Merge pull request #781 from RosettaCommons/vmullig/fix_tom
Trying to fix the Mac issue with BridgeChainsTests unit test.
There were two instances in the code of something along the lines of:
std::string const & test_id = ids.top();
ids.pop();
<pass test_id to a function that uses it>
This doesn't work, because in plain English, it reads as:
-- Give me a const reference to the top element of the ids stack.
-- Remove the top element of the ids stack (so that my const reference is now invalid -- references are NOT owning pointers).
-- Do something with that const reference (resulting in an error).
The simple solution was to remove the ampersand, so that I'm creating a copy of the top element before destroying it.
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Merge pull request #717 from RosettaCommons/everyday847/pna
I can't believe that I haven't merged this relatively simple PR yet! I also used it to fix mm_params.
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Merge pull request #741 from RosettaCommons/everyday847/triazolamers
HBS linkers on peptoid residues, corrected HBS and OOP coordinates, and triazolamer incorporation
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Merge pull request #761 from RosettaCommons/rfalford12/remove_illegal_using_namespace_from_mpframework
Remove bad "using namespace" statements in membrane code
it seems that all of this time, I've been breaking coding conventions by including "using namespace" at the top of headers (and sometimes the cc files). I've removed this from all offending files in core/conformation/membrane and protocols/membrane. There were also a few pilot apps affected. Hopefully, this merge will make the membrane code in better alignment with the coding conventions and reduce the number of "ambiguous namespace" errors I constantly see
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Merge pull request #766 from RosettaCommons/JWLabonte/sugars/loops
Carbohydrates: Further removal of bad assumptions preventing loop modeling
Unit test failures are the same instabilities currently plaguing master and were not caused by this change set.
CCD_loop_closure, c-term_conjugation, carbohydrates, and rings integration test changes expected due to output changes.
inverse_rotamer_remodel, and the match tests are unstable
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Merge pull request #773 from RosettaCommons/vmullig/muteall_issue
Fixing crash bug when "-mute all" option is used.
This seems to be an issue with using boost::format with the new tracer << macros when tracers are muted. The solution seems to be to enclose the tracer output in an "if(TR.visible()) {}" check. This problem was noticed in Remodel, though it might recur elsewhere. To err to the side of caution, I've also bracketed a few other cases where boost::format is used in "if(TR.visible()) {}" checks.
All unit and integration tests pass on my machine. Merging without branch testing due to test server backlog. Hopefully this is the last of the bugs currently plaguing master.
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Merge pull request #772 from RosettaCommons/revert-770-dimaio/envdep_elec
Revert "Dimaio/envdep elec"
Hi, Frank. I'm temporarily reverting this for two reasons:
- There are compile errors with this (unused variables -- check the debug build).
- Master currently has a number of issues, and we're waiting for the test server to catch up. Until we're sure that master's okay, we should avoid new merges with master (i.e. commit freeze).
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Merge pull request #770 from RosettaCommons/dimaio/envdep_elec
Fixing two issues with lk_ball:
1) remove derivative discontinuity in between water positions by replacing a min with a soft min
2) implement proper cartesian derivatives for movement of the stub atoms used to build waters
The changes from result in very small changes to scoring, and no noticeable runtime changes.
Three parameters controlling the potential are exposed through the options system/
These fixes are also implemented for using lk_ball with -nblist_autoupdate.
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