Modifications to support android_arm 9 platform. There are some manual steps for a successful build: 1. You must install the android ndk and run android-ndk-install-dir/build/tools/make-standalone-toolchain.sh to create the 'androidarm-tc' toolchain directory. 2. You must set environment variables NDKROOT, TOOLCHAIN, SYSROOT 3. The final link command must be manually run to dynamically link -lz. I couldn't figure out a way for scons to run the correct link command.

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Improved parsing of motif in connectjumps

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commenting out new residue types to test relative performance changes

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Adding ResidueType::has(const char *name) as workaround for what seems to be MSVC bug (thanks to Luki for suggesting it!)

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Merge branch 'master' of https://github.com/RosettaCommons/main

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Adding option extreme_value_removal to DdgFilter. If set to true and repeats>=3 then in computing the average of several repeats the filter will remove the values at the bottom and top. For instance, if repeats=5, 5 evaluations will take place but only the 3 values at the middle will be used to compute the average. This should reduce the sometimes quite significant extreme values observed when 1000s of ddG evaluations are made in a single trajectory. Log change expected in ddG using integration tests. See wiki for details.

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A few fixes for symmetric docking RigidBodyTrans mover no longer resets all dimensions if one dimension slides out of the boundary. SwitchResidueTypeSetMover is quieter with symmetric poses.

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Fixing Windows build project files make script.

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add temperature level based interpolated sampling weights for 2d Hamiltonian Exchange fixed a bug for docking metric Fnonnat calculation in /protocols/docking/metrics.cc'

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Fixing PyRosetta monolith build

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merged with master

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Modified std::cout and std::cerr calls to use the Tracer object. Expect trivial integration log changes.

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Fixing PyRosetta build

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fix debug build

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prints out the size of search space

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Adding option to output the score file in JSON format (concatenation of valid JSON objects), and a python utility script to parse and extract data from such score files. To output score files in the JSON format, use the option -out:file:scorefile_format json. The utility script scorefile.py in main/source/tools can convert the JSON score file to the legacy format or CSV, extract selected fields, and compute some quick stats. Further, scorefile.py can be imported into your python scripts and provides the ScoreFile class for easy access to score data. Unit Tests: All Pass Integration Tests: Cosmetic changes to score term order and naming in scorefiles; output is now consistent for silent and PDB files. Affected tests: assemble_domains_jd2 fold_and_dock membrane_relax score_only_silence score_jd2 ThreadingInputter

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