branch: master 「№61352」
Commited by: Sarah Biehn
GitHub commit link: 「1b17f26a5290e07e」 「№4880」
Difference from previous tested commit:  code diff
Commit date: 2020-07-31 11:12:05

Merge pull request #4880 from RosettaCommons/sarahbiehn/hrf_bug_fix Bug fix: adding missing option_values in EnergyMethodOptions.cc

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branch: master 「№61351」
Commited by: Rocco Moretti
GitHub commit link: 「34b2a46cfee6502d」 「№4877」
Difference from previous tested commit:  code diff
Commit date: 2020-07-30 11:43:04

Merge pull request #4877 from RosettaCommons/roccomoretti/fix_master_tests Fix zeromq test and some other tests.

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branch: master 「№61350」
Commited by: Rocco Moretti
GitHub commit link: 「dfbee7af523706bc」 「№4846」
Difference from previous tested commit:  code diff
Commit date: 2020-07-27 14:55:50

Merge pull request #4846 from RosettaCommons/roccomoretti/calculator_sm Convert the CalculatorFilter to a CalculatorMetric In light of the push to move from Filters to SimpleMetrics for value calculation, this PR adds a new RealMetric, the CalculatorMetric, which can take other RealMetrics and compute a value with them. This is very similar in intent and function to the CalculatorFilter. (In fact, the CalculatorFilter was re-implemented in terms of the CalculatorMetric, using the FilterValueMetric as a bridge.) Also, because I could, you can now define the metrics being used for variables "in-line" under the CalculatorMetric tag. (The name parameter is not optional in this case.)

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branch: master 「№61349」
Commited by: Sarah Biehn
GitHub commit link: 「7dbc20d1b2d94e5f」 「№4840」
Difference from previous tested commit:  code diff
Commit date: 2020-07-27 14:31:14

Merge pull request #4840 from RosettaCommons/sarahbiehn/hrf_dynamics Rosetta script nma_relax.xml and score term hrf_dynamics

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branch: master 「№61348」
Commited by: Rocco Moretti
GitHub commit link: 「949ade4c6b4b882b」 「№4832」
Difference from previous tested commit:  code diff
Commit date: 2020-07-27 14:11:12

Merge pull request #4832 from RosettaCommons/roccomoretti/deboost De-Boostification C++11 introduced a fair number of constructs and standard library features which make pre-C++11 Boost library functionality redundant. (Primarily by elevating various Boost library features to standard library features.) On a bit of a whim, I went through the Rosetta codebase and converted a number of Boost usages to their C++11 equivalents. The hope is that be refocusing the usage on the standard library versions, the code will be easier to approach by new people. There are a few places where I didn't convert the existing usage, in part because the boost version has a feature which the std version doesn't. I tried to leave notes as to the rationale. This merge also doesn't convert unordered_map and unordered_sets, due to slight behavioral differences between them.

Vikram K. Mulligan 4 years
Rocco: looks like this merge (the de-Boostification merge) broke the header only test. It's probably just a missing #include.
Rocco Moretti 4 years
The fix has been rolled into https://github.com/RosettaCommons/main/pull/4877
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branch: master 「№61347」
Commited by: Steven Lewis
GitHub commit link: 「4756f8ab7940542c」 「№4876」
Difference from previous tested commit:  code diff
Commit date: 2020-07-24 21:46:56

Merge pull request #4876 from RosettaCommons/smlewis/remove_inappropriate_comment remove inappropriate comment

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branch: master 「№61346」
Commited by: Jared Adolf-Bryfogle
GitHub commit link: 「451a3019d88dd81d」 「№4860」
Difference from previous tested commit:  code diff
Commit date: 2020-07-23 17:50:07

Merge pull request #4860 from RosettaCommons/jadolfbr/strongt Add default constructor for StrongType to allow use in maps. Thanks to @JackMaguire for the constructor fix here! - Add default constructor to StrongType to allow use in maps - Add a const ref operator to allow more common functionality - Add decrement operators - Add note that +/- operators are implicit

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branch: master 「№61345」
Commited by: Frank DiMaio
GitHub commit link: 「49768c722bb77f26」 「№4863」
Difference from previous tested commit:  code diff
Commit date: 2020-07-23 15:09:02

