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James Graham authoredJames Graham authored
pycgtool.py 2.25 KiB
#!/usr/bin/env python3
import argparse
import sys
from pycgtool.pycgtool import main, map_only
from pycgtool.interface import Options
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Perform coarse-grain mapping of atomistic trajectory")
input_files = parser.add_argument_group("Input files")
input_files.add_argument('-g', '--gro', type=str, required=True, help="GROMACS GRO file")
input_files.add_argument('-m', '--map', type=str, help="Mapping file")
input_files.add_argument('-x', '--xtc', type=str, help="GROMACS XTC file")
input_files.add_argument('-b', '--bnd', type=str, help="Bonds file")
input_files.add_argument('-i', '--itp', type=str, help="GROMACS ITP file")
parser.add_argument('--interactive', default=False, action='store_true')
parser.add_argument('--outputxtc', default=False, action='store_true')
parser.add_argument('--quiet', default=False, action='store_true')
input_files.add_argument('--begin', type=int, default=0, help="Frame number to begin")
input_files.add_argument('--end', type=int, default=-1, help="Frame number to end")
args = parser.parse_args()
config = Options([("output_name", "out"),
("output", "gro"),
("output_xtc", args.outputxtc),
("map_only", not bool(args.bnd)),
("map_center", "geom"),
("constr_threshold", 100000),
("dump_measurements", bool(args.bnd) and not bool(args.map)),
("dump_n_values", 100000),
("output_forcefield", False),
("temperature", 310),
("angle_default_fc", True),
("generate_angles", True),
("generate_dihedrals", False)],
args)
if not args.map and not args.bnd:
parser.error("One or both of -m and -b is required.")
if args.interactive:
try:
config.interactive()
except KeyboardInterrupt:
sys.exit(0)
else:
print("Using GRO: {0}".format(args.gro))
print("Using XTC: {0}".format(args.xtc))
if config.map_only:
map_only(args, config)
else:
main(args, config)