Todo List

Global ost::conop::Builder::IsResidueComplete (const mol::ResidueHandle &rh)

Add hydrogen flag

Global ost::mol::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 ost::gfx::Entity::PickAtom (const geom::Line3 &line, Real line_width=0.5)

honour object transformation

Global ost::gfx::Entity::PickBond (const geom::Line3 &line, Real line_width=0.5)

honour object transformation

Global ost::mol::EntityVisitor::VisitBond (const BondHandle &b)

not implemented for views

Global ost::mol::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 ost::mol::impl::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 ost::conop::RuleBasedBuilder::OnUnknownAtom (mol::AtomHandle atom)

what should be done when the atom name is changed? it would be neccessary to rerun CheckResidueCompleteness().

Class Sanitizer

Sanitizer acts both as the checker and the instance responsible for cleaning up structural problems. Is this desired?