correctly implemented other_rel_AO_per_edge_per_frag

troyvvgroup · Jan 28, 2025 · c695d22 · c695d22
1 parent 9a0313d
commit c695d22
Showing 1 changed file with 29 additions and 0 deletions.
diff --git a/src/quemb/molbe/chemfrag.py b/src/quemb/molbe/chemfrag.py
@@ -455,8 +455,19 @@ class FragmentedMolecule:
     #: in motif `i_motif`.
     AO_per_motif_per_frag: Final[Sequence[Mapping[MotifIdx, Sequence[AOIdx]]]]
 
+    #: The relative atomic orbital indices per motif per fragment.
+    #: Relative means that the AO indices are relative to
+    #: the **own** fragment.
     rel_AO_per_motif_per_frag: Final[Sequence[Mapping[MotifIdx, Sequence[OwnRelAOIdx]]]]
 
+    #: The relative atomic orbital indices per edge per fragment.
+    #: Relative means that the AO indices are relative to the **other**
+    #: fragment where the edge is a center.
+    #: This variable was formerly known as `center_idx`.
+    other_rel_AO_per_edge_per_frag: Final[
+        Sequence[Mapping[EdgeIdx, Sequence[OtherRelAOIdx]]]
+    ]
+
     @classmethod
     def from_frag_structure(
         cls, mol: Mole, frag_structure: FragmentedStructure
@@ -502,13 +513,31 @@ def from_frag_structure(
                 rel_AO_per_motif[motif] = [OwnRelAOIdx(AOIdx(i)) for i in indices]
             rel_AO_per_motif_per_frag.append(rel_AO_per_motif)
 
+        other_rel_AO_per_edge_per_frag: list[
+            Mapping[EdgeIdx, Sequence[OtherRelAOIdx]]
+        ] = [
+            {
+                i_edge: [
+                    # We correctly reinterpet the AO indices as
+                    # indices of the other fragment
+                    cast(OtherRelAOIdx, i)
+                    for i in rel_AO_per_motif_per_frag[frag_per_edge[i_edge]][i_edge]
+                ]
+                for i_edge in edges
+            }
+            for edges, frag_per_edge in zip(
+                frag_structure.edges_per_frag, frag_structure.frag_idx_per_edge
+            )
+        ]
+
         return cls(
             frag_structure,
             mol,
             AO_per_atom,
             AO_per_frag,
             AO_per_motif_per_frag,
             rel_AO_per_motif_per_frag,
+            other_rel_AO_per_edge_per_frag,
         )