/usr/share/pyshared/ase/io/mol.py is in python-ase 3.6.0.2515-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | from math import pi, cos, sin, sqrt, acos
from ase.atoms import Atoms
from ase.parallel import paropen
def read_mol(fileobj, index=-1):
if isinstance(fileobj, str):
fileobj = open(fileobj)
lines = fileobj.readlines()
del(lines[:3])
L1 = lines[0].split()
del(lines[0])
natoms = int(L1[0])
positions = []
symbols = []
for line in lines[: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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