"""haddock3-restraints restrain_bodies subcommand.
The restrain_bodies subcommand creates distance restraints to lock several
chains together. Useful to avoid unnatural flexibility or movement due to
sequence/numbering gaps.
Usage::
haddock3-restraints restrain_bodies <structure> [--exclude] [--verbose]
"""
import logging
import sys
import random
from haddock.libs.librestraints import read_structure, get_bodies, build_restraints, generate_tbl
# Set random seed to have reproducibility
random.seed(917)
[docs]def add_restrain_bodies_arguments(restraint_bodies_subcommand):
restraint_bodies_subcommand.add_argument(
"structure",
help="The PDB structure to be restrained.",
)
restraint_bodies_subcommand.add_argument(
"-e",
"--exclude",
help="Chains to exclude from the calculation.",
required=False,
type=str,
)
restraint_bodies_subcommand.add_argument(
"-v",
"--verbose",
help="Tune verbosity of the output.",
required=False,
default=0,
type=int,
)
restraint_bodies_subcommand
[docs]def restrain_bodies(structure, exclude=None, verbose=0): # noqa: E501
"""Create distance restraints to lock several chains together.
Parameters
----------
structure : str
The PDB structure to be restrained.
exclude : str
Chains to exclude from the calculation.
verbose : int
Tune verbosity of the output.
"""
if verbose== 1:
logging.basicConfig(level=logging.INFO)
elif verbose > 1:
logging.basicConfig(level=logging.DEBUG)
else:
logging.basicConfig(level=logging.WARNING)
# Main logic
atom_lst = read_structure(structure, exclude=exclude)
bodies = get_bodies(atom_lst)
restraints = build_restraints(bodies)
generate_tbl(atom_lst, restraints)