Fix ROCS scoring correctness and robustness - #6
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Recreating as upstream PR against CDDLeiden/DrugEx |
Correct OpenEye color-optimization flags, duplicate score remapping, shape-only report parsing, worker semantics, and configurable timeouts. Add portable regression coverage that does not require an OpenEye license.
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What changed
Root cause
The OpenEye wrapper did not consistently connect public options to CLI flags and report columns. Shape-only output does not contain TanimotoCombo, so parsing that default column could silently return no scores. Duplicate conformer generation also lost the mapping to repeated inputs.
Compatibility
The existing constructor remains compatible. n_jobs is accepted for backend API consistency but OpenEye ROCS remains one CLI subprocess. This PR does not introduce the separate explicit optimization-mode API.
Validation