def refine(sample_filename, rec_filename):
"""
Refine the molecule against the map
"""
# Load the sample
sample = parakeet.sample.load(sample_filename)
# Get the molecule name
assert sample.number_of_molecules == 1
name, _ = list(sample.iter_molecules())[0]
# Get the PDB filename
pdb_filename = parakeet.data.get_pdb(name)
# Fit the molecule to the map
maptools.fit(
rec_filename,
pdb_filename,
output_pdb_filename="refined.pdb",
resolution=3,
ncycle=10,
mode="rigid_body",
log_filename="fit.log",
)
def test_fit(ideal_map_filename, pdb_filename):
_, output_filename = tempfile.mkstemp()
_, log_filename = tempfile.mkstemp()
maptools.fit(
input_map_filename=ideal_map_filename,
input_pdb_filename=pdb_filename,
output_pdb_filename=output_filename,
mode="rigid_body",
resolution=8,
ncycle=2,
log_filename=log_filename,
)
assert os.path.exists(output_filename)
def fit(args):
"""
Compute the map fit
Args:
args (object): The parsed arguments
"""
maptools.fit(
input_map_filename=args.input,
input_pdb_filename=args.input2,
output_pdb_filename=args.output,
resolution=args.resolution,
ncycle=args.ncycle,
mode=args.mode,
log_filename=args.logfile,
)