def test_subst_ibond_equals_ipos():
with pytest.raises(ValueError, match=r'sub and bond indices .*'):
elem, xyz, vec = substitute.subst(eg.c2h4[0],
eg.c2h4[1],
'f',
2,
ibond=2)
def test_subst_fluoro_vec():
vec = np.ones_like(eg.c2h4[1])
elem, xyz, vec = substitute.subst(eg.c2h4[0], eg.c2h4[1], 'f', 2, vec=vec)
soln = np.copy(vec)
soln[2] = 0.
assert np.all(elem == eg.c2h3f[0])
assert np.allclose(xyz, eg.c2h3f[1])
assert np.allclose(vec, soln)
def test_subst_pl_equals_ibond():
with pytest.raises(ValueError, match=r'plane and bond indices .*'):
elem, xyz, vec = substitute.subst(eg.c2h4[0],
eg.c2h4[1],
'f',
2,
ibond=3,
pl=3)
def test_subst_methyl_plane_vec():
elem, xyz, vec = substitute.subst(eg.c2h4[0],
eg.c2h4[1],
'ch3',
2,
pl=[1, 1, 1])
assert np.all(elem == eg.c2h3me_ax[0])
assert np.allclose(xyz, eg.c2h3me_ax[1])
def test_subst_fluoro_vec():
vec = np.ones_like(eg.c2h4[1])
elem, xyz, vec = substitute.subst(eg.c2h4[0], eg.c2h4[1], 'f', 2, vec=vec)
soln = np.copy(vec)
soln[2] = 0.
assert np.all(elem == eg.c2h3f[0])
assert np.allclose(xyz, eg.c2h3f[1])
assert np.allclose(vec, soln)
def subst(self, lbl, isub, ibond=None, pl=None):
"""Replaces an atom or set of atoms with a substituent.
Parameters
----------
lbl : str
The substituent label.
isub : int or list
The atomic index (or indices) to be replaced by the substituent.
ibond : int, optional
The atomic index of the atom bonded to position isub. If None
(default), the nearest atom is chosen.
pl : int or array_like, optional
The atomic index or vector defining the xz-plane of the
substituent. See :func:`substitute.subst` for more details.
"""
args = (self._elem, self._xyz, lbl, isub)
kwargs = dict(ibond=ibond, pl=pl, vec=self._vec)
self._elem, self._xyz, vec = substitute.subst(*args, **kwargs)
if self.print_vec:
self._vec = vec
else:
self._vec = np.zeros_like(self._xyz)
self._check()
def test_subst_methyl_plane_vec():
elem, xyz, vec = substitute.subst(eg.c2h4[0], eg.c2h4[1], 'ch3', 2,
pl=[1, 1, 1])
assert np.all(elem == eg.c2h3me_ax[0])
assert np.allclose(xyz, eg.c2h3me_ax[1])
def test_subst_fluoro_ibond():
elem, xyz, vec = substitute.subst(eg.c2h4[0], eg.c2h4[1], 'f', 2, ibond=0)
assert np.all(elem == eg.c2h3f[0])
assert np.allclose(xyz, eg.c2h3f[1])
def test_subst_fluoro_with_fluoro():
inp_xyz = np.copy(eg.c2h3f[1])
inp_xyz[2] += np.ones(3)
elem, xyz, vec = substitute.subst(eg.c2h3f[0], inp_xyz, 'f', 2)
assert np.all(elem == eg.c2h3f[0])
assert np.allclose(xyz, inp_xyz)
def test_subst_fluoro_multisub():
elem, xyz, vec = substitute.subst(eg.c2h4[0], eg.c2h4[1], 'f', [2, 3])
assert np.all(elem == np.hstack((eg.c2h3f[0][:3], eg.c2h3f[0][4:])))
assert np.allclose(xyz, np.vstack((eg.c2h3f[1][:3], eg.c2h3f[1][4:])))
def test_subst_fluoro_default():
elem, xyz, vec = substitute.subst(eg.c2h4[0], eg.c2h4[1], 'f', 2)
assert np.all(elem == eg.c2h3f[0])
assert np.allclose(xyz, eg.c2h3f[1])
assert np.allclose(vec, np.zeros_like(xyz))
def test_subst_fluoro_multisub():
elem, xyz, vec = substitute.subst(eg.c2h4[0], eg.c2h4[1], 'f', [2, 3])
assert np.all(elem == np.hstack((eg.c2h3f[0][:3], eg.c2h3f[0][4:])))
assert np.allclose(xyz, np.vstack((eg.c2h3f[1][:3], eg.c2h3f[1][4:])))
def subst(self, lbl, isub, ibond=None, pl=None):
"""Replaces an atom or set of atoms with a substituent."""
args = (self._elem, self._xyz, lbl, isub)
kwargs = dict(ibond=ibond, pl=pl, vec=self._vec)
self._elem, self._xyz, self._vec = substitute.subst(*args, **kwargs)
self._check()
def test_subst_fluoro_ibond():
elem, xyz, vec = substitute.subst(eg.c2h4[0], eg.c2h4[1], 'f', 2, ibond=0)
assert np.all(elem == eg.c2h3f[0])
assert np.allclose(xyz, eg.c2h3f[1])
def test_subst_fluoro_with_fluoro():
inp_xyz = np.copy(eg.c2h3f[1])
inp_xyz[2] += np.ones(3)
elem, xyz, vec = substitute.subst(eg.c2h3f[0], inp_xyz, 'f', 2)
assert np.all(elem == eg.c2h3f[0])
assert np.allclose(xyz, inp_xyz)
def test_subst_ibond_equals_ipos():
with pytest.raises(ValueError, match=r'sub and bond indices .*'):
elem, xyz, vec = substitute.subst(eg.c2h4[0], eg.c2h4[1], 'f', 2,
ibond=2)
def test_subst_pl_equals_ibond():
with pytest.raises(ValueError, match=r'plane and bond indices .*'):
elem, xyz, vec = substitute.subst(eg.c2h4[0], eg.c2h4[1], 'f', 2,
ibond=3, pl=3)
def test_subst_fluoro_default():
elem, xyz, vec = substitute.subst(eg.c2h4[0], eg.c2h4[1], 'f', 2)
assert np.all(elem == eg.c2h3f[0])
assert np.allclose(xyz, eg.c2h3f[1])
assert vec is None