol. At the moment, the standard generator gives the user the choice between element symbol and compact element. I did mean at some point to make the highlighting more powerful, to allow for such things, as well as path-based outlines around fragments. It's on the large list of things to maybe do at some point... gilleain On 11/22/13, Nina Jeliazkova <jel...@gm...> wrote: > Hi John, > > > On 22 November 2013 13:35, John May <joh...@gm...> wrote: > >> Hi Gilleain, Nina >> >> Thanks for the examples. >> >> Do you mean the text of the atom labels should be different colors, or >> >> do you want colored circles underneath the atoms? >> >> >> Circles underneath like Nina linked to in Ambit. >> >> There are several ways, >> >> >> I thought as much :-) >> >> ambit code is at >> http://sourceforge.net/p/ambit/code/HEAD/tree/trunk/ambit2-all/ambit2-rendering/src/main/java/ambit2/rendering/CompoundImageTools.java >> >> >> >> Hmmm the SelectAtomGenerator… doesn’t exist in 1.4.x or master? >> >> IAtomColorer atomColorer = new IAtomColorer() { … //implement this >> somehow >> BasicAtomGenerator atomGenerator = //etc >> atomGenerator.set(BasicAtomGenerator.AtomColorer.class, atomColorer); >> >> this version uses CDK 1.4.11 - CDK renderers only, not JChemPaint >> (JCP > is a pain to have server side). The CDK renderer part might have changed in > later version. > > > >> >> This colours the atom symbol / glyph, is there a non-extension way to do >> the highlight. >> > > > There is a custom MySelectAtomGenerator which does the highlighting based > on atom property (in the demo link the three colors corresponds to ranks > 1,2,3 as calculated by SmartCYP) . > > I think Bioclipse does the highlighting differently, may be someone from > Bioclipse team could elaborate. > > Regards, > Nina > > >> >> Cheers, >> John >> >> On 22 Nov 2013, at 11:24, gilleain torrance <gil...@gm...> >> wrote: >> >> Ah, Nina's code seems quite comprehensive, and looks like it will do >> all sorts of useful things here. >> >> However, the 'standard' way to do things (inherited from the old JCP >> code) was to use an instance of an IAtomColorer, eg: >> >> IAtomColorer atomColorer = new IAtomColorer() { … //implement this >> somehow >> BasicAtomGenerator atomGenerator = //etc >> atomGenerator.set(BasicAtomGenerator.AtomColorer.class, atomColorer); >> >> should work, I think? >> >> gilleain >> >> >> >> >> On 11/22/13, Nina Jeliazkova <jel...@gm...> wrote: >> >> Hi John, >> >> >> On 22 November 2013 13:01, John May <jo...@eb...> wrote: >> >> Hi All, >> >> Does anyone know how to highlight atoms in different colours using the >> CDK >> renders? >> >> >> Yes :) >> >> >> http://apps.ideaconsult.net:8080/ambit2/dataset/1736?model_uri=http://apps.ideaconsult.net:8080/ambit2/model/48 >> >> There are several ways, ambit code is at >> >> http://sourceforge.net/p/ambit/code/HEAD/tree/trunk/ambit2-all/ambit2-rendering/src/main/java/ambit2/rendering/CompoundImageTools.java >> >> >> Regards, >> Nina >> >> >> Stephan and I have been scratching our heads and really looks like it’s >> not possible. We have code for this in Knime but simply can’t believe >> it’s >> not in the main rendering code. >> >> I always thought the ColorHash was how it was done but this (see below) >> only works for bonds :/. >> >> Map<IChemObject,Color> highlight = Maps.newHashMap(); >> highlight.put(m.getAtom(0), Color.green); >> highlight.put(m.getAtom(1), Color.red); >> renderer.getRenderer2DModel().set(RendererModel.ColorHash.class, >> highlight); >> >> Cheers, >> J >> >> >> >> >> ------------------------------------------------------------------------------ >> Shape the Mobile Experience: Free Subscription >> Software experts and developers: Be at the forefront of tech innovation. >> Intel(R) Software Adrenaline delivers strategic insight and game-changing >> conversations that shape the rapidly evolving mobile landscape. Sign up >> now. >> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk >> _______________________________________________ >> Cdk-devel mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-devel >> >> >> >> >> >> ------------------------------------------------------------------------------ >> Shape the Mobile Experience: Free Subscription >> Software experts and developers: Be at the forefront of tech innovation. >> Intel(R) Software Adrenaline delivers strategic insight and game-changing >> conversations that shape the rapidly evolving mobile landscape. Sign up >> now. >> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk >> _______________________________________________ >> Cdk-devel mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-devel >> >> >> >> >> ------------------------------------------------------------------------------ >> Shape the Mobile Experience: Free Subscription >> Software experts and developers: Be at the forefront of tech innovation. >> Intel(R) Software Adrenaline delivers strategic insight and game-changing >> conversations that shape the rapidly evolving mobile landscape. Sign up >> now. >> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk >> _______________________________________________ >> Cdk-devel mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-devel >> >> > |
From: John M. <joh...@gm...> - 2013-11-22 11:53:01
|
Hi Nina, I think that class was from JChemPaint… here’s the package in 1.4.11: https://github.com/cdk/cdk/tree/cdk-1.4.11/src/main/org/openscience/cdk/renderer/generators I guess the short answer is that no it’s not possible to highlight atoms (with different colours) in the CDK without writing a custom generator or porting from downstream projects. Thanks, John On 22 Nov 2013, at 11:45, Nina Jeliazkova <jel...@gm...> wrote: > Hi John, > > > On 22 November 2013 13:35, John May <joh...@gm...> wrote: > Hi Gilleain, Nina > > Thanks for the examples. > >> Do you mean the text of the atom labels should be different colors, or >> do you want colored circles underneath the atoms? > > > Circles underneath like Nina linked to in Ambit. > >> There are several ways, > > I thought as much :-) > >> ambit code is at http://sourceforge.net/p/ambit/code/HEAD/tree/trunk/ambit2-all/ambit2-rendering/src/main/java/ambit2/rendering/CompoundImageTools.java > > > Hmmm the SelectAtomGenerator… doesn’t exist in 1.4.x or master? > >> IAtomColorer atomColorer = new IAtomColorer() { … //implement this somehow >> BasicAtomGenerator atomGenerator = //etc >> atomGenerator.set(BasicAtomGenerator.AtomColorer.class, atomColorer); > > this version uses CDK 1.4.11 - CDK renderers only, not JChemPaint (JCP is a pain to have server side). The CDK renderer part might have changed in later version. > > > > This colours the atom symbol / glyph, is there a non-extension way to do the highlight. > > > There is a custom MySelectAtomGenerator which does the highlighting based on atom property (in the demo link the three colors corresponds to ranks 1,2,3 as calculated by SmartCYP) . > > I think Bioclipse does the highlighting differently, may be someone from Bioclipse team could elaborate. > > Regards, > Nina > > > Cheers, > John > > On 22 Nov 2013, at 11:24, gilleain torrance <gil...@gm...> wrote: > >> Ah, Nina's code seems quite comprehensive, and looks like it will do >> all sorts of useful things here. >> >> However, the 'standard' way to do things (inherited from the old JCP >> code) was to use an instance of an IAtomColorer, eg: >> >> IAtomColorer atomColorer = new IAtomColorer() { … //implement this somehow >> BasicAtomGenerator atomGenerator = //etc >> atomGenerator.set(BasicAtomGenerator.AtomColorer.class, atomColorer); >> >> should work, I think? >> >> gilleain >> >> >> >> >> On 11/22/13, Nina Jeliazkova <jel...@gm...> wrote: >>> Hi John, >>> >>> >>> On 22 November 2013 13:01, John May <jo...@eb...> wrote: >>> >>>> Hi All, >>>> >>>> Does anyone know how to highlight atoms in different colours using the >>>> CDK >>>> renders? >>>> >>> >>> Yes :) >>> >>> http://apps.ideaconsult.net:8080/ambit2/dataset/1736?model_uri=http://apps.ideaconsult.net:8080/ambit2/model/48 >>> >>> There are several ways, ambit code is at >>> http://sourceforge.net/p/ambit/code/HEAD/tree/trunk/ambit2-all/ambit2-rendering/src/main/java/ambit2/rendering/CompoundImageTools.java >>> >>> >>> Regards, >>> Nina >>> >>> >>>> Stephan and I have been scratching our heads and really looks like it’s >>>> not possible. We have code for this in Knime but simply can’t believe >>>> it’s >>>> not in the main rendering code. >>>> >>>> I always thought the ColorHash was how it was done but this (see below) >>>> only works for bonds :/. >>>> >>>> Map<IChemObject,Color> highlight = Maps.newHashMap(); >>>> highlight.put(m.getAtom(0), Color.green); >>>> highlight.put(m.getAtom(1), Color.red); >>>> renderer.getRenderer2DModel().set(RendererModel.ColorHash.class, >>>> highlight); >>>> >>>> Cheers, >>>> J >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Shape the Mobile Experience: Free Subscription >>>> Software experts and developers: Be at the forefront of tech innovation. >>>> Intel(R) Software Adrenaline delivers strategic insight and game-changing >>>> conversations that shape the rapidly evolving mobile landscape. Sign up >>>> now. >>>> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk >>>> _______________________________________________ >>>> Cdk-devel mailing list >>>> Cdk...