Merge pull request #4948 from RosettaCommons/bfrenz/refactored-ddg-fixes
Bfrenz/refactored ddg fixes: This PR has recent fixes for the refactored version of the ddg code. They included fixes to the way in which the movemap is set up. It also resets the default values of certain options based on new findings with the debugged version. (from Brandon Frenz).
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Merge pull request #4714 from RosettaCommons/roccomoretti/rdkit_submodule2
Add RDKit as a submodule to Rosetta.
While Rosetta has a bunch of functionality for macromolecule modeling, it's lacking functionality for small molecule modeling.
The RDKit (http://rdkit.org/) is a widely-used BSD-licensed library for chemoinformatics and analysis & manipulation of small molecules. While primarily used as a Python package, RDKit has a C++ library backing. This PR adds RDKit as a submodule in the external/ directory, and hooks the C++ library into Rosetta compilation. (Such that the files will be compiled with Rosetta.)
In addition to the library, included in this PR are two classes to facilitate transformation from a Rosetta ResidueType to an RDKit molecule and back again. It also includes a SimpleMetric and a Mover which can be used to run a number of chemoinformatic measures (such as logP, TPSA, etc.) over a specified ResidueType.
Other functionality such as rotamer library generation and ligand manipulation will be added in future PRs. (This PR is one in a series to merge my drug_design branch into master.)
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Merge pull request #4993 from RosettaCommons/vmullig/fix_unit_test_werror_clang12
Fix a warning-as-error in the unit test suite, raised by clang 12
Fixing the following error raised by clang 12's warnings-as-errors:
```
./test/protocols/indexed_structure_store/utility.hh:96:21: error: loop variable 'pair' is always a copy because the range of type 'combined_range<decltype(boost::make_tuple(boost::begin(rngs), boost::begin(rngs)))>' (aka
'combined_range<tuple<ndarray::detail::StridedIterator<protocols::indexed_structure_store::ResidueEntry>, ndarray::detail::StridedIterator<protocols::indexed_structure_store::ResidueEntry>, boost::tuples::null_type,
boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type> >') does not return a reference
[-Werror,-Wrange-loop-analysis]
for ( const auto & pair : boost::combine(a, b) ) {
```
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Merge pull request #4989 from RosettaCommons/vmullig/add_beta_branched_property
Adding BETA_BRANCHED_SIDECHAIN property for amino acids.
This is important for machine learning, if one wants to learn based on amino acid properties rather than based on one-hot encodings of amino acid identities. Without this, leucine and isoleucine are identical from properties alone.
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Merge pull request #4981 from RosettaCommons/vmullig/update_clang_macos_settings
Adding -Wno-implicit-function-declaration to the Mac/clang build options.
Unfortunately, the recent update from clang 11 to clang 12 adds new warnings-as-errors that break the build of the C files in the external libraries.
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Merge pull request #4871 from RosettaCommons/dimaio/dna_phil_modes
A few general fixes for DNA.
- Enabling (plus fix a few deriv discontinuities) in Phil's dna_dihedral_* terms.
- Fix cart_bonded for DNA
- Change default of -excluded_dna_dna to true.
- Adding some utility functions (from Phil) for minimizing DNA with a zig-zag atom tree
Integration test changes are due to: a) changes to cart_bonded database (and consequent changes in summation order of cart_bonded terms); b) integration tests that print EnergyMethodOptions or HbondOptions (which have had defaults changed).
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Add a Release and Debug Windows build definition (#4975)
* Add a Release and Debug Windows build definition
* Add `windows` and `windows_debug` CMake build definitions.
* Add rules to build with MSVC (aka. cl).
* Don't double-define `NOMINMAX` in `httplib.`.
* Add a `types.hh` to use with the MSVC build.
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Make Python build scripts for Ninja work on Windows (#4962)
* Make Python build scripts for Ninja work on Windows
Issue Details:
Currently the Python build scripts that set up the Ninja build uses Linux/Mac OS specific commands/assumptions.
Fix Details:
* Explicitly run Python scripts using `sys.executable` (instead of assuming that the OS knows how to handle `.py` files).
* Handle Windows executables having a `.exe` suffix.
* Either change `git` commands, or use Python to process output instead of using other tools that don't exist on Windows.
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Lift uses of `make_shared` that cause MSVC to crash into their own functions (#4966)
Issue Details:
When `make_shared` is used via a using declaration as a default parameter value, it causes MSVC to crash (see https://developercommunity.visualstudio.com/content/problem/1170468/ice-when-using-make-shared-via-a-using-declaration.html).
Fix Details:
Move the use of `make_shared` from the default parameter value into a function, then call that function as the default parameter value.
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