Error creating new molecule

## Bug report
#### Description
TypeError when copying atoms out of a molecule then creating a new one

#### Steps to reproduce

```python
mol = mdt.from_smiles('[H][H]')
atoms = mol.atoms.copy()
atoms.append(mdt.Atom(1))
newmol = mdt.Molecule(atoms)
```

raises

```python
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
in ()
2 atoms = mol.atoms.copy()
3 atoms.append(mdt.Atom(1))
----> 4 newmol = mdt.Molecule(atoms)

~/mycode/molecular-design-toolkit/moldesign/molecules/molecule.py in __init__(self, atomcontainer, name, bond_graph, copy_atoms, pdbname, charge, metadata)
1058 self.chains = Instance(molecule=self)
1059 self.residues = []
-> 1060 self._rebuild_topology(bond_graph=bond_graph)
1061
1062 if name is not None:

~/mycode/molecular-design-toolkit/moldesign/molecules/molecule.py in _rebuild_topology(self, bond_graph)
486 self.dim_masses = u.broadcast_to(self.masses, (3, self.num_atoms)).T
487 self._assign_atom_indices()
--> 488 self._assign_residue_indices()
489 self._dof = None
490

~/mycode/molecular-design-toolkit/moldesign/molecules/molecule.py in _assign_residue_indices(self)
559
560 for atom in self.atoms:
--> 561 if last_pdb_idx is not None and atom.pdbindex <= last_pdb_idx:
562 atom.pdbindex = last_pdb_idx + 1
563 conflicts.add('atom numbers')

TypeError: unorderable types: NoneType() <= int()
```

#### Environment
- Operating system: OS X High Sierra
- `python --version` output: Python 3.5.2 :: Continuum Analytics, Inc.
- `pip show moldesign nbmolviz | grep -B1 Version` output: 0.8.0a2

Start with moldesign/molecules/molecule.py, especially Molecule.__init__, _rebuild_topology, and _assign_residue_indices around the reported line. Run the supplied Python reproduction to inspect the failure. Done means constructing a new Molecule from the copied and appended atoms no longer raises the shown TypeError.

Written by the indexing model from the issue text.