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Bacting := acting as the Bioclipse TNG
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License DOI Maven Central

Bacting := acting as the Bioclipse TNG

How to cite

If you use this software, please cite the Bioclipse 2 paper.


First, you need a working Maven installation and then install this software:

mvn clean install

Bumping the version

Use this command to change the version number (and update BioclipseManager.version()):

mvn versions:set -DgroupId=io.github.egonw.bacting -DartifactId=bioclipse-* -DoldVersion=2.8.0 -DnewVersion=
mvn versions:set -DgroupId=io.github.egonw.bacting -DartifactId=managers-* -DoldVersion=0.0.4 -DnewVersion=0.0.5-SNAPSHOT


It can be used in Groovy by including the Bacting managers you need:

@Grab(group='io.github.egonw.bacting', module='managers-cdk', version='0.0.5')

workspaceRoot = "."
def cdk = new net.bioclipse.managers.CDKManager(workspaceRoot);

println cdk.fromSMILES("COC")

API Coverage

For the time being, the API is incomplete. Particularly, manager functionality around graphical UX in the original Bioclipse may never be implemented. Each Bacting release will implement more APIs and the release notes will mention which managers and which methods have been added.

For a description of the API, I refer to the book A lot of Bioclipse Scripting Language examples that Jonathan and I compiled.

All Bacting scripts will be backwards compatible with Bioclipse. If you want to install Bioclipse and see its wonderful UX in actions, download Bioclipse 2.6.2 here.

Using SNAPSHOT versions

You may need to occassionally delete the modules cached by Groovy, by doing something like, to remove earlier SNAPSHOT versions:

\rm -Rf ~/.groovy/grapes/net.bioclipse.managers/

Copyright and authors

All code in the /bioclipse/ folder contains Bioclipse 2 code and the headers of the individual source code files describe who contributed to that code of that class, but unfortunately this code ownership is not always clear. I refer to the various Bioclipse code repositories for the git history for more information.

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