Order of monomer bond lists in random builder

[cwalker7]

Figure out why this monomer definition fails to build with the random builder:

       monomer_dict = {
            "monomer_name": A,
            "particle_sequence": [b,sa,sb,sc],
            "bond_list": [[0,1],[1,3],[0,2]],
            "start": 0,
            "end": 0,
        }

And this one succeeds:

       monomer_dict = {
            "monomer_name": A,
            "particle_sequence": [b,sa,sb,sc],
            "bond_list": [[0,1],[0,2],[1,3]],
            "start": 0,
            "end": 0,
        }

Seems like the order matters when the monomers are parsed. This model has separate 2 sidechain and 1 sidechain connections to one backbone bead. Ideally it should work in both cases above. Details of the error for the first case are:

Traceback (most recent call last):
  File "/projects/chwa2399/software/anaconda/envs/cg_openmm_py39/lib/python3.9/site-packages/flow/project.py", line 3396, in _execute_operation
    self._operations[operation.name](*operation._jobs)
  File "/projects/chwa2399/software/anaconda/envs/cg_openmm_py39/lib/python3.9/site-packages/flow/project.py", line 630, in __call__
    return self._op_func(*jobs)
  File "/gpfs/alpine1/scratch/chwa2399/cg_openmm_signac_scans/helix_3sc_triangle_opt_111_exclusions_9_13_22/pitch_1_40_go_vary_bond_closures_10_6_22/2sc_diag_1sc/project.py", line 278, in signac_run_replica_exchange
    cgmodel_torsion_off = CGModel(
  File "/projects/chwa2399/software/anaconda/envs/cg_openmm_py39/lib/python3.9/site-packages/cg_openmm-1.0-py3.9.egg/cg_openmm/cg_model/cgmodel.py", line 282, in __init__
    self.positions = get_random_positions(self, use_library=use_structure_library)
  File "/projects/chwa2399/software/anaconda/envs/cg_openmm_py39/lib/python3.9/site-packages/cg_openmm-1.0-py3.9.egg/cg_openmm/utilities/random_builder.py", line 732, in get_random_positions
    trial_positions, placement = assign_position_lattice_style(
  File "/projects/chwa2399/software/anaconda/envs/cg_openmm_py39/lib/python3.9/site-packages/cg_openmm-1.0-py3.9.egg/cg_openmm/utilities/random_builder.py", line 289, in assign_position_lattice_style
    positions = np.insert(positions, bead_index, new_coordinates, axis=0) * positions.unit
  File "<__array_function__ internals>", line 180, in insert
  File "/projects/chwa2399/software/anaconda/envs/cg_openmm_py39/lib/python3.9/site-packages/numpy/lib/function_base.py", line 5280, in insert
    raise IndexError(f"index {obj} is out of bounds for axis {axis} "
IndexError: index 3 is out of bounds for axis 0 with size 2
Execute with '--show-traceback' or '--debug' to show the full traceback.