lib/rubabel/molecule/fragmentable.rb in rubabel-0.3.0 vs lib/rubabel/molecule/fragmentable.rb in rubabel-0.4.0
- old
+ new
@@ -56,14 +56,15 @@
# breaks the bond and gives the electrons to the oxygen
def carbon_oxygen_esteal(carbon, oxygen)
nmol = self.dup
ncarbon = nmol.atom(carbon.id)
noxygen = nmol.atom(oxygen.id)
+
+ is_carboxyl = noxygen.carboxyl_oxygen?
+
nmol.delete_bond(ncarbon, noxygen)
- ncarbon.remove_an_h!
- #noxygen.ob.set_spin_multiplicity 1
- noxygen.spin = 1
- noxygen.charge = -1
+ ncarbon.remove_a_hydride!
+ noxygen.remove_a_proton!
nmol.split
end
# returns the duplicated molecule and the equivalent atoms
def dup_molecule(atoms=[])