Merge pull request #1569 from RosettaCommons/everyday847/handle_insertions_pdbinfo
Unit test added--note that I'm setting up the unit test so that it tests only the unit I'm interested in, i.e., how this function works on the PDBInfo. So I'm setting up a PDBInfo with the exact defect I want to repair and then repairing it. Actually inserting a residue via a call from Conformation, then repairing the result, would be an integration test!
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Merge pull request #1572 from RosettaCommons/revert-1571-sofibali/sofia_summer_work
Revert "Sofibali/sofia summer work"
This merge caused the following problems:
- The PyRosetta C001_Carbohydrates_Demo01 unit test failed to run.
- Several integration tests were complaining about the INAME line in the changed params file (a typo).
- The carbohydrates integration test failed to run.
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Merge pull request #1364 from RosettaCommons/ch.norn@gmail.com/evolution
Ch.norn@gmail.com/evolution. Contains code for simulating evolution: NucleotideMutatationMover to mutate between amino acids, but restrained by the codon table (single nucleotide mutations), and EvolutionaryDynamicsMover to accept and reject mutations, not according to the boltzmann function, but according to evolutionary dynamics.
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Merge pull request #1562 from RosettaCommons/sergey/binder
Adding release.PyRosetta4.documentation test. Refactoring rosetta release source/binary tests so they use new release API.
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Merge pull request #1567 from RosettaCommons/dougrenfrew/2-amino-3-methylamino-propanoic_acid
Adding 2-amino-3-methylamino-propanoic acid (also know as beta-methylamino-alanine, BMAA) to the NCAAs.
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Merge pull request #1563 from RosettaCommons/dougrenfrew/C-linked-glycosolation
Adding C-mannosyl tryptophan patch. TRP can now be mannosylated at the delta-carbon.
Carbohydrate integration test is expected to change.
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Merge pull request #1564 from RosettaCommons/vmullig/calc_pnear
Minor bugfix to BinTransitionData, and small tweak to PNear output in simple_cycpep_predict (MPI mode)
The BinTransitionData module was using utility_exit instead of throwing an exception, which brought down MPI jobs since it couldn't be handled by a try/catch block to kill the current job without bringing everything down. Also, PNear output was happening even if no native structure was provided.
Minor, cosmetic changes expected to MPI-mode integration test output.
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Merge pull request #1566 from RosettaCommons/dimaio/mg_cartmin_issue
Rosetta crashes when bondangles were minimized with an Mg-containing pose. The issue arises due to the input_stub logic selecting three collinear atoms to build the stub. As a quick and dirty fix, reorder the Mg atoms so this does not happen.
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Merge pull request #1557 from RosettaCommons/tlinsky/fix_bridgechains_integration
Make BridgeChains outputting pdbs off by default. Should fix integration test
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Merge pull request #1558 from RosettaCommons/vmullig/calc_pnear
Adding support for calculating PNear (funnel quality metric) to SimpleCycpepPredictApplication_MPI.
This will eliminate a manual calculation step from the SSMs that @hssnzdh2 and I want to do on Blue Gene.
Tasks:
- Add calculation.
- Add output.
- Add options for controlling Gaussian breadth (lambda) and Boltzmann temperature (kbt).
- Check integration test changes in MPI mode. (New output lines should appear.)
- Beauty.
- Documentation.
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