1"""Reads chemical data in MDL Molfile format. 

2 

3See https://en.wikipedia.org/wiki/Chemical_table_file 

4""" 

5from ase.atoms import Atoms 

6 

7 

8def read_mol(fileobj): 

9 lines = fileobj.readlines() 

10 L1 = lines[3] 

11 

12 # The V2000 dialect uses a fixed field length of 3, which means there 

13 # won't be space between the numbers if there are 100+ atoms, and 

14 # the format doesn't support 1000+ atoms at all. 

15 if L1.rstrip().endswith('V2000'): 

16 natoms = int(L1[:3].strip()) 

17 else: 

18 natoms = int(L1.split()[0]) 

19 positions = [] 

20 symbols = [] 

21 for line in lines[4:4 + natoms]: 

22 x, y, z, symbol = line.split()[:4] 

23 symbols.append(symbol) 

24 positions.append([float(x), float(y), float(z)]) 

25 return Atoms(symbols=symbols, positions=positions)