When calling the copy ctor of PrepResidue you ran into trouble. Specifically because you have to call the base class:
PrepResidue::PrepResidue(const PrepResidue& other) : cds::Residue(other)
The base class copies the atoms as type cds::Atom. They get sliced bro.
So any attempt to cast the new PrepResidue atoms as PrepAtom causes undefined behaviour aka seggies.
If you don’t call the base class via cds::Residue(other), then you can’t call it’s base class of Node, so you lose any connectivity.
(Failed) Ideas that don’t require a complete redesign:
1) In the copy ctor of prepResidue you clear all the atoms in the base class after they’re constructed. Then copy each atom manually with the addAtom function, which is disgustingly wasteful.
2) Don’t allow the ctor of prepResidue to be called? Just read in a new copy and move/edit it directly to what you want.
The ultimate issue is that even if you do that, what you want to do is edit the prep residue by deleting atoms, but that would require re-creating the whole prep file tree M 3 E madness for each delete, so while you can read/write a PrepResidue and keep it as a PrepResidue, as soon as you edit it you’ll want to have a generic writePrepResidue function that takes in the base class cds::Residue. That way the origin doesn’t matter. However we don’t even want prep files, they suck, so you’re going to use the pre-existing generic lib/off file writer and make the jump to lib files. We want that anyway.
You thought of this (but it won’t work):
in cds::Residue:
virtual std::vector<Atom*> getAtoms() const;
in prep::PrepResidue:
std::vector<PrepAtom*> PrepResidue::getAtoms() const
But you can’t make getAtoms() be virtual in the base class (cds::Residue) of prep::PrepResidue and then have the returned vector be of type PrepAtom* because a vector of PrepAtom* is not covariant with a vector of cds::Atom*, even though the classes themselves are covariant, their vectors are not.
https://stackoverflow.com/questions/4807643/container-covariance-in-c