Merge pull request #1064 from RosettaCommons/vmullig/nicer_conect_behaviour2
XRW -- Make dumping of CONECT records default for noncanonicals/nonsolvent
This changes the default behaviour of CONECT records in PDB files, dumping them for all noncanonicals by default (the PDB standard). Unfortunately, this is another one that changes a lot of integration tests.
Details:
- [x] Turn CONECT record writing on by default.
- [x] Set default distance cutoff to 0.
- [x] Add concept of CANONICAL_AA to database.
- [x] Add concept of CANONICAL_NUCLEIC to database.
- [x] Add concept of SOLVENT to database.
- [x] Add logic to only write internal bonds if the current residue is not a CANONICAL_AA, CANONICAL_NUCLEIC, or SOLVENT.
- [x] Add logic to only write inter-residue bonds if one of the residues involved is not a CANONICAL_AA, CANONICAL_NUCLEIC, or SOLVENT.
- [x] Add option to dump <i>all</i> CONECT records if one so wishes.
- [x] Add option to prevent CONECT record dumping, if one so wishes.
- [x] Documentation.
This is part of the 2016 Chemical XRW. It should be tested and merged AFTER pull request #1060 and AFTER pull request #1066.