def aromatizeRing(self, ring, center_x, center_y):
'''
render a ring that is aromatic and is a regular polygon
'''
# first, set all bonds to aromatic
ringbonds = list(ring.iterateBonds())
for tkbond in ringbonds:
bond = self._getBond(tkbond)
bond.bond_type = 'aromatic'
# any bond can serve as the anchor for the circle,
# so we'll just use the last one from the loop
atom = bond.end_atom
outer_r, angle = compare_positions(atom.x, atom.y, center_x, center_y)
# angle is based on raw coordinates - adjust for user-set rotation
angle += self.options['rotate']
# outer_r calculated from raw coordinates, must be adjusted
# for bond scaling that may have taken place
outer_r *= self.bond_scale
alpha = ( math.pi / 2 - math.pi / len(ringbonds) )
inner_r = math.sin(alpha) * outer_r
arb = AromaticRingBond(self.options, bond, angle, outer_r, inner_r)
bond.descendants.append(arb)
def annotateRing(self, ring, is_aromatic):
'''
determine center, symmetry and aromatic character of ring
I wonder if indigo would tell us directly about these ...
annotate double bonds in rings, or alternatively decorate
ring with aromatic circle.
'''
atoms = set()
bond_lengths = []
bonds = []
for tkbond in ring.iterateBonds():
bond = self._getBond(tkbond)
bonds.append(bond)
atoms.add(self.atoms[bond.start_atom.idx])
atoms.add(self.atoms[bond.end_atom.idx])
bond_lengths.append(bond.length)
if len(bonds) > 8: # large rings may foul things up, so we skip them.
return
bl_max = max(bond_lengths)
bl_spread = (bl_max - min(bond_lengths)) / bl_max
# determine ring center
center_x = sum([atom.x for atom in atoms]) / len(atoms)
center_y = sum([atom.y for atom in atoms]) / len(atoms)
# compare distances from center. Also remember atoms and bond
# angles; if the ring ends up being aromatized, we flag those
# angles as occupied (by the fancy circle inside the ring).
atom_angles = []
center_distances = []
for atom in atoms:
length, angle = compare_positions(atom.x, atom.y, center_x, center_y)
center_distances.append(length)
atom_angles.append((atom, angle))
cd_max = max(center_distances)
cd_spread = (cd_max - min(center_distances)) / cd_max
tolerance = 0.05
is_symmetric = (cd_spread <= tolerance and bl_spread <= tolerance)
if is_aromatic and is_symmetric and self.options['aromatic_circles']:
# ring meets all requirements to be displayed with circle inside
self.aromatizeRing(ring, center_x, center_y)
# flag bond angles as occupied
for atom, angle in atom_angles:
atom.bond_angles.append(angle)
else: # flag orientation individual bonds - will influence
# rendering of double bonds
for bond in bonds:
bond.is_clockwise(center_x, center_y)
