Hello,
In the paper: "Graph Networks as a Universal Machine Learning
Framework for Molecules and Crystals", authors introduce chirality as an
atom feature input to analyze QM9 dataset. I was trying to recreate this
atom feature as following
> Chirality: (categorical) R, S, or not a Chiral center (one-hot encoded).
The code I used is:
from chainer_chemistry import datasets
from chainer_chemistry.dataset.preprocessors.ggnn_preprocessor import
GGNNPreprocessor
from rdkit import Chem
import numpy as np
dataset, dataset_smiles = datasets.get_qm9(GGNNPreprocessor(),
return_smiles=True)
for i in range(len(dataset_smiles)):
mol = Chem.MolFromSmiles(dataset_smiles[i])
Chem.AssignAtomChiralTagsFromStructure(mol)
chiral_cc = Chem.FindMolChiralCenters(mol)
if not len(chiral_cc) == 0:
print(chiral_cc)
The output shows no Chiral centers for this dataset. When I use
`includeUnassigned=True`, code gives a list of tuples, but instead of
"R/S", I get "?". I was wondering if there is a mistake in my
implementation. If this is expected, any thoughts on how chirality was
assigned in the above paper? Thanks.
Sincerely,
Navid
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