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Mufei Li d3560b7155 [DGL-LifeSci] Documentation (#1414) 
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# -*- coding:utf-8 -*-
"""Tencent Alchemy Dataset https://alchemy.tencent.com/"""
import numpy as np
import os
import os.path as osp
import pandas as pd
import pathlib
import zipfile
from collections import defaultdict
from dgl import backend as F
from dgl.data.utils import download, get_download_dir, _get_dgl_url, save_graphs, load_graphs
from rdkit import Chem
from rdkit.Chem import ChemicalFeatures
from rdkit import RDConfig
from ..utils.mol_to_graph import mol_to_complete_graph
from ..utils.featurizers import atom_type_one_hot, atom_hybridization_one_hot, atom_is_aromatic
__all__ = ['TencentAlchemyDataset']
def alchemy_nodes(mol):
"""Featurization for all atoms in a molecule. The atom indices
will be preserved.
Parameters
----------
mol : rdkit.Chem.rdchem.Mol
RDKit molecule object
Returns
-------
atom_feats_dict : dict
Dictionary for atom features
"""
atom_feats_dict = defaultdict(list)
is_donor = defaultdict(int)
is_acceptor = defaultdict(int)
fdef_name = osp.join(RDConfig.RDDataDir, 'BaseFeatures.fdef')
mol_featurizer = ChemicalFeatures.BuildFeatureFactory(fdef_name)
mol_feats = mol_featurizer.GetFeaturesForMol(mol)
mol_conformers = mol.GetConformers()
assert len(mol_conformers) == 1
for i in range(len(mol_feats)):
if mol_feats[i].GetFamily() == 'Donor':
node_list = mol_feats[i].GetAtomIds()
for u in node_list:
is_donor[u] = 1
elif mol_feats[i].GetFamily() == 'Acceptor':
node_list = mol_feats[i].GetAtomIds()
for u in node_list:
is_acceptor[u] = 1
num_atoms = mol.GetNumAtoms()
for u in range(num_atoms):
atom = mol.GetAtomWithIdx(u)
atom_type = atom.GetAtomicNum()
num_h = atom.GetTotalNumHs()
atom_feats_dict['node_type'].append(atom_type)
h_u = []
h_u += atom_type_one_hot(atom, ['H', 'C', 'N', 'O', 'F', 'S', 'Cl'])
h_u.append(atom_type)
h_u.append(is_acceptor[u])
h_u.append(is_donor[u])
h_u += atom_is_aromatic(atom)
h_u += atom_hybridization_one_hot(atom, [Chem.rdchem.HybridizationType.SP,
Chem.rdchem.HybridizationType.SP2,
Chem.rdchem.HybridizationType.SP3])
h_u.append(num_h)
atom_feats_dict['n_feat'].append(F.tensor(np.array(h_u).astype(np.float32)))
atom_feats_dict['n_feat'] = F.stack(atom_feats_dict['n_feat'], dim=0)
atom_feats_dict['node_type'] = F.tensor(np.array(
atom_feats_dict['node_type']).astype(np.int64))
return atom_feats_dict
def alchemy_edges(mol, self_loop=False):
"""Featurization for all bonds in a molecule.
The bond indices will be preserved.
Parameters
----------
mol : rdkit.Chem.rdchem.Mol
RDKit molecule object
self_loop : bool
Whether to add self loops. Default to be False.
Returns
-------
bond_feats_dict : dict
Dictionary for bond features
"""
bond_feats_dict = defaultdict(list)
mol_conformers = mol.GetConformers()
assert len(mol_conformers) == 1
geom = mol_conformers[0].GetPositions()
num_atoms = mol.GetNumAtoms()
for u in range(num_atoms):
for v in range(num_atoms):
if u == v and not self_loop:
continue
e_uv = mol.GetBondBetweenAtoms(u, v)
if e_uv is None:
bond_type = None
else:
bond_type = e_uv.GetBondType()
bond_feats_dict['e_feat'].append([
float(bond_type == x)
for x in (Chem.rdchem.BondType.SINGLE,
Chem.rdchem.BondType.DOUBLE,
Chem.rdchem.BondType.TRIPLE,
Chem.rdchem.BondType.AROMATIC, None)
])
bond_feats_dict['distance'].append(
np.linalg.norm(geom[u] - geom[v]))
bond_feats_dict['e_feat'] = F.tensor(
np.array(bond_feats_dict['e_feat']).astype(np.float32))
bond_feats_dict['distance'] = F.tensor(
np.array(bond_feats_dict['distance']).astype(np.float32)).reshape(-1 , 1)
return bond_feats_dict
class TencentAlchemyDataset(object):
"""
Developed by the Tencent Quantum Lab, the dataset lists 12 quantum mechanical
properties of 130, 000+ organic molecules, comprising up to 12 heavy atoms
(C, N, O, S, F and Cl), sampled from the GDBMedChem database. These properties
have been calculated using the open-source computational chemistry program
Python-based Simulation of Chemistry Framework (PySCF).
For more details, check the `paper <https://arxiv.org/abs/1906.09427>`__.
Parameters
----------
mode : str
'dev', 'valid' or 'test', separately for training, validation and test.
Default to be 'dev'. Note that 'test' is not available as the Alchemy
contest is ongoing.
mol_to_graph: callable, str -> DGLGraph
A function turning an RDKit molecule instance into a DGLGraph.
