args = parser.parse_args()
# Read solute data file
solute_data = lammps.Datafile(filename=args.solute)
if args.pdb is not None:
pdbfile = pdb.PDBFile(filename=args.pdb)
for datom, patom in zip(solute_data.atoms, pdbfile.atoms):
datom.set_xyz(patom.xyz)
# Read box data file and force field
box_data = lammps.Datafile(filename=args.box)
for atom in box_data.atoms:
atom.ix = None
atom.iy = None
atom.iz = None
box_ff = lammps.Includefile(filename=args.ff)
if args.dihfunc_box is not None:
for dih in box_ff.dihedralparams:
if dih.func == "": dih.func = args.dihfunc_box
ELBA_FUNC = "lj/sf/dipole/sf"
for pair in box_ff.pair_coeff:
if pair.func == "": pair.func = ELBA_FUNC
if not args.norespa and pair.hybrid == -1 and pair.func == ELBA_FUNC:
pair.hybrid = 2
lj_hybrid = -1
if not args.norespa: lj_hybrid = 1
lj_func = {ELBA_FUNC: ELBA_FUNC}
outdata.box = np.array(box, copy=True)
outdata.title = "Converted to CG with convert_aa.py from %s" % os.path.basename(
infilename)
outdata.write("data.%s-chexanebox" % ligand)
if __name__ == '__main__':
filename = sys.argv[1]
filehead = os.path.splitext(os.path.basename(filename))[0]
solvent = filehead.split("-")[0]
ligand = filehead.split("_")[1]
aadata = lammps.Datafile(filename)
aapairparams = lammps.Includefile(os.path.splitext(filename)[0] + ".input")
solutedata = lammps.Datafile()
solatypes = []
solidx = []
solutemasses = []
solventatoms = []
# Split up solute and solvent atoms
for atom in aadata.atoms:
if atom.molecule == 1:
solatypes.append(atom.atype)
solidx.append(atom.idx)
solutedata.atoms.append(atom)
solutemasses.append(aadata.atomtypes[atom.atype - 1].mass)
else:
solventatoms.append(atom)
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
for i, (res, takethis) in enumerate(zip(pdbfile.residues, takeres)):
if not takethis: continue
moli += 1
res2 = res.resname.strip().lower()
found = False
help="the scaling factors",
default=[])
parser.add_argument(
'-p',
'--param',
choices=["e", "s", "c"],
nargs="+",
help="the parameter to scale, either e(psilon), s(igma), or c(oulomb)",
default=[])
args = parser.parse_args()
if args.file is None:
print "No input file specified. Exiting!"
quit()
infile = lammps.Includefile(filename=args.file)
# Find all mixed pairs
mixed_pairs = []
for pair in infile.pair_coeff:
if (pair.comment.find("AA-CG mixed") > -1 or
pair.comment.find("Mixed using Lorentz-Berthelot rules") > -1):
mixed_pairs.append(pair)
lj_same = infile.lj_same_dict()
# Loop over all the bead specification and change the given parameter
for beadspec, fac, param in zip(args.beads, args.scale, args.param):
beads = [int(b) for b in beadspec.strip().split(",")]
for pair in mixed_pairs:
if pair.iatom in beads:
if param.lower()[0] == "e":
Example:
lmp_duplicate_atype.py forcefield.elba
"""
import argparse
from sgenlib import lammps
if __name__ == '__main__' :
# Command-line input
parser = argparse.ArgumentParser(description="Duplicating atom type in Lammps include file")
parser.add_argument('file',help="the lammps include file")
parser.add_argument('-o','--out',help="the output file")
parser.add_argument('-t','--type',type=int,help="the type to duplicate")
args = parser.parse_args()
ifile = lammps.Includefile(args.file)
# Duplicate masses and pair coefficients
newmass,newpairs = ifile.duplicate_type(args.type)
newmass.comment = "# duplicate of %d"%(args.type)
ifile.masses.append(newmass)
ifile.pair_coeff.extend(newpairs)
ifile.pair_coeff.sort(cmp=lammps.comp_pair)
if args.out is None :
args.out = args.file+"_mod"
ifile.write(args.out)
"""
import argparse
from sgenlib import lammps
if __name__ == '__main__':
# Command-line input
parser = argparse.ArgumentParser(
description="Write out atom types of heavy atoms")
parser.add_argument('file', help="the lammps include file")
parser.add_argument('-x',
'--exclude',
type=float,
nargs="+",
help="exclude these",
default=[40.0, 90.0, 62.0, 42.0])
parser.add_argument('-m',
'--mass',
type=float,
help="the mass of hydrogen",
default=1.00800)
args = parser.parse_args()
atypes = []
for m in lammps.Includefile(args.file).masses:
if not (m.mass in args.exclude or m.mass == args.mass):
atypes.append(m.idx)
print " ".join(["%d" % i for i in atypes])