Small changes.

ecoli/composites/ecoli_configs/ecoli/composites/ecoli_configs/run_parca.json

@@ -0,0 +1,3 @@
+{
+    "sim_data_path": null
+}

ecoli/experiments/metabolism_redux_sim.py

@@ -55,18 +55,19 @@ def run_ecoli_with_metabolism_redux(
 # disables growth rate control
 def run_ecoli_with_metabolism_redux_classic(
     filename="metabolism_redux_classic",
-    total_time=10,
+    total_time=5000,
     divide=True,
     # initial_state_file='wcecoli_t0', # 'met_division_test_state',
     progress_bar=True,
     log_updates=False,
     emitter="timeseries",  # 'timeseries',
-    name="convex_kinetics_minimal",
+    name="cofactors",
     raw_output=False,
+    emit_unique=True,
     save=True,
     save_times=[1, 10],
-    condition="basal",  # basal, with_aa
-    fixed_media="minimal",  # minimal, minimal_plus_amino_acids
+    condition="with_aa",  # basal, with_aa
+    fixed_media="minimal_plus_amino_acids",  # minimal, minimal_plus_amino_acids
 ):
     # filename = 'default'
     sim = EcoliSim.from_file(CONFIG_DIR_PATH + filename + ".json")
@@ -77,6 +78,7 @@ def run_ecoli_with_metabolism_redux_classic(
     sim.emitter = emitter
     # sim.initial_state = get_state_from_file(path=f'data/{initial_state_file}.json')
     sim.raw_output = raw_output
+    sim.emit_unique = emit_unique
     sim.save = save
     sim.save_times = save_times
 
@@ -104,13 +106,13 @@ def run_ecoli_with_metabolism_redux_classic(
     sim.run()
 
     query = []
-    folder = f"out/cofactors/{name}_{total_time}_{datetime.date.today()}/"
+    folder = f"out/cofactors/colony/"
     save_sim_output(folder, query, sim, save_model=True)
 
 
 def run_colony(
     filename="metabolism_redux_classic",
-    total_time=1400,
+    total_time=2700,
     divide=True,
     # initial_state_file='wcecoli_t0', # 'met_division_test_state',
     progress_bar=True,
@@ -120,8 +122,8 @@ def run_colony(
     raw_output=False,
     save=True,
     save_times=[1, 200, 400, 1300],
-    condition="with_aa",  # basal, with_aa
-    fixed_media="minimal_plus_amino_acids",  # minimal, minimal_plus_amino_acids
+    condition="basal",  # basal, with_aa
+    fixed_media="minimal",  # minimal, minimal_plus_amino_acids
 ):
     # filename = 'default'
     sim = EcoliSim.from_file(CONFIG_DIR_PATH + filename + ".json")
@@ -138,17 +140,61 @@ def run_colony(
     sim.condition = condition
     sim.fixed_media = fixed_media
 
-    for seed in [i for i in range(4, 9, 1)]:
+    for seed in [i for i in range(11, 20, 1)]:
         sim.seed = seed
 
         sim.build_ecoli()
 
         sim.run()
 
         query = []
-        folder = f"out/cofactors/rich-{seed}/"
+        folder = f"out/cofactors/minimal-{seed}/"
         save_sim_output(folder, query, sim, save_model=False)
 
+def run_lineage(
+    filename="metabolism_redux_classic",
+    total_time=2900,
+    divide=True,
+    initial_state_file='lineage_min_2', # 'wcecoli_t0', # 'met_division_test_state',
+    progress_bar=True,
+    log_updates=False,
+    emitter="timeseries",  # 'timeseries',
+    name="metabolism-redux-classic-rich",
+    raw_output=False,
+    save=True,
+    save_times=[1, 2500, 2600, 2700, 2800, 2900],
+    condition="basal",  # basal, with_aa
+    fixed_media="minimal",  # minimal, minimal_plus_amino_acids
+):
+    # filename = 'default'
+    sim = EcoliSim.from_file(CONFIG_DIR_PATH + filename + ".json")
+    sim.total_time = total_time
+    sim.divide = divide
+    sim.progress_bar = progress_bar
+    sim.log_updates = log_updates
+    sim.emitter = emitter
+    sim.initial_state = get_state_from_file(path=f'data/{initial_state_file}.json')
+    sim.raw_output = raw_output
+    sim.save = save
+    sim.save_times = save_times
+
+    sim.condition = condition
+    sim.fixed_media = fixed_media
+
+    sim.seed = 1
+
+    # this means that sims will not create conflicting random indices when loading from saved state
+    if initial_state_file != 'wcecoli_t0':
+        sim.seed += int(sim.initial_state['global_time'])
+
+    sim.build_ecoli()
+
+    sim.run()
+
+    query = []
+    folder = f"out/cofactors/lineage-min-{initial_state_file}/"
+    save_sim_output(folder, query, sim, save_model=False)
+
 
 @pytest.mark.slow
 def test_ecoli_with_metabolism_redux(
@@ -293,6 +339,7 @@ def run_ecoli_with_default_metabolism(
     "2": run_ecoli_with_metabolism_redux,
     "2a": run_ecoli_with_metabolism_redux_classic,
     "2b": run_colony,
+    "2c": run_lineage,
     "3": test_ecoli_with_metabolism_redux,
     "3a": test_ecoli_with_metabolism_classic,
     "4": test_ecoli_with_metabolism_redux_div,
@@ -309,6 +356,8 @@ def save_sim_output(folder, query, sim, save_model=False):
                 ("agents", agent, "listeners", "fba_results"),
                 ("agents", agent, "listeners", "mass"),
                 ("agents", agent, "listeners", "unique_molecule_counts"),
+                ("agents", agent, "listeners", "rna_synth_prob"),
+                ("agents", agent, "listeners", "rna_counts"),
                 ("agents", agent, "bulk"),
             ]
         )

ecoli/processes/metabolism_redux_classic.py

@@ -63,6 +63,12 @@
     "RXN-22461",
     "RXN-22462",
     "RXN-22463",
+    "PYRROLINECARBDEHYDROG-RXN",
+    "RXN0-7008-PRO/UBIQUINONE-8//L-DELTA1-PYRROLINE_5-CARBOXYLATE/CPD-9956/PROTON.67.",
+    "GLUCOKIN-RXN-GLC/ATP//ALPHA-GLC-6-P/ADP/PROTON.34.", # gets confused with PTS
+    "PRPPSYN-RXN-CPD-15318/ATP//PRPP/AMP/PROTON.31.", # duplicate
+    "TRANS-RXN0-574-GLC//GLC.9.", # duplicate
+    "GLUCOKIN-RXN-GLC/ATP//D-glucopyranose-6-phosphate/ADP/PROTON.48.", # duplicate
 ]
 
 # not key central carbon met