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 Entity::PickAtom (const geom::Line3 &line, Real line_width=0.5): honour object transformation
Global Entity::PickBond (const geom::Line3 &line, Real line_width=0.5): honour object transformation
Global EntityVisitor::VisitBond (const BondHandle &b): not implemented for views
Global EntityVisitor::VisitTorsion (const TorsionHandle &t): Not implemented for views
Class Primitive: transparent primitives would require the gfx objects to be ordered back to front. This has to be properly implemented in the rendering system.
Class Quad: this class should be part of a more sophisticated polygon rendering class.
Global ResidueImpl::FindAtom (const String &aname) const: make the return type a AtomImplList, since there may be several atoms with the given name.