def mark_aromatic_bonds(self):
sssr = self.get_smallest_independent_cycles()
if len(sssr) > 10:
# turn off processing of all cycles - it would be too slow, just use SSSR
rings = sssr
else:
rings = self.get_all_cycles(
) #self.get_smallest_independent_cycles()
solved = [1]
# we need to repeat it to mark such things as 'badly' drawn naphtalene (no double bond in the centre)
while solved:
solved = []
for aring in rings:
els = [
self._get_atoms_possible_aromatic_electrons(a, aring)
for a in aring
]
if () in els:
continue
for comb in common.gen_combinations_of_series(els):
if sum(comb) % 4 == 2:
bring = self.vertex_subgraph_to_edge_subgraph(aring)
for b in bring:
b.aromatic = 1
#b.order = 4
solved.append(aring)
break
for r in solved:
rings.remove(r)
def mark_aromatic_bonds( self):
sssr = self.get_smallest_independent_cycles()
if len( sssr) > 10:
# turn off processing of all cycles - it would be too slow, just use SSSR
rings = sssr
else:
rings = self.get_all_cycles() #self.get_smallest_independent_cycles()
solved = [1]
# we need to repeat it to mark such things as 'badly' drawn naphtalene (no double bond in the centre)
while solved:
solved = []
for aring in rings:
els = [self._get_atoms_possible_aromatic_electrons( a, aring) for a in aring]
if () in els:
continue
for comb in common.gen_combinations_of_series( els):
if sum( comb) % 4 == 2:
bring = self.vertex_subgraph_to_edge_subgraph( aring)
for b in bring:
b.aromatic = 1
#b.order = 4
solved.append( aring)
break
for r in solved:
rings.remove( r)
def localize_aromatic_bonds(self):
"""localizes aromatic bonds (does not relocalize already localized ones),
for those that are not aromatic but marked so
(it is for instance possible to misuse 'cccc' in smiles to create butadiene)
they will be properly localized but marked as non-aromatic"""
erings = self.get_smallest_independent_cycles_e()
# filter off rings without aromatic bonds
erings = filter(lambda x: len([b for b in x if b.aromatic]), erings)
rings = map(self.edge_subgraph_to_vertex_subgraph, erings)
# sort rings
rings.sort(
lambda x, y: len(y) % 2 - len(x) % 2) # odd size rings first
last_rings = []
while rings:
# we have to continue with the neighbor rings of the last_ring (or the rings before)
intersection = None
if last_rings:
aring = None
while last_rings:
last_ring = last_rings.pop(-1)
for ring in rings:
intersection = ring & last_ring
if intersection:
aring = ring
last_rings.append(last_ring)
break
if aring:
break
if not aring:
aring = rings.pop(0)
else:
rings.remove(aring)
else:
aring = rings.pop(0)
last_rings.append(aring)
# convert ring from set to list
aring = self.sort_vertices_in_path(
aring, start_from=intersection and intersection.pop() or None)
# taken from mark_aromatic_bonds
els = [
self._get_atoms_possible_aromatic_electrons(a, aring)
for a in aring
]
if () in els:
continue # misuse of aromatic bonds (e.g. by smiles) or e.g. tetrahydronaphtalene
for comb in common.gen_combinations_of_series(els):
if sum(comb) % 4 == 2:
aring.append(aring[0])
comb.append(comb[0])
# at first we process the bonds that are surely single (like C-S-C in thiophene)
already_set = None
for i in range(len(aring) - 1):
if comb[i] + comb[i + 1] != 2:
# these bonds must be single
b = aring[i].get_edge_leading_to(aring[i + 1])
b.order = 1
already_set = i
if already_set != None:
# we reorder the comb and aring to start from the already set bonds
j = already_set + 1
aring = aring[j:len(aring)] + aring[1:j]
aring.insert(0, aring[-1])
comb = comb[j:len(comb)] + comb[1:j]
comb.insert(0, comb[-1])
i = 0
while i + 1 < len(aring):
if comb[i] + comb[i + 1] == 2:
b = aring[i].get_edge_leading_to(aring[i + 1])
assert b != None # should be
# to assure alternating bonds
bs1 = [
bo for bo in aring[i].get_neighbor_edges()
if bo.order == 2 and bo.aromatic and bo != b
]
bs2 = [
bo for bo in aring[i + 1].get_neighbor_edges()
if bo.order == 2 and bo.aromatic and bo != b
]
if len(bs1) == 0 and len(bs2) == 0:
b.order = 2
else:
b.order = 1
i += 1
break
self.localize_fake_aromatic_bonds()
def localize_aromatic_bonds( self):
"""localizes aromatic bonds (does not relocalize already localized ones),
for those that are not aromatic but marked so
(it is for instance possible to misuse 'cccc' in smiles to create butadiene)
they will be properly localized but marked as non-aromatic"""
erings = self.get_smallest_independent_cycles_e()
# filter off rings without aromatic bonds
erings = filter( lambda x: len( [b for b in x if b.aromatic]), erings)
rings = map( self.edge_subgraph_to_vertex_subgraph, erings)
# sort rings
rings.sort( lambda x,y: len(y)%2 - len(x)%2) # odd size rings first
last_rings = []
while rings:
# we have to continue with the neighbor rings of the last_ring (or the rings before)
intersection = None
if last_rings:
aring = None
while last_rings:
last_ring = last_rings.pop( -1)
for ring in rings:
intersection = ring & last_ring
if intersection:
aring = ring
last_rings.append( last_ring)
break
if aring:
break
if not aring:
aring = rings.pop(0)
else:
rings.remove( aring)
else:
aring = rings.pop(0)
last_rings.append( aring)
# convert ring from set to list
aring = self.sort_vertices_in_path( aring, start_from=intersection and intersection.pop() or None)
# taken from mark_aromatic_bonds
els = [self._get_atoms_possible_aromatic_electrons( a, aring) for a in aring]
if () in els:
continue # misuse of aromatic bonds (e.g. by smiles) or e.g. tetrahydronaphtalene
for comb in common.gen_combinations_of_series( els):
if sum( comb) % 4 == 2:
aring.append( aring[0])
comb.append( comb[0])
# at first we process the bonds that are surely single (like C-S-C in thiophene)
already_set = None
for i in range( len( aring) -1):
if comb[i] + comb[i+1] != 2:
# these bonds must be single
b = aring[i].get_edge_leading_to( aring[i+1])
b.order = 1
already_set = i
if already_set != None:
# we reorder the comb and aring to start from the already set bonds
j = already_set + 1
aring = aring[j:len(aring)] + aring[1:j]
aring.insert( 0, aring[-1])
comb = comb[j:len(comb)] + comb[1:j]
comb.insert( 0, comb[-1])
i = 0
while i+1 < len( aring):
if comb[i] + comb[i+1] == 2:
b = aring[i].get_edge_leading_to( aring[i+1])
assert b != None # should be
# to assure alternating bonds
bs1 = [bo for bo in aring[i].get_neighbor_edges() if bo.order == 2 and bo.aromatic and bo!=b]
bs2 = [bo for bo in aring[i+1].get_neighbor_edges() if bo.order == 2 and bo.aromatic and bo!=b]
if len( bs1) == 0 and len( bs2) == 0:
b.order = 2
else:
b.order = 1
i += 1
break
self.localize_fake_aromatic_bonds()