def linear_atoms(geo, gra=None, tol=5.):
""" find linear atoms in a geometry (atoms with 180 degree bond angle)
:param geo: the geometry
:type geo: automol geometry data structure
:param gra: the graph describing connectivity; if None, a connectivity
graph will be generated using default distance thresholds
:type gra: automol graph data structure
:param tol: the tolerance threshold for linearity, in degrees
:type tol: float
:rtype: tuple(int)
"""
gra = connectivity_graph(geo) if gra is None else gra
ngb_idxs_dct = atoms_neighbor_atom_keys(gra)
lin_idxs = []
for idx in range(count(geo)):
nidxs = ngb_idxs_dct[idx]
if len(nidxs) >= 2:
for nidx1, nidx2 in itertools.combinations(nidxs, 2):
ang = central_angle(geo, nidx1, idx, nidx2, degree=True)
if numpy.abs(ang - 180.) < tol:
lin_idxs.append(idx)
lin_idxs = tuple(lin_idxs)
return lin_idxs
def inchi_with_sort(geo, stereo=True):
""" Generate an InChI string from a molecular geometry. (Sort?)
:param geo: molecular geometry
:type geo: automol geometry data structure
:param stereo: parameter to include stereochemistry information
:type stereo: bool
:rtype: str
"""
ich = object_to_hardcoded_inchi_by_key('geom', geo, comp=_compare)
nums = None
if ich is None:
gra = connectivity_graph(geo)
if not stereo:
geo = None
geo_idx_dct = None
else:
geo_idx_dct = dict(enumerate(range(count(geo))))
ich, nums = inchi_with_sort_from_geometry(gra=gra,
geo=geo,
geo_idx_dct=geo_idx_dct)
return ich, nums
def insert_dummies_on_linear_atoms(geo,
lin_idxs=None,
gra=None,
dist=1.,
tol=5.):
""" Insert dummy atoms over linear atoms in the geometry.
:param geo: the geometry
:type geo: automol molecular geometry data structure
:param lin_idxs: the indices of the linear atoms; if None, indices are
automatically determined from the geometry based on the graph
:type lin_idxs: tuple(int)
:param gra: the graph describing connectivity; if None, a connectivity
graph will be generated using default distance thresholds
:type gra: automol molecular graph data structure
:param dist: distance of dummy atom from the linear atom, in angstroms
:type dist: float
:param tol: the tolerance threshold for linearity, in degrees
:type tol: float
:returns: geometry with dummy atoms inserted, along with a dictionary
mapping the linear atoms onto their associated dummy atoms
:rtype: automol molecular geometry data structure
"""
lin_idxs = linear_atoms(geo) if lin_idxs is None else lin_idxs
gra = connectivity_graph(geo) if gra is None else gra
dummy_ngb_idxs = set(dummy_atoms_neighbor_atom_key(gra).values())
assert not dummy_ngb_idxs & set(lin_idxs), (
"Attempting to add dummy atoms on atoms that already have them: {}".
format(dummy_ngb_idxs & set(lin_idxs)))
ngb_idxs_dct = atoms_sorted_neighbor_atom_keys(gra)
xyzs = coordinates(geo, angstrom=True)
def _perpendicular_direction(idxs):
""" find a nice perpendicular direction for a series of linear atoms
"""
triplets = []
for idx in idxs:
for n1idx in ngb_idxs_dct[idx]:
for n2idx in ngb_idxs_dct[n1idx]:
if n2idx != idx:
ang = central_angle(geo,
idx,
n1idx,
n2idx,
degree=True)
if numpy.abs(ang - 180.) > tol:
triplets.append((idx, n1idx, n2idx))
if triplets:
idx1, idx2, idx3 = min(triplets, key=lambda x: x[1:])
xyz1, xyz2, xyz3 = map(xyzs.__getitem__, (idx1, idx2, idx3))
r12 = util.vec.unit_direction(xyz1, xyz2)
r23 = util.vec.unit_direction(xyz2, xyz3)
direc = util.vec.orthogonalize(r12, r23, normalize=True)
else:
if len(idxs) > 1:
idx1, idx2 = idxs[:2]
else:
idx1, = idxs
idx2, = ngb_idxs_dct[idx1]
xyz1, xyz2 = map(xyzs.__getitem__, (idx1, idx2))
r12 = util.vec.unit_direction(xyz1, xyz2)
for i in range(3):
disp = numpy.zeros((3, ))
disp[i] = -1.
alt = numpy.add(r12, disp)
direc = util.vec.unit_perpendicular(r12, alt)
if numpy.linalg.norm(direc) > 1e-2:
break
return direc
# partition the linear atoms into adjacent groups, to be handled together
lin_idxs_lst = sorted(
map(
sorted,
util.equivalence_partition(lin_idxs,
lambda x, y: x in ngb_idxs_dct[y])))
dummy_key_dct = {}
for idxs in lin_idxs_lst:
direc = _perpendicular_direction(idxs)
for idx in idxs:
xyz = numpy.add(xyzs[idx], numpy.multiply(dist, direc))
dummy_key_dct[idx] = count(geo)
geo = insert(geo, 'X', xyz, angstrom=True)
return geo, dummy_key_dct