fix PyRosetta builds (#69)

• Summary

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.

• Summary

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.

• Summary

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.

• Summary

Update SCons for compilation with Python 3.12 (#54) Python 3.12 removed the imp module, which means our current SCons 3.0.4 doesn't work with it. Upgrading to SCons 4 will fix this. However, this removes support for building with Python 2.7 -- I think at this point this is acceptable, as anyone compiling Rosetta will likely have a Python3 version installed for RFDiffusion, etc. anyway. Additionally, the error message printed is relatively user friendly: ``` scons: *** SCons version 4.2.0 does not run under Python version 2.7. Python >= 3.5 is required. ``` SCons 4.2.0 was selected as it's the last version which supports Python 3.5 -- I don't know how many people that will actually help, but we don't need to be bleeding edge. Some additional files were changed to address warning messages with a Python 3.12 build. (Note that the current external/scons-local directory was deleted and then re-created from the official download. No manual changes were made, save for deleting some unnecessary documentation files.)

• Summary

Update benchmark scripts for Python3.12. (#51) Python 3.12 gets rid of the imp module. Moreover, it gets rid of imp.load_source() altogether. We thus need to change around how we do the magic 'import from parent directory' statement. There are also a few other things which were popping up warnings when I ran things locally.

• Summary
• linux.gcc.unit 「6」

QOL update to the PerResidueEsmProbabilitiesMetric (#26) This short PR: * Adds the proper citation for ESM * Adds some checks for NaNs/Infs to the Perplexity/softmax calculation * fixes a typo in MIFST.cc * Prevents an error in SampleSequenceFromProbabilities when calling the SimpleThreadingMover without mutations * Fixes const behavior in SampleSequenceFromProbabilities --------- Co-authored-by: moritzertelt <moritz.ertelt@gmail.com>

• Summary

fix PyRosetta build on Ubuntu-22.04 (#45)

• Summary

rename torch extras and defines (#43) * rename torch extras and defines * fix integration tests

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update documentation and remove deprecated scripts (#41) * Update README.md * add reference docker files * add reference Docker files readme * remove deprecated Conda setup and instructions * remove PyRosetta deprecated build option and update readme

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libxml2 build: strcasecmp needs strings.h (#39) The exact error (by clang) was that a missing declaration is no longer supported with the latest C++ standards.

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add support for PyRosetta ML builds (#32)

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• profile 「4」

Add Link to CLA website

• Summary
• performance 「18」
• profile 「8」

Support multiple clients and resource constraints in PyRosettaCluster (#21)

• Summary
• performance 「18」
• profile 「7」

triggering release (#23)

• Summary
• performance 「2」

Fix some currently broken tests. (#17) There are clang-tidy errors for ImplicitMembraneCoulomb & ImplicitMembraneElecEnergy due to virtual/override. There are running errors for the scientific tests due to a typo I made earlier.

• Summary
• m1.clang.cxx11thread.serialization.python310.release.PyRosetta.conda.Release
• m1.clang.cxx11thread.serialization.python311.release.PyRosetta.conda.Release
• m1.clang.cxx11thread.serialization.python312.release.PyRosetta.conda.Release
• m1.clang.cxx11thread.serialization.python39.release.PyRosetta.conda.Release
• 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.python38.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python39.release.PyRosetta.conda.Release

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