setup_target

Description:

manipulate a specific setup of a target

Usage:

setup_target.py [-h] [-target_dir TARGET_DIR]
[-target_prefix TARGET_PREFIX] [-quiet]
[-flag_lib FLAG_LIB] [-label LABEL]
[-method {abrelax,autoNOE,contacts,cyana,fixbb,rasrec,replica_dock,vanilla_dock}]
[-remove [REMOVE [REMOVE ...]]] [-patch PATCH]
[-target TARGET] [-transfer_method TRANSFER_METHOD]
[-transfer_label TRANSFER_LABEL] [-overwrite]
[-traceback]

Detailed Help:

-h, --help show this help message and exit
-target_dir TARGET_DIR input-files are used from/put into this path, instead of directly into the run-directory
-target_prefix TARGET_PREFIX target dirs are found here
-quiet suppress output
-flag_lib FLAG_LIB directory with meta files for generation of Rosetta cmd-line flag-files
-label LABEL give a special label to this setup -- reflected in file-name for method-options
-method {abrelax,autoNOE,contacts,cyana,fixbb,rasrec,replica_dock,vanilla_dock} choose algorithm; use together with -h to see additional method-specific options
-remove [REMOVE [REMOVE ...]] remove one or more options from the SETUP
-patch PATCH provide some python code that patches file-library content
-target TARGET target_dir is target_prefix/target
-transfer_method TRANSFER_METHOD start with this setup and modify according to flags
-transfer_label TRANSFER_LABEL start with this setup and modify according to flags
-overwrite force overwriting of files in the target-database
-traceback print full traceback in case of error

Examples:

setup_target.py -target t000_ -method abrelax -frags frags9.dat frags3.dat -fasta t000_.fasta

prepare a basic abrelax run for target t000_ (use default target-library location $CS3_BENCH_TARGETLIB)

setup_target.py -target t000_ -method rasrec -transfer_method abrelax

copy settings from Setup (t000_, abrelax, standard) to Setup (t000_, rasrec, standard)

setup_target.py -target t000_ -method rasrec -transfer_label standard -label with_rdc -rdc med1.rdc med2.rdc

add rdc data to existing Setup (t000_, rasrec, standard) and call it Setup (t000_, rasrec, with_rdc)

application: