Support changing atoms in trajectory

[utf]

I'm trying to use hofmann to render a trajectory from a diffusion model. At the beginning all atoms are masked (for this I'm used Og at the atom type) and during the trajectory they are progressively unmasked and become a different atom type.

I've tried rendering this with hofmann but get the error:

ValueError                                Traceback (most recent call last)
Cell In[30], [line 1](vscode-notebook-cell:?execution_count=30&line=1)
----> [1](vscode-notebook-cell:?execution_count=30&line=1) scene = StructureScene.from_ase(traj)
      2 scene.render_animation("output.gif")

File ~/opt/miniconda3/envs/py313/lib/python3.13/site-packages/hofmann/model/structure_scene.py:253, in StructureScene.from_ase(cls, atoms, bond_specs, polyhedra, centre_atom, atom_styles, title, view, atom_data)
    202 """Create a StructureScene from ASE ``Atoms`` object(s).
    203 
    204 For periodic systems, fractional coordinates are wrapped to
   (...)    249     :func:`hofmann.construction.scene_builders.from_ase`
    250 """
    251 from hofmann.construction.scene_builders import from_ase
--> [253](https://file+.vscode-resource.vscode-cdn.net/Users/alexganose/Library/CloudStorage/OneDrive-ImperialCollegeLondon/Notebooks/2026/hoffman/~/opt/miniconda3/envs/py313/lib/python3.13/site-packages/hofmann/model/structure_scene.py:253) return from_ase(
    254     atoms, bond_specs, polyhedra=polyhedra,
    255     centre_atom=centre_atom,
    256     atom_styles=atom_styles, title=title, view=view,
    257     atom_data=atom_data,
    258 )

File ~/opt/miniconda3/envs/py313/lib/python3.13/site-packages/hofmann/construction/scene_builders.py:180, in from_ase(atoms, bond_specs, polyhedra, centre_atom, atom_styles, title, view, atom_data)
    174     raise ValueError(
    175         f"all Atoms in a trajectory must have the same number "
    176         f"of atoms. Frame 0 has {len(first)} but frame {i} "
    177         f"has {len(a)}."
    178     )
    179 if a.get_chemical_symbols() != species:
--> [180](https://file+.vscode-resource.vscode-cdn.net/Users/alexganose/Library/CloudStorage/OneDrive-ImperialCollegeLondon/Notebooks/2026/hoffman/~/opt/miniconda3/envs/py313/lib/python3.13/site-packages/hofmann/construction/scene_builders.py:180)     raise ValueError(
    181         f"all Atoms in a trajectory must have the same "
    182         f"species. Frame 0 has {species} but frame {i} has "
    183         f"{a.get_chemical_symbols()}."
    184     )
    185 frame_periodic = a.pbc.any() and a.cell.rank == 3
    186 if frame_periodic != periodic:

ValueError: all Atoms in a trajectory must have the same species. Frame 0 has ['Og', 'Og', 'Ts', 'Ts', 'Lv', 'Lv'] but frame 31 has ['Tb', 'Tb', 'Ts', 'Ts', 'Lv', 'Lv'].

Is there a reason why atom types cannot differ during a trajectory? I'm not plotting any octahedra or bonds.