Merge pull request #4863 from RosettaCommons/dimaio/denovo_bugfix Fix a bug in denovo density that arises when a fragment contains all …

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branch: master 「№61344」
Commited by: Jack Maguire
GitHub commit link: 「bdbdc16e45a0b7d4」 「№4734」
Difference from previous tested commit:  code diff
Commit date: 2020-07-21 10:51:02

Merge pull request #4734 from RosettaCommons/MentenAI/PeptideStubMover Adding Residue Labels From The PeptideStubMover

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branch: master 「№61343」
Commited by: Sergey Lyskov
GitHub commit link: 「ab8a1461ccd0c42e」 「№4857」
Difference from previous tested commit:  code diff
Commit date: 2020-07-18 18:22:46

Merge pull request #4857 from RosettaCommons/sergey/f Adding support for `extras` in scientific tests

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branch: master 「№61342」
Commited by: Jack Maguire
GitHub commit link: 「59f52f9adf470b99」 「№4853」
Difference from previous tested commit:  code diff
Commit date: 2020-07-15 21:20:59

Merge pull request #4853 from RosettaCommons/JackMaguire/HBondMetricXML Fixing HbondMetric XML Interface

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branch: master 「№61341」
Commited by: Vikram K. Mulligan
GitHub commit link: 「886e40432568875a」 「№4769」
Difference from previous tested commit:  code diff
Commit date: 2020-07-15 18:55:38

Merge pull request #4769 from RosettaCommons/vmullig/peptide_pnear_vs_ic_scitest Add a scientific test for the correlation between peptide computed PNear and experimentally-measured IC50. The rigidity of a peptide macrocycle is a determinant of binding affinity. When peptides are optimized for favourable interactions with a target, computed PNear (or DeltaG_folding) values correlate well with experimentally-measured IC50 values. This correlation has improved as the Rosetta energy function has improved, from a vague correlation with talaris2013 and talaris2014 to a pretty good correlation that actually predicts rank order with ref2015. (This is likely due to the practice of training against physics-based fluid simulations used for ref2015.) It would be good to ensure that this trend continues for future versions of the energy function, so I'm adding a scientific test.

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branch: master 「№61340」
Commited by: Vikram K. Mulligan
GitHub commit link: 「6a9ffca35846c858」 「№4847」
Difference from previous tested commit:  code diff
Commit date: 2020-07-15 15:45:10

Merge pull request #4847 from RosettaCommons/vmullig/fix_clang_tidy_une_fois_de_plus Fix clang-tidy tests. A few more little issues have crept in. One, the failure to mark AddResidueCouplingConstraint::clone() as virtual or override, probably really is a minor bug.

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branch: master 「№61339」
Commited by: Theodore Fobe
GitHub commit link: 「b90fa2e009b74e12」 「№4790」
Difference from previous tested commit:  code diff
Commit date: 2020-07-15 12:18:59

Merge pull request #4790 from RosettaCommons/tlfobe/add_atoms_flag Adding `-add_atom_types` flag

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branch: master 「№61338」
Commited by: Sergey Lyskov
GitHub commit link: 「43e678f19df4de04」 「№4843」
Difference from previous tested commit:  code diff
Commit date: 2020-07-12 23:53:52

Merge pull request #4843 from RosettaCommons/benchmark - fixing scientific tests Python environment deployment on Mac - fixing Symmetry tutorial - updating unit tests timeout for core:ContactOrderEnergy_Tests and core:RotamerSetsTests test suites

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branch: master 「№61337」
Commited by: Rocco Moretti
GitHub commit link: 「6c72cc81148950c3」 「№4834」
Difference from previous tested commit:  code diff
Commit date: 2020-07-11 12:01:16

Merge pull request #4834 from RosettaCommons/roccomoretti/iosfwd Convert stream header usage to iosfwd As the templated stream headers can be rather bulky, the C++ standard library provides an iosfwd header to forward declare many of the classes & objects which are provided by them. By using the iosfwd header instead of something like iostream in the hh files, we can possibly simplify & speed up compiles, by not forcing the compiler to include/compile the stream headers when they're not needed. Most of this was an automated replacement of includes in header files, followed by a "will it compile" fixup. There were some movement of functions to cc files, and some conversions of izstream and ozstream to plain std::istream and std::ostream in function signatures. (You can pass an ozstream to a std::ostream reference.)

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