How to Get Chirality tag and BondDir for canonical smiles

yuyangw / MolCLR

Implementation of MolCLR: "Molecular Contrastive Learning of Representations via Graph Neural Networks" in PyG.

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How to Get Chirality tag and BondDir for canonical smiles #22

Closed shrimonmuke0202 closed 1 year ago

shrimonmuke0202 commented 1 year ago

Hi Team,

I have a canonical smile "CCC[NH2+]C(CCc1ccccn1)c1ccc(Cl)s1" and obtain rdkit.Chem.rdchem.ChiralType.CHI_UNSPECIFIED as chiral tag and rdkit.Chem.rdchem.BondDir.NONE for all atoms and bonds. Why does this happen? is there any alternative way to include those two properties in the molecular graph?

Again for all smiles strings that are used for pertaining of the iMolCLR produces rdkit.Chem.rdchem.ChiralType.CHI_UNSPECIFIED for chiraltag and rdkit.Chem.rdchem.BondDir.NONE for BondDIR.

yuyangw commented 1 year ago

See https://github.com/yuyangw/iMolCLR/issues/6.