Add explicit ROCS optimization modes - #9
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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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What changed
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
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.