return 1.4
elif atom.mass == 32.06 :
return 1.85
else :
return 2.0
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Program make a PQR file")
parser.add_argument('-f','--file',help="the input gro-file")
parser.add_argument('-p','--topol',help="the topology file")
parser.add_argument('-o','--out',help="the output pqr-file",default="conv.pqr")
parser.add_argument('-m','--mol',nargs="+",help="the molecule to write out",default=["protein"])
args = parser.parse_args()
ref = gmx.TopFile(args.topol)
pdbfile = pdb.PDBFile(args.file)
mols = []
for topol_mol in ref.moleculetypes :
for argmol in args.mol :
if topol_mol.name.lower() == argmol.lower() :
mols.append(topol_mol)
break
natom = sum([len(mol.atoms) for mol in mols])
pdbfile.residues = [res for res in pdbfile.residues if res.atoms[0].serial <= natom]
pdbfile.atoms = pdbfile.atoms[:natom]
start = 0
for mol in mols :
"""
import argparse
import math
from sgenlib import gmx
if __name__ == "__main__":
parser = argparse.ArgumentParser(
description="Program make Glycam pair params")
parser.add_argument('-f', '--file', help="the input top-file")
parser.add_argument('-m', '--molecule', help="the molecule name")
args = parser.parse_args()
reftop = gmx.TopFile(args.file)
atypes = {}
for atype in reftop.atomtypes:
atypes[atype.name] = atype
refmol = None
for mol in reftop.moleculetypes:
if mol.name == args.molecule:
refmol = mol
break
if refmol is None:
print "Could not find moleculetype %s. Exit." % args.molecule
quit()
for pair in refmol.pairs:
'--nreplace',
type=int,
help="how many POPI molecules to replace")
args = parser.parse_args()
# Read in a gro-file
popimem = pdb.PDBFile()
popimem.read(args.file, gro=True)
# Read in a template IPC-file
ipc_pdb = pdb.PDBFile(filename=args.template)
# Read in the z-matrix of the IPC molecule
ipc_zmat = [
line.strip().split() for line in open(args.zmat, "r").readlines()
]
# Read in the atom order of the IPC itp-file
ipctop = gmx.TopFile(args.itp)
ipc_atomlist = [atom.name for atom in ipctop.moleculetypes[0].atoms]
nreplace = args.nreplace
# Check where the middle of the membrane is
midz = popimem.xyz[:, 2].mean()
# Hash the IPC atoms
ipc_hash = {}
for atom in ipc_pdb.atoms:
ipc_hash[atom.name.strip()] = atom.xyz
# Find POPI residues in lower and upper part of the membrane
popires_low = []
popires_upp = []
for residue in popimem.residues:
help="the protein molecule")
args = parser.parse_args()
# Read a Xrya structure file
xray = gpcr_lib.load_xray(args.mol, loadsigma=True)
pdb = xray.pdbfile
# Remove cholesterols at the end
while pdb.residues[-1].resname == "CHOL":
for atom in pdb.residues[-1].atoms:
pdb.atoms.remove(atom)
del pdb.residues[-1]
pdb.xyz = np.array([atom.xyz for atom in pdb.atoms])
# Read a Gromacs topology file
top = gmx.TopFile(args.top)
# Store away all interesting LJ parameter pairs
roh_type = "SP1" #"SC1"
roh_pairs = []
for p in top.pairtypes:
if p.atomi == roh_type or p.atomj == roh_type: roh_pairs.append(p)
# Find the protein molecule definition
protein_type = None
for m in top.moleculetypes:
if m.name == "Protein": protein_type = m
if protein_type is None:
raise Exception("Could not find a protein molecule type")
# Check that the given structure is compatible with the found protein force field