Chem::Structure

Splits the structure into molecules and returns those that are ligands (see AtomView#ligand?). A molecule is a set of residues joined by covalent bonds; each residue is whole regardless of its internal bonds (e.g. ferrocene, whose Fe–C bonds may be zero-order or dropped by #guess_bonds). Solvent and excluded residues are never part of a ligand. Bonds are guessed first when a hetero residue has none.

Fixes upstream reset_connectivity, which deletes from atom.bonds while iterating it and so leaves every other bond in place (stale bonds then survive #guess_bonds with their original order).