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