{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2010/04/05/cdk-jchempaint-2-rendering-reactions.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/wyfzs-jsm57", "url": "https://chem-bla-ics.linkedchemistry.info/2010/04/05/cdk-jchempaint-2-rendering-reactions.html", "title": "CDK-JChemPaint #2: rendering reactions", "content_html": "

I posted earlier today a Groovy script to render molecules \nwith CDK-JChemPaint 8. Now, the new JChemPaint rendering engine also contains the functionality to render reactions. So, I can also do:

\n\n
$ groovy renderReaction.groovy\n
\n\n

\"\"

\n\n

The matching script:

\n\n
import java.util.List;\n\nimport java.awt.*;\nimport java.awt.image.*;\n\nimport javax.imageio.*;\nimport javax.vecmath.*;\n\nimport org.openscience.cdk.*;\nimport org.openscience.cdk.geometry.*;\nimport org.openscience.cdk.interfaces.*;\nimport org.openscience.cdk.layout.*;\nimport org.openscience.cdk.renderer.*;\nimport org.openscience.cdk.renderer.font.*;\nimport org.openscience.cdk.renderer.generators.*;\nimport org.openscience.cdk.renderer.visitor.*;\nimport org.openscience.cdk.templates.*;\n\nint WIDTH = 600;\nint HEIGHT = 600;\n\n// the draw area and the image should be the same size\nRectangle drawArea = new Rectangle(WIDTH, HEIGHT);\nImage image = new BufferedImage(\n  WIDTH, HEIGHT, BufferedImage.TYPE_INT_RGB\n);\n\nIMolecule benzene = MoleculeFactory.makeBenzene();\nIMolecule triazole = MoleculeFactory.make123Triazole();\nIReaction reaction = new Reaction();\n\nStructureDiagramGenerator sdg = new StructureDiagramGenerator();\nsdg.setMolecule(triazole);\nsdg.generateCoordinates();\ntriazole = sdg.getMolecule();\nsdg.setMolecule(benzene);\nsdg.generateCoordinates();\nbenzene = sdg.getMolecule();\ntry {\nGeometryTools.translate2DCenterTo(benzene, new Point2d(-4,0))\nGeometryTools.translate2DCenterTo(triazole, new Point2d(4,0))\n} catch (Exception e) {\n e.printStackTrace();\n}\n\nreaction.addReactant(benzene);\nreaction.addProduct(triazole);\n\n// generators make the image elements\nList generators = new ArrayList();\ngenerators.add(new BasicSceneGenerator());\ngenerators.add(new BasicBondGenerator());\ngenerators.add(new BasicAtomGenerator());\n\n List reactiongenerators =\n  new ArrayList();\nreactiongenerators.add(new ReactionArrowGenerator());\nreactiongenerators.add(new ReactionPlusGenerator());\n\n// the renderer needs to have a toolkit-specific font manager\nRenderer renderer = new Renderer(\n  generators, reactiongenerators, new AWTFontManager()\n);\n\n// the call to 'setup' only needs to be done on the first paint\nrenderer.setup(reaction, drawArea);\n\n// paint the background\nGraphics2D g2 = (Graphics2D)image.getGraphics();\ng2.setColor(Color.WHITE);\ng2.fillRect(0, 0, WIDTH, HEIGHT);\n\n// the paint method also needs a toolkit-specific renderer\nrenderer.paintReaction(reaction, new AWTDrawVisitor(g2));\n\nImageIO.write(\n  (RenderedImage)image, \"PNG\", new File(\"reaction.png\")\n);\n
", "summary": "I posted earlier today a Groovy script to render molecules with CDK-JChemPaint 8. Now, the new JChemPaint rendering engine also contains the functionality to render reactions. So, I can also do:", "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/reaction.png", "date_published": "2010-04-05T00:10:00+00:00", "date_modified": "2026-07-05T00:00:00+00:00", "tags": ["cdk","jchempaint"], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }