def distance_bounds_matrices(gra, keys, sp_dct=None):
""" initial distance bounds matrices
:param gra: molecular graph
:param keys: atom keys specifying the order of indices in the matrix
:param sp_dct: a 2d dictionary giving the shortest path between any pair of
atoms in the graph
"""
assert set(keys) <= set(atom_keys(gra))
sub_gra = subgraph(gra, keys, stereo=True)
sp_dct = atom_shortest_paths(sub_gra) if sp_dct is None else sp_dct
bounds_ = path_distance_bounds_(gra)
natms = len(keys)
umat = numpy.zeros((natms, natms))
lmat = numpy.zeros((natms, natms))
for (idx1, key1), (idx2,
key2) in itertools.combinations(enumerate(keys), 2):
if key2 in sp_dct[key1]:
path = sp_dct[key1][key2]
ldist, udist = bounds_(path)
lmat[idx1, idx2] = lmat[idx2, idx1] = ldist
umat[idx1, idx2] = umat[idx2, idx1] = udist
else:
# they are disconnected
lmat[idx1, idx2] = lmat[idx2,
idx1] = closest_approach(gra, key1, key2)
umat[idx1, idx2] = umat[idx2, idx1] = 999
assert lmat[idx1, idx2] <= umat[idx1, idx2], (
"Lower bound exceeds upper bound. This is a bug!\n"
f"{string(gra, one_indexed=False)}\npath: {str(path)}\n")
return lmat, umat
def ts_distance_bounds_matrices(gra,
keys,
frm_bnds_dct,
rct_geos=None,
relax_torsions=False,
sp_dct=None):
""" distance bounds matrices for a transition state
:param gra: molecular graph
:param keys: atom keys specifying the order of indices in the matrix
:param frm_bnds_dct: bounds for bonds formed in the reaction; the keys are
bond keys and the values are lower and upper distance bounds for those
forming bonds
:param rct_geos: reactant geometries; must follow the same order as the
atoms in `keys
:param relax_torsions: whether or not to allow torsions to change from
their value in the reactant geometries
:param sp_dct: a 2d dictionary giving the shortest path between any pair of
atoms in the graph
"""
sp_dct = atom_shortest_paths(gra) if sp_dct is None else sp_dct
natms = len(keys)
lmat, umat = distance_bounds_matrices(gra, keys)
# save the current values so that we can overwrite the fixed torsions below
lmat_old = numpy.copy(lmat)
umat_old = numpy.copy(umat)
# 2. set known geometric parameters
if rct_geos:
xmats = [
automol.geom.base.coordinates(geo, angstrom=True)
for geo in rct_geos
]
dmats = list(map(embed.distance_matrix_from_coordinates, xmats))
start = 0
for dmat in dmats:
dim, _ = numpy.shape(dmat)
end = start + dim
lmat[start:end, start:end] = dmat
umat[start:end, start:end] = dmat
start = end
# 3. reopen bounds on the torsions from the reactant
if relax_torsions:
tors_ijs = [[i, j] for i, j in itertools.combinations(range(natms), 2)
if j in sp_dct[i] and len(sp_dct[i][j]) >= 4]
tors_ijs += list(map(list, map(reversed, tors_ijs)))
tors_idxs = tuple(map(list, zip(*tors_ijs)))
lmat[tors_idxs] = lmat_old[tors_idxs]
umat[tors_idxs] = umat_old[tors_idxs]
# 1. set distance bounds for the forming bonds
for bnd, (ldist, udist) in frm_bnds_dct.items():
idx1 = tuple(bnd)
idx2 = tuple(reversed(idx1))
lmat[idx1] = lmat[idx2] = ldist
umat[idx1] = umat[idx2] = udist
return lmat, umat
def join_distance_bounds_matrices(gra,
keys,
dist_range_dct,
geos=None,
relax_angles=False,
relax_torsions=False,
sp_dct=None,
angstrom=True):
""" distance bounds matrices for joining multiple geometries
:param gra: molecular graph:
:param keys: atom keys specifying the order of indices in the matrix
:param dist_range_dct: distance ranges for specific atoms in the graph
:param geos: (optional) geometries which will be used to fix the bond
angles, bond distances, and chiralities of all connected atoms in the
graph; if `relax_torsions` is False, the 4-atom dihedral angles will be
allowed to vary as well
:param relax_torsions: whether or not to allow torsions to change from
their value in the reactant geometries
:param sp_dct: a 2d dictionary giving the shortest path between any pair of
atoms in the graph
"""
sp_dct = atom_shortest_paths(gra) if sp_dct is None else sp_dct
natms = len(keys)
lmat, umat = distance_bounds_matrices(gra, keys)
# save the current values so that we can overwrite the fixed torsions below
lmat_old = numpy.copy(lmat)
umat_old = numpy.copy(umat)
# 1. set known geometric parameters
if geos:
xmats = [
automol.geom.base.coordinates(geo, angstrom=angstrom)
for geo in geos
]
dmats = list(map(embed.distance_matrix_from_coordinates, xmats))
start = 0
for dmat in dmats:
dim, _ = numpy.shape(dmat)
end = start + dim
lmat[start:end, start:end] = dmat
umat[start:end, start:end] = dmat
start = end
# 2. reopen bounds on the torsions from the reactant
if relax_torsions:
tors_ijs = [[i, j] for i, j in itertools.combinations(range(natms), 2)
if j in sp_dct[i] and len(sp_dct[i][j]) >= 4]
tors_ijs += list(map(list, map(reversed, tors_ijs)))
tors_idxs = tuple(map(list, zip(*tors_ijs)))
lmat[tors_idxs] = lmat_old[tors_idxs]
umat[tors_idxs] = umat_old[tors_idxs]
# 3. reopen bounds on the angles from the reactant
if relax_angles:
ang_ijs = [[i, j] for i, j in itertools.combinations(range(natms), 2)
if j in sp_dct[i] and len(sp_dct[i][j]) >= 3]
ang_ijs += list(map(list, map(reversed, ang_ijs)))
ang_idxs = tuple(map(list, zip(*ang_ijs)))
lmat[ang_idxs] = lmat_old[ang_idxs]
umat[ang_idxs] = umat_old[ang_idxs]
# 4. set distance bounds for the forming bonds
for bnd, (ldist, udist) in dist_range_dct.items():
idx1 = tuple(bnd)
idx2 = tuple(reversed(idx1))
lmat[idx1] = lmat[idx2] = ldist
umat[idx1] = umat[idx2] = udist
return lmat, umat