{ "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/2007/08/24/jchempaint-too-png-embedded.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/rxpr6-t1772", "url": "https://chem-bla-ics.linkedchemistry.info/2007/08/24/jchempaint-too-png-embedded.html", "title": "JChemPaint too: PNG embedded connectivity tables", "content_html": "

Rich blogged about Firefly embedding MDL molfiles in PNG images ,\nwhich I found really cool.\nRich and Noel later showed how that metadata can be retrieved again ,\npossibly with Python.

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But I did not like that Firefly could do this, and JChemPaint not.\nSo, I started hacking. First I discovered I had to get rid of the use of JAI; then I had to adapt the\nJChemPaintPanel takeSnaphot() API to return a RendererImage; and finally, I had to figure out how to write the extra metadata. Now, Firefly is not opensource\n(yet), so it took me some time to figure out how that was done, and this is how:

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ImageWriter writer = ImageIO.getImageWriters(\n  new ImageTypeSpecifier(awtImage), \"png\"\n).next();\nImageTypeSpecifier specifier = new ImageTypeSpecifier(awtImage);\nIIOMetadata meta = writer.getDefaultImageMetadata( specifier, null );\n\nNode node = meta.getAsTree( \"javax_imageio_png_1.0\" );\nIIOMetadataNode tExtNode = new IIOMetadataNode(\"tEXt\");\nIIOMetadataNode tExtEntryNode = new IIOMetadataNode(\"tEXtEntry\");\ntExtEntryNode.setAttribute( \"keyword\", \"molfile\" );\ntExtEntryNode.setAttribute( \"value\", mdlMolfile);\ntExtNode.appendChild(tExtEntryNode);\nnode.appendChild(tExtNode);\nmeta.mergeTree(\"javax_imageio_png_1.0\", node);\nImageOutputStream ios = ImageIO.createImageOutputStream(\n  new FileOutputStream(filename)\n);\nwriter.setOutput(ios);\nwriter.write( meta, new IIOImage(awtImage, null, meta), null );\n
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Now I can create my own test files for the Strigi’s ability to extract chemical metadata from PNG images.\nHere is the JChemPaint generator PNG image for benzophenone:

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\"\"

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Another issue, unrelated to this patch, is that writing PNG images changes the location of the structure in the JChemPaint editor,\nand that the placing of the element symbol in image writing is seriously broken. But that will soon be solved with\nNiels’ new renderer.

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The metadata looks like:

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\"\"

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(Newlines are lost in the XML display.)

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JChemPaint does not yet write InChIs, and it also does not open PNG images for input yet (as Firefly does).

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References

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Apodaca, R. (2007). Never Draw the Same Molecule Twice: Image Metadata for Cheminformatics. In Front Matter. Front Matter. https://doi.org/10.59350/j026p-17z02 CrossRef Scholia
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Apodaca, R. (2007). Never Draw the Same Molecule Twice: Viewing Image Metadata. In Front Matter. Front Matter. https://doi.org/10.59350/wgy8j-brx45 CrossRef Scholia
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", "summary": "Rich blogged about Firefly embedding MDL molfiles in PNG images , which I found really cool. Rich and Noel later showed how that metadata can be retrieved again , possibly with Python.", "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/jcpPNGmolfile.png", "date_published": "2007-08-24T00:00:00+00:00", "date_modified": "2025-02-08T00:00:00+00:00", "tags": ["jchempaint","cheminf"], "_references": [ { "url": "https://doi.org/10.59350/j026p-17z02", "doi": "10.59350/j026p-17z02" } , { "url": "https://doi.org/10.59350/wgy8j-brx45", "doi": "10.59350/wgy8j-brx45" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }