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For PCQM4M-v2, I want to use the provided pcqm4m-v2-train.sdf.However, because I do not know much about chemistry and I am not familiar with RDkit toolkit, I do not know how to get 3D information from SDF. Here are some of my attempts. I'm not sure if I did it right.
I first try GetPropNames() to get the list of the properties of mol.
suppl = Chem.SDMolSupplier('/data/pcqm4m-v2-train.sdf')
for idx, mol in enumerate(suppl):
print(f'{idx}-th rdkit mol obj: {mol}')
print(mol.GetPropNames())
But what I got was {}.
Then I tried mol.GetConformer().GetPositions() and I can get the coordinates, but I'm not sure whether the coordinates are correct, because I don't particularly understand the specific meaning of conformer.
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Hi OGB-LSC Team,
For PCQM4M-v2, I want to use the provided
pcqm4m-v2-train.sdf
.However, because I do not know much about chemistry and I am not familiar with RDkit toolkit, I do not know how to get 3D information from SDF. Here are some of my attempts. I'm not sure if I did it right.I first try GetPropNames() to get the list of the properties of mol.
But what I got was
{}
.Then I tried
mol.GetConformer().GetPositions()
and I can get the coordinates, but I'm not sure whether the coordinates are correct, because I don't particularly understand the specific meaning ofconformer
.Thanks
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