Merge pull request #256 from RosettaCommons/kalekundert/fix_integration_tests
Fix the instability in the loop_creation integration test. I decided to do this because I already spent a day figuring out how to run valgrind for my own unstable integration test, and it turned out to be a really easy process. So I thought I might as well fix the other unstable test while I still remembered how.
The problem in this case was related to the prevent_nonloop_modifications_ variable being declared in the parent class and the child class, but only defined in the child class. I fixed this by removing the child class declaration and forcing everything through the parent class.
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Merge pull request #245 from RosettaCommons/vmullig/for_chris
This creates a new mover, BundleGridSampler, which samples Crick parameter space in user-defined ranges and returns the parameters corresponding to the lowest-energy pose, along with that low-energy pose. The mover can also dump out PDB files for all structures sampled.
Tasks completed:
Update protocols_c.5.src.settings and the MoverCreators/MoverRegistrators init files.
Create the BundleGridSampler mover.
Add RosettaScripts support. Let the mover parse all options accessible to the MakeBundle mover (using parsing code that dwells in that mover), and additionally let the user specify custom parameter ranges.
Add PDB output support for all states sampled.
Add a sample low / sample high option, and let the user specify a custom scorefunction.
Let the user specify a custom mover for the grid sampler to apply at each grid point before final scoring.
Possibly add warnings for unreasonably high numbers of samples?
Select lowest-energy structure sampled, and return this as the output pose.
Documentation.
Integration test.
I expect very minor cosmetic changes to the helical_bundle, helical_bundle_nonideal, and perturb_helical_bundle integration tests (I think one line of output, related to delta_t, will now occur slightly later or earlier in sequence than it did before). The newly-added bundlegridsampler and bundlegridsampler_design integration tests should also fail, because they're new.
Note that the KIC_with_fragments integration test has been failing consistently, and the Linux PyRosetta unit tests have intermittently been failing with memory errors (all independent of this merge). I didn't wait for the Windows PyRosetta build test since it completed successfully on a slightly earlier version of this branch, and since there is a major backlog with that test.
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Fix an uninitialized variable in the loop modeling code.
I think this bug has been responsible for the instabilities in the
KIC_with_fragments test, but it shouldn't have had any real effect on
loop modeling performance.
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Merge pull request #251 from RosettaCommons/kalekundert/fix_integration_tests
Fix three integration tests that I accidentally broke a while back: favor_native_residue, hotspot_graft, and place_simultaneously. Three tests remain broken: antibody_graft, pocket_suggest_targets, and mpframework_syndock. The former two were broken before my original commit and the latter one was broken after, so I won't be doing anything about those.
The instabilities in the KIC_with_fragments test are also probably related to my original commit, since the instabilities started around then and my commit made a lot of changes to that code. So my next goal will be to track down that bug.
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Merge pull request #249 from RosettaCommons/rhiju/inner_score_delta_clarification
renaming inner_score_temperature_delta to inner_score_delta_over_tempera...
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Merge pull request #248 from RosettaCommons/daslab
Daslab -- proper docking in stepwise modeling
all tests confirmed OK (except windows_pyrosetta_build -- seems to be a big backlog in that build queue...)
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Merge pull request #246 from RosettaCommons/rhiju/fix_default_for_sampler_perform_phosphate_pack
Rhiju/fix default for sampler perform phosphate pack
setting allow_internal_local_moves (erraser-style moves) to true in step...
test changes are in 3 expected stepwise tests, and rest are 'usual suspects'.
windows pyrosetta build not queued yet, but I'll keep an eye on master after this merge.
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Merge pull request #247 from RosettaCommons/rhiju/allow_internal_local_moves_true
setting allow_internal_local_moves (erraser-style moves) to true in step...
test changes are acceptable (and minimal). windows pyrosetta build not queued yet, but I'll keep an eye on master after this merge.
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