def parseBonds(self):
'''
read some bond attributes
'''
bonds = {} # dictionary with bond objects, both orientations
atom_pairs = [] # atom index pairs only, unique
for bond in self.tkmol.iterateBonds():
# start, end, bond_type, stereo = numbers
start = bond.source().index()
end = bond.destination().index()
bond_type = bond.bondOrder() # 1,2,3,4 for single, double, triple, aromatic
stereo = bond.bondStereo()
start_atom = self.atoms[start]
end_atom = self.atoms[end]
bond = Bond(self.options, start_atom, end_atom, bond_type, stereo)
# we store both orientations of the bond, since we don't know yet
# which way it will be used
bonds[(start, end)] = bond
bonds[(end, start)] = bond.invert()
atom_pairs.append((start, end))
return bonds, atom_pairs
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)
