Hi, I have started to use Standard Generator for depicting structures, (described in: https://github.com/cdk/cdk/wiki/Standard-Generator).
The generated depictions are nicer before, but I have found some structures
that make StandardGenerator fail.
Following the part to the code used to create the depiction:
[...]
final DOMImplementation domImplementation =
GenericDOMImplementation.getDOMImplementation();
final Document document = domImplementation.createDocument("
http://www.w3.org/2000/svg";, "svg", null);
final SVGGeneratorContext context =
SVGGeneratorContext.createDefault(document);
final SVGGraphics2D svgGraphics2D = new SVGGraphics2D(context,
true);
final List<IGenerator<IAtomContainer>> listOfGenerators = new
ArrayList<IGenerator<IAtomContainer>>();
listOfGenerators.add(new BasicSceneGenerator());
listOfGenerators.add(new StandardGenerator(new Font("Verdana",
Font.PLAIN, 18)));
final AtomContainerRenderer atomContainerRenderer = new
AtomContainerRenderer(listOfGenerators, new AWTFontManager());
final RendererModel rendererModel =
atomContainerRenderer.getRenderer2DModel();
rendererModel.set(StandardGenerator.Visibility.class,
SymbolVisibility.iupacRecommendations());
rendererModel.set(StandardGenerator.AtomColor.class, new
CDK2DAtomColors());
try {
atomContainerRenderer.paint(pIAtomContainer, new
AWTDrawVisitor(svgGraphics2D), new Rectangle(0, 0, width, height), true);
} catch (final Exception e) {
throw new CDKException("Error during image depiction.", e);
}
final StringWriter stringWriter = new StringWriter();
final Element root = svgGraphics2D.getRoot();
root.setAttributeNS(null, SVGConstants.SVG_VIEW_BOX_ATTRIBUTE, "0 0
"
+ (width) + " "
+ height);
svgGraphics2D.stream(root, stringWriter);
[...]
With some structures the following exception is raised:
Caused by: java.lang.ArrayIndexOutOfBoundsException: 34
at
org.openscience.cdk.renderer.generators.standard.StandardBondGenerator$RingBondOffsetComparator.countLightElements(StandardBondGenerator.java:1303)
at
org.openscience.cdk.renderer.generators.standard.StandardBondGenerator$RingBondOffsetComparator.compare(StandardBondGenerator.java:1248)
at
org.openscience.cdk.renderer.generators.standard.StandardBondGenerator$RingBondOffsetComparator.compare(StandardBondGenerator.java:1214)
at java.util.TimSort.countRunAndMakeAscending(Unknown Source)
at java.util.TimSort.sort(Unknown Source)
at java.util.TimSort.sort(Unknown Source)
at java.util.Arrays.sort(Unknown Source)
at java.util.Collections.sort(Unknown Source)
at
org.openscience.cdk.renderer.generators.standard.StandardBondGenerator.ringPreferenceMap(StandardBondGenerator.java:1143)
at
org.openscience.cdk.renderer.generators.standard.StandardBondGenerator.<init>(StandardBondGenerator.java:146)
at
org.openscience.cdk.renderer.generators.standard.StandardBondGenerator.generateBonds(StandardBondGenerator.java:181)
at
org.openscience.cdk.renderer.generators.standard.StandardGenerator.generate(StandardGenerator.java:197)
at
org.openscience.cdk.renderer.generators.standard.StandardGenerator.generate(StandardGenerator.java:82)
at
org.openscience.cdk.renderer.AbstractRenderer.generateDiagram(AbstractRenderer.java:120)
at
org.openscience.cdk.renderer.AtomContainerRenderer.paint(AtomContainerRenderer.java:235)
Attached to this mail you will find an structure (.SDF format) which
produces the error.
Has anybody experienced similar behavior ? Is there any workaround ?
Thanks in advance.
Oscar
EXAMPLE.sdf
Description: Binary data
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