This is a collections of scripts for closing loops in pdb files (or silent files) as an add-on for the Rosetta protein suite.
If something doesn't run, please don't hesitate to email me! (d.zorine@gmail.com)
You must have pyrosetta inside of the environment you install this package in. It is recommended that you install this inside of a conda environment where you have pyrosetta.
python -m pip install git+https://github.com/dmitropher/hashed_loop.git import_default_loop_table /path/to/loop.hf5 /path/to/loop.silent (Tables are typically large, the copy operation can take a long time. The table is copied to the package resource directory rather than referenced.)
prebuilt data is available at: https://files.ipd.uw.edu/dzorine/full.hf5 https://files.ipd.uw.edu/dzorine/default.silent
If you have access to IPD computational resources, contact me directly and I can send you the paths to these resources on the shared filesystem so that you don't have to maintain your own copy and use up disk space quota.
The loop closer should be usable by running:
close_loop /path/to/my.pdb
It is hightly reccommended that you run the following for options and help
close_loop --help
You can use:
build_hash_loop_table --help
for info on how to build your table. There is currently no default or best practice for this procedure until a global benchmark is complete. Email d.zorine@gmail.com for guidelines on making your own archive. This also typically takes a long time and a lot of RAM. This table can be set as default using the table install script above.