def continue_ring_system(gra, keys_lst, vma, zma_keys):
""" continue constructing a v-matrix for a ring system
Exactly one atom in the ring system must already be in the v-matrix, and
this atom must be in the starting ring of the decomposed ring system key
list.
"""
# First, get the ring keys
keys_lst = list(keys_lst)
keys = keys_lst.pop(0)
# Break the bonds joining the last pair of atoms in each arc
gra = remove_bonds(gra, [(k[-1], k[-2]) for k in keys_lst])
# Start by constructing the v-matrix for the first ring
vma, zma_keys = continue_ring(gra, keys, vma, zma_keys)
# Now, complete the ring system by continuing the v-matrix along each arc
for keys in keys_lst:
# Note that the atoms on each end of the arc are already in the
# v-matrix, so we ignore those
vma, zma_keys = continue_chain(gra, keys[1:-1], vma, zma_keys,
term_hydrogens=False)
return vma, zma_keys
def ring_system(gra, keys_lst):
""" generate a v-matrix for a ring system
:param gra: the graph
:param keys_lst: the first entry contains keys for a ring and each next one
contains keys for an arc that starts and ends on atoms in the preceding
entries
"""
# First, get the ring keys
keys_lst = list(keys_lst)
keys = keys_lst.pop(0)
# Break the bonds joining the last pair of atoms in each arc
gra = remove_bonds(gra, [(k[-1], k[-2]) for k in keys_lst])
# Start by constructing the v-matrix for the first ring
vma, zma_keys = ring(gra, keys)
# Now, complete the ring system by continuing the v-matrix along each arc
for keys in keys_lst:
# Note that the atoms on each end of the arc are already in the
# v-matrix, so we ignore those
vma, zma_keys = continue_chain(gra, keys[1:-1], vma, zma_keys)
return vma, zma_keys
def ring(gra, keys):
""" generate a v-matrix for a ring
All neighboring atoms along the ring will be included
:param gra: the graph
:param keys: ring keys, in the order they should appear in the z-matrix
"""
# Break the bond between the first and last atoms to make this a chain
gra = remove_bonds(gra, [(keys[0], keys[-1])])
# Now, construct a v-matrix for the chain
vma, zma_keys = chain(gra, keys, term_hydrogens=True)
return vma, zma_keys
def continue_ring(gra, keys, vma, zma_keys):
""" continue constructing a v-matrix around a ring
All neighboring atoms along the ring will be included
Exactly one atom in the ring must already be in the v-matrix.
"""
# Find the connecting key
key = next((k for k in keys if k in zma_keys), None)
assert key is not None, (
"There must be a ring atom already in the v-matrix")
# Cycle the connecting key to the front of the ring
keys = cycle_ring_atom_key_to_front(keys, key)
# Break the bond between the first and last atoms to make this a chain
gra = remove_bonds(gra, [(keys[0], keys[-1])])
# Now, construct a v-matrix for the chain
vma, zma_keys = continue_chain(gra, keys, vma, zma_keys)
return vma, zma_keys
