Select active ligand torsions for Vina preparation

[dprada]

What — Allow the docking protocol to choose which candidate ligand bonds are active torsions.
How — Consume MolSysMT rotatable-bond and rigid-fragment information, expose explicit selection or a documented default, and pass the selected torsions to the PDBQT writer.
Why — The present ligand preparator defaults to zero torsional degrees of freedom, while flexible-ligand Vina input requires a valid torsion tree.
Record — devguide/pending_proposals/select_active_ligand_torsions_for_vina_preparation.md
Related — #3

[dprada]

Partial progress in c68cc7d: DockingMT's current ligand writer produces a rigid ROOT block only. It now rejects nonzero torsion_dof at preparation and export instead of writing a TORSDOF count without a valid ROOT/BRANCH tree. The rigid policy is recorded in prepared ligand metadata and Vina provenance. Guard: tests/test_preparation.py::test_ligand_writer_rejects_torsion_count_without_branch_tree.

The proposal remains open. Selecting active bonds and writing a validated flexible-ligand tree still depends on uibcdf/molsysmt#214 and uibcdf/molsysmt#224. Local report: devguide/pending_proposals/select_active_ligand_torsions_for_vina_preparation.md (partial).