- Global Builder::IsResidueComplete (const mol::ResidueHandle &rh)
- Add hydrogen flag
- Global ChainView::GetResidueList () const
- Residue list may be unordered. Is it the responsibility of the method building the view to have them ordered or is it our job?
- Global EntityVisitor::VisitBond (const BondHandle &b)
- not implemented for views
- Global EntityVisitor::VisitTorsion (const TorsionHandle &t)
- Not implemented for views
- Global ResidueImpl::FindAtom (const String &aname) const
- make the return type a AtomImplList, since there may be several atoms with the given name.
- Class RuleBasedBuilder
- Sorting of the residues directly uses impl layer of the base module. Would be much nicer if the order could be assigned in the public interface and then tell the residues to sort the atoms in ascending order.
- Global RuleBasedBuilder::OnUnknownAtom (mol::AtomHandle atom)
- what should be done when the atom name is changed? it would be neccessary to rerun CheckResidueCompleteness().
