kortemme-lab / loop_modeling Goto Github PK

The analysis/analysis.py script uses the tools package which has now been renamed to https://github.com/Kortemme-Lab/klab.

1. "pip install -e git+ssh://[email protected]/Kortemme-Lab/klab.git#egg=klab" in the virtual environment containing the loop_modeling clone
2. Fix the analysis.py script to use klab rather than tools.
3. Update the main documentation to tell users to install the klab package as a dependency.

change ./run_benchmark to ./run_benchmark.py in README.rst

and change benchmarks/full.pdbs to input/full.pdbs

Make each protocol self contained in their own folder under protocols/

typo in directory name

In the 14-17 benchmark, some reference structures (input/structures/14_17_res/rosetta/reference/ folder) have HETATMS:

1r6x
1ra0
1rdq
1s95
2aeb
2b0t
2bwr
2puh
3a3p
3a64
3b40
3cnq
3ea1

These blow up the RMSD step for some ways of calculating RMSD. My use of this benchmark isn't totally "inside" - I'm doing the RMSD in its own separate RosettaScripts step - so it might affect only me. I'm filing the issue because I'm having to remove the heteroatoms to get it to work for my purposes. I can PR fixed structures if it is determined that they are wanted, but I'm not sure that it's relevant for the "official" use of the data.