Hi,
I try to generate molecule images from MDL(SDF) files using CDK, but it throws
NullPointerException:
org.openscience.cdk.io.MDLReader cdkMDL = new
org.openscience.cdk.io.MDLReader(mdl);
org.openscience.cdk.Molecule mol = new org.openscience.cdk.Molecule();
cdkMDL.read(mol);
org.openscience.cdk.renderer.SimpleRenderer2D renderer = new
org.openscience.cdk.renderer.SimpleRenderer2D();
Rectangle2D bounds = new Rectangle2D.Double(0, 0, 180, 180);
BufferedImage bufferedImage = new BufferedImage( 180,
180,BufferedImage.TYPE_INT_RGB );
Graphics2D graphics = bufferedImage.createGraphics();
renderer.paintMolecule(mol, graphics, bounds);
javax.imageio.ImageIO.write(bufferedImage, "png", out);
java.lang.NullPointerException
at
org.openscience.cdk.geometry.GeometryTools.getBestAlignmentForLabel(GeometryTools.java:801)
at
org.openscience.cdk.renderer.AbstractRenderer2D.paintAtom(AbstractRenderer2D.java:230)
at
org.openscience.cdk.renderer.AbstractRenderer2D.paintAtoms(AbstractRenderer2D.java:206)
at
org.openscience.cdk.renderer.SimpleRenderer2D.paintMolecule(SimpleRenderer2D.java:148)
at
org.openscience.cdk.renderer.SimpleRenderer2D.paintMolecule(SimpleRenderer2D.java:100)
the mdl file is as follows:
3D_NCI753
3D_NCI
9 10 0 0 0 0 0 0 0 0 1 V2000
-0.0170 1.4060 0.0100 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0020 -0.0040 0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.2560 2.0480 0.0300 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0610 0.7840 -0.0130 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2920 -0.0100 0.0250 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2730 1.8200 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1.3260 -0.3630 -0.0130 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.1490 -0.6630 0.0100 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.3520 1.3100 0.0410 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 4 0 0 0 0
1 3 4 0 0 0 0
1 6 4 0 0 0 0
2 7 4 0 0 0 0
2 8 4 0 0 0 0
3 9 4 0 0 0 0
4 6 4 0 0 0 0
4 7 4 0 0 0 0
5 8 4 0 0 0 0
5 9 4 0 0 0 0
M END
--
Adel Golovin EMBL-EBI/PDBe 44 1223 492531 [EMAIL PROTECTED]
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