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Update README
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wukevin committed Dec 10, 2024
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Expand Up @@ -69,4 +69,4 @@ We have included an example of how glycans can be specified under `predict_glyco

### A note on leaving atoms

One might notice that in the above example, we are specifying CCD codes for sugar rings and connecting them to each other and an amino acid residue via various bonds. A subtle point is that the reference conformer for these sugar rings include OH hydroxyl groups that leave when bonds are formed. Under the hood, Chai-1 tries to automatically find and remove these atoms (see `AllAtomStructureContext.drop_leaving_atoms` for implementation), but this logic only drops leaving atoms within non-polymeric residues, and only removes leaving hydroxyl groups. For other, non-sugar covalently attached ligands, consider specifying a SMILES string that leaves out the leaving atoms, or open a GitHub issue.
One might notice that in the above example, we are specifying CCD codes for sugar rings and connecting them to each other and an amino acid residue via various bonds. A subtle point is that the reference conformer for these sugar rings include OH hydroxyl groups that leave when bonds are formed. Under the hood, Chai-1 tries to automatically find and remove these atoms (see `AllAtomStructureContext.drop_glycan_leaving_atoms_inplace` for implementation), but this logic only drops leaving hydroxyl groups within glycan sugar rings. For other, non-sugar covalently attached ligands, please specify a SMILES string without the leaving atoms. If this does not work for your use case, please open a GitHub issue.

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