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Add explicit ROCS optimization modes - #9

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fulopjoz wants to merge 2 commits into
fix/rocs-scoring-followupfrom
fix/rocs-optimization-modes
Draft

Add explicit ROCS optimization modes#9
fulopjoz wants to merge 2 commits into
fix/rocs-scoring-followupfrom
fix/rocs-optimization-modes

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@fulopjoz

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What changed

  • add a consistent optional optimization_mode argument to RDKit, CDPKit, and OpenEye ROCS scorers
  • preserve exact legacy behavior and keys when the argument is omitted
  • make explicit shape, combo, and color modes control both overlay selection and returned score
  • give every explicit mode a distinct scorer key, including explicit combo
  • document score ranges, compatibility, and threshold recalibration

Scientific behavior

RDKit uses opt_param values 1.0, 0.5, and 0.0 for shape, combo, and color. CDPKit color mode uses color-feature-centred starts and color ranking because CDPKit exposes no color-overlap gradient. OpenEye maps modes to internally consistent CLI flags and report columns.

Explicit RDKit combo and color can differ from legacy values because legacy DrugEx evaluated them at a shape-optimized pose. Existing tutorials remain legacy unless they opt in.

Validation

  • python -m drugex.training.scorers.tests: 15 passed
  • includes a flexible RDKit objective test and CDPKit end-to-end worker test
  • python -m drugex.training.tests: passed
  • source compilation and diff checks: passed
  • licensed OpenEye CLI integration: not run

Dependency

This is a stacked fork review based on PR #6. After PR #6 is accepted, this branch should be rebased onto the updated dev branch before any upstream proposal.

fulopjoz added 2 commits July 29, 2026 16:42
Preserve omitted-mode behavior while allowing shape, combo, and color to control both overlay selection and the returned metric. Distinguish every explicit mode in scorer keys and document CDPKit color seeding as an approximation.
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