Merge pull request #1217 from RosettaCommons/aleaverfay/fix_cloud_pdb_output_in_matcher_postXRW
Aleaverfay/fix cloud pdb output in matcher post xrw
Fixing a bug from the ChemXRW that broke cloud PDB writing.
This patch activats the "skip_connect_info" in the StructFileRepOptions
object in the CloudPDBWriter's call to dump_pdb_residue helping to
avoid assertion failures stemming from non-polymeric inter-residue
connections being seen as asymmetric (residue i's connection to residue
j isn't mirrored in residue j -- because residue j isn't being output).
It's not clear that dump_pdb_residue can function properly without
the skip_connect_info flag. This should be looked at more closely.
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Merge pull request #1219 from RosettaCommons/yhsia/fixRestrictNativeResiduesOperation
Invert option default not set to "off" when the invert option is not directly set to false. If no invert option is set, the code reads random memory and performs the invert function.
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Merge pull request #1218 from RosettaCommons/fixStoreCompoundTaskMover
Clears the cache at the end of the nstruct so that the selected residues do not carry over to the next nstruct.
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Merge pull request #1215 from RosettaCommons/aleaverfay/fix_matcher_chi_building_bug2
One-line fix to ProteinUpstreamBuilder::recover_hits to output NCAAs with discontiguous chis
This is the second half to the bug fix merged into master with PR #1085;
in that PR, ProteinUpstreamBuilder::build was updated to multiply the
pre_chitip_transform HomogeneousTransform when building the chitip
frame while actually building hits. There is a second place in the code,
however, where the geometries of the upstream residues are computed, and
this second location was not updated to use the new transforms.
This fixes the geometry of the NCAA in the test case given to me
by Sophia Tan. Thanks Sophia!
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Merge pull request #1206 from RosettaCommons/vmullig/phi_selector
Create a ResidueSelector for selecting alpha-amino acids in the positive- or negative-phi region of Ramachandran space
This is convenient for mixed D/L design: it's nice to be able to require that residues in the positive-phi region are only allowed to be D-amino acids, and that residues in the negative-phi region are only allowed to be L-amino acids. This can also be used for conventional design to ensure that positive-phi positions are only glycine, and negative-phi positions are never glycine. Or this can be used in conjunction with the aa_composition score term to limit the number of D-amino acids in the negative-phi region or L-amino acids in the positive-phi region. Or it can be used just to count residues in the positive-phi region as part of the process of filtering out bad designs.
So it should be useful.
@dabaker, @gbhardwaj, @hssnzdh2
Tasks:
Add the ResidueSelector using Jared's nifty scripts.
Actually write the apply() function.
Write the parse_my_tag() function.
ResidueSelectors require XSD stuff, don't they?
Additional checks for termini and whatnot.
Unit test.
Documentation.
Beauty.
Unit tests all pass on my machine. No integration test or other test changes expected. Merging.
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Merge pull request #1213 from RosettaCommons/dimaio/PolymerBondedContainer_fixes
Small bugfixes for cart_bonded/PolymerBondedEnergyContainer.
Previously there was special logic in the container specifically for cart_bonded. Instead, the special case is handled by cart_bonded (moving some logic to compute intrares energies/derivatives), and the energy container behaves more reasonably. In doing so, we fix a bug where cart_bonded was not getting scored for some terminal residues.
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Merge pull request #1214 from RosettaCommons/vmullig/amberperiodic
Add the AmberPeriodicFunc to the FuncFactory.
The AmberPeriodicFunc is in the Rosetta documentation and is well-covered by unit tests, but is apparently inaccessible to the constraint file parser. This rectifies this.
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Merge pull request #1212 from RosettaCommons/vmullig/split_spacegroup
Splitting the giant get_symmops() function in spacegroups.cc for more efficient compilation.
The 32-bit Linux BOINC build was running out of memory and crashing when compiling this function.
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Merge pull request #1209 from RosettaCommons/jadolfbr/sugars/enable_n_omegas
Glycan Relax Updates
Updates
======
- This PR will enable omega2 sampling for the ASN-glycan linkage and enable n-omega sampling for all other glycan linkages.
- The BBDihedralSamplerMover now can take any number of BBSamplers for any torsion and sample on these. It can also now use the MoveMap's TorsionID functionality to set specific BB torsions. This makes GlycanRelaxMover sample evenly on the glycan residues and removes biases where we were over-sampling omega torsion angles for those glycan linkages where this angle is present.
- Bug Fix for SugarBBSampler where phi dihedral was not being sampled if omega was present.
Integration Tests
============
Integration Test changes expected for glycan_relax and simple_glycosylation. Also expected for those using out:level debug as I added a debug tracer output to RandomMovers apply if the TR.Debug is visible.
Code Templates
============
Make it so that templates created using the code_templates framework are compilable after generation, which was suggested during WinterRosettaCon 2016 and is very cool to be able to do.
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Merge pull request #1207 from RosettaCommons/dougrenfrew/uniformrigidbodymover_creation_registration
Adding UniformRigidBodyMover to list of registered movers
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Merge pull request #1201 from RosettaCommons/jadolfbr/in_file_seed
EnsembleJobInputter
Merges a JD2 Job Inputter that is specifically for working with an ensemble of input structures. Simple. Fun to code. Two modes. Seed Ensemble and Grid Ensemble.
Seed Ensemble
============
Randomly choose the starting files using the list of structures given by -s and -l
-jd2:seed_ensemble_weights (RealVector)
- Will give weights to the input PDBs and trigger seed_ensemble mode and the JI. We then use the weighted sampler to choose the input pdb for each nstruct. The weights could be the size of the cluster, the energy, that you like some structure better, etc. Must match number of inputs.
-jd2:seed_ensemble_weight_file (File)
- A file specifying weights to use for each input structure. Enables seed_ensemble mode and the JI. Two columns. basename with extension (or relative path or full path), weight. Any not given in file will be set to 0 by default. Can give a line that is [ALL weight] to set all input pdbs to a given weight. Used for example, to upweight a specific structure:
```
#name weight
ALL 1
awesome_model.pdb 3
```
-jd2:seed_ensemble (Bool)
- Enable seed ensemble mode, but simply randomly choose the input pdb for each nstruct. For seed ensemble mode, the number of input pdbs can be larger than nstruct.
Grid Ensemble
===========
Use the input files given in -s and -l and nstruct to cover a grid.
-in:jd2:grid_ensemble (Bool)
- Will enable the basic component of the JI. Here, instead of sampling nstruct for every input pdb, we only sample nstruct no matter the number of input PDBs (with nstruct split as evenly as possible over the input PDBs).
To Do
=====
- [x] Add Test
- [x] Update Documentation
- [x] Add more documentation to header
Etc:
===
- Implemented as a Subclass of PDBJI - Does not work with silent files.
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