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>

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• m1.clang.cxx11thread.serialization.python312.release.PyRosetta.conda.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.

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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.

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fix Conda release procedure (#306)

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trigger clean rebuild

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• 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

Attempt to fix failing tests in main. (#299) This PR attempts to address (in part) the following failures: * code_template_tests_src integration -- Update test (and script documentation) for the new scheme * unit valgrind -- fix for Python3 * clang tidy -- update NULL/nullptr * mp_f19_tilt_angle scientific -- Make more robust, and remove unneeded (for the scientific test) repacking step added with RosettaCommons/main#5551 * protein_data_bank_diagnostic scientific -- Errors are due to running out of pseudotty handles, attempt to recognize that situation and use a fall-back approach. * glycan_structure_prediction scientific -- Adjust number of processors and runtime to run on single node. I've also made some changes to better support the GCC 11 & Rocky9 build I'm now doing locally. I've also attempted to fix the replica_docking MPI integration test timeout, but there some additional issues which mean it's not quite working correctly.

• 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

removing "defaults" Conda channel in favor of "conda-forge" (#241) Conda recently changed the licensing terms for they "defaults" channel so let use conda-forge instead.

• 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
• mac.clang.cxx11thread.serialization.python312.release.rosetta.conda.release

Fix issue related to PackerTask usage in homodimer_design. (#115) With a -pack_min_runs of 2 or greater, there's a chance that the sequence of the structure changes. This is a problem for a fixed PackerTask run, as `task_is_valid( pose )` fails if the base residue types don't match up properly. This is an issue found in Discussion #112 The fix is simple -- just use the TaskFactory which we already have lying around instead of manually generating the packer task. (The PackRotamersMover will properly re-apply the TaskFactory.) We can also make the interface of PackRotamersMover a bit nicer.

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trigger test run

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• m1.clang.cxx11thread.serialization.python313.release.PyRosetta.Release
• mac.clang.cxx11thread.serialization.python313.release.PyRosetta.Release
• ubuntu.clang.cxx11thread.serialization.python313.release.PyRosetta.Release
• m1.clang.cxx11thread.serialization.python313.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python313.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python313.release.PyRosetta.conda.Release

rename pytorch → torch extras and defines (#170)

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Update README.md, add Conda install instructions. (#151)

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add bindings for vector1<WaterBuilder> and test script (#131)

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fix PyRosetta builds (#69)

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set a prefix for util files (#57) The prefix is the argument passed via class_name. It is added in the description of --class_name.

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Crosslinker Mover lanthionine (#24) This is the code to enable lanthipeptide modeling in Rosetta. Crosslinker updated to include lanthionine and methyllanthionine connections. -This includes D/L ALA steriochem for lanthionine and D/L and 3 R/S steriochem for methylanthionine (B(L/D)(R/S)) Dehydrated amino acid patches for DBU and DHU were updated/added The AmbiguouosNMRDistanceConstraints were updated to work for NCAA (hardcoding was generalized) Additionally, I noticed that the thioether lariat in simple cyc pep predict only samples cis omega bonds for the N terminal residue. I changed this to trans, which should be energetically preferred.

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Fix pre-compile script calls on Windows build (#58) The windows build test on the test server doesn't seem to be updating options appropriately. It looks like the issue is that the *.sh files aren't being properly called -- adding "bash" to the front of them allows them to run properly.

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