Refactor Molecules class

[serk12]

I've refactored the RWMolecule, QtGui::Molecule and Core::Molecule so the Molecule graph is dynamic and also compute the connectivity between nodes.

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[ghutchis]

The build failures are from the pybind11 Python bindings. Looks like most boil down to:

2021-07-05T15:39:52.3786938Z        .def("add_atom", &Molecule::addAtom, "Add an atom")

I think the problem is that you've now added the overload, pybind can't figure out which method to bind:
https://pybind11.readthedocs.io/en/stable/classes.html#overloaded-methods

So you'll just need to tweak python/core.cpp:
https://github.com/OpenChemistry/avogadrolibs/blob/master/python/core.cpp#L46

Probably users would want to access both methods...

[github-actions]

Here are the build results
macOS.dmg
Ubuntu-2004.tar.gz
Win64.exe
Artifacts will only be retained for 90 days.

[ghutchis]

Overall, it's good, but I'd really like to keep more inline functions and combine the MoleculeGraph and Molecule classes - I'm not sure I see the point of separating them.

[ghutchis]

Looks pretty good, although it seems like there are some merge conflicts?

[github-actions]

Here are the build results
macOS.dmg
Ubuntu-2004.tar.gz
Win64.exe
Artifacts will only be retained for 90 days.

[ghutchis]

The "Wheel" failures can be fixed with this patch:

diff --git a/python/core.cpp b/python/core.cpp
index ae4e9901..f105d38e 100644
--- a/python/core.cpp
+++ b/python/core.cpp
@@ -43,7 +43,7 @@ PYBIND11_MODULE(core, m)
 
   py::class_<Molecule>(m, "Molecule")
     .def(py::init<>())
-    .def("add_atom", &Molecule::addAtom, "Add an atom")
+    .def("add_atom", static_cast<Atom (Molecule::*)(unsigned char)>(&Molecule::addAtom), "Add an atom")
     .def("atom_count", atomCount0, "The number of atoms")
     .def("atom_count", atomCount1,
          "The number of atoms with the supplied atomic number")

[github-actions]

Here are the build results
macOS.dmg
Ubuntu-2004.tar.gz
Win64.exe
Artifacts will only be retained for 90 days.

[github-actions]

Here are the build results
macOS.dmg
Ubuntu-2004.tar.gz
Win64.exe
Artifacts will only be retained for 90 days.

[ghutchis]

Everything looks good from my side. @cryos if you're busy, I'm just going to go ahead and merge this on Wednesday.