Merge pull request #2833 from RosettaCommons/jadolfbr/glycosylation_pdbinfo
Fix writing Link Records for Glycans
Glycan PDB Link Record output only worked for branch points, which is good, but not quite what we want. @BrandonFrenz Fixed this, but it was under an option that only worked for certain circumstances.
This allows proper Link output for all glycans - which allows us to manually create the glycans, de novo model them, and then output them properly. Next step is to allow the atom aliases to work with Rosetta-created ResidueTypes.
This also moves the `GlycanInfoMover` code out of the app and enables its use in RosettaScripts, which makes debugging easier.
Fixed a few GlycanTreeRelax bugs for quench mode and multiple round runs.
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Merge pull request #2752 from RosettaCommons/jadolfbr/ab_design_optimize_interface
MonteCarlo Interface
Main
===
This PR adds a new derived MonteCarlo class called `MonteCarloInterface`, located in `simple_moves`. It uses the `InterfaceAnalyzerMover` to score the interface and optimize the **dG** of the interface specified. **dG** and **total_energy** CAN be weighted, with default of dG at 1.0. This can be integrated into protocols at will. Due to the need of a specific interface, it is implemented as protocol-specific instead of within `MonteCarlo` itself.
The relevant option that can be accessed by a protocol to appropriately construct the `MonteCarloInterface` is `-mc_optimize_dG`. Options to change weights are given by `-mc_interface_weight` and `-mc_total_weight`
Etc.
===
- This has been integrated into the `RosettaAntibodyDesign` protocol (enabled using `-mc_optimize_dG`) and shows significant improvement in interface quality in resulting models. The models should still be pruned/filtered by total energy, only considering the top 10 or 25 percent of decoys.
- `RosettaAntibodyDesign` now minimizes using the neighbor list. I still don't know why this is not the default across Rosetta. Not using it is a pathology.
- Small bug fix in RAbD to only add atom-pair constraints by default if using docking. Otherwise, they should be turned off.
- Change the way cluster cutoffs work in RaBD to now be gene and cluster specific.
Unit Tests
=======
Add decently comprehensive tests for MonteCarlo(!!!) And MonteCarloInterface
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Merge pull request #2882 from RosettaCommons/aleaverfay/fix_BuriedUnsatFilter2_copy_ctor
Aleaverfay/fix buried unsat filter2 copy ctor
The homodimer_fnd_ref2015_memb and ppi_v3_suiteA integration tests have been failing in master for quite a while now, and it's only due to this copy constructor being incorrectly written. This integration test was broken with PR #2411 and remained broken quite long after that PR was merged to master. Trapping the bug in GDB very quickly illuminated the problem -- this should have been done much sooner.
Also altering the command file in the homodimer_fnd_ref2015_memb integration test so that the Tracers don't pollute the terminal when you're running it locally.
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Merge pull request #2886 from RosettaCommons/revert-2883-vmullig/rotamer_read_refactor
Revert "Incremental merge of fix to rotamer scoring bug identified by Adam."
Sorry about that. The fix to the Intel build in the PR that I just merged broke the gcc build. Reverting until I can fix.
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Merge pull request #2883 from RosettaCommons/vmullig/rotamer_read_refactor
Incremental merge of fix to rotamer scoring bug idenfied by Adam.
This merge should change nothing about current functionality, and does not itself fix the bug identified by @atom-moyer. Internally, it separates rotamer library reading into a parse step and a configure rotamer library step. This will make it easier for me to add correction steps in between.
Vikram K. Mulligan 7 years This broke everything. Am reverting. Apologies![list]
Vikram K. Mulligan 7 years @Sergey -- is there any way to cancel tests for this revision to master? I have reverted it.[list]
Vikram K. Mulligan 7 years (Though it is satisfying to note that, despite breaking almost everything else, the linux.icc.build.debug test passes. The icc build still works! :P)
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Merge pull request #2875 from RosettaCommons/vmullig/nmethyl_update
Updates to N-methyl amino acids
After adding support for spinny N-methyls, the rotamer libraries for N-methyl amino acids need some updates. I plan to merge this after pull request #2855, since that will affect this.
Tasks:
- [x] Update TRP N-methyl rotamer library in database with new version from Tim.
- [x] Update other N-mehtyl rotamer libraries in Git LFS repository with new versions from Tim.
- [x] Update N-methyl atom types and charges:
```
From Tim:
ATOM N Nbb NH1 -0.6046255 0.000 ---> ATOM N Npro NXX -0.7438 0.000
The partial charges should be:
N : -0.7438
CN : -0.2352
1HN : 0.1920
2HN : 0.1920
3HN : 0.1920
```
@twcraven
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Merge pull request #2869 from RosettaCommons/roccomoretti/case_sensitive_filename_test
Add a test to check for case sensitive filenames in the repository.
This PR adds an integration test which should throw up an error (even on Linux) if a commit in the `main` repository accidentally contains two files which are only distinguished by case.
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Merge pull request #2868 from RosettaCommons/vmullig/oligourea_design_fix
Attempting to fix failing integration test.
I had changed the way that you specify oligourea residues but had forgotten to update the test.
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Merge pull request #2799 from RosettaCommons/rfalford12/serlialize-MathMatrix
Adding Serialization functions for MathMatrix: Added MathMatrix.srlz.hh and MathMatrix.srlz.cc to serialize the MathMatrix class
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