Вы можете попытаться извлечь данные с помощью модуля re
( regex101 ):
import re
from itertools import zip_longest
data = '''
//Text file starts
---------------------------SOFTWARE NAME------------------------------------
I/O Filenames: abc.txt
Variables:______
------------------------------------------------------------------------
Method name.
Coordinates : 0 0
S.No. X(No.) Y(No.) Z(Beta) A(Alpha)
1 3.541 0
2 7.821 180
3 2.160 0
4 4.143 0 3.69 0
5 2.186 0 2.18 0
6 3.490 0 2.45 0
//End of text file
'''
l = [g.split() for g in re.findall(r'^\s+\d+\s+[^\n]+$', data, flags=re.M)]
for v in zip(*zip_longest(*l)):
print(v)
Отпечатки:
('1', '3.541', '0', None, None)
('2', '7.821', '180', None, None)
('3', '2.160', '0', None, None)
('4', '4.143', '0', '3.69', '0')
('5', '2.186', '0', '2.18', '0')
('6', '3.490', '0', '2.45', '0')