Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Grow fragments when stereochemistry can not be fixed #118

Closed
jthorton opened this issue Jul 19, 2021 · 0 comments · Fixed by #123
Closed

Grow fragments when stereochemistry can not be fixed #118

jthorton opened this issue Jul 19, 2021 · 0 comments · Fixed by #123

Comments

@jthorton
Copy link
Contributor

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]",)

@jthorton jthorton mentioned this issue Aug 11, 2021
1 task
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging a pull request may close this issue.

1 participant