Default to :func:`dgllife.utils.mol_to_complete_graph`.
node_featurizer : callable, rdkit.Chem.rdchem.Mol -> dict
Featurization for nodes like atoms in a molecule, which can be used to update
ndata for a DGLGraph. By default, we construct graphs where nodes represent atoms
and node features represent atom features. We store the atomic numbers under the
name ``"node_type"`` and store the atom features under the name ``"n_feat"``.
The atom features include:
* One hot encoding for atom types
* Atomic number of atoms
* Whether the atom is a donor
* Whether the atom is an acceptor
* Whether the atom is aromatic
* One hot encoding for atom hybridization
* Total number of Hs on the atom
edge_featurizer : callable, rdkit.Chem.rdchem.Mol -> dict
Featurization for edges like bonds in a molecule, which can be used to update
edata for a DGLGraph. By default, we construct edges between every pair of atoms,
excluding the self loops. We store the distance between the end atoms under the name
``"distance"`` and store the edge features under the name ``"e_feat"``. The edge
features represent one hot encoding of edge types (bond types and non-bond edges).
load : bool
Whether to load the previously pre-processed dataset or pre-process from scratch.
``load`` should be False when we want to try different graph construction and
featurization methods and need to preprocess from scratch. Default to True.
"""
def __init__(self, mode='dev',
mol_to_graph=mol_to_complete_graph,
node_featurizer=alchemy_nodes,
edge_featurizer=alchemy_edges,
load=True):
if mode == 'test':
raise ValueError('The test mode is not supported before '
'the Alchemy contest finishes.')
assert mode in ['dev', 'valid', 'test'], \
'Expect mode to be dev, valid or test, got {}.'.format(mode)
self.mode = mode
# Construct DGLGraphs from raw data or use the preprocessed data
self.load = load
file_dir = osp.join(get_download_dir(), 'Alchemy_data')
if load:
file_name = "{}_processed_dgl".format(mode)
else:
file_name = "{}_single_sdf".format(mode)
self.file_dir = pathlib.Path(file_dir, file_name)
self._url = 'dataset/alchemy/'
self.zip_file_path = pathlib.Path(file_dir, file_name + '.zip')
download(_get_dgl_url(self._url + file_name + '.zip'), path=str(self.zip_file_path))
if not os.path.exists(str(self.file_dir)):
archive = zipfile.ZipFile(self.zip_file_path)
archive.extractall(file_dir)
archive.close()
self._load(mol_to_graph, node_featurizer, edge_featurizer)
def _load(self, mol_to_graph, node_featurizer, edge_featurizer):
if self.load:
self.graphs, label_dict = load_graphs(osp.join(self.file_dir, "{}_graphs.bin".format(self.mode)))
self.labels = label_dict['labels']
with open(osp.join(self.file_dir, "{}_smiles.txt".format(self.mode)), 'r') as f:
smiles_ = f.readlines()
self.smiles = [s.strip() for s in smiles_]
else:
print('Start preprocessing dataset...')
target_file = pathlib.Path(self.file_dir, "{}_target.csv".format(self.mode))
self.target = pd.read_csv(
target_file,
index_col=0,
usecols=['gdb_idx',] + ['property_{:d}'.format(x) for x in range(12)])
self.target = self.target[['property_{:d}'.format(x) for x in range(12)]]
self.graphs, self.labels, self.smiles = [], [], []
supp = Chem.SDMolSupplier(osp.join(self.file_dir, self.mode + ".sdf"))
cnt = 0
dataset_size = len(self.target)
for mol, label in zip(supp, self.target.iterrows()):
cnt += 1
print('Processing molecule {:d}/{:d}'.format(cnt, dataset_size))
graph = mol_to_graph(mol, node_featurizer=node_featurizer,
edge_featurizer=edge_featurizer)
smiles = Chem.MolToSmiles(mol)
self.smiles.append(smiles)
self.graphs.append(graph)
label = F.tensor(np.array(label[1].tolist()).astype(np.float32))
self.labels.append(label)
save_graphs(osp.join(self.file_dir, "{}_graphs.bin".format(self.mode)), self.graphs,
labels={'labels': F.stack(self.labels, dim=0)})
with open(osp.join(self.file_dir, "{}_smiles.txt".format(self.mode)), 'w') as f:
for s in self.smiles:
f.write(s + '\n')
self.set_mean_and_std()
print(len(self.graphs), "loaded!")
def __getitem__(self, item):
"""Get datapoint with index
Parameters
----------
item : int
Datapoint index
Returns
-------
str
SMILES for the ith datapoint
DGLGraph
DGLGraph for the ith datapoint
Tensor of dtype float32 and shape (T)
Labels of the datapoint for all tasks.
"""
return self.smiles[item], self.graphs[item], self.labels[item]
def __len__(self):
"""Size for the dataset.
Returns
-------
int
Size for the dataset.
"""
return len(self.graphs)
def set_mean_and_std(self, mean=None, std=None):
"""Set mean and std or compute from labels for future normalization.
The mean and std can be fetched later with ``self.mean`` and ``self.std``.
Parameters
----------
mean : float32 tensor of shape (T)
Mean of labels for all tasks.
std : float32 tensor of shape (T)
Std of labels for all tasks.
"""
labels = np.array([i.numpy() for i in self.labels])
if mean is None:
mean = np.mean(labels, axis=0)
if std is None:
std = np.std(labels, axis=0)
self.mean = mean
self.std = std
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