Dan Nealschneider 67fc0708e5 CIPLabeler performance: Store vector of bonds (#9250) ...

* CIPLabeler performance: Store vector of bonds

CIPLabelling refers to bonds by index over and over again. This
causes a measurable hit in performance in findConfigs() because
we iterate over a bitset of "allowed" bonds. For very large
molecules with many bonds, this can be a rate-limiting step!

This affects many PDB-sized structures.

2J3N goes from 0.7s to 0.25s with this change.

I had another example for which the findBondWithIdx() call was
taking 500ms of a 700ms call (after the performance update
in #9171 was implemented)

* yikes, XXL reserve

thanks, greg

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

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Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

2026-05-06 11:57:28 +02:00

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