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Aleaverfay/bump check#363

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aleaverfay wants to merge 23 commits intomasterfrom
aleaverfay/bump_check
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Aleaverfay/bump check#363
aleaverfay wants to merge 23 commits intomasterfrom
aleaverfay/bump_check

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This examines the energies of the rotamers after they have all been computed to remove rotamers that are very unlikely to be selected in the final rotamer assignment because their total energy is greater than 5 kcal/mol under even the most favorable rotamer assignment of its neighbors. This eliminates about 1/3rd of the rotamers that are originally built. This should give a modest performance boost to packing.

I'll do some measurements.

fdimaio and others added 23 commits April 8, 2026 11:08
…ance check in biotite-to-pose-stack to properly handle missing density; c) set semirotameric prob cumsum to 0.98 (was 0.95)
…annot compute them in advance and stash in PBT. Revert back to computing at build-time.
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