Backlog

Backlog

Replace quick_protein_donor_acceptors with a dictionary-aware donor/acceptor lookup

coot::quick_protein_donor_acceptors (geometry/protein-donor-acceptors.{hh,cc}) is a hard-coded (residue-name, atom-name) → hb_type map for the standard amino acids only. It is used by the environment-distances display (“Constructor G” in coords/Bond_lines.cc, ~line 3000) to decide whether a close contact is drawn as a hydrogen bond (purple) or a plain contact.

Because it knows nothing about ligands, any non-protein atom pair fails the lookup and gets the fallback colour — so ligand H-bonds are never properly classified (e.g. the t3ND4 lactam O27 ↔ ASP main-chain O pair, acceptor + acceptor, 2026-09-13). The replacement should get hb types from the dictionaries: protein_geometry::get_h_bond_type(atom_name, monomer_name, imol_enc) already maps _chem_comp_atom.type_energy → hb_t via the energy lib, and protein_geom_p is in scope at the call site. The quick table could remain as a fast path for protein atoms, or go entirely.

Quick-table defects all fixed 2026-09-13: THR “ OG1”, THR in the main-chain list, HOH “ O “ = HB_BOTH (explicit entry after the loop, overriding the loop’s blanket HB_ACCEPTOR), and n_res_types now comes from std::size(l). Consider #include <iterator> for std::size portability (GCC’s <iostream> provides it transitively; libc++ may not).