Merge pull request #1913 from RosettaCommons/vmullig/cycpep_align
Add a mover to align a quasi-symmetric peptide to the origin and Z-axis, for true symmetry setup
Currently I do this with some manual editing of PDB files, a script, and the minimizer, but a specialized mover could do this more easily and more efficiently. This will be a needed part of the symmetric cyclic peptide design pipeline.
Tasks:
- [x] Create the mover with Jared's code template scripts.
- [x] Register it.
- [x] Add options to parse_my_tag() for specifying symmetry.
- [x] XSD information for these.
- [x] Add length check and symmetry check (with the CycpepSymmetryFilter) to apply() function.
- [x] Add origin alignment to apply() function.
- [x] Add Z-axis alignment to apply() function.
- [x] Ensure above handles non-protein residues properly (ignores them).
- [x] Allow auto-detection of symmetry.
- [x] In parse_my_tag().
- [x] XSD information.
- [x] In apply() function.
- [x] Add option to delete all but a selected repeat:
- [x] To parse_my_tag().
- [x] XSD information.
- [x] To apply() function.
- [x] Ensure this deletes non-protein residues like TBMB. (Symmetric versions can be added back after symmetry is set up, using the ThreefoldCrosslinkerMover.)
- [x] Document this deletion of non-protein residues.
- [x] Unit tests.
- [x] Integration test.
- [x] Beauty.
- [x] Documentation.
Merge pull request #1899 from RosettaCommons/dougrenfrew/fix_mrl
This PR should fix a bug in the MakeRotLib protocol that caused the omega and epsilon torsion to not minimize correctly in alpha-/beta-peptides, and caused peptoids to minimize the wrong dihedrals.
Merge pull request #1873 from RosettaCommons/aleaverfay/fix_abscript_xsd
Ok, AbscriptMover looks like it ought to be able to read multiple
"Fragments" subtags, and not just a single one, and that "Stage" and
"Fragments" subtags can be interleaved. This PR updates the XSD to reflect that.
Merge pull request #1811 from RosettaCommons/everyday847/devel_init_like_your_life_depended_on_it
Use devel::init in apps
If you're in an app, you want to call devel::init to go through the whole cascade of initializations.
If you only call protocols::init or, don't even say it, core::init, weird stuff can happen, especially if you try to use any job distributor.
We need to fix this issue before merging XRW stuff because it affects integration tests in a hardware-dependent manner. It's also the cause of some ubsan/addsan issues.
resolves #1375
Merge pull request #1621 from RosettaCommons/vmullig/fix_icc16
Fix additional issues to allow compilation with icc 16.0.2.
This doesn't fix everything, yet, but gets us closer to being able to compile with icc. No test changes expected.
Merge pull request #1775 from RosettaCommons/rhiju/declare_chemical_bond_at_loop_cutpoints
declare chemical bond when CUTPOINT_UPPER and CUTPOINT_LOWER are assigned at a chainbreak
Only tests that change are ones that failed before (cppcheck; thermal_sampler in debug_release), and bridge_chains gets a much lower energy due to absence of repulsion between the atoms bonded across the chainbreak.
Merge pull request #1690 from RosettaCommons/everyday847/dont_make_bad_promises
You will see all those EnergyMethod integration test changes, just in the other direction. Do not be alarmed.
Merge pull request #1671 from RosettaCommons/vmullig/simple_cycpep_predict_features
Adding needed features to simple_cycpep_predict application
Tasks:
- Add options for torsion/angle/length space relaxation with:
- Flexible bond angles.
- Flexible bond angles and bond lengths.
- Add option for full Cartesian-space relaxation.
- Have the above options actually trigger appropriate rounds of relaxation.
- Bond angles.
- Bond angles + bond lengths.
- Cartesian-space relaxation.
- Integration tests for the above.
- Add output of number of cis-peptide bonds.
- Plus unit test for sorting by cis-peptide bond count.
- Add hard energy cutoff for output.
- Add to one integration test.
- Turn cis-pro sampling on by default. (Do this last, after confirming that above changes do not change existing behaviour of integration tests.)
- Disable cis-pro sampling explicitly in existing integration tests that did not sample cis-pro before.
- Documentation.
- Beauty.
Merge pull request #1652 from RosettaCommons/vmullig/chunli_metal_issue
Fixing crash with -auto_setup_metals when poses were resized
Correcting issue that lead to crashes whenever -auto_setup_metals was used with a pose that was subsequently resized. Since NamedAtomPairConstraint and NamedAngleConstraint didn't implement a remap_resid() function, the parent class (AtomPairConstraint or AngleConstraint) function was called, resulting in the NamedAtomPairConstraint being replaced with an AtomPairConstraint, or the NamedAngleConstraint being replaced with an AngleConstraint, with atom IDs set to zero.