Merging vmullig/cycpep into master. This tweaks GeneralizedKIC a bit, as well as fixing a problem in setting the position of atoms dependent on non-polymer connections on PDB import. (This might fix the problem with the UBQ_E2_thioester_extra_bodies and UBQ_E2_thioester_two_ubiquitins integration tests on the test server -- I'm not sure. I haven't been able to reproduce that failure.)
Unit test status: All pass except the two that have been failing (protocols:DdgFilter:test_filter_parsing and protocols:DdgFilter:test_use_filter)
Integration test status: No changed tests; two were already failing (app_exception_handling and buried_unsat_kinemage). As mentioned, the UBQ tests that fail on the test server don't fail when I run the integration tests.
Changes to be committed:
(use "git reset HEAD <file>..." to unstage)
modified: source/src/core/chemical/AtomICoor.cc
modified: source/src/core/chemical/AtomICoor.hh
modified: source/src/core/conformation/Conformation.cc
modified: source/src/protocols/generalized_kinematic_closure/GeneralizedKIC.cc
modified: source/src/protocols/generalized_kinematic_closure/util.cc