1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
|
"""Reads chemical data in SDF format (wraps the molfile format).
See https://en.wikipedia.org/wiki/Chemical_table_file#SDF
"""
from ase.atoms import Atoms
def read_sdf(fileobj):
if isinstance(fileobj, str):
fileobj = open(fileobj)
lines = fileobj.readlines()
# first three lines header
del lines[:3]
L1 = lines.pop(0).split()
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)
|
