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Revisions №61052

branch: master 「№61052」
Commited by: Vikram K. Mulligan
GitHub commit link: 「f82d28a98d8d025c」 「№4197」
Difference from previous tested commit:  code diff
Commit date: 2019-11-22 14:14:54
linux.clang linux.gcc linux.srlz mac.clang
PyRosetta4.notebook gcc-9.gcc.python37.PyRosetta4.unit linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck alpine.gcc.build.debug gcc-9.gcc.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL mac.clang.python36.build.debug build.header build.levels ninja graphics static linux.ui mac.ui build.xcode beautification code_quality.clang_analysis code_quality.clang_tidy serialization integration.mpi integration.release_debug integration.tensorflow integration.thread integration performance profile release.source scientific.cofactor_binding_sites scientific.simple_cycpep_predict.debug scientific.simple_cycpep_predict linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release util.apps

Merge pull request #4197 from RosettaCommons/vmullig/add_options_to_simple_cycpep_predict Adding a few features to simple_cycpep_predict and helical_bundle_predict. This pull request adds: - The ability to automatically calculate RMSD to the lowest-energy structure encountered to `simple_cycpep_predict` and `helical_bundle_predict`. - The ability to calculate various metrics related to solubility and membrane permeability for each sample, and to compute the Boltzmann-weighted ensemble average for these metrics. - Support for sampling bond lengths and angles. I'll flesh this out more as I go along. <u>TODO:</u> - [x] Pull request #4216 should be merged before this one. - ~~Pull request #4220 should be merged before this one.~~ --> Merged into this one and closed that one, since this one fixes some bugs that persist in that one. - [x] Add the options. - [x] Register them as relevant to `simple_cycpep_predict`. - [x] Register them as relevant to `helical_bundle_predict`. - [x] Write the ensemble lowest-energy RMSD calculator. - [x] Output. - [x] Integration test. - [x] Add to scientific test. - [x] Document new flag. - [x] Write the ensemble SASA calculator. - [x] Total, polar, and hydrophobic SASA. - [x] Compute ensemble average. - [x] Output. - [x] Integration test. - [x] Add to scientific test. - [x] Document new flag. - [x] Add support for sampling bond lengths and angles. - [x] Add options. - [ ] Document new options. - [x] Add GenKIC bond angle and bond length perturbers. - [ ] Document new GenKIC features. - [x] Register with `simple_cycpep_predict` (but _not_ `helical_bundle_predict`). - [x] Have the options do something. - [x] Integration test. - [x] Check scientific test with new features: queued here (https://b3.graylab.jhu.edu/revision/commits/14270). - [x] Beautify.