Fix complex (#526)

Related Issues: #524

The existing implementation was overwriting the existing host
vertex if the guest was the same building block as the vertex.
Fix this by appending to the list of vertices that a given building
block is attached to.

justfile

@@ -19,7 +19,7 @@ check:
   trap error=1 ERR
 
   echo
-  (set -x; ruff . )
+  (set -x; ruff check . )
 
   echo
   ( set -x; ruff format --check . )
@@ -38,7 +38,7 @@ check:
 # Auto-fix code issues.
 fix:
   ruff format .
-  ruff --fix .
+  ruff check --fix .
 
 # Start a MongoDB instance in docker.
 mongo:

src/stk/_internal/constructed_molecule.py

@@ -366,10 +366,10 @@ def get_atom_info(atom: Atom) -> AtomInfo:
 
             canonical_building_block = building_blocks[old_building_block]
 
-            (
-                canonical_building_block_atom,
-            ) = canonical_building_block.get_atoms(
-                atom_ids=canonical_building_block_atom_id,
+            (canonical_building_block_atom,) = (
+                canonical_building_block.get_atoms(
+                    atom_ids=canonical_building_block_atom_id,
+                )
             )
 
             return AtomInfo(

src/stk/_internal/construction_state/molecule_state/molecule_state.py

@@ -100,9 +100,9 @@ def _with_placement_results(
             edge_id,
             functional_groups,
         ) in summary.get_edge_functional_groups():
-            self._edge_functional_groups[
-                edge_id
-            ] = self._edge_functional_groups.get(edge_id, [])
+            self._edge_functional_groups[edge_id] = (
+                self._edge_functional_groups.get(edge_id, [])
+            )
             self._edge_functional_groups[edge_id].extend(functional_groups)
         return self
 

src/stk/_internal/topology_graphs/cage/cage.py

@@ -1378,9 +1378,9 @@ def _get_building_block_vertices(
         for vertex in cls._vertex_prototypes:
             vertex_degree = cls._vertex_degrees[vertex.get_id()]
             building_block = building_blocks_by_degree[vertex_degree]
-            building_block_vertices[
-                building_block
-            ] = building_block_vertices.get(building_block, [])
+            building_block_vertices[building_block] = (
+                building_block_vertices.get(building_block, [])
+            )
             building_block_vertices[building_block].append(vertex)
         return typing.cast(
             dict[BuildingBlock, abc.Sequence[_CageVertex]],

src/stk/_internal/topology_graphs/cage/cage_construction_state.py

@@ -179,9 +179,9 @@ def _update_neighbor_positions(
                 (functional_group,) = building_block.get_functional_groups(
                     fg_id
                 )
-                self._neighbor_positions[
-                    neighbor_id
-                ] = self._neighbor_positions.get(neighbor_id, [])
+                self._neighbor_positions[neighbor_id] = (
+                    self._neighbor_positions.get(neighbor_id, [])
+                )
                 self._neighbor_positions[neighbor_id].append(
                     building_block.get_centroid(
                         atom_ids=functional_group.get_placer_ids(),

src/stk/_internal/topology_graphs/cof/cof.py

@@ -780,9 +780,9 @@ def _get_building_block_vertices(
         for vertex in vertices:
             vertex_degree = vertex_degrees[vertex.get_id()]
             building_block = building_blocks_by_degree[vertex_degree]
-            building_block_vertices[
-                building_block
-            ] = building_block_vertices.get(building_block, [])
+            building_block_vertices[building_block] = (
+                building_block_vertices.get(building_block, [])
+            )
             building_block_vertices[building_block].append(vertex)
         return building_block_vertices
 

src/stk/_internal/topology_graphs/host_guest/complex.py

@@ -499,22 +499,29 @@ def _get_vertices_from_guests(
         if isinstance(guests, Guest):
             guests = (guests,)
 
-        building_block_vertices: dict[BuildingBlock, abc.Sequence[Vertex]]
-        building_block_vertices = {host: (HostVertex(0, (0.0, 0.0, 0.0)),)}
-        guest_vertices = {
-            guest.get_building_block(): (
-                GuestVertex(
-                    id=i + 1,
-                    position=guest.get_displacement(),
-                    start=guest.get_start_vector(),
-                    target=guest.get_end_vector(),
-                ),
-            )
-            for i, guest in enumerate(guests)
-        }
-        building_block_vertices.update(guest_vertices)
-
-        return building_block_vertices
+        building_block_vertices: dict[BuildingBlock, list[Vertex]]
+        building_block_vertices = {host: [HostVertex(0, (0.0, 0.0, 0.0))]}
+        for id_, guest in enumerate(guests, 1):
+            building_block = guest.get_building_block()
+            if building_block in building_block_vertices:
+                building_block_vertices[building_block].append(
+                    GuestVertex(
+                        id=id_,
+                        position=guest.get_displacement(),
+                        start=guest.get_start_vector(),
+                        target=guest.get_end_vector(),
+                    ),
+                )
+            else:
+                building_block_vertices[building_block] = [
+                    GuestVertex(
+                        id=id_,
+                        position=guest.get_displacement(),
+                        start=guest.get_start_vector(),
+                        target=guest.get_end_vector(),
+                    ),
+                ]
+        return building_block_vertices  # type: ignore
 
     def clone(self) -> Complex:
         return self._clone()