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Calculating molecular descriptors with OpenTox
While working during office hours on Oscar, I am also trying to finish up some work left from Uppsala. One such thing is the Bioclipse-OpenTox project (see Using Bioclipse to upload data to an OpenTox server and Oxford, August 2010: eCheminfo Predictive ADME & Toxicology 2010 Workshop). Today I finished calculating molecular descriptor values with OpenTox servers:
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Algorithm or Model: OpenTox API quiz
Nina (who still does not seem to blog) wrote up this interesting question, triggered by the OpenTox API ontology:
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Oscar4 Java API: chemical name dictionaries
Besides getting Oscar used by ChEBI (hopefully via Taverna ), my main task in my three month Oscar project is to refactor things to make it more modular, and remove some features no longer needed (e.g. an automatically created workspace environment). Clearly, I need to define a lot of new unit tests to ensure my assumptions on how to code works are valid.
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CDK 1.2 to 1.4 API changes #2: implicit hydrogens
A second API change lies deep in the IAtom interface. To reflect more accurately the meaning of the method, the IAtomType.getHydrogenCount() has been renamed to IAtomType.getImplicitHydrogenCount(), and likewise the setter methods.
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CDK 1.2 to 1.4 API changes #1: creating objects with an IChemObjectBuilder
Later this year (planned) a new stable branch of the CDK library will be released. Time to look at some API changes, to ease migration. In this first post of the series, I will show how the IChemObjectBuilder functionality has changed.
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Multiple unit test inheritance with JExample
Two months ago I wrote about JExample (see Specifying unit test dependencies with JExample ). At the time, my examples did not include multiple unit test inheritance, but was informed later by @jexample that is possible. I just got time to try it in the Oscar project:
