Minor updates to general_class code_templates (include refcount for general class hh template, fix class include hh for general class cc template.). Make no default type argument for generator - it was too easy to accidently create movers.
integration test changes expected for code_template_tests_src.
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Merge pull request #979 from RosettaCommons/vmullig/symmgly_mintests
Add unit tests for minimization of mirrored poses
Tasks:
- [x] Add unit test for symmetric glycine minimization (with the --symmetric_gly_tables flag).
- [x] Add unit test for minimization of mirrored D/L amino acid poses.
- [x] Debug p_aa_pp.
- [x] Debug dslf_fa13.
This pull request does fix a bug in minimization of D-amino acids with p_aa_pp: the derivatives for the p_aa_pp score term were not being calculated properly for D-amino acids.
The following integration tests fail. All failures are expected, due to change to p_aa_pp minimization with D-residues:
- simple_cycpep_predict
- simple_cycpep_predict_symm_gly
- d_workflow
- dcys_disulfidize
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Merge pull request #955 from RosettaCommons/vmullig/glysymm_problem
Add unit tests for glycine with the -symmetric_gly_tables option
Tasks:
- [x] Add unit tests for each of the talaris2014 terms, confirming that glycine in a given conformation scores identically to glycine in the mirror-image conformation when the flag is used.
- [x] Debug any issues with scoring.
- [x] Add unit tests confirming that L-amino acid conformations (including glycine) score identically to mirror-image D-amino acid conformations (including glycine).
- [x] Debug any issues with scoring:
- [x] yhh_planarity was not scoring D-tyrosine (fixed)
- [x] dslf_fa13 was not currently scoring D-disulfides properly.
- [x] fa_dun was not scoring terminal D-residues properly.
This corrects fa_dun scoring of D-residues at termini, dslf_fa13 scoring of D-disulfides, and dslf_fa13 scoring of mixed D/L disulfides.
All unit tests pass.
The test server is a bit backed up due to hardware outages. Testing on the Baker lab's development box ("jojo"), I see the following integration test changes:
- vancomycin: Due to corrections to fa_dun term for terminal D-residues, resulting in somewhat different packing and minimization trajectories. Structures are still reasonable, and changes are expected.
- ligand_dock_7cpa: This test often produces tiny numerical differences on repeated runs on jojo. I don't know why, but that's what I'm seeing here. There is no visible difference to the output structure, and the energy difference is in the sixth decimal point with the dihedral constraint.
- dcys_disulfidize: Expected changes. More reasonable mixed D/L disulfides are forming, now, as expected.
- d_workflow: Subtle differences, largely due to packer changes at termini, I think. This is expected, given the correction to fa_dun.
- simple_cycpep_predict_symm_gly: Expected changes due to addition of symmetrization of gly params file when the -symmetric_gly_tables option is used.
- posttranslational_mod_io: D-hydroxyproline (0AZ) in isolation (by definition, at a terminus) scores slightly differently because of the fa_dun correction to D-residue scoring at termini.
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Merge pull request #973 from RosettaCommons/rhiju/stepwise_lores_with_submotif_info
Rhiju/stepwise lores with submotif info
+ three rna tests (rna_denovo_bps, rna_denovo_bps_fixed_ends, and stepwise_lores) are expected to change due to a bug fix in closing chainbreaks in FARNA with base pair steps.
+ code_template_tests_src does not run in master (but a fix went in after these tests were queued)
+ mm_params changes -- one of those sporadic errors, presumably due to an ambiguous sort.
+ performance and profile have not run, but they appear to not be running on recent master commits.
+ unit test: CarbohydratePoseIOTests:test_sugar_modifications_from_suffix is broken -- as discussed on developer's list, this is a sporadic error.
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Merge pull request #961 from RosettaCommons/aleaverfay/manual_serialization
Merging branch aleaverfay/manual_serialization into master.
Preliminary work on bringing serialization code into master as progress toward JD3.
This branch builds on pull request #751, making several large changes to the implementation of constraints and to the way Poses can be copied.
300 some classes now have serialization routines -- basically, Pose, and everything that can be cached inside of a Pose can be serialized.
Separately, there is code in the tools repository to ensure that all classes with serialization routines serialize all of their data members.
ResidueSelectors now define an XSD to describe the format in which they may be specified in XML files.
Constraints comparison semantics have been improved, and a bug in the way ConstraintSets are cloned and remapped has been fixed. Func objects can now be compared. ConstraintSet copying should now be quite a bit faster, since the ResidueConstraints objects are more efficiently copied between ConstraintSets.
Significant integration test changes are likely the result of adding a new data member to class Residue; Residue now contains both a ResidueType const & and a ResidueTypeCOP. There were four integration test changes up to revision a06365a that were all explainable, and the only changes after that point that could have an impact on existing code was to have Residue hold this smart pointer. This will change inlining and lead to integration test trajectory changes.
Full documentation of the utility::tag::XMLSchema classes will arrive shortly.
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Merge pull request #971 from RosettaCommons/rhiju/stepwise_fixes_for_kalli
Rhiju/stepwise fixes for kalli
only tests that change are stepwise/erraser -- expected, since some post-packing 2'-OH torsions were not being copied appropriate before, but are now.
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Merge pull request #910 from RosettaCommons/jadolfbr/code_templates
Jadolfbr/code templates
This merge adds a directory in source and associated scripts for generating Rosetta classes and util files from stub-like templates. Two other scripts are added for unit tests and JD2 public and pilot applications.
It uses a simple replacement syntax with python lambda functions that should be easy to add to.
Integration tests for these scripts have been added, and each subtype is tested.
See README.md in the directory for more.
Implemented template types:
General Rosetta Class
Mover
Task Operation
Residue Selector
abstract class
util
Unit Test
Pilot/Public App
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