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primaryodors / primarydock

PrimaryOdors.org molecular docker.
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Active Clash Compensation. #405

Closed primaryodors closed 6 months ago

primaryodors commented 6 months ago

When running a prediction, if any ligand-receptor clashes are observed in the active state, the directions and magnitudes (defined as ∑r(vdW) - r) of the clashes are recorded and a new temporary model PDB is generated based on adjusting the positions of the TM helices to resolve the clashes, within the constraint that the total adjustments do not exceed a fixed number of standard deviations (currently 2Σ) according to the positional variability from the cryo-EM models.

primaryodors commented 6 months ago

All tests succeeding so far.

primaryodors commented 6 months ago

There is a lot to this PR. However, aside from a few minor fixes, all of it is interrelated and pertinent to the application of cryo-EM models to the prediction system.

primaryodors commented 6 months ago

All tests successful.

primaryodors commented 6 months ago

All functionality in this PR has either been merged, is part of an open PR, or was causing unit test failures.