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In some cases, fragmenter will stop and raise an error if a fragment molecules stereochemistry can not be fixed to match the parent. It may be better, in this case, to keep growing the fragment until the stereochemistry can be matched all the way until the parent molecule is returned where there would be no issues. This would avoid downstream workflows like bespokefit from having to do this and they might miss a smaller possible fragment that does fix the issue.
An example molecule which fails mol = Molecule.from_smiles("[H][O][C]([H])([H])[C]([H])([H])[C]([H])([N]([H])[C]1=[N][C]([H])=[C]2[C](=[N]1)[N]([C]([H])([H])[H])[C](=[O])[C]([O][C]1=[C]([F])[C]([H])=[C]([F])[C]([H])=[C]1[H])=[C]2[H])[C]([H])([H])[C]([H])([H])[O][H]",)
The text was updated successfully, but these errors were encountered:
In some cases, fragmenter will stop and raise an error if a fragment molecules stereochemistry can not be fixed to match the parent. It may be better, in this case, to keep growing the fragment until the stereochemistry can be matched all the way until the parent molecule is returned where there would be no issues. This would avoid downstream workflows like bespokefit from having to do this and they might miss a smaller possible fragment that does fix the issue.
An example molecule which fails
mol = Molecule.from_smiles("[H][O][C]([H])([H])[C]([H])([H])[C]([H])([N]([H])[C]1=[N][C]([H])=[C]2[C](=[N]1)[N]([C]([H])([H])[H])[C](=[O])[C]([O][C]1=[C]([F])[C]([H])=[C]([F])[C]([H])=[C]1[H])=[C]2[H])[C]([H])([H])[C]([H])([H])[O][H]",)
The text was updated successfully, but these errors were encountered: