Make dssp info programmatically available

[Greg Couch]

I'm looking for the sheets, the strands in the sheets, the residues in the strands, and the pairwise relationship of the strands (parallel or not). So, dssp's ladder summary and the sheet membership in the residue summary. Having the helix summary and residue summary's secondary structure type would let me fill in the helix type, so that would be good too. The turn information is not used by the PDB right now, so that can be skipped.

[pett]

Thought about working on this and just wanted to verify that this is what you actually want. You are aware that doing this will change the secondary structure assignments from whatever they currently are to whatever dssp thinks they should be?

[Greg Couch]

I consider it a stop gap measure until the information is actually retained. And it will only be done if the user requests it. Of course, it would be better if were it possible to get the information without altering the secondary structure.

[pett]

You will have to do the same thing that MatchMaker does: remember atoms.ss_types and .ss_ids before calling dssp, and restore them afterwards.

[pett]

residues.ss_types, etc., I mean

[pett]

Added an optional argument to Structure.compute_secondary_structure(), a pointer to a CompSSInfo instance as defined in CompSS.h, and which will contain the information requested in this ticket after the call.