Ola has released the second beta for Bioclipse 2.0.\nThings are getting along, and I will not go into details on the molecules table Arvid is working on,\nthe 1GB+ SD file support, the validating CML editor ,\nthe support for XMPP services ,\nor the brand new welcome page\nwhich will guide new users around in what Bioclipse has to offer.
\n\nThis blog will focus on what Bioclipse has to offer CDK developers.
\n\nWhile Bioclipse 1.x (doi:10.1186/1471-2105-8-59) was a prototype that showed the\npower if integrating different bio- and cheminformatics tools, Bioclipse2 was designed from scratch, taking advantage of\nthe latest Eclipse RCP technologies. More importantly, the\nteam in Uppsala decided to have all functionality work via managers, allowing all actions to be recorded. And,\nscripting of Bioclipse. I blogged earlier about scripting JChemPaint ,\nand creating UFF optimized 3D structures from SMILES .\nExample scripts can be found on\nGitHub (this is their coverage), and are\nindexed on Delicious.
\n\nThe fact that we can script everything makes Bioclipse an ideal platform for doing cheminformatics: we have access to a variety of\ncheminformatics libraries, and the means to visualize results via JChemPaint and\nJmol. It is like R for cheminformatics: Bioclipse being the R command line, Bioclipse plugins the R\npackages. Eclipse provides an mechanism called Update Sites, which makes something like CRAN redundant. Back to the Chemistry\nDevelopment Kit.
\n\nOver the next weeks, I will blog about scripts aimed at CDK developers and people who want to learn more on how the CDK\ninternals work. This series assumes Bioclipse 2.0 beta2 (or better) and the CDK Feature installed. I’ll be using the Gist\nwidget to embed scripts in this blog, but you can always download the Gist directly into Bioclipse, with the GUI as described\nhere .
\n\nBioclipse uses JavaScript (maybe other scripting languages in the future. File a wishlist report if you like to see Jython,\nBeanShell or other support in the Bioclipse bug track system.)\nBioclipse managers are visible using special variables, such as:
\n\n| Bioclipse Feature | \nui | \nBioclipse UI interaction | \n
| Cheminformatics Feature | \ncdk | \nCDK functionality | \n
| \n | jmol | \nJmol functionality | \n
| CDK Feature | \ncdx | \nCDK Developer functionality | \n
Bioclipse scripting has TAB completion support, so you can type cdk. (notice the dot at the end) to which methods the cdk manager provides.
\n\nAs I wrote last week with the email on the first CDK 1.2 release candidate ,\nthe new CDK atom typer is a core component of the new CDK. The new implementation covers all atom types used in CDK 1.0, and many more.\nIn particular, Miguel boosted support for charged and radical atom types.
\n\nHowever, the atom types in your data set may not be covered, or perception fails otherwise. That happens. Bioclipse2 makes\ndebugging of this important step in cheminformatics quite insightful. The following script reads a molecule from SMILES,\nvisualizes 2D diagram in JChemPaint, and perceives atom types: The atom type perception results are return to the JavaScript\nconsole, and if there are nulls given, then the CDK algorithm did not find a matching atom type for that atom. If you are\nsure your cheminformatics representation is in order, I welcome a bug report\nhere.
\n\nCDK developers can take advantage of this functionality, to eliminate possible causes why a certain algorithm fails. CDK atom typing is used for a variate of algorithms, including counting implicit hydrogens, which many other algorithms need to know.
\n\nA use case for people who want to know if a particular SMILES feature is read or to make sure it is read correctly:\nThis script uses the diff functionality introduced in CDK 1.2, and shows two aspects of the SMILES specification: 1. it\npicked up the isotope information given in the second SMILES; 2. the second SMILES does not include the implicit hydrogen\ncount, which the SMILES specification then defaults as zero.
\n\nThe CDK managers in Bioclipse (cdk and cdx) expose functionality of the CDK, and allows using it in Bioclipse’ rich\nvisual workbench environment.
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