Broaden PyRosetta conda package dependency version requirements for NumPy (#496)

• Summary
• icc.icc.build.debug

Add the deterministic_flag option to the ProteinMPNNProbabilitiesMetric SimpleMetric (#485) This PR adds the `deterministic_flag` option to the `ProteinMPNNProbabilitiesMetric` PerResidueProbabilitiesMetric. After some evidence provided in #429, the `ProteinMPNNMover` already has the `deterministic_flag` option set to `false` by default, and therefore due to Torch randomness the `ProteinMPNNProbabilitiesMetric` can return non-deterministic PSSM tables, even with the `-run:constant_seed 1` Rosetta option enabled. This PR just adds some control of the `ProteinMPNNMover` from the `ProteinMPNNProbabilitiesMetric` to enable deterministic mode when calculating per-residue ProteinMPNN probabilities.

• Summary
• PyRosetta.unit 「1」
• icc.icc.build.debug
• performance 「1」
• ubuntu.clang.python312.release.PyRosetta.MinSizeRel
• ubuntu.clang.python37.release.PyRosetta.MinSizeRel
• ubuntu.clang.cxx11thread.serialization.python311.release.PyRosetta.Release
• ubuntu.clang.python312.release.PyRosetta.Release
• ubuntu.clang.cxx11thread.serialization.python312.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python313.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python38.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python312.release.rosetta.conda.release

Add option to control intermediate dumping in BackrubProtocol (#372) Especially with XML (where the Backrub protocol is part of a more extensive protocol), you don't necessarily want an unconditional dumping of the last & low results from the Backrub stage. This commit adds an XML option which will allow the dumping of the poses (old behavior), but turns it off by default. This only changes XML usage -- I didn't change how the backrub application behaves. Changes to the backrub_interface_ddG integration test is expected.

• Summary
• ubuntu.clang.python311.release.PyRosetta.MinSizeRel
• ubuntu.clang.cxx11thread.serialization.python310.release.PyRosetta.Release
• ubuntu.clang.cxx11thread.serialization.python38.release.PyRosetta.Release
• ubuntu.clang.cxx11thread.serialization.python39.release.PyRosetta.Release
• ubuntu.clang.python311.release.PyRosetta.Release
• ubuntu.clang.python312.release.PyRosetta.Release
• ubuntu.clang.python39.release.PyRosetta.Release

Add support for various package versions in pyrosetta.distributed #434 Merging changes originated in #434 which was authored by @klimaj Co-authored-by: Jason C. Klima <klimaj@uw.edu>

• Summary

Fixes for failing tests in main (#426) Address some currently failing tests: * Update the documentation repo with autogenerated data (and update the submodule SHA1) * Fix clang tidy issues from the AMRLD code * Make log file parsing in peptide_pnear_vs_ic50 scientific test more robust * Fix compilation issues with Clang 19 (Issue #404)

• Summary
• PyRosetta.unit
• ubuntu.clang.cxx11thread.serialization.python38.release.PyRosetta.conda.Release
• ubuntu.clang.python312.scripts.pyrosetta

Add cmath includes (#277) `std::abs(Real)` needs the real-valued version of std::abs() function, which is found in the cmath header. (Versus the integer-valued versions, which can also be found in the cstdlib header.) We were missing those imports in a few locations, which was causing my compiler to complain.

• Summary
• PyRosetta.unit
• ubuntu.clang.cxx11thread.serialization.python38.release.PyRosetta.conda.Release

Rosetta automated reaction-based ligand design (RosettaAMRLD) (#403) This is code for the new application RosettaAMRLD. The framework is based on the Monte Carlo Drug Design branch (PR #282) by Rocco Moretti (@roccomoretti) The algorithm use Monte Carlo Metropolis methods and similarity-guided sampling to iteratively optimize molecules within a combinatorial library. The changes are primarily new Filters and Chemistries added to `src/protocols/drug_design/` and modifications to the DrugDesignMover for RosettaAMRLD related functionalities and Simulated Annealing options. Other changes include: * Added a python script that plot the distribution of (RDKit) metrics (by RM) * Added an edge case handling when removing charges in RDKit utils (by RM) * Modified the recompute function in `source/src/core/pose/metrics/simple_calculators/InterfaceDeltaEnergeticsCalculator.cc` to handle multiple chains. (calculate energies between the first and second chains -> between all chains and the last chain) --------- Co-authored-by: Rocco Moretti <rmorettiase@gmail.com>

• Summary

fix Mac build on Clang-17 (#406)

• Summary

Unfolded state tlc bugfix (#336) This changes two lines that were preventing mpi rosetta from compiling. It seems that two mentions of slave_data_vector should actually be slave_tlc_vector. The comments imply that this is the case and changing the mentions enables rosetta with mpi to compile again.

• Summary

trigger clean rebuild

• Summary

fix clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug build (#392)

• Summary
• PyRosetta.unit
• ubuntu.clang.cxx11thread.serialization.python38.release.PyRosetta.Release

Rosetta Evolutionary Ligand (REvoLd) (#303) This PR aims to include the newly developed application REvoLd into Rosetta. REvoLd preprint: https://arxiv.org/abs/2404.17329 The algorithm optimizes small molecule ligands within combinatorial libraries like Enamine REAL. Most code changes are self enclosed and do not affect any functionality outside of the application. The only exception are changes to cmake compile directives for mpi which were broken. A guide on how to run REvoLd is available here: https://docs.rosettacommons.org/docs/wiki/revold Unit and integration test run locally and passed all. --------- Co-authored-by: Paul Eisenhuth <eisenhuth@informatik.uni-leipzig.de>

• Summary
• m1.clang.python311.release.PyRosetta.MinSizeRel
• m1.clang.python311.release.PyRosetta.Release

Better debugging on CIF file read in. (#356) Issue #355 indicates that errors in mmCIF parsing are not well handled. This commit attempts to fix that in two ways. The first is to add a 'from extension' fallback if the from-contents parser doesn't like it. We assume that if you're naming it xyz.pdb, you want it parsed as a PDB. The second is to print the diagnostics report for mmCIF files to the tracer -- this is what's being used to autodetect mmCIF format, so better transparency of what the failure issue is would be warranted.

• Summary

Bugfix for RosettaCM and branched glycans (#221) RosettaCM, with a branched glycan ligand, was segfaulting. In 2 locations, the "previous residue" of the given polymer entity was selected by choosing the position prior to the one in question, which is not appropriate for a branched glycan. The fix was to set a conditional for carbohydrates that uses conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue to find the previous residue.

• Summary

fix Conda release procedure (#306)

• Summary

trigger clean rebuild

• Summary
• mac.clang.cxx11thread.serialization.python310.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python311.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python312.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python313.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python38.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python39.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python310.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python311.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python312.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python313.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python38.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python39.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python312.release.rosetta.conda.release
• ubuntu.clang.cxx11thread.serialization.python312.release.rosetta.conda.release

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