[chimera-dev] Publishing an extension

Sébastien Cuendet sebastien.cuendet at gmail.com
Wed Jun 24 07:59:52 PDT 2009


At the Molecular Modelling Group (http://www.molecular-modelling.ch/)  
in Lausanne, Switzerland, we've developed a Chimera extension with 3  
    * GUI for CHARMM setups: inspect, clean up and prepare molecules  
for use with CHARMM
    * GUI for the EADock docking software: setup a receptor, a ligand,  
choose the docking parameters that suit your needs, and run your docking
    * access to the S3DB database, a database containing more than 250  
manually curated complexes

The extension is reaching the end of the test phase and we plan on  
releasing it soon. However, coming closer to the release day brought  
up several questions:

1) We needed a slightly modified version of the writeMol2 function (in  
writeMol2.py), and had to include a modified version of the writeMol2  
and midas package in our extension. Of course we're not claiming any  
intellectual property on any of those two modified files, but is it a  
problem to integrate them into our extension?

2) More or less the same situation appears for the rotamers window,  
from which we took a part to integrate it in part of our extension  
that allows a user to fix residues with missing atoms. We basically  
copied and pasted the code we needed. The problem is slightly  
different since this isn't a built-in function of Chimera, as opposed  
to writeMol2, for example. But again, is that a problem?

3) We plan to add some features to the awesome ViewDock extension that  
is already part of Chimera. However, we really only want to implement  
shortcut commands that are helpful when using EADock, but  since  
ViewDock is already so complete, it makes no sense to start from  
scratch. We see two options: either extend the ViewDock extension with  
our features, or inherit a large part of the ViewDock extension and  
customize it in our own extension. Option 1 seems possible only if the  
owner of the ViewDock extension agrees to integrate our features in  
his extension and brings up questions of supporting/updating those  
features, whereas option 2 brings up the question already mentioned  

Could someone let us know what the standard policy is to deal with  
those issues?


Sébastien Cuendet
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