Table 1 Molecular graph attributes used at the atom level.
From: Prediction of peptide cleavage sites using protein language models and graph neural networks
Graph component | Attributes | Description |
|---|---|---|
Nodes (atoms) | Atom-type | Type of atoms |
Degree | Number of covalent bonds | |
Charge | Formal charge | |
Chirality | R or S (null if not applicable) | |
Number of hydrogens | Number of attached H atoms | |
Hybridization | sp, sp2, sp3, sp3d, sp3d2 | |
Valance | Total valence electrons | |
Edges (bonds between atoms) | Bond-type | Single, double, triple, aromatic |
Conjugation | Is conjugated | |
Ring | Bond is part of a ring | |
Stereochemistry | None, any, Z, E |