@li... >>>> https://lists.sourceforge.net/lists/listinfo/cdk-devel >>>> >>>> >>> >> >> ------------------------------------------------------------------------------ >> Shape the Mobile Experience: Free Subscription >> Software experts and developers: Be at the forefront of tech innovation. >> Intel(R) Software Adrenaline delivers strategic insight and game-changing >> conversations that shape the rapidly evolving mobile landscape. Sign up now. >> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk >> _______________________________________________ >> Cdk-devel mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-devel > > > ------------------------------------------------------------------------------ > Shape the Mobile Experience: Free Subscription > Software experts and developers: Be at the forefront of tech innovation. > Intel(R) Software Adrenaline delivers strategic insight and game-changing > conversations that shape the rapidly evolving mobile landscape. Sign up now. > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > > > ------------------------------------------------------------------------------ > Shape the Mobile Experience: Free Subscription > Software experts and developers: Be at the forefront of tech innovation. > Intel(R) Software Adrenaline delivers strategic insight and game-changing > conversations that shape the rapidly evolving mobile landscape. Sign up now. > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk_______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel |
From: Egon W. <ego...@gm...> - 2013-11-22 11:57:05
|
not really got time to go into details, but CDK-JChemPaint has this class: cdk-jchempaint$ find . -name "SelectAtomGenerator.java" ./build/src/rendercontrol/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java ./src/main/org/openscience/cdk/renderer/generators/SelectAtomGenerator.java Grtz, Egon On Fri, Nov 22, 2013 at 12:52 PM, John May <joh...@gm...> wrote: > Hi Nina, > > I think that class was from JChemPaint… here’s the package in 1.4.11: > https://github.com/cdk/cdk/tree/cdk-1.4.11/src/main/org/openscience/cdk/renderer/generators > > I guess the short answer is that no it’s not possible to highlight atoms > (with different colours) in the CDK without writing a custom generator or > porting from downstream projects. > > Thanks, > John > > On 22 Nov 2013, at 11:45, Nina Jeliazkova <jel...@gm...> wrote: > > Hi John, > > > On 22 November 2013 13:35, John May <joh...@gm...> wrote: >> >> Hi Gilleain, Nina >> >> Thanks for the examples. >> >> Do you mean the text of the atom labels should be different colors, or >> >> do you want colored circles underneath the atoms? >> >> >> Circles underneath like Nina linked to in Ambit. >> >> There are several ways, >> >> >> I thought as much :-) >> >> ambit code is at >> http://sourceforge.net/p/ambit/code/HEAD/tree/trunk/ambit2-all/ambit2-rendering/src/main/java/ambit2/rendering/CompoundImageTools.java >> >> >> Hmmm the SelectAtomGenerator… doesn’t exist in 1.4.x or master? >> >> IAtomColorer atomColorer = new IAtomColorer() { … //implement this somehow >> BasicAtomGenerator atomGenerator = //etc >> atomGenerator.set(BasicAtomGenerator.AtomColorer.class, atomColorer); > > this version uses CDK 1.4.11 - CDK renderers only, not JChemPaint (JCP > is a pain to have server side). The CDK renderer part might have changed in > later version. > > >> >> >> This colours the atom symbol / glyph, is there a non-extension way to do >> the highlight. > > > > There is a custom MySelectAtomGenerator which does the highlighting based > on atom property (in the demo link the three colors corresponds to ranks > 1,2,3 as calculated by SmartCYP) . > > I think Bioclipse does the highlighting differently, may be someone from > Bioclipse team could elaborate. > > Regards, > Nina > >> >> >> Cheers, >> John >> >> On 22 Nov 2013, at 11:24, gilleain torrance <gil...@gm...> >> wrote: >> >> Ah, Nina's code seems quite comprehensive, and looks like it will do >> all sorts of useful things here. >> >> However, the 'standard' way to do things (inherited from the old JCP >> code) was to use an instance of an IAtomColorer, eg: >> >> IAtomColorer atomColorer = new IAtomColorer() { … //implement this somehow >> BasicAtomGenerator atomGenerator = //etc >> atomGenerator.set(BasicAtomGenerator.AtomColorer.class, atomColorer); >> >> should work, I think? >> >> gilleain >> >> >> >> >> On 11/22/13, Nina Jeliazkova <jel...