def _make_waterdata(atoms, box, ligands, infilename):
"""
Make a datafile for a CG box with water molecules
"""
outdata = lammps.Datafile()
atoms = atoms[::3] # Map to the oxygen
for i, aaatom in enumerate(atoms, 1):
cgatom = lammps.Atom()
cgatom.idx = i
cgatom.atype = 1
cgatom.set_xyz(aaatom.xyz) # This is the only thing used from all-atom
cgatom.charge = 0
cgatom.set_mu(geo.sphere_rand(0.541)) # Random dipole direction
cgatom.diameter = 3.0
cgatom.density = 2.7
cgatom.kind = "cg"
outdata.atoms.append(cgatom)
outdata.atomtypes = [None] * 6
outdata.bondtypes = [None] * 5
outdata.angletypes = [None] * 5
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-waterbox" % ligand)
def _make_cyclohexanedata(atoms, box, ligands, infilename):
"""
Make a datafile for a CG box with cyclohexane molecules
"""
outdata = lammps.Datafile()
c1_atoms = atoms[::18] # Map to first carbon
c2_atoms = atoms[1::18] # Map to second carbon
c3_atoms = atoms[3::18] # Map to fourth carbon
for i, (c1atom, c2atom,
c3atom) in enumerate(zip(c1_atoms, c2_atoms, c3_atoms)):
aatoms = [c1atom, c2atom, c3atom]
for j in range(3):
cgatom = lammps.Atom()
cgatom.idx = i * 3 + j + 1
cgatom.atype = 6
cgatom.set_xyz(aatoms[j].xyz)
cgatom.charge = 0
cgatom.set_mu([0, 0, 0])
cgatom.diameter = 4.5
cgatom.density = 0.9
cgatom.kind = "cg"
cgatom.molecule = i + 1
outdata.atoms.append(cgatom)
outdata.bonds.append(
lammps.Connectivity(
"%d 5 %d %d" % (len(outdata.bonds) + 1, i * 3 + 1, i * 3 + 2)))
outdata.bonds.append(
lammps.Connectivity(
"%d 5 %d %d" % (len(outdata.bonds) + 1, i * 3 + 1, i * 3 + 3)))
outdata.bonds.append(
lammps.Connectivity(
"%d 5 %d %d" % (len(outdata.bonds) + 1, i * 3 + 3, i * 3 + 2)))
outdata.atomtypes = [None] * 6
outdata.bondtypes = [None] * 5
outdata.angletypes = [None] * 5
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)
default="lj/charmm/coul/long")
parser.add_argument('--dihfunc',
help="the dihedral function for the solute")
parser.add_argument('--dihfunc_box',
help="the dihedral function for the box")
parser.add_argument('--pairmix',
nargs="+",
help="pair functions to use when mixing pairs")
parser.add_argument('--noff',
action="store_true",
help="turns off the creating of force field file",
default=False)
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:
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
for residue in converter.residues:
if residue.name == res2:
coord = residue.generate_cg(res, moli + 1, data, mapping=False)
all_coords.extend(coord)
found = True
outdata.angletypes = [None] * 5
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:
parser.add_argument('data', help="the lammps data file")
parser.add_argument('-o', '--out', help="the output file")
parser.add_argument('-a', '--atoms', nargs="+", help="the atoms to change")
parser.add_argument('-t', '--type', type=int, help="the new atom type")
parser.add_argument('--increase',
help="increase number of atom types",
action='store_true',
default=False)
parser.add_argument('--decrease',
help="decrease number of atom types",
action='store_true',
default=False)
args = parser.parse_args()
# Read datafile and parse into molecules
datafile = lammps.Datafile(filename=args.data)
mols = lammps.parse_molecules(datafile)
# Loop over all atom selections and modify atom type
for atom in args.atoms:
molrange, atomi = atom.split(":")
atomi = int(atomi)
first, last = map(int, molrange.split("-"))
print "Changing: ", first, last, atomi
for m in range(first, last + 1):
mols[m][atomi - 1].atype = args.type
# Increase or decrease the atomtype list
if args.increase:
datafile.atomtypes.append(None)
elif args.decrease:
"""
import argparse
from sgenlib import lammps
if __name__ == '__main__':
parser = argparse.ArgumentParser(description="Truncate a LAMMPS datafile")
parser.add_argument('file', help="the data file.")
parser.add_argument('-m',
'--mol',
type=int,
help="the molecule id of the QM system")
parser.add_argument('-o', '--out', help="the output file")
args = parser.parse_args()
if args.file is None:
print "No input file specified. Exiting!"
quit()
datafile = lammps.Datafile(args.file)
for atom in datafile.atoms:
if atom.molecule == args.mol:
atom.q = 0.0
if args.out is None:
datafile.write(args.file)
else:
datafile.write(args.out)
import numpy as np
from sgenlib import lammps
from sgenlib import pdb
from sgenlib import pbc
if __name__ == '__main__':
# Command-line input
parser = argparse.ArgumentParser(
description="Making molecules whole in a LAMMPS datafile")
parser.add_argument('file', help="the lammps data file")
parser.add_argument('-o', '--out', help="the output file")
args = parser.parse_args()
data = lammps.Datafile(filename=args.file)
# Create a box with the length of the datafile box
box = np.zeros(3)
box[0] = data.box[3] - data.box[0]
box[1] = data.box[4] - data.box[1]
box[2] = data.box[5] - data.box[2]
mols = lammps.parse_molecules(data)
for atom in data.atoms:
if atom.ix != None:
atom.ix = None
atom.iy = None
atom.iz = None
for mol in mols:
}
harmonic {
colvars solute
forceConstant %.3f
centers %.1f
outputCenters on
}
"""
# Find the first and last atom of the membrane and solute
mfirst = 10000
mlast = -10000
sfirst = 10000
slast = -10000
for atom in lammps.Datafile(args.file).atoms :
if atom.molecule >= args.membrane[0] and atom.molecule <= args.membrane[1] :
mfirst = min(atom.idx,mfirst)
mlast = max(atom.idx,mlast)
elif atom.molecule == args.solute :
sfirst = min(atom.idx,sfirst)
slast = max(atom.idx,slast)
# Create an output file for each depth
for z in args.zdepth :
with open("%sz%0.f"%(args.out,z),"w") as f:
f.write(strtempl%(sfirst,slast,mfirst,mlast,args.weight,z))
'--watrad',
type=float,
help="the water radius to keep atomistic")
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)
# Create a Datafile and PDBFile
pdbfile = pdb.PDBFile(args.file) # Input PDB
takeres = [True for res in pdbfile.residues]
data = lammps.Datafile()
pdbout = pdb.PDBFile() # Output PDB
# Load the force field file
include = lammps.Includefile(args.include)
if args.atomistic:
# At the moment, multiple AA solutes are not supported with atomistic water radius
if len(args.atomistic) > 1:
args.watrad = None
natomtypes = _ntypes(include.masses)
contypes = [
_ntypes(include.bondparams),
_ntypes(include.angleparams),
_ntypes(include.dihedralparams)
]