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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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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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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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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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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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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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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