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"""Reads chemical data in MDL Molfile format.
See https://en.wikipedia.org/wiki/Chemical_table_file
"""
from ase.atoms import Atoms
def read_mol(fileobj):
lines = fileobj.readlines()
L1 = lines[3]
# The V2000 dialect uses a fixed field length of 3, which means there
# won't be space between the numbers if there are 100+ atoms, and
# the format doesn't support 1000+ atoms at all.
if L1.rstrip().endswith('V2000'):
natoms = int(L1[:3].strip())
else:
natoms = int(L1.split()[0])
positions = []
symbols = []
for line in lines[4:4 + natoms]:
x, y, z, symbol = line.split()[:4]
symbols.append(symbol)
positions.append([float(x), float(y), float(z)])
return Atoms(symbols=symbols, positions=positions)
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