Merge pull request #1271 from RosettaCommons/rfalford12/fix-fa-pH-test
Fix Membrane Fa pH Score Function Fingerprint Test - Adding missing atoms to 1qd6_tr_C.pdb which caused problems with the score function fingerprint test.
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Merge pull request #1509 from RosettaCommons/rfalford12/energy-method-code-templates
Code Templates for Energy Methods:
Adding code templates for one body, two body, and whole structure energy methods to the collection. These interfaces are based off of the base class interfaces. I don't have a pressing energy term to implement right now as a better test, but I will adjust these as I go in the next few weeks.
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Merge pull request #1512 from RosettaCommons/vmullig/noisier_flipping_tests
Make flipping tests noisier
About eighteen integration tests are showing weird "flipping" behaviour on the test server, and no one knows why. Making two of these tests noisier (-out:level 500) to try to track down the problem. (It would be good to know at least what Rosetta modules were being invoked when the trajectory changes start to appear.)
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Merge pull request #1505 from RosettaCommons/rhiju/fix_amw_ribosome_tether_example
Rhiju/fix amw ribosome tether example
+ @everyday847 the bug is fixed in master.
+ some integration tests change, but they look like the 'usual' ones that are sensitive to floating point inaccuracies.
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Merge pull request #1504 from RosettaCommons/vmullig/fix_mpi_tests
Fix error in MPI-mode integration tests introduced in Documentation XRW
The tests were failing to run due to a small error in integration.py. Fixed now.
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Merge pull request #1499 from RosettaCommons/rpavlovicz/fastsaxs_fix
fastsaxs scoring was failing in centroid mode and when dealing with symmetric poses due to virtual atoms and virtual residues being considered during COM calculations. these changes fix this issue.
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Merge pull request #1494 from RosettaCommons/jkleman/mp_updates_stats
Jkleman/mp updates stats
adding small app for lipid accessibility
14 integration tests change, these are the unstable ones, this can only be because I added new options and Rosetta was rebuild from the ground up as I am not changing anything that could cause these tests to fail
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Merge pull request #1457 from RosettaCommons/jadolfbr/fix_seed_ensemble
Fix Seed Ensemble integration test
This should properly run the integration test for seed ensemble JD2. Thanks for @roccomoretti for the find!
This also properly reinstates certain protocol movers to work better with multiple different poses - AKA calls proper Mover functions to tell JD2 what to do. Most were already coded this way, but this explicitly says what to do.
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Merge pull request #1275 from RosettaCommons/jadolfbr/pyrosetta/setup_pyrosetta
Add PyRosetta Setup Script
Add a script for setting up PyRosetta - ```setup_pyrosetta.py```. This has been needed for years. Thanks to @raemisch for the suggestion. It runs SetPyRosettaEnvironment (which is now updated), and creates a new file for PyRosetta paths (which are usually exported at the end of the shell file). This file should then sourced in your profile, which this script can append for you if it is not already present in the file.
The script interactively asks you if you would like to add this to your profile if not already present
```
## PyRosetta ##
source /Users/jadolfbr/.pyrosetta_env
```
The new file looks like this:
```
# PyRosetta Paths. Source this within your profile.
# Date Created: 04/13/2016
export PYROSETTA=path/To/PyRosetta.namespace.mac.release
export PYTHONPATH=$PYROSETTA${PYTHONPATH+:$PYTHONPATH}
export DYLD_LIBRARY_PATH=$PYROSETTA:$PYROSETTA/rosetta${DYLD_LIBRARY_PATH+:$DYLD_LIBRARY_PATH}
export export LD_LIBRARY_PATH=$PYROSETTA:$PYROSETTA/rosetta${LD_LIBRARY_PATH+:$LD_LIBRARY_PATH}
export PYROSETTA_DATABASE=$PYROSETTA/database
```
You can either use SetPyRosettaEnvironment or setup_pyrosetta.py script. The setup_pyrosetta.py script should be run anytime directories are changed (Which is now actually able to be done through the dylib - this never actually worked before).
Here is the help output of the python script:
```
usage: This file adds a file to your home directory, .pyrosetta_env, and by default adds a line to your bash or zsh profile (if not already present) to source this file. After running this script, you will no longer need to run anything before using PyRosetta or add anything to your profile.
[-h] [--source SOURCE] [--outname OUTNAME] [--outdir OUTDIR]
[--shell_profile_path SHELL_PROFILE_PATH]
optional arguments:
-h, --help show this help message and exit
--source SOURCE, -s SOURCE
The file to source in order to set the environment.
Default is SetPyRosettaEnvironment.sh
--outname OUTNAME, -o OUTNAME
Name of the output file we will eventually source.
Default is .pyrosetta_env
--outdir OUTDIR, -d OUTDIR
Output directory of the env file. Default is $HOME
directory
--shell_profile_path SHELL_PROFILE_PATH, -p SHELL_PROFILE_PATH
If your shell profile path is different than the
common ones, please set the path here.
```
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