def process_cross_bonds(self):
'''
if cross bonds have been declared:
1. tag the corresponding bonds within the tree as no-ops
2. create a ghost-bond connection from exit_atom to start atom
3. create a drawn duplicate of the cross bond
4. append 2 and 3 as branch to the exit atom
this is unfortunately all a little hackish.
'''
cross_bonds = self.options['cross_bond']
for start1, end1 in cross_bonds:
start = start1 - 1
end = end1 - 1
# retrieve the matching bond that's in the parse tree
for combo in ((start, end), (end, start)):
if combo in self.seen_bonds:
bond = self.bonds[combo]
break
else: # referenced bond doesn't exist
raise MCFError, "bond %s-%s doesn't exist" % (start1, end1)
# very special case: the bond _might_ already be the very
# last one to be rendered - then we just tag it
if self.exit_bond.descendants and bond is self.exit_bond.descendants[-1]:
bond.set_cross(last=True)
continue
# create a copy of the bond that will be rendered later
bond_copy = bond.clone()
# tag original bond as no-op
bond.set_link()
# modify bond copy
bond_copy.set_cross()
bond_copy.to_phantom = True # don't render atom again
bond_copy.descendants = [] # forget copied descendants
if bond_copy.start_atom is not self.exit_atom: # usual case
# create a pseudo bond from the exit atom to the start atom
# pseudo bond will not be drawn, serves only to "move the pen"
pseudo_bond = Bond(self.options,
self.exit_atom,
bond_copy.start_atom)
pseudo_bond.set_link()
pseudo_bond.to_phantom = True # don't render the atom, either
bond_copy.parent = pseudo_bond
pseudo_bond.descendants.append(bond_copy)
pseudo_bond.parent = self.exit_bond
self.exit_bond.descendants.append(pseudo_bond)
else: # occasionally, the molecule's exit atom may be the starting point
# of the elevated bond
self.exit_bond.descendants.append(bond_copy)
def link_atoms(self, x, y):
'''
connect atoms with indexes x and y using a pseudo bond.
Helper for connect_fragments
'''
start_atom = self.atoms[x]
end_atom = self.atoms[y]
bond = Bond(self.options, start_atom, end_atom)
bond.set_link()
self.bonds[(x, y)] = bond
self.bonds[(y, x)] = bond.invert()
start_atom.neighbors.append(y)
end_atom.neighbors.append(x)
