QM9EdgeDataset
- class dgl.data.QM9EdgeDataset(label_keys=None, raw_dir=None, force_reload=False, verbose=True, transform=None)[source]
Bases:
DGLDataset
QM9Edge dataset for graph property prediction (regression)
This dataset consists of 130,831 molecules with 19 regression targets. Nodes correspond to atoms and edges correspond to bonds.
- This dataset differs from
QM9Dataset
in the following aspects: It includes the bonds in a molecule in the edges of the corresponding graph while the edges in
QM9Dataset
are purely distance-based.It provides edge features, and node features in addition to the atoms’ coordinates and atomic numbers.
It provides another 7 regression tasks(from 12 to 19).
This class is built based on a preprocessed version of the dataset, and we provide the preprocessing datails here.
Reference:
For Statistics:
Number of graphs: 130,831.
Number of regression targets: 19.
Node attributes:
pos: the 3D coordinates of each atom.
attr: the 11D atom features.
Edge attributes:
edge_attr: the 4D bond features.
Regression targets:
Keys
Property
Description
Unit
mu
Dipole moment
alpha
Isotropic polarizability
homo
Highest occupied molecular orbital energy
lumo
Lowest unoccupied molecular orbital energy
gap
Gap between
andr2
Electronic spatial extent
zpve
Zero point vibrational energy
U0
Internal energy at 0K
U
Internal energy at 298.15K
H
Enthalpy at 298.15K
G
Free energy at 298.15K
Cv
Heat capavity at 298.15K
U0_atom
Atomization energy at 0K
U_atom
Atomization energy at 298.15K
H_atom
Atomization enthalpy at 298.15K
G_atom
Atomization free energy at 298.15K
A
Rotational constant
B
Rotational constant
C
Rotational constant
- Parameters:
label_keys (list) – Names of the regression property, which should be a subset of the keys in the table above. If not provided, it will load all the labels.
raw_dir (str) – Raw file directory to download/contains the input data directory. Default: ~/.dgl/
force_reload (bool) – Whether to reload the dataset. Default: False.
verbose (bool) – Whether to print out progress information. Default: True.
transform (callable, optional) – A transform that takes in a
DGLGraph
object and returns a transformed version. TheDGLGraph
object will be transformed before every access.
- Raises:
UserWarning – If the raw data is changed in the remote server by the author.
Examples
>>> data = QM9EdgeDataset(label_keys=['mu', 'alpha']) >>> data.num_tasks 2
>>> # iterate over the dataset >>> for graph, labels in data: ... print(graph) # get information of each graph ... print(labels) # get labels of the corresponding graph ... # your code here... >>>
- __getitem__(idx)[source]
Get graph and label by index
- Parameters:
idx (int) – Item index
- Returns:
dgl.DGLGraph – The graph contains:
ndata['pos']
: the coordinates of each atomndata['attr']
: the features of each atomedata['edge_attr']
: the features of each bond
Tensor – Property values of molecular graphs
- This dataset differs from