Merge pull request #3846 from RosettaCommons/sergey/f Increasing default unit tests timeout if clean-clone detected

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Merge pull request #3836 from RosettaCommons/jadolfbr/fix_sm_filter This fixes the Sum option for the `SimpleMetricFilter` in parse_my_tag, which is used for `PerResidueMetrics`. It also adds output for action options to the doc XSD doc string in the `ResidueSummaryMetric`, which is a meta-metric that calculates different values for `PerResidueMetrics`. Thanks to @tjbrunette for identifying these issues!

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Merge pull request #3843 from RosettaCommons/JackMaguire/MCHBNetProfileTest Adding a profile test for Monte Carlo HBNet. Thanks for the review, @lyskov !

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Merge pull request #3837 from RosettaCommons/JWLabonte/quick_fix Integration Testing: Adding missing test flag Several of the integration tests are missing the -testing:INTEGRATION_TEST flag. This merge adds it. This will fix the 11 integration tests that I recently broke.

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updating benchmark signature file to create clean-rebuild wall with PR3825

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Merge pull request #3841 from RosettaCommons/aleaverfay/fix_force_dslf_mvr_schema Update ForceDisulfideMover's schema to cover valid residue strings ForceDisulfideMover uses core::pose::parse_resnum, which allows chain ids, but the schema previously refused anything that was a letter. This PR updates the schema to accept a comma-separated list of colon-separated refpose_enabled_residue_number_strings. HT: David Nannemann

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Merge pull request #3131 from CyrusBiotechnology/smlewis/rescue_indigo/nmer_refactor_plus_commonsmerge2 This PR merges @indigogo 's re-factored NMerSVMEnergy (currently used by Cyrus) into the Rosetta master branch, and now uses the `EnergyMethodOptions` system (courtesy of @vmullig ). This paves the way for @cbaileykellogg and myself to complete and merge #3464 (`MHCEpitopeEnergy`), which integrates nmer into the packer-compatible mhc_energy scoreterm. Integration test failures are due to writing out `EnergyMethodOptions` lists to PDB files, and are purely cosmetic. @indigogo 's description of these changes: Changes to NMerSVMEnergy scoring method and associated filter. This adds normalized score rank percentage calculation to NMerSVMEnergy. Why? Here's the problem: when using NMerSVMEnergy to predict T cell epitopes from MHC binding predictions, some MHC allele types bind more or less strongly on average. However, this is not indicative of more or less average predisposition to causing T cell activation. To correctly combine predictions across a repertoire of MHC types, we need to normalize the scores reported by different SVM models. To do this, I predicted MHC binding for 100k random 15mers from the human genome for every allele svm in the rosetta database and stored those distributions back in the database. Every time NMerSVMEnergy calculates a score, it also calculates the rank fraction of that score against the precalculated distribution; this info is retrievable from the scoring method directly, or you can pass a non-default cmdline option to switch to reporting that rank fraction as the score terms 'energy' instead of using the raw score. This allows one to properly combine the predictions of multiple alleles during deimmunization design in rosetta. Also tagging @smlewis ,

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Merge pull request #3814 from RosettaCommons/yingyue0414-patch-1 Add L-Galactopyranosyl parameters

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Merge pull request #3829 from RosettaCommons/vmullig/fix_shape_grid_water Tweak ShapeGrid so that it doesn't crash with ligands. Looks like it's pretty hard-coded for canonical amino acids. I started to generalize it but gave up. The main change here is an if statement to skip ligands.

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Merge pull request #2468 from RosettaCommons/JWLabonte/PDB_IO PDB IO: Title Section IO Following an idea/request from @cdbahl at RosettaCON 2017, I have added functionality for automatically adding a time stamp and Rosetta version number to all output `.pdb` files. The default output uses proper/standard/PDB-defined records, _e.g._: ``` HEADER 21-FEB-19 XXXX EXPDTA THEORETICAL MODEL REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 DATE OF DATA COLLECTION : 21-FEB-19 REMARK 220 REMARK 220 REMARK: MODEL GENERATED BY ROSETTA REMARK 220 VERSION 2019.04.post.dev+165.HEAD.646026d ``` This way, one will always know whence a `.pdb` came, and it will lead to better reproducibility of results. One could also easily adapt this system, using JD2 or JD3, to automatically include specific protocol information to the file. This merge will also allow input and output of `AUTHOR` records: ``` HEADER 21-FEB-19 XXXX EXPDTA THEORETICAL MODEL AUTHOR LABONTE ``` To include a list of authors, simply use the option flag `-set_pdb_author` with a comma-delimited list of names, according to the PDB format: ``` -set_pdb_author "I.M.A.JUNIOR JR.,I.HYPHENATE-MY-SURNAME,LABONTE" ``` If integration tests are running, the system automatically outputs the date as `xx-MMM-xx` and the version number as `INTEGRATION TEST` to ensure that integration tests do not fail every time from the changing date and version output. This merge also corrects some bugs in `HeaderInformation`. All unit tests pass. Almost every single integration test changes, as every `.pdb` file now has a default title section prepended. I have looked through about 10% of the >400 tests and did not find any unexpected changes. Likewise, 5 score tests are changed and 2 mpi integration tests.

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Merge pull request #3807 from RosettaCommons/JackMaguire/FastDesignScriptsInDatabase Refactored FastDesign's ability to support scorefunction-dependent relax scripts. Now KillA2019 supports score12, talaris2013, and talaris2014. Lot's of integration test changes but those are all just small FastRelax differences.

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Merge pull request #3830 from RosettaCommons/vmullig/buried_unsat_penalty_support_water Fix the burial calculator used by buried_unsatisfied_penalty so that it doesn't choke on water. The burial calculator currently assumes that all residues used to determine burial are polymeric, and runs into trouble with ligands, including water. This fixes that.

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Merge pull request #3817 from RosettaCommons/roccomoretti/cloud_multithread Move multithreaded cloud usage behind compiler directive. To enable better compilation on platforms where std::thread requires pthread, move multithreading in protocols/network/cloud.cc to behind the MULTI_THREADING directive. This also involves moving some of the code in external/include/httplib.h behind that compiler directive. The single-threading logic for protocols/network/cloud.cc has also been adjusted, such that it works without any resort to std::thread.

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Merge pull request #3819 from RosettaCommons/vmullig/fix_bg_yet_again Fixing Blue Gene compilation. Minor change to an included file's path. Might fix compilation on certain other systems, too. (Note that this is not a BG-specific change. This corrects an incorrect path; other systems were largely _robust_ to the incorrect path, but some might not be.)

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Merge pull request #3619 from RosettaCommons/smlewis/update_PDBdiagnostic_refs PDB diagnostic: update reference lists. Reformat readme per Julia's formatting (This was left open forever, merging it now so I can make a new one to update the refs again)

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Merge pull request #3812 from RosettaCommons/jkleman/benchmarks updating relax scientific tests to have 90% of values below threshold

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