def process_traj():
"""
process traj of xyz file
"""
line = raw_input("enter the filename (xyz format): \n > ")
fname = line.strip()
line = raw_input("enter the index range (from zero) <i.e. 1-5,9,11>: \n >")
frg_ndx1 = line.strip()
line = raw_input(
"enter the index range (from zero) <i.e. 20-37, 39, 41, 42-48>: \n >")
frg_ndx2 = line.strip()
# traj. info
traj = xyzTraj()
traj.read_it(filename=fname)
# det. shape
shape = bMolShape()
while True:
frg1 = traj.fragment(frg_ndx1)
frg2 = traj.fragment(frg_ndx2)
t = shape.plane_angle(frg1, frg2)
print t
if traj.next_model() == 0:
break
return t
def process_struct():
"""
process on structure of xyz file
"""
line = raw_input("enter the filename (xyz format): \n > ")
fname = line.strip()
line = raw_input("enter the index range (from zero) <i.e. 1-5,9,11>: \n >")
frg_ndx1 = line.strip()
line = raw_input("enter the index range (from zero) <i.e. 20-37, 39, 41, 42-48>: \n >")
frg_ndx2 = line.strip()
# mol. info.
mol = xyzStruct()
mol.read_it(filename = fname)
frg1 = mol.fragment(frg_ndx1)
frg2 = mol.fragment(frg_ndx2)
# det. shape
shape = bMolShape()
t = shape.plane_angle(frg1, frg2)
return t
def process_struct():
"""
process on structure of xyz file
"""
line = raw_input("enter the filename (xyz format): \n > ")
fname = line.strip()
line = raw_input("enter the index range (from zero) <i.e. 1-5,9,11>: \n >")
frg_ndx1 = line.strip()
line = raw_input(
"enter the index range (from zero) <i.e. 20-37, 39, 41, 42-48>: \n >")
frg_ndx2 = line.strip()
# mol. info.
mol = xyzStruct()
mol.read_it(filename=fname)
frg1 = mol.fragment(frg_ndx1)
frg2 = mol.fragment(frg_ndx2)
# det. shape
shape = bMolShape()
t = shape.plane_angle(frg1, frg2)
return t
def process_traj():
"""
process traj of xyz file
"""
line = raw_input("enter the filename (xyz format): \n > ")
fname = line.strip()
line = raw_input("enter the index range (from zero) <i.e. 1-5,9,11>: \n >")
frg_ndx1 = line.strip()
line = raw_input("enter the index range (from zero) <i.e. 20-37, 39, 41, 42-48>: \n >")
frg_ndx2 = line.strip()
# traj. info
traj = xyzTraj()
traj.read_it(filename = fname)
# det. shape
shape = bMolShape()
while True:
frg1 = traj.fragment(frg_ndx1)
frg2 = traj.fragment(frg_ndx2)
t = shape.plane_angle(frg1, frg2)
print t
if traj.next_model() == 0:
break
return t
