fix glycan O1 leaving-atom cleanup for standalone glycans

[magnusbauer]

Summary

Currently, glycan O1 can be removed during leaving-atom cleanup even when no glycan bond context exists. This incorrectly affects standalone glycans, where O1 should be preserved. This PR makes the cleanup logic bond-aware, so O1 is only dropped when glycan bond information indicates that it should be treated as a leaving atom.

The 6MJ ligand in 7zdy is one example where this occurs, the same issue applies more generally to standalone glycans containing O1. The image below shows the effect of the change, with the structure before the fix on the left (red) and after the fix on the right (green).

Changes

• require glycan bond context before dropping glycan O1
• preserve O1 on standalone glycans
• skip the fast-path O1 removal when no glycan bonds are present

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[magnusbauer]

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