def setup(self, printargs=False):
super(AaCgTrajectoryProcessor, self).setup(printargs)
self.ff = elbalib.Elba()
self.ff.load(self.args.xml)
self.refuniverse = md.Universe(self.args.ref)
# Check if we need to translate the atom names
self.namtrans = None
if self.args.naming is not None:
namref = [
line.strip()
for line in open(self.args.naming[0], 'r').readlines()
]
nammob = [
line.strip()
for line in open(self.args.naming[1], 'r').readlines()
]
self.namtrans = {}
for nr, nm in zip(namref, nammob):
if nm != "*":
self.namtrans[nm] = nr
# Setup of a list of residues defined in the force field that can be processed
self.residues = []
for r in self.refuniverse.selectAtoms("all").residues:
if self.args.mol is not None and r.name.lower(
) != self.args.mol.lower():
continue
ffmol = self.ff.find_molecule(r.name)
if ffmol is None or not ffmol.beadnames:
continue
self.residues.append(_Residue(r.id, ffmol, self.universe))
if not self.iscgtraj:
self.residues[-1].make_transmat(self.namtrans)
for action in self.actions:
action.setup_residues()
bond.contype = elbalib.BondType()
bond.contype.set(id=di+1,kf=2,k=data[di,0],r0=data[di,1])
ff.bondtypes[di+1]=bond.contype
di += 1
ai = 0
prev = len(ff.angletypes)
ff.angletypes = {}
for angle in ffmol.angles :
angle.contype = elbalib.AngleType()
angle.contype.set(id=ai+1,kf=2,k=data[di,0],theta0=data[di,1])
ff.angletypes[ai+1]=angle.contype
di += 1
ai += 1
if __name__ == '__main__':
print " ".join(sys.argv)
argparser = argparse.ArgumentParser(description="Program the generate LAMMPS input files")
argparser.add_argument('-x', '--xml', help="an XML file with force field definitions")
argparser.add_argument('-b','--bonded',nargs=2,help="replace bonded parameters")
args = argparser.parse_args()
ff = elbalib.Elba()
ff.load(args.xml)
modify_bonded(ff,args.bonded[0],args.bonded[1])
generate_gmxinput(ff.molecules[args.bonded[0]])