Python toMsd Examples

Example #1

def withPbc(testfile="supper.pdb", args=''):
    a = Pdb(testfile)
    b = a.parser()
    b.assignAtomTypes()
    b.assignEleTypes()
    b.assignIdNumbers()
    b.toFrac()
    #b.translate(12.0, "z")
    toXyz(b, "out.xyz")
    toMusic(b, "out.music")
    if len(b.pbc) == 0:
        b.geotag = "BIOGRF 200"
    else:
        b.geotag = "XTLGRF 200"
    toReaxLammps(b, "lammps.data")
    toGeo(b, "sim.geo")
    toMsd(b, "sim.msd")
    toPoscar(b, )
    toCfg(b, )
    toJdft(b, )
    toTowheecoords(b)
    if args:
        if args.element:
            toPdb(b, "out.pdb", 1)
    else:
        toPdb(b, "out.pdb")

Example #2

def fortranOut(testfile="output.pdb", args=''):
    a = Pdb(testfile)
    b = a.parser()
    b.assignAtomTypes()
    b.assignEleTypes()
    b.pbc = [50.00, 50.00, 50.00, 90.0, 90.0, 90.0]
    b.geotag = "XTLGRF 200"
    toReaxLammps(b, "lammps.data")
    if args:
        if args.element:
            toPdb(b, "out.pdb", 1)
    else:
        toPdb(b, "out.pdb")
    toMsd(b, "sim.msd")
    toGeo(b, "sim.geo")

Example #3

File: e_2_pdb.py Project: karthipitt/simpy

def fortranOut(testfile = "output.pdb", args=''):
    a = Pdb(testfile)
    b = a.parser()
    b.assignAtomTypes()
    b.assignEleTypes()
    b.pbc = [50.00, 50.00, 50.00, 90.0, 90.0, 90.0]
    b.geotag = "XTLGRF 200"
    toReaxLammps(b, "lammps.data")
    if args:
        if args.element:
            toPdb(b, "out.pdb", 1)
    else:
        toPdb(b, "out.pdb")
    toMsd(b, "sim.msd")
    toGeo(b, "sim.geo")

Example #4

File: e_2_pdb.py Project: karthipitt/simpy

def withPbc(testfile="supper.pdb", args=''):
    a = Pdb(testfile)
    b = a.parser()
    b.assignAtomTypes()
    b.assignEleTypes()
    #b.translate(12.0, "z")
    toXyz(b, "out.xyz")
    toMusic(b, "out.music")
    if len(b.pbc) == 0:
        b.geotag = "BIOGRF 200"
    else:
        b.geotag = "XTLGRF 200"
    toReaxLammps(b, "lammps.data")
    toGeo(b, "sim.geo")
    toMsd(b, "sim.msd")
    if args:
        if args.element:
            toPdb(b, "out.pdb", 1)
    else:
        toPdb(b, "out.pdb")