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. 2023 Jan 26;19(1):e1010812. doi: 10.1371/journal.pcbi.1010812

Table 3. Atom and bond features.

atom feature Description Size
atom type [B, C, N, O, F, Si, P, S, Cl, As, Se, Br, Te, I, At, meta 16 (one-hot)
degree number of covalent bonds [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10] 11 (one-hot)
hybridization [sp, sp2, sp3, sp3d, sp3d2] 5 (one-hot)
implicit valence implicit valence of the atom [0, 1, 2, 3, 4, 5, 6,] 7 (one-hot)
radical electrons number of radical electrons 1(integer)
formal charge formal charge of the atom 1 (integer)
aromatic whether the atom is part of an aromatic system 1 (integer)
bond feature Description Size
bone type [single, double, triple, aromatic] 4 (one-hot)
conjugated whether the bond is part of a conjugated system 1 (integer)
ring whether the bond is part of a ring 1 (integer)