Merging vmullig/ncaas into master to alter the way rama handles nonstandard connections.
--Eliminated the rama_score_nonstandard_connections option. This is now the default behaviour. (That is, if a residue is connected to something that is not the i+1 or i-1 residue, or if the connection is not a traditional C->N connection, rama can still score the residue).
--Fixed a few problems with Ramachandran.cc that were causing unit tests to fail with the new behaviour.
--Added connect_map_size() method to the Residue object (useful for a quick check in Ramachandran.cc to fix one of the afore-mentioned bugs).
Unit test status: All pass (EXCEPT for DdgFilter:test_filter_parsing and DdgFilter:test_use_filter, which were failing before.)
Integration test status: 4 changed tests
--These are all expected changes, due to backbone-to-sidechain connections in which the terminal backbone residue is now scoring with rama.
--The changed tests are:
UBQ_E2_thioester_extra_bodies
UBQ_Gp_LYX-Cterm
UBQ_E2_thioester
UBQ_E2_thioester_two_ubiquitins
--Note that some of the above tests seem to be failing to run sometimes. I couldn't reproduce this on my system, but it seems to happen on the test server, and might be related to my earlier changes to the CYX residue type. I'll try to diagnose and fix this at some point in the future.
On branch master
Changes to be committed:
(use "git reset HEAD <file>..." to unstage)
new file: source/src/apps/pilot/vmullig/ncaa_notes.txt
modified: source/src/basic/options/options_rosetta.py
modified: source/src/core/conformation/Residue.hh
modified: source/src/core/scoring/Ramachandran.cc
modified: source/src/core/scoring/methods/RamachandranEnergy.cc