Enhance the pocket detection - #50
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`detect_pocket_cavity` maps the void space of a binding pocket by placing probes on a regular grid within the TM bundle and keeping those that lie inside the convex hull of the TM centerlines and clear of every protein atom. `pocket_pharmacophore` packages inward-residue selection and feature extraction into a single call describing the receptor side of the pocket. `complementary_pharmacophore` converts such a receptor description into the ligand-side query needed for virtual screening, swapping donors with acceptors and cations with anions. Given a cavity it also projects each feature onto the nearest void probe, so the resulting positions lie in accessible space rather than inside the receptor's van der Waals surface; :Steric is dropped in that form because the cavity parametrizes the pocket's free volume directly. Assisted-by: Claude Opus 4.8 <noreply@anthropic.com>
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This adds cavity detection and complementary pharmacophore model construction. The intent is to then be able to align ligands to the pocket pharamacophore model and use that for ligand-based virtual screening.