The following features are available for atom featurization in one-hot encoding format and are available in the atom_onehot_feature_names_to_array function. They are also listed in the list_all_atom_onehot_features function.
| Feature | Description |
|---|---|
atomic-number |
All atomic numbers from 1 - 100 |
atomic-number-common |
First 4 rows of periodic table and Iodine |
atomic-number-organic |
Organic chemistry elements only |
degree |
Number of explicit neighboring atoms |
total-degree |
Number of neighboring atoms including hydrogens |
valence |
Total valence of the atom |
implicit-valence |
Implicit valence of the atom |
hybridization |
Hybridization type of the atom (SP, SP2, SP3, SP3D, SP3D2) |
hybridization-organic |
Hybridization type of the atom for organic elements (S, SP, SP2, SP3) |
chirality |
Chirality of the atom |
group |
Periodic table group of the atom |
period |
Periodic table period of the atom |
formal-charge |
Formal charge on atom |
num-hydrogens |
Total number of hydrogens (explicit and implicit) on an atom |
ring-size |
Size of the ring the atom is present in (ring size 3 - 8 are multi-hot encoded) |
The following features are available for atom featurization in floating-point format and are available in the atom_float_feature_names_to_array function. They are also listed in the list_all_atom_float_features function.
| Feature | Description |
|---|---|
atomic-number |
Atomic number of the atom |
mass |
Atomic mass of the atom |
valence |
Total valence of the atom |
implicit-valence |
Implicit valence of the atom |
hybridization |
Numerical representation of hybridization state |
chirality |
Numerical encoding of atom chirality |
aromatic |
Whether the atom is aromatic (1.0) or not (0.0) |
in-ring |
Whether the atom is in a ring (1.0) or not (0.0) |
min-ring |
Size of the smallest ring containing this atom |
max-ring |
Size of the largest ring containing this atom |
num-ring |
Number of rings the atom is part of |
degree |
Number of bonded neighbors |
radical-electron |
Number of radical electrons |
formal-charge |
Formal charge on the atom |
group |
Periodic table group number |
period |
Periodic table period number |
single-bond |
Number of single bonds |
aromatic-bond |
Number of aromatic bonds |
double-bond |
Number of double bonds |
triple-bond |
Number of triple bonds |
is-carbon |
Whether the atom is carbon (1.0) or not (0.0) |
hydrogen-bond-donor |
Whether the atom can donate hydrogen bonds (1.0) or not (0.0) determined by SMARTS match |
hydrogen-bond-acceptor |
Whether the atom can accept hydrogen bonds (1.0) or not (0.0) determined by SMARTS match |
acidic |
Whether the atom is acidic (1.0) or not (0.0) determined by SMARTS match |
basic |
Whether the atom is basic (1.0) or not (0.0) determined by SMARTS match |
The following features are available for bond featurization and are available in the bond_feature_names_to_array function. They are also listed in the list_all_bond_features function.
| Feature | Description |
|---|---|
is-null |
Binary indicator: 1 if a bond is present, 0 otherwise |
bond-type-float |
Numerical representation of bond type (e.g., 2.0 for double bond, 1.5 for aromatic) |
bond-type-onehot |
One-hot encoding of selected bond types |
in-ring |
Binary indicator: 1.0 if the bond is in at least one ring, 0.0 otherwise |
conjugated |
Binary indicator: 1.0 if the bond is conjugated, 0.0 otherwise |
stereo |
One-hot encoding of bond stereo configurations |
conformer-bond-length |
Length of the bond from a conformer (either first or computed) |
estimated-bond-length |
Length of the bond estimated using a fast heuristic |