Merge pull request #3085 from RosettaCommons/MelanieAprahamian/HRFMSLabeling
Melanie aprahamian/hrfms labeling
Vikram K. Mulligan 6 years The ubsan and addsan failures are unrelated to Melanie's changes, and are caused by a known issue with the SIDECHAIN_CONJUGATION patch which is corrected in pull request #3090. If someone could approve that pull request, we can get that fixed in master.[list]
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Merge pull request #3075 from RosettaCommons/aleaverfay/fix_jd3_outputter_for_job_confusion
Fixing output-filename specification for silent files in JD3. Also fixing an issue with -out:path:all for score files in JD3
Vikram K. Mulligan 6 years The unit test failure is not introduced by this merge. It's a random, intermittent failure that's fixed by pull request #3090, which will hopefully be merged today.
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Merge pull request #3086 from RosettaCommons/vmullig/fix_betanov16_metals_issue
Fix issue with beta_nov16 scorefunction and -auto_setup_metals
This pull request addresses issue #3066. The problem is that when -auto_setup_metals strips off a proton from a residue that coordinates a metal, the hydroxyl torsional potential chokes because it expects that proton to be there. This adds a simple check that all the relevant atoms are, indeed, present.
Bug found independently by @senord25 and @aroy10.
Tasks:
- [x] Fix the bug.
- [x] Unit test.
- [x] Beauty.
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Merge pull request #3006 from RosettaCommons/vmullig/tweak_fit_helixparams_restype_access
Small tweak to a pilot app.
In older code, I had a bad habit of using pose.residue(i).type() instead of pose.residue_type(i). This, unfortunately, can trigger a refold, which is computationally expensive if you just want to interrogate the residue type for some information. This pull request updates a pilot app that others might be using for reference to avoid doing this.
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Merge pull request #3000 from RosettaCommons/vmullig/lariats_for_kris
Add support for isopeptide-bonded lariats to simple_cycpep_predict
This pull request adds support to `simple_cycpep_predict` for peptides in which a D/L-aspartate or D/L-glutamate side-chain is connected to the N-terminus. Requested by @deiblerk.
Tasks:
- [x] Add sidechain conjugation patch for D/L-aspartate.
- [x] Add sidechain conjugation patch for D/L-glutamate.
- [x] Add `SET_NET_FORMAL_CHARGE` patch operation.
- [x] Add flags to `simple_cycpep_predict` for specifying lariat closure.
- [x] Have them do something internally.
- [x] Add flags to `simple_cycpep_predict` for specifying sidechain isopeptide closure.
- [x] Have them do something internally.
- [x] Integration tests:
- [x] N-terminal lariat.
- [x] Debug alignment code.
- [x] C-terminal lariat.
- [x] Sidechain isopeptide bond.
- [x] Sidechain isopeptide bond - reverse direction.
- [x] Documentation.
- [x] Include note about ASX and GLX not being used in `simple_cycpep_predict`.
- [x] Beauty.
Also:
- [x] Deprecate the old carboxy sidechain-conjugation patch.
- [x] ~~Update code that called it~~ --> I don't think there was any.
- [x] Add unit tests for isopeptide bonded peptide scoring.
- [x] ~~Fix `rama`~~. --> Not necessary. Not fully compatible with NCAAs in any case, and `rama_prepro` is its replacement.
- [x] Fix `rama_prepro`.
- [x] Note: I found a little bug in rama_prepro that's also fixed in this pull request. This creates a number of minor trajectory changes in integration tests.
- [x] Remove debug output from unit test.
- [x] Update `ResidueType` and `Conformation` to allow easy, efficient updating of coordinates that depend on nonpolymeric connections (or on other atoms that depend on non polymeric connections).
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Merge pull request #3081 from RosettaCommons/vmullig/fit_jorge_structure
Adding support for fitting Crick parameters from a repeating unit defined by an input pose.
Feature needed for @jfv1812.
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Merge pull request #2876 from RosettaCommons/everyday847/protocols_3_split
More protocols.3 splitting
Integration test changes only in logfile. I'm glad PyRosetta folks are prepared to shim, and I am prepared to help them out. This just couldn't wait any longer or it would die entirely.
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Merge pull request #3023 from RosettaCommons/vmullig/add_metal_csts
Adding `metalbinding_constraint` to weights files in database that have constraints turned on
The -auto_setup_metals flag turns on the metalbinding_constraint score term in the default scorefunction, but if a user specifies a custom scorefunction (or uses Sharon's very useful SetupMetalsMover in RosettaScripts with a script-defined scorefunction), this is not on by default. To make it a bit easier for users, I think it makes sense to turn on the metalbinding_constraint term in all of the scorefunctions that are defined with *_cst.wts files in the database. (All other constraint types are on in these scorefunctions.)
Integration test changes are due to extra column in score line in tests that use the *_cst.wts files. This is exactly the expected behaviour. Merging.
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Merge pull request #3071 from RosettaCommons/vmullig/better_mc_error_message
Trying to make some error messages in the GenericMonteCarloMover more informative.
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Merge pull request #3063 from RosettaCommons/BYachnin/symmetric_SimpleThreadingMover
Make SimpleThreadingMover symmetry aware. Also adds additional user input checking.
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Include last residue of constraint chain in setup_csts method in SiteConstraint
SiteConstraint did not include last residue of constraint chain due to an off-by-one error when iterating through residues
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