@gm...> wrote: >> >> Hi John, >> >> >> On 22 November 2013 13:01, John May <jo...@eb...> wrote: >> >> Hi All, >> >> Does anyone know how to highlight atoms in different colours using the >> CDK >> renders? >> >> >> Yes :) >> >> >> http://apps.ideaconsult.net:8080/ambit2/dataset/1736?model_uri=http://apps.ideaconsult.net:8080/ambit2/model/48 >> >> There are several ways, ambit code is at >> >> http://sourceforge.net/p/ambit/code/HEAD/tree/trunk/ambit2-all/ambit2-rendering/src/main/java/ambit2/rendering/CompoundImageTools.java >> >> >> Regards, >> Nina >> >> >> Stephan and I have been scratching our heads and really looks like it’s >> not possible. We have code for this in Knime but simply can’t believe >> it’s >> not in the main rendering code. >> >> I always thought the ColorHash was how it was done but this (see below) >> only works for bonds :/. >> >> Map<IChemObject,Color> highlight = Maps.newHashMap(); >> highlight.put(m.getAtom(0), Color.green); >> highlight.put(m.getAtom(1), Color.red); >> renderer.getRenderer2DModel().set(RendererModel.ColorHash.class, >> highlight); >> >> Cheers, >> J >> >> >> >> >> ------------------------------------------------------------------------------ >> Shape the Mobile Experience: Free Subscription >> Software experts and developers: Be at the forefront of tech innovation. >> Intel(R) Software Adrenaline delivers strategic insight and game-changing >> conversations that shape the rapidly evolving mobile landscape. 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Sign up >> now. >> >> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk >> _______________________________________________ >> Cdk-devel mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-devel >> > > ------------------------------------------------------------------------------ > Shape the Mobile Experience: Free Subscription > Software experts and developers: Be at the forefront of tech innovation. > Intel(R) Software Adrenaline delivers strategic insight and game-changing > conversations that shape the rapidly evolving mobile landscape. Sign up now. > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk_______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > > > > ------------------------------------------------------------------------------ > Shape the Mobile Experience: Free Subscription > Software experts and developers: Be at the forefront of tech innovation. > Intel(R) Software Adrenaline delivers strategic insight and game-changing > conversations that shape the rapidly evolving mobile landscape. Sign up now. > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > -- 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 ORCID: 0000-0001-7542-0286 |
From: Nina J. <jel...@gm...> - 2013-11-22 11:58:25
|
On 22 November 2013 13:52, John May <joh...@gm...> wrote: > Hi Nina, > > I think that class was from JChemPaint… here’s the package in 1.4.11: > https://github.com/cdk/cdk/tree/cdk-1.4.11/src/main/org/openscience/cdk/renderer/generators > It's probably be from cdk-jchempaint , not JChemPaint itself (according to maven dependencies in ambit ;) > > I guess the short answer is that no it’s not possible to highlight atoms > (with different colours) in the CDK without writing a custom generator or > porting from downstream projects. > Guess so - otherwise I would not invent a custom class. Regards, Nina > > Thanks, > John > > On 22 Nov 2013, at 11:45, Nina Jeliazkova <jel...@gm...> > wrote: > > Hi John, > > > On 22 November 2013 13:35, John May <joh...@gm...> wrote: > >> Hi Gilleain, Nina >> >> Thanks for the examples. >> >> Do you mean the text of the atom labels should be different colors, or >> >> do you want colored circles underneath the atoms? >> >> >> Circles underneath like Nina linked to in Ambit. >> >> There are several ways, >> >> >> I thought as much :-) >> >> ambit code is at >> http://sourceforge.net/p/ambit/code/HEAD/tree/trunk/ambit2-all/ambit2-rendering/src/main/java/ambit2/rendering/CompoundImageTools.java >> >> >> >> Hmmm the SelectAtomGenerator… doesn’t exist in 1.4.x or master? >> >> IAtomColorer atomColorer = new IAtomColorer() { … //implement this somehow >> BasicAtomGenerator atomGenerator = //etc >> atomGenerator.set(BasicAtomGenerator.AtomColorer.class, atomColorer); >> >> this