Bioperl: 3D biomolecular structure handling for Bioperl

[Eser Ayanoglu]

We had a meeting recently about revisiting the Bio::Struct module issue
about handling 3D molecular structures, as part of the Bioperl project. 
This matter was discussed several years ago (1995-96) in some detail. 
Because of new developments, software availability, and possible changes
in our approaches, we wanted to open the issue to your ideas and
suggestions.  Among others, we would especially like to hear your comments
on the following areas: 


 - In what sort of program would you use such a module?
 - How would you want to access the data, and what methods should be
    available?

Responses from this message will be employed to create a requirements
specification for uses of 3D macromolecular structural information. Such
requirements will aid the design of 3D structure modules within the
Bioperl project.

The preliminary page has been set up and an Initial Requirements List was
prepared primarily by one of us (SteveC) at:

http://bio.perl.org/Projects/Structure/requirements.html

to further compile such requirements and consolidate structure-related
issues at the moment. Any other ideas/suggestions/contributions will be
appreciated.  Thank you.

Eser Ayanoglu
Steve Chervitz
Steven Brenner


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