"""QM9 dataset for graph property prediction (regression)."""
import os
import numpy as np
import scipy.sparse as sp
from .dgl_dataset import DGLDataset
from .utils import download, _get_dgl_url
from ..convert import graph as dgl_graph
from ..transforms import to_bidirected
from .. import backend as F
[docs]class QM9Dataset(DGLDataset):
r"""QM9 dataset for graph property prediction (regression)
This dataset consists of 130,831 molecules with 12 regression targets.
Nodes correspond to atoms and edges correspond to close atom pairs.
This dataset differs from :class:`~dgl.data.QM9EdgeDataset` in the following aspects:
1. Edges in this dataset are purely distance-based.
2. It only provides atoms' coordinates and atomic numbers as node features
3. It only provides 12 regression targets.
Reference:
- `"Quantum-Machine.org" <http://quantum-machine.org/datasets/>`_,
- `"Directional Message Passing for Molecular Graphs" <https://arxiv.org/abs/2003.03123>`_
Statistics:
- Number of graphs: 130,831
- Number of regression targets: 12
+--------+----------------------------------+-----------------------------------------------------------------------------------+---------------------------------------------+
| Keys | Property | Description | Unit |
+========+==================================+===================================================================================+=============================================+
| mu | :math:`\mu` | Dipole moment | :math:`\textrm{D}` |
+--------+----------------------------------+-----------------------------------------------------------------------------------+---------------------------------------------+
| alpha | :math:`\alpha` | Isotropic polarizability | :math:`{a_0}^3` |
+--------+----------------------------------+-----------------------------------------------------------------------------------+---------------------------------------------+
| homo | :math:`\epsilon_{\textrm{HOMO}}` | Highest occupied molecular orbital energy | :math:`\textrm{eV}` |
+--------+----------------------------------+-----------------------------------------------------------------------------------+---------------------------------------------+
| lumo | :math:`\epsilon_{\textrm{LUMO}}` | Lowest unoccupied molecular orbital energy | :math:`\textrm{eV}` |
+--------+----------------------------------+-----------------------------------------------------------------------------------+---------------------------------------------+
| gap | :math:`\Delta \epsilon` | Gap between :math:`\epsilon_{\textrm{HOMO}}` and :math:`\epsilon_{\textrm{LUMO}}` | :math:`\textrm{eV}` |
+--------+----------------------------------+-----------------------------------------------------------------------------------+---------------------------------------------+
| r2 | :math:`\langle R^2 \rangle` | Electronic spatial extent | :math:`{a_0}^2` |
+--------+----------------------------------+-----------------------------------------------------------------------------------+---------------------------------------------+
| zpve | :math:`\textrm{ZPVE}` | Zero point vibrational energy | :math:`\textrm{eV}` |
+--------+----------------------------------+-----------------------------------------------------------------------------------+---------------------------------------------+
| U0 | :math:`U_0` | Internal energy at 0K | :math:`\textrm{eV}` |
+--------+----------------------------------+-----------------------------------------------------------------------------------+---------------------------------------------+
| U | :math:`U` | Internal energy at 298.15K | :math:`\textrm{eV}` |
+--------+----------------------------------+-----------------------------------------------------------------------------------+---------------------------------------------+
| H | :math:`H` | Enthalpy at 298.15K | :math:`\textrm{eV}` |
+--------+----------------------------------+-----------------------------------------------------------------------------------+---------------------------------------------+
| G | :math:`G` | Free energy at 298.15K | :math:`\textrm{eV}` |
+--------+----------------------------------+-----------------------------------------------------------------------------------+---------------------------------------------+
| Cv | :math:`c_{\textrm{v}}` | Heat capavity at 298.15K | :math:`\frac{\textrm{cal}}{\textrm{mol K}}` |
+--------+----------------------------------+-----------------------------------------------------------------------------------+---------------------------------------------+
Parameters
----------
label_keys : list
Names of the regression property, which should be a subset of the keys in the table above.
cutoff : float
Cutoff distance for interatomic interactions, i.e. two atoms are connected in the corresponding graph if the distance between them is no larger than this.
Default: 5.0 Angstrom
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 :class:`~dgl.DGLGraph` object and returns
a transformed version. The :class:`~dgl.DGLGraph` object will be
transformed before every access.
Attributes
----------
num_tasks : int
Number of prediction tasks
num_labels : int
(DEPRECATED, use num_tasks instead) Number of prediction tasks
Raises
------
UserWarning
If the raw data is changed in the remote server by the author.
Examples
--------
>>> data = QM9Dataset(label_keys=['mu', 'gap'], cutoff=5.0)
>>> data.num_tasks
2
>>>
>>> # iterate over the dataset
>>> for g, label in data:
... R = g.ndata['R'] # get coordinates of each atom
... Z = g.ndata['Z'] # get atomic numbers of each atom
... # your code here...
>>>
"""
def __init__(self,
label_keys,
cutoff=5.0,
raw_dir=None,
force_reload=False,
verbose=False,
transform=None):
self.cutoff = cutoff
self.label_keys = label_keys
self._url = _get_dgl_url('dataset/qm9_eV.npz')
super(QM9Dataset, self).__init__(name='qm9',
url=self._url,
raw_dir=raw_dir,
force_reload=force_reload,
verbose=verbose,
transform=transform)
def process(self):
npz_path = f'{self.raw_dir}/qm9_eV.npz'
data_dict = np.load(npz_path, allow_pickle=True)
# data_dict['N'] contains the number of atoms in each molecule.
# Atomic properties (Z and R) of all molecules are concatenated as single tensors,
# so you need this value to select the correct atoms for each molecule.
self.N = data_dict['N']
self.R = data_dict['R']
self.Z = data_dict['Z']
self.label = np.stack([data_dict[key] for key in self.label_keys], axis=1)
self.N_cumsum = np.concatenate([[0], np.cumsum(self.N)])
def download(self):
file_path = f'{self.raw_dir}/qm9_eV.npz'
if not os.path.exists(file_path):
download(self._url, path=file_path)
@property
def num_labels(self):
r"""
Returns
--------
int
Number of prediction tasks.
"""
return self.label.shape[1]
@property
def num_tasks(self):
r"""
Returns
--------
int
Number of prediction tasks.
"""
return self.label.shape[1]
[docs] def __getitem__(self, idx):
r""" Get graph and label by index
Parameters
----------
idx : int
Item index
Returns
-------
dgl.DGLGraph
The graph contains:
- ``ndata['R']``: the coordinates of each atom
- ``ndata['Z']``: the atomic number
Tensor
Property values of molecular graphs
"""
label = F.tensor(self.label[idx], dtype=F.data_type_dict['float32'])
n_atoms = self.N[idx]
R = self.R[self.N_cumsum[idx]:self.N_cumsum[idx + 1]]
dist = np.linalg.norm(R[:, None, :] - R[None, :, :], axis=-1)
adj = sp.csr_matrix(dist <= self.cutoff) - sp.eye(n_atoms, dtype=np.bool)
adj = adj.tocoo()
u, v = F.tensor(adj.row), F.tensor(adj.col)
g = dgl_graph((u, v))
g = to_bidirected(g)
g.ndata['R'] = F.tensor(R, dtype=F.data_type_dict['float32'])
g.ndata['Z'] = F.tensor(self.Z[self.N_cumsum[idx]:self.N_cumsum[idx + 1]],
dtype=F.data_type_dict['int64'])
if self._transform is not None:
g = self._transform(g)
return g, label
[docs] def __len__(self):
r"""Number of graphs in the dataset.
Return
-------
int
"""
return self.label.shape[0]
QM9 = QM9Dataset