[Biopython-dev] Structure and LDNe

Peter biopython at maubp.freeserve.co.uk
Fri Jan 9 07:59:00 EST 2009


On Thu, Jan 8, 2009 at 10:24 PM, Jason Eshleman <jae at lmi.net> wrote:
> Greetings all,
>
> Presently, the code I have for dealing with STRUCTURE is similar to the code
> for interacting with Clustal, in that it does not modify any of the STRUCTURE
> source code by merely initiates the compiled executable.

Biopython has code for interacting with lots of command line tools,
and this neatly avoids any copyright/licence questions about being a
derived work.

> Initially, I have used my code in place of their Java front end as it allows
> for more control of the run-time variables for successive runs with varying
> run parameters.  At some point, I'd like to get it to interface more
> directly with the STRUCTURE code to be able to pipe results directly to
> python for parsing rather than working with the STRUCTURE text output but
> that's a ways off still.

I'm not quite clear what you have in mind, but this would probably
need a little more thought from the legal perspective.  If STRUCTURE
provides an API with header files you can compile against, that should
be OK (but I am not a lawyer).  Note that do this within Biopython
would then mean adding another build time dependency, which would need
to be justified in terms of the benefits it brings.

Peter


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