version uses CDK 1.4.11 - CDK renderers only, not JChemPaint > (JCP is a pain to have server side). The CDK renderer part might have > changed in later version. > > > >> >> This colours the atom symbol / glyph, is there a non-extension way to do >> the highlight. >> > > > There is a custom MySelectAtomGenerator which does the highlighting based > on atom property (in the demo link the three colors corresponds to ranks > 1,2,3 as calculated by SmartCYP) . > > I think Bioclipse does the highlighting differently, may be someone from > Bioclipse team could elaborate. > > Regards, > Nina > > >> >> Cheers, >> John >> >> On 22 Nov 2013, at 11:24, gilleain torrance <gil...@gm...> >> wrote: >> >> Ah, Nina's code seems quite comprehensive, and looks like it will do >> all sorts of useful things here. >> >> However, the 'standard' way to do things (inherited from the old JCP >> code) was to use an instance of an IAtomColorer, eg: >> >> IAtomColorer atomColorer = new IAtomColorer() { … //implement this somehow >> BasicAtomGenerator atomGenerator = //etc >> atomGenerator.set(BasicAtomGenerator.AtomColorer.class, atomColorer); >> >> should work, I think? >> >> gilleain >> >> >> >> >> On 11/22/13, Nina Jeliazkova <jel...@gm...> wrote: >> >> Hi John, >> >> >> On 22 November 2013 13:01, John May <jo...@eb...> wrote: >> >> Hi All, >> >> Does anyone know how to highlight atoms in different colours using the >> CDK >> renders? >> >> >> Yes :) >> >> >> http://apps.ideaconsult.net:8080/ambit2/dataset/1736?model_uri=http://apps.ideaconsult.net:8080/ambit2/model/48 >> >> There are several ways, ambit code is at >> >> http://sourceforge.net/p/ambit/code/HEAD/tree/trunk/ambit2-all/ambit2-rendering/src/main/java/ambit2/rendering/CompoundImageTools.java >> >> >> Regards, >> Nina >> >> >> Stephan and I have been scratching our heads and really looks like it’s >> not possible. We have code for this in Knime but simply can’t believe >> it’s >> not in the main rendering code. >> >> I always thought the ColorHash was how it was done but this (see below) >> only works for bonds :/. >> >> Map<IChemObject,Color> highlight = Maps.newHashMap(); >> highlight.put(m.getAtom(0), Color.green); >> highlight.put(m.getAtom(1), Color.red); >> renderer.getRenderer2DModel().set(RendererModel.ColorHash.class, >> highlight); >> >> Cheers, >> J >> >> >> >> >> ------------------------------------------------------------------------------ >> Shape the Mobile Experience: Free Subscription >> Software experts and developers: Be at the forefront of tech innovation. >> Intel(R) Software Adrenaline delivers strategic insight and game-changing >> conversations that shape the rapidly evolving mobile landscape. Sign up >> now. >> >> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk >> _______________________________________________ >> Cdk-devel mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-devel >> >> >> >> >> >> ------------------------------------------------------------------------------ >> Shape the Mobile Experience: Free Subscription >> Software experts and developers: Be at the forefront of tech innovation. >> Intel(R) Software Adrenaline delivers strategic insight and game-changing >> conversations that shape the rapidly evolving mobile landscape. Sign up >> now. >> >> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk >> _______________________________________________ >> Cdk-devel mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-devel >> >> >> >> >> ------------------------------------------------------------------------------ >> Shape the Mobile Experience: Free Subscription >> Software experts and developers: Be at the forefront of tech innovation. >> Intel(R) Software Adrenaline delivers strategic insight and game-changing >> conversations that shape the rapidly evolving mobile landscape. Sign up >> now. >> >> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk >> _______________________________________________ >> Cdk-devel mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-devel >> >> > > ------------------------------------------------------------------------------ > Shape the Mobile Experience: Free Subscription > Software experts and developers: Be at the forefront of tech innovation. > Intel(R) Software Adrenaline delivers strategic insight and game-changing > conversations that shape the rapidly evolving mobile landscape. Sign up > now. > > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk_______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > > > > > ------------------------------------------------------------------------------ > Shape the Mobile Experience: Free Subscription > Software experts and developers: Be at the forefront of tech innovation. > Intel(R) Software Adrenaline delivers strategic insight and game-changing > conversations that shape the rapidly evolving mobile landscape. Sign up > now. > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > > |
