Merge pull request #2628 from RosettaCommons/aleaverfay/fix_invrottree_atom_indexing_bug
PDB I/O from the InvrotTree indexing-from-0 bug
The InvrotTree code was constructing a PDB file counting from atom index 0,
but large sections of PDB writing assumes that atom indices start from 1.
This bug was recently uncovered by the (several) fixes to the behavior of
CONECT record creation in PDB writing with PR #2595 and disrupted the behavior
of the cstfile_to_theozyme_pdb integration test