# Command-line input
parser = argparse.ArgumentParser(description="Make a Lammps data file")
parser.add_argument('file',help="the PDB or GRO file")
parser.add_argument('-i','--include',help="the LAMMPS include file")
parser.add_argument('-o','--out',help="the output prefix")
parser.add_argument('-b','--box',type=float,nargs=3,help="the box dimensions",default=[0.0,0.0,0.0])
#parser.add_argument('-a','--atomistic',nargs="+",help="data file(s) for atomistic solutes",default=[])
parser.add_argument('-c','--converter',help="the dictionary with conversion rules")
#parser.add_argument('-p','--pairfunc',help="the pair function for the AA",default="lj/charmm/coul/long")
args = parser.parse_args()
# Load a converter
converter = lammps.Aa2Cg()
if args.converter is None :
converter.read(lammps.get_filename("aa2cg.dat")) # The default
else :
converter.read(args.converter)
# Load the force field file
include = lammps.Includefile(args.include)
# Create a Datafile and PDBFile
pdbfile = pdb.PDBFile(args.file) # Input PDB
takeres = [True for res in pdbfile.residues]
data = lammps.Datafile()
# Convert residues
all_coords = []
nwat = 0
moli = 0
default=[0.0, 0.0, 0.0])
#parser.add_argument('-a','--atomistic',nargs="+",help="data file(s) for atomistic solutes",default=[])
parser.add_argument('-c',
'--converter',
help="the dictionary with conversion rules")
parser.add_argument('-k',
'--kind',
help="the kind of particles",
default="cg")
#parser.add_argument('-p','--pairfunc',help="the pair function for the AA",default="lj/charmm/coul/long")
args = parser.parse_args()
# Load a converter
converter = lammps.Aa2Cg()
if args.converter is None:
converter.read(lammps.get_filename("aa2cg.dat")) # The default
else:
converter.read(args.converter)
# Load the force field file
include = lammps.Includefile(args.include)
# Create a Datafile and PDBFile
pdbfile = pdb.PDBFile(args.file) # Input PDB
takeres = [True for res in pdbfile.residues]
data = lammps.Datafile()
# Convert residues
all_coords = []
nwat = 0
moli = 0