Ensure uniqueness of unique_indices field

ecoli/library/initial_conditions.py

@@ -1240,10 +1240,7 @@ def initialize_transcription(
     unique_molecules["RNA"] = np.concatenate((partial_rnas, full_rnas))
     # Have to recreate unique indices or else there will be conflicts between
     # full and partial RNAs
-    unique_mol_names = list(
-        sim_data.internal_state.unique_molecule.unique_molecule_definitions.keys()
-    )
-    unique_prefix = unique_mol_names.index("RNA") << 59
+    unique_prefix = np.min(unique_molecules["RNA"]["unique_index"])
     unique_molecules["RNA"]["unique_index"] = np.arange(
         unique_prefix, unique_prefix + len(unique_molecules["RNA"])
     )

ecoli/library/schema.py

@@ -116,6 +116,18 @@ class MetadataArray(np.ndarray):
     def __new__(cls, input_array, metadata=None):
         # Input array should be an array instance
         obj = np.asarray(input_array).view(cls)
+        # Ensure unique_index field exists and is unique
+        if "unique_index" in obj.dtype.names:
+            if "_entryState" in obj.dtype.names:
+                unique_indices = obj["unique_index"][obj["_entryState"].view(np.bool_)]
+                if len(unique_indices) != len(set(unique_indices)):
+                    raise ValueError(
+                        "All elements in the 'unique_index' field must be unique."
+                    )
+            else:
+                raise ValueError("Input array must have an '_entryState' field.")
+        else:
+            raise ValueError("Input array must have a 'unique_index' field.")
         obj.metadata = metadata
         return obj
 

ecoli/processes/chromosome_structure.py

@@ -1391,6 +1391,7 @@ def generate_flow(self, config):
     full_chromosomes.flags.writeable = True
     full_chromosomes["_entryState"][0] = 1
     full_chromosomes["domain_index"][0] = 0
+    full_chromosomes["unique_index"][0] = 0
     full_chromosomes.flags.writeable = False
     # Set up chromosome domains
     chromosome_domains, replisome_idx = get_free_indices(
@@ -1399,6 +1400,7 @@ def generate_flow(self, config):
     chromosome_domains.flags.writeable = True
     chromosome_domains["_entryState"][replisome_idx] = 1
     chromosome_domains["domain_index"][replisome_idx] = np.arange(5)
+    chromosome_domains["unique_index"][replisome_idx] = np.arange(5)
     chromosome_domains["child_domains"][replisome_idx] = [
         [1, 2],
         [3, 4],
@@ -1413,6 +1415,7 @@ def generate_flow(self, config):
     oriCs.flags.writeable = True
     oriCs["_entryState"][oriC_idx] = 1
     oriCs["domain_index"][oriC_idx] = [2, 3, 4]
+    oriCs["unique_index"][oriC_idx] = np.arange(3)
     oriCs.flags.writeable = False
     template_initial_state["unique"]["oriC"] = oriCs
     # Set up replisome for actively replicating domain
@@ -1538,6 +1541,7 @@ def generate_flow(self, config):
     )
     chromosomal_segments["domain_index"][segment_idx] = domain_index
     chromosomal_segments["linking_number"][segment_idx] = linking_number
+    chromosomal_segments["unique_index"][segment_idx] = np.arange(len(linking_number))
     chromosomal_segments.flags.writeable = False
     template_initial_state["unique"]["chromosomal_segment"] = chromosomal_segments
     # Since unique numpy updater is an class method, internal