Add reconciliation buffer to codon sequences

Author: thalassemia

ecoli/library/sim_data.py

@@ -1109,6 +1109,7 @@ def get_polypeptide_elongation_config(self, time_step=1):
             "K_M_trna__per_L": K_M_trna__per_L,
             "max_curated_kcats": max_curated_kcats,
             "kcats_curated": curated,
+            "reconciliation_buffer": relation.reconciliation_buffer,
             "elongation_max": (
                 constants.ribosome_elongation_rate_max
                 if self.variable_elongation_translation

ecoli/processes/polypeptide_elongation.py

@@ -2323,7 +2323,7 @@ def __init__(self, parameters, process):
         # kinetics and sequence limits. This width buffer describes
         # the additional sequence positions (towards the C terminal)
         # to view during each time step.
-        self.buffer = 10
+        self.buffer = self.parameters["reconciliation_buffer"]
 
         # Previous rate: the previous ribosome elongation rate is
         # recorded to warm start the next time step's binary search. For

reconstruction/ecoli/dataclasses/relation.py

@@ -345,6 +345,9 @@ def _build_codon_based_translation(self, raw_data, sim_data):
         molecule_ids = [protein_id[:-3] for protein_id in protein_ids]
         sequences = [self._codon_sequences[molecule_id] for molecule_id in molecule_ids]
 
+        # See ecoli.processes.polypeptide_elongation.KineticTrnaChargingModel.
+        self.reconciliation_buffer = 10
+
         # Calculate the number of columns required to read beyond
         # (towards the C-terminal) the longest mRNA coding region.
         # Note: For polypeptides undergoing N-terminal cleavage of the
@@ -360,6 +363,8 @@ def _build_codon_based_translation(self, raw_data, sim_data):
                     units.aa / units.s
                 )
             )
+            # Add read-ahead buffer for reconciliation
+            + self.reconciliation_buffer
         )
 
         self.codon_sequences = np.full(