Update of naming and comments

python/chemiscope/jupyter.py

@@ -249,7 +249,8 @@ def show(
                 "values": (
                     list(range(len(frames)))
                     if hasattr(frames, "__len__")
-                    # MDAnalysis `frames` will not be a list, and does not have a `__len__`
+                    # MDAnalysis `frames` will not be a list, and does not have
+                    # a `__len__`
                     else list(range(len(frames.trajectory)))
                 ),
             }

python/chemiscope/structures/__init__.py

@@ -71,7 +71,9 @@ def frames_to_json(frames):
     elif adapter == "stk":
         return [_stk_to_json(frame) for frame in frames]
     elif adapter == "mda":
-        return [_mda_to_json(frames.atoms) for frame in frames.trajectory]
+        # Be careful of the lazy loading of `frames.atoms`, which is updated during the
+        # iteration of the trajectory
+        return [_mda_to_json(frames.atoms) for _ in frames.trajectory]
     else:
         raise Exception("reached unreachable code")
 

python/chemiscope/structures/_mda.py

@@ -18,7 +18,7 @@ def _mda_valid_structures(frames):
 def _mda_to_json(ag):
     data = {}
     data["size"] = len(ag)
-    data["names"] = [atom.name for atom in ag]
+    data["names"] = [atom.type for atom in ag]
     data["x"] = [float(value) for value in ag.positions[:, 0]]
     data["y"] = [float(value) for value in ag.positions[:, 1]]
     data["z"] = [float(value) for value in ag.positions[:, 2]]

python/chemiscope/structures/_stk.py

@@ -18,7 +18,7 @@ def _stk_valid_structures(
     if HAVE_STK and isinstance(frames, Molecule):
         # deal with the user passing a single frame
         return [frames], True
-    elif HAVE_STK and hasattr(frames, "__iter__") and isinstance(frames[0], Molecule):
+    elif HAVE_STK and isinstance(frames, list) and isinstance(frames[0], Molecule):
         for frame in frames:
             assert isinstance(frame, Molecule)
         return frames, True

python/tests/mda_structures.py

@@ -6,7 +6,7 @@
 import chemiscope
 
 BASE_FRAME = mda.Universe.empty(n_atoms=3, trajectory=True)
-BASE_FRAME.add_TopologyAttr("name", ["C", "O", "O"])
+BASE_FRAME.add_TopologyAttr("type", ["C", "O", "O"])
 BASE_FRAME.atoms.positions = np.array([[0, 0, 0], [1, 1, 1], [2, 2, 5]])