Some oxygens appear to be SP3 hybridized and aromatic at the same time

[Boxylmer]

Hey Mojaie!

Should this be happening? I've found a few molecules that have oxygens showing up as SP3 and aromatic, see the MWE below for the ones I've caught.

smiles = [
    "C1=CC=C2C(=C1)C=CC(=O)O2"
    "CC1=NOC=C1"
    "C1=CON=C1"
    "C1=CC=C2C(=C1)C=CO2"
    "C1=COC(=C1)C=O"
    "C1=COC(=C1)C#N"
]
for smile in smiles
    mol = smilestomol(smile)
    hybs = hybridization(mol)
    as = atomsymbol(mol)
    ar = is_aromatic(mol)
    for i in eachindex(hybs, as, ar)
        if hybs[i] == :sp3 && as[i] == :O && ar[i]
            println(smile)
            break
        end
    end
end

Best, Will.

[Boxylmer]

Similarly I'm catching some sp3 aromatic nitrogen and sulfur as well, but not carbon. The full table of the combinations are shown below (I'm working on some fragmentation schemes)

sp3 O (aromatic) => 6
sp3 S => 11
H => 1875
sp3 N => 39
sp2 N (aromatic) => 18
sp2 C (aromatic) => 1425
sp3 O => 166
sp2 C => 118
sp3 I => 2
sp3 Cl => 152
sp2 O => 134
sp3 P => 1
S => 10
sp2 N => 34
sp3 S (aromatic) => 5
P => 2
sp3 F => 35
sp3 N (aromatic) => 11
sp2 S => 3
sp3 Br => 40
sp3 C => 344
sp N => 11
sp C => 16

[mojaie]

Thank you for the comment. I'm working on hybridization now and there maybe some degradation. For now, newly introduced hybridization_delocalized(mol) method may work better.

[mojaie]

Still discretized aromaticity and orbital hybridization is a difficult problem and there should be options which types of atoms are considered aromatic/hybridized

[mojaie]

5556424f 16308956 f9a99c29 and 51ca339a may improved hybridization and aromaticity determination. This will be available on upcoming v0.17.0.