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

Rewrite alpha/beta stereochemistry assignment handling code #41

Open
dan2097 opened this issue Feb 23, 2017 · 0 comments
Open

Rewrite alpha/beta stereochemistry assignment handling code #41

dan2097 opened this issue Feb 23, 2017 · 0 comments
Labels
enhancement New feature or request major

Comments

@dan2097
Copy link
Owner

dan2097 commented Feb 23, 2017

Original report by Daniel Lowe (Bitbucket: dan2097, GitHub: dan2097).


Currently alpha/beta stereo are treated like other stereochemistry terms and applied to the stereoparent after it has been constructed. Alpha/beta stereochemistry indicates the position of a group relative to the plane of the unsubstituted parent, hence to do this in general the term must be associated with the atom through which the group that was added attached.
[The current implementation makes the assumption that the non-hydrogen is the atom added and hence fails when a position is double substituted]
Proposal: Keep alpha/beta stereochemistry in much the way it is originally parsed. In bridge assignment, suffix assignment and substitutent attachment add consider being preceded either by a locant or a stereochemistry element of this type. Once the group is attached, the stereochemistry term should be moved in front of the stereoparent and associanted with the atomid of the atom that attached to the stereoparent.

Bracketed alpha/beta stereochemistry can be handled as it is currently. Alpha/beta stereo directly in front of a stereoparent should probably be recognized at the point that it is currently applied.

@dan2097 dan2097 added major enhancement New feature or request labels Apr 5, 2020
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request major
Projects
None yet
Development

No branches or pull requests

1 participant