[chimera-dev] Publishing an extension

Eric Pettersen pett at cgl.ucsf.edu
Mon Jun 29 18:04:00 PDT 2009

Hi Sébastien,
	I made mods to writeMol2() (and the Midas module write()) so that you  
no longer need to include those modules with your extension (details  
sent separately).  With your extension no longer including entire  
Chimera modules, the small parts of the Rotamers interface that you  
copied and changed for you use we don't believe constitute  
"distributing the Software" as far as the license is concerned and  
therefore you can distribute your extension without any explicit  
permission from us.  Basically basing your own code on an example from  
the Chimera source is okay, given that we're not talking about the  
better part of entire modules -- which would be a gray area.


On Jun 24, 2009, at 10:40 PM, Eric Pettersen wrote:

> Hi Sébastien,
> 	Your extension will be really useful to a lot of people.  Thanks  
> for developing it!
> 	As for the question about distributing the extension:  if the  
> extension contained only code you'd written yourself (that possibly  
> called Chimera functions) without copying Chimera modules then I'm  
> certain that you could distribute it freely.  That's explicitly  
> allowed by the last sentence of section 3 of the license agreement.   
> With copies of Chimera modules included it's less clear that the  
> license allows it directly, though since extensions such as yours  
> are exactly what we're trying to encourage with Chimera (and why  
> extensibility is a basic design goal of Chimera) I am certain that  
> we will grant permission to distribute the Chimera code with your  
> extension.
> 	I'm waiting to hear back from the head of our lab (Tom Ferrin) as  
> to whether explicit permission is actually needed in this case since  
> I'm no expert in reading license legalese.  I'll let you know when I  
> hear something.
> 	  Perhaps it isn't necessary to include modified Chimera code in  
> your extension.  I wrote the WriteMol2 and Rotamers modules and  
> Conrad Huang in our lab wrote ViewDock.  If you sent me the diffs to  
> the writeMol2 function I'm sure I could incorporate them (perhaps  
> activated by a keyword arg if the changes make the Mol2 file non- 
> standard).  Same thing for the Midas module.  As for Rotamers, if  
> you let me know what part of the Rotamers interface you copied I  
> could refactor the module so that you could import that element  
> separately and avoid duplicating code.  This kind of integration has  
> the benefit that any improvements we make to the base code flow  
> through to your extension.  I guess it has the drawback that those  
> particular functions are less "hackable" on your side. :-)
> 	Conrad has already made changes to support viewing MORDOR output (http://mondale.ucsf.edu/index_mordor.html 
> ) so I'm sure he'd be interested in investigating EADock support.
> --Eric
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> On Jun 24, 2009, at 7:59 AM, Sébastien Cuendet wrote:
>> Hi,
>> At the Molecular Modelling Group (http://www.molecular- 
>> modelling.ch/) in Lausanne, Switzerland, we've developed a Chimera  
>> extension with 3 functionalities:
>>    * 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 above.
>> Could someone let us know what the standard policy is to deal with  
>> those issues?
>> Thanks,
>> Sébastien Cuendet
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