atoms
Atom features for GNN models.
An atom featurization scheme is a tuple of instances of the classes in this module:
>>> atom_features = (
... AtomicElement(),
... AtomHybridization(),
... AtomConnectivity(),
... AtomAverageFormalCharge(),
... AtomGasteigerCharge(),
... AtomInRingOfSize(3),
... AtomInRingOfSize(4),
... AtomInRingOfSize(5),
... AtomInRingOfSize(6),
... ...
... )
The AtomFeature
and AtomFeatureMeta
classes may be used
to implement your own features.
Classes
Abstract base class for features of atoms. |
|
One-hot encodings for specified elements |
|
One-hot encodings for the number of other atoms this atom is connected to. |
|
One-hot encodings for the specified atomic orbital hybridization modes. |
|
One-hot encoding for whether the atom is aromatic or not. |
|
One-hot encoding for whether the atom is in a ring of any size. |
|
One-hot encoding for whether the atom is in a ring of the given size. |
|
One-hot encoding of the formal charge on an atom. |
|
The formal charge of the atom, averaged over all resonance forms. |
|
The Gasteiger partial charge of the atom. |