def read_geometry(self):
""" Read geometry from the contained file """
# First we read in the geometry
sc = self.read_supercell()
# Try and go to the first model record
in_model, l = self._step_record('MODEL')
idx = []
tags = []
xyz = []
Z = []
if in_model:
l = self.readline()
def is_atom(line):
return l.startswith('ATOM') or l.startswith('HETATM')
def is_end_model(line):
return l.startswith('ENDMDL') or l == ''
while not is_end_model(l):
if is_atom(l):
idx.append(int(l[6:11]))
tags.append(l[12:16].strip())
xyz.append(
[float(l[30:38]),
float(l[38:46]),
float(l[46:54])])
Z.append(l[76:78].strip())
l = self.readline()
# First sort all atoms according to the idx array
idx = np.array(idx)
idx = np.argsort(idx)
xyz = np.array(xyz)[idx, :]
tags = [tags[i] for i in idx]
Z = [Z[i] for i in idx]
# Create the atom list
atoms = Atoms(Atom(Z[0], tag=tags[0]), na=len(Z))
for i, a in enumerate(map(Atom, Z, tags)):
try:
s = atoms.index(a)
except:
s = len(atoms.atom)
atoms._atom.append(a)
atoms._specie[i] = s
return Geometry(xyz, atoms, sc=sc)
def test_index1():
atom = Atoms(['C', 'Au'])
with pytest.raises(KeyError):
atom.index(Atom('B'))
def test_index1():
atom = Atoms(['C', 'Au'])
atom.index(Atom('B'))