From: John M. <joh...@gm...> - 2013-11-22 12:05:20
|
Thanks for the help everyone. If I have time I will see if I can add it this weekend. Cheers, J On 22 Nov 2013, at 11:58, Nina Jeliazkova <jel...@gm...> wrote: > > > > On 22 November 2013 13:52, John May <joh...@gm...> wrote: > Hi Nina, > > I think that class was from JChemPaint… here’s the package in 1.4.11: https://github.com/cdk/cdk/tree/cdk-1.4.11/src/main/org/openscience/cdk/renderer/generators > > It's probably be from cdk-jchempaint , not JChemPaint itself (according to maven dependencies in ambit ;) > > > I guess the short answer is that no it’s not possible to highlight atoms (with different colours) in the CDK without writing a custom generator or porting from downstream projects. > > Guess so - otherwise I would not invent a custom class. > > Regards, > Nina > > > Thanks, > John > > On 22 Nov 2013, at 11:45, Nina Jeliazkova <jel...@gm...> wrote: > >> Hi John, >> >> >> On 22 November 2013 13:35, John May <joh...@gm...> wrote: >> Hi Gilleain, Nina >> >> Thanks for the examples. >> >>> Do you mean the text of the atom labels should be different colors, or >>> do you want colored circles underneath the atoms? >> >> >> Circles underneath like Nina linked to in Ambit. >> >>> There are several ways, >> >> I thought as much :-) >> >>> ambit code is at http://sourceforge.net/p/ambit/code/HEAD/tree/trunk/ambit2-all/ambit2-rendering/src/main/java/ambit2/rendering/CompoundImageTools.java >> >> >> Hmmm the SelectAtomGenerator… doesn’t exist in 1.4.x or master? >> >>> IAtomColorer atomColorer = new IAtomColorer() { … //implement this somehow >>> BasicAtomGenerator atomGenerator = //etc >>> atomGenerator.set(BasicAtomGenerator.AtomColorer.class, atomColorer); >> >> this version uses CDK 1.4.11 - CDK renderers only, not JChemPaint (JCP is a pain to have server side). The CDK renderer part might have changed in later version. >> >> >> >> This colours the atom symbol / glyph, is there a non-extension way to do the highlight. >> >> >> There is a custom MySelectAtomGenerator which does the highlighting based on atom property (in the demo link the three colors corresponds to ranks 1,2,3 as calculated by SmartCYP) . >> >> I think Bioclipse does the highlighting differently, may be someone from Bioclipse team could elaborate. >> >> Regards, >> Nina >> >> >> Cheers, >> John >> >> On 22 Nov 2013, at 11:24, gilleain torrance <gil...@gm...> wrote: >> >>> Ah, Nina's code seems quite comprehensive, and looks like it will do >>> all sorts of useful things here. >>> >>> However, the 'standard' way to do things (inherited from the old JCP >>> code) was to use an instance of an IAtomColorer, eg: >>> >>> IAtomColorer atomColorer = new IAtomColorer() { … //implement this somehow >>> BasicAtomGenerator atomGenerator = //etc >>> atomGenerator.set(BasicAtomGenerator.AtomColorer.class, atomColorer); >>> >>> should work, I think? >>> >>> gilleain >>> >>> >>> >>> >>> On 11/22/13, Nina Jeliazkova <jel...@gm...> wrote: >>>> Hi John, >>>> >>>> >>>> On 22 November 2013 13:01, John May <jo...@eb...> wrote: >>>> >>>>> Hi All, >>>>> >>>>> Does anyone know how to highlight atoms in different colours using the >>>>> CDK >>>>> renders? >>>>> >>>> >>>> Yes :) >>>> >>>> http://apps.ideaconsult.net:8080/ambit2/dataset/1736?model_uri=http://apps.ideaconsult.net:8080/ambit2/model/48 >>>> >>>> There are several ways, ambit code is at >>>> http://sourceforge.net/p/ambit/code/HEAD/tree/trunk/ambit2-all/ambit2-rendering/src/main/java/ambit2/rendering/CompoundImageTools.java >>>> >>>> >>>> Regards, >>>> Nina >>>> >>>> >>>>> Stephan and I have been scratching our heads and really looks like it’s >>>>> not possible. We have code for this in Knime but simply can’t believe >>>>> it’s >>>>> not in the main rendering code. >>>>> >>>>> I always thought the ColorHash was how it was done but this (see below) >>>>> only works for bonds :/. >>>>> >>>>> Map<IChemObject,Color> highlight = Maps.newHashMap(); >>>>> highlight.put(m.getAtom(0), Color.green); >>>>> highlight.put(m.getAtom(1), Color.red); >>>>> renderer.getRenderer2DModel().set(RendererModel.ColorHash.class, >>>>> highlight); >>>>> >>>>> Cheers, >>>>> J >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Shape the Mobile Experience: Free Subscription >>>>> Software experts and developers: Be at the forefront of tech innovation. >>>>> Intel(R) Software Adrenaline delivers strategic insight and game-changing >>>>> conversations that shape the rapidly evolving mobile landscape. Sign up >>>>> now. >>>>> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk >>>>> _______________________________________________ >>>>> Cdk-devel mailing list >>>>> Cdk...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/cdk-devel >>>>> >>>>> >>>> >>> >>> ------------------------------------------------------------------------------ >>> Shape the Mobile Experience: Free Subscription >>> Software experts and developers: Be at the forefront of tech innovation. >>> Intel(R) Software Adrenaline delivers strategic insight and game-changing >>> conversations that shape the rapidly evolving mobile landscape. Sign up now. >>> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk >>> _______________________________________________ >>> Cdk-devel mailing list >>> Cdk...@li... >>> https://lists.sourceforge.net/lists/listinfo/cdk-devel >> >> >> ------------------------------------------------------------------------------ >> Shape the Mobile Experience: Free Subscription >> Software experts and developers: Be at the forefront of tech innovation. >> Intel(R) Software Adrenaline delivers strategic insight and game-changing >> conversations that shape the rapidly evolving mobile landscape. Sign up now. >> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk >> _______________________________________________ >> Cdk-devel mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-devel >> >> >> ------------------------------------------------------------------------------ >> Shape the Mobile Experience: Free Subscription >> Software experts and developers: Be at the forefront of tech innovation. >> Intel(R) Software Adrenaline delivers strategic insight and game-changing >> conversations that shape the rapidly evolving mobile landscape. Sign up now. >> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk_______________________________________________ >> Cdk-devel mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-devel > > > ------------------------------------------------------------------------------ > Shape the Mobile Experience: Free Subscription > Software experts and developers: Be at the forefront of tech innovation. > Intel(R) Software Adrenaline delivers strategic insight and game-changing > conversations that shape the rapidly evolving mobile landscape. Sign up now. > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > > > ------------------------------------------------------------------------------ > Shape the Mobile Experience: Free Subscription > Software experts and developers: Be at the forefront of tech innovation. > Intel(R) Software Adrenaline delivers strategic insight and game-changing > conversations that shape the rapidly evolving mobile landscape. Sign up now. > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk_______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel |
From: John M. <joh...@gm...> - 2013-11-27 12:56:48
|
Hi All, I played around with the highlight the other day (see. attached). The current bond highlighting changes the colour of bond lines based on a ColorHash given to the render model. Atom highlight via a glow is only available in JChemPaint (or CDK-JChemPaint?). I kind of think it might be nicer to have the ‘colour class’ on the container and then use the render options to change change colour palette (similar to how R handles plot colours)? This means you can create one renderer and pass it different molecules with different highlights and don’t need to touch the renderer parameters. Currently the colour class is simply and ‘int’ in a hashmap for atoms/bonds. Multiple colours is also nice but it gets complicated for bonds when they are highlighted with a different ‘glow’ from their atoms - do you think how it’s handled below is okay? Here’s an example for a use of multiple colours from CDK/JChemPaint/SMSD/EC-Blast atom mapping: http://www.ebi.ac.uk/thornton-srv/software/ecblast/rbl/images/reaction/bc/R00994.png Oh I also spotted how to fix the skeletal/really thin bonds in large depictions and will add the atom symbol alignment fix. Cheers, J |