I think we can start thinking in redesigning the structure module, getting rid of the current design, which is tightly coupled to PDB representation.
Some of the details would include: - Separating I/O from the model (i.e. creating specialized I/O classes PDBReadr/Writer, MOL2Reader/Writer, etc). - redefining terms like group, molecule, bond, and model. As well as redistributing attributes among them. (e.g. a model is an entity that has properties, not just a list of chains. Also an atom has more properties like partial charge. a carbon atom can be SP2 or SP3). If the idea is accepted in principle, we can start discuss it here or off-list. Amr Best Regards, Amr AL-HOSSARY Amr Ali AL-HOSSARY | Ph.D. Student | International PhD program in Computational Biology and Bioinformatics | School of Computer Engineering | Nanyang Technological University | Singapore (GMT+8) | Email: [email protected] | Mobile: +65-94572816 -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Eric Talevich Sent: Monday, February 03, 2014 3:14 PM To: [email protected] Subject: [Biojava-l] Google Summer of Code 2014 - Call for project ideas Hi everyone, Google Summer of Code is on again for 2014, and the Open Bioinformatics Foundation (OBF) is once again applying as a mentoring organization. Participating in GSoC as an organization is very competitive, and we will need your help in gathering a good set of ideas and potential mentors for BioJava's role in GSoC this year. If you have an idea for a Summer of Code project, please post your idea here on the BioJava mailing list for discussion and start an outline on the wiki page: http://biojava.org/wiki/Google_Summer_of_Code We also welcome ideas that fit with OBF's mission but are not part of a single Bio* project, or span multiple projects -- these ideas can be posted on the OBF wiki and discussed on the OBF mailing list: http://www.open-bio.org/wiki/Google_Summer_of_Code#Project_ideas http://lists.open-bio.org/mailman/listinfo/open-bio-l Here's to another fun and productive Summer of Code! Cheers, Eric & Raoul _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
