With the 1.3.6 jar and the jchempaint 15 jar I can't compile
Are there any plans to finally get the rendering in sync with the CDK
so that one could actually use it, rather than spend an afternoon
hacking on it?
compile:
[mkdir] Created dir: /Users/guhar/src/cdkr/rcdkjar/classes
[javac] Compiling 15 source files to /Users/guhar/src/cdkr/rcdkjar/classes
[javac]
/Users/guhar/src/cdkr/rcdkjar/src/org/guha/rcdk/view/MoleculeImage.java:59:
cannot find symbol
[javac] symbol : constructor
Renderer(java.util.List<org.openscience.cdk.renderer.generators.IGenerator>,org.openscience.cdk.renderer.font.AWTFontManager)
[javac] location: class org.openscience.cdk.renderer.Renderer
[javac] Renderer renderer = new Renderer(generators, new
AWTFontManager());
[javac] ^
[javac]
/Users/guhar/src/cdkr/rcdkjar/src/org/guha/rcdk/view/panels/MoleculeCell.java:56:
cannot find symbol
[javac] symbol : constructor
Renderer(java.util.List<org.openscience.cdk.renderer.generators.IGenerator>,org.openscience.cdk.renderer.font.AWTFontManager)
[javac] location: class org.openscience.cdk.renderer.Renderer
[javac] this.renderer = new Renderer(generators, new
AWTFontManager());
[javac] ^
[javac] 2 errors
On Thu, Sep 23, 2010 at 8:50 AM, Özgür Demir <[email protected]> wrote:
> Hi,
>
> I'm trying to implement some "simple" tasks using CDK. Given a Molecule
> I want to retrieve its Formula, Smiles Code, Molecular Weight and
> finally render an image. I was able to compute the smiles string and
> formula using CDK 1.2.7:
>
> //smiles
> SmilesGenerator sg = new SmilesGenerator();
> molecule.setSmiles(sg.createSMILES(cdkmolecule));
> //formula
> IMolecularFormula moleculeFormula =
> MolecularFormulaManipulator.getMolecularFormula(cdkmolecule);
> molecule.setFormula(MolecularFormulaManipulator.getString(moleculeFormula));
>
> next I wanted to render an image. I found an example on
> http://chem-bla-ics.blogspot.com/2010/04/cdk-jchempaint-1-rendering-molecules.html
> which assumes cdk-1.3.x and cdk-jchempaint. Trying to run this code with
> cdk-1.3.6 and cdk-jchempaint-15 (I got both via sourceforge) reveals the
> following exception:
>
> Exception in thread "main" java.lang.NoSuchMethodError:
> org.openscience.cdk.interfaces.IChemObjectBuilder.newInstance(Ljava/lang/Class;[Ljava/lang/Object;)Lorg/openscience/cdk/interfaces/ICDKObject;
> at
> org.openscience.cdk.renderer.generators.BasicBondGenerator.getRingSet(BasicBondGenerator.java:142)
> at
> org.openscience.cdk.renderer.generators.BasicBondGenerator.generate(BasicBondGenerator.java:204)
> at
> org.openscience.cdk.renderer.generators.BasicBondGenerator.generate(BasicBondGenerator.java:57)
> at
> org.openscience.cdk.renderer.AtomContainerRenderer.generateDiagram(AtomContainerRenderer.java:585)
> at
> org.openscience.cdk.renderer.AtomContainerRenderer.paint(AtomContainerRenderer.java:240)
>
>
> The code for the smiles string generation does not work either with cdk
> 1.3.x. I get the following exception:
>
> Exception in thread "main" java.lang.NoSuchMethodError:
> org.openscience.cdk.smiles.SmilesGenerator.createSMILES(Lorg/openscience/cdk/interfaces/IAtomContainer;)Ljava/lang/String;
>
> Hence, 1.3.x does not seem to be compatible to 1.2.x? Is that true? So
> I'm a little bit confused which version to use and how to calculate the
> desired properties?
> Regards
>
> Özgür Demir
>
>
>
> heres the code for image creation:
>
> private static void renderImage(IMolecule molecule, File file, int
> width, int height) throws Exception {
> Rectangle drawArea = new Rectangle(width, height);
> Image image = new BufferedImage(width, height,
> BufferedImage.TYPE_INT_RGB);
> StructureDiagramGenerator sdg = new StructureDiagramGenerator();
> sdg.setMolecule(molecule);
> sdg.generateCoordinates();
> molecule = sdg.getMolecule();
> List<IGenerator<IAtomContainer>> generators = new
> ArrayList<IGenerator<IAtomContainer>>();
> generators.add(new BasicSceneGenerator());
> generators.add(new BasicBondGenerator());
> generators.add(new BasicAtomGenerator());
> AtomContainerRenderer renderer = new
> AtomContainerRenderer(generators, new AWTFontManager());
> renderer.setup(molecule, drawArea);
> Graphics2D g2 = (Graphics2D) image.getGraphics();
> g2.setColor(Color.WHITE);
> g2.fillRect(0, 0, width, height);
> renderer.paint(molecule, new AWTDrawVisitor(g2));
> ImageIO.write((RenderedImage) image, "PNG", file);
> }
>
>
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--
Rajarshi Guha
NIH Chemical Genomics Center
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