{ "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-1-rendering-molecules.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/zp98c-wkb92", "url": "https://chem-bla-ics.linkedchemistry.info/2010/04/05/cdk-jchempaint-1-rendering-molecules.html", "title": "CDK-JChemPaint #1: rendering molecules", "content_html": "

I reported earlier that the CDK-JChemPaint patch is now a clean add-on from the CDK releases.\nThis means that you download cdk-1.3.4.jar and\ncdk-jchempaint-8.jar separately, put them in your class path, and get started\nwith, for example, Groovy:

\n\n
$ export CLASSPATH=cdk-1.3.4.jar:cdk-jchempaint-8.jar\n$ groovy renderMol.groovy\n
\n\n

\"\"

\n\n

I have tuned to code in this tutorial\nby Gilleain a bit, resulting in this code:

\n\n
import java.util.List;\n\nimport java.awt.*;\nimport java.awt.image.*;\n\nimport javax.imageio.*;\n\nimport org.openscience.cdk.*;\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 triazole = MoleculeFactory.make123Triazole();\nStructureDiagramGenerator sdg = new StructureDiagramGenerator();\nsdg.setMolecule(triazole);\nsdg.generateCoordinates();\ntriazole = sdg.getMolecule();\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// the renderer needs to have a toolkit-specific font manager\nAtomContainerRenderer renderer =\n  new AtomContainerRenderer(generators, new AWTFontManager());\n\n// the call to 'setup' only needs to be done on the first paint\nrenderer.setup(triazole, 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.paint(triazole, new AWTDrawVisitor(g2));\n\nImageIO.write((RenderedImage)image, \"PNG\", new File(\"triazole.png\"));\n
", "summary": "I reported earlier that the CDK-JChemPaint patch is now a clean add-on from the CDK releases. This means that you download cdk-1.3.4.jar and cdk-jchempaint-8.jar separately, put them in your class path, and get started with, for example, Groovy:", "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/triazole.png", "date_published": "2010-04-05T00:00:00+00:00", "date_modified": "2010-04-05T00:00:00+00:00", "tags": ["cdk","jchempaint"], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }