Table 4 Descriptions of atomic and bond features
From: Deep clustering of small molecules at large-scale via variational autoencoder embedding and K-means
Feature type | Attribute | Size | Description |
|---|---|---|---|
Atomic features | Atom type | 118 | Known chemical elements (by atomic number) |
| Â | Degree | 6 | Number of bonds the atom is involved in |
| Â | Formal charge | 5 | Electronic charge assigned to an atom |
| Â | Chirality | 4 | Unspecified, tetrahedral CW/CCW, or other types of chirality |
| Â | Number of H | 5 | Number of bonded hydrogen atoms |
| Â | Hybridization | 5 | sp, sp2, sp3, sp3d, or sp3d2 |
| Â | Aromaticity | 1 | Whether the atom is aromatic |
| Â | Atomic mass | 1 | Mass of the atom |
Bond features | Bond type | 4 | Single, double, triple, or aromatic |
| Â | Conjugated | 1 | Whether the bond is conjugated |
| Â | Ring | 1 | Whether the bond is in a ring |
| Â | Stereo | 6 | Stereochemistry of bonds (none, any, E/Z or cis/trans) |