{ "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/2007/12/20/molecular-qsar-descriptors-in-cdk.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/10.59350/47rre-wwc20", "url": "https://chem-bla-ics.linkedchemistry.info/2007/12/20/molecular-qsar-descriptors-in-cdk.html", "title": "The molecular QSAR descriptors in the CDK", "content_html": "

Pending the release of Bioclipse 1.2.0, Ola asked me to do some additional feature\nimplementation for the QSAR feature, such as having the filenames as labels in the descriptor matrix. See also\nthese earlier items:

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(How more open notebook science can you get?)

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But I ran into some trouble when both JOElib and CDK descriptors\nwere selected, or Ola really. Now, nothing much I plan to do on the JOElib code, but at least I code investigate\nthe CDK code.

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The QSAR descriptor framework has been published in the Recent developments of the chemistry development kit (CDK) -\nan open-source java library for chemo- and bioinformatics paper (DOI:10.2174/138161206777585274).\nHowever, while most molecular descriptors had JUnit tests for at least the calculate() method, a full\nand proper module testing was not set up. This involves a rough coverage testing and test methods for all\nmethods in the classes.

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So, I set up a new CDK module called qsarmolecular, and added the coverage test class\nQsarmolecularCoverageTest.\nThis class is really short and basically only requires a module to be set up, as reflected by the line:

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private final static String CLASS_LIST = \"qsarmolecular.javafiles\";\n
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The actual functionality is inherited from the CoverageTest.\nThe coverage testing requires, unlike tools like Emma \nfor which reports are generated by Nightly,\na certain naming scheme (explained in Development Tools. 1. Unit testing in\nCDK News 2.2).

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Now, testing for a lot of the methods in the IMolecularDescriptor\nand IDescriptor\ninterfaces are actually identical for all descriptors. Therefore, I wrote a\nMolecularDescriptorTest\nand made all JUnit test classes for the molecular descriptors extend this new class. This means that by writing only 10 new tests,\nwith 29 assert statements, for the 45 molecular descriptor classes, 450 new unit tests are run without special effort, making to\ntotal sum of unit tests run each night by Nightly for trunk/\npass the 4500 unit tests.

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Now, this turned out to be necessary. I count 52 new failing tests, which should hit Nightly in the next 24 hours.

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References

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Steinbeck, C., Hoppe, C., Kuhn, S., Floris, M., Guha, R., & Willighagen, E. (2006). Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics. Current Pharmaceutical Design, 12(17), 2111–2120. https://doi.org/10.2174/138161206777585274 CrossRef Scholia
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", "summary": "Pending the release of Bioclipse 1.2.0, Ola asked me to do some additional feature implementation for the QSAR feature, such as having the filenames as labels in the descriptor matrix. See also these earlier items:", "date_published": "2007-12-20T00:00:00+00:00", "date_modified": "2025-04-20T00:00:00+00:00", "tags": ["cdk","qsar","bioclipse"], "_references": [ { "url": "https://doi.org/10.2174/138161206777585274", "doi": "10.2174/138161206777585274" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }