Bioclipse : Safe When Used As Directed

Finally used bioclipse for a real purpose, and to good effect, too:

what this shows (the images do get larger if you click on them! :) is the following basic workflow:

1) Exploring manager functions in the js console (bottom).

2) Writing a script in the js editor (top left).

3) Running and getting feedback in the rhino console (far right).

4) Viewing the results in the sdf viewer (top right).

What I was doing was searching through an sdf file (C10H16_filtered.sdf) for all structures with a cyclohexane ring as a substructure, then writing those out to a file.

Probably could have been done 5 other ways, but, well, it was more fun this way.

Oh, and it is a gist here.

Comments

Egon Willighagen said…

The only thing that worries me here, is that the statelessness of managers do not easily allow making a fully efficient iterative process... it seems CDK classes would need to be used directly for that.

28 April 2009 at 08:13

gilleain said…

This is true. It would have been nicer to have a call like:

cdk.writeToSDF(mol, sdfFileHandle)

in the loop. Even better would be a manager method that takes user-defined filter functions like:

cdk.filterSDF(my_func, inputPath, outputPath)

but that's very much a pipe-dream :)

28 April 2009 at 12:01

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