Chimie Théorique » QMX

from math import pi, cos, sin, sqrt, acos

from ase.atoms import Atoms

from ase.parallel import paropen

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)