Split media update and uptake constraint processes

ecoli/composites/ecoli_configs/default.json

@@ -45,6 +45,7 @@
     "profile": false,
     "processes": [
         "bulk-timeline",
+        "media_update",
         "exchange_data",
 
         "ecoli-tf-unbinding",
@@ -91,9 +92,10 @@
         }
     },
     "flow": {
-        "exchange_data": [],
+        "media_update": [],
+        "exchange_data": [["media_update"]],
 
-        "ecoli-tf-unbinding": [["exchange_data"]],
+        "ecoli-tf-unbinding": [["media_update"]],
 
         "ecoli-equilibrium": [["ecoli-tf-unbinding"]],
         "ecoli-two-component-system": [["ecoli-tf-unbinding"]],

ecoli/composites/ecoli_configs/fba_redux.json

@@ -6,8 +6,6 @@
     },
     "exclude_processes": ["exchange_data"],
     "flow": {
-        "ecoli-tf-unbinding": [],
-
         "ecoli-metabolism-redux": [["ecoli-chromosome-structure"]],
         "ecoli-mass-listener": [["ecoli-metabolism-redux"]],
         "RNA_counts_listener": [["ecoli-metabolism-redux"]],

ecoli/composites/ecoli_configs/fba_redux_div.json

@@ -6,8 +6,6 @@
     },
     "exclude_processes": ["exchange_data"],
     "flow": {
-        "ecoli-tf-unbinding": [],
-
         "ecoli-metabolism-redux": [["ecoli-chromosome-structure"]],
         "ecoli-mass-listener": [["ecoli-metabolism-redux"]],
         "RNA_counts_listener": [["ecoli-metabolism-redux"]],

ecoli/library/sim_data.py

@@ -400,6 +400,7 @@ def get_config_by_name(self, name, time_step=1, parallel=False):
             'rnap_data_listener': self.get_rnap_data_listener_config,
             'unique_molecule_counts': self.get_unique_molecule_counts_config,
             'exchange_data': self.get_exchange_data_config,
+            'media_update': self.get_media_update_config,
             'bulk-timeline': self.get_bulk_timeline_config,
         }
 
@@ -1470,6 +1471,12 @@ def get_exchange_data_config(self, time_step=1, parallel=False):
             '_parallel': parallel,
             'exchange_data_from_concentrations': self.sim_data.external_state.exchange_data_from_concentrations,
             'environment_molecules': list(self.sim_data.external_state.env_to_exchange_map.keys()),
+        }
+
+    def get_media_update_config(self, time_step=1, parallel=False):
+        return {
+            'time_step': time_step,
+            '_parallel': parallel,
             'saved_media': self.sim_data.external_state.saved_media
         }
 

ecoli/processes/__init__.py

@@ -32,6 +32,7 @@
 from ecoli.processes.environment.local_field import LocalField
 from ecoli.processes.environment.field_timeline import FieldTimeline
 from ecoli.processes.environment.exchange_data import ExchangeData
+from ecoli.processes.environment.media_update import MediaUpdate
 from ecoli.processes.shape import Shape
 from ecoli.processes.antibiotics.cell_wall import CellWall
 from ecoli.processes.antibiotics.pbp_binding import PBPBinding
@@ -91,6 +92,7 @@
 process_registry.register(LocalField.name, LocalField)
 process_registry.register(FieldTimeline.name, FieldTimeline)
 process_registry.register(ExchangeData.name, ExchangeData)
+process_registry.register(MediaUpdate.name, MediaUpdate)
 
 # auxiliary processes
 process_registry.register(Chemostat.name, Chemostat)

ecoli/processes/environment/exchange_data.py

@@ -12,7 +12,7 @@
 
 class ExchangeData(Step):
     """
-    Update environment concentrations and metabolism exchange constraints.
+    Update metabolism exchange constraints according to environment concs.
     """
     name = NAME
     topology = TOPOLOGY
@@ -28,7 +28,6 @@ def __init__(self, parameters=None):
         self.exchange_data_from_concentrations = self.parameters[
             'exchange_data_from_concentrations']
         self.environment_molecules = self.parameters['environment_molecules']
-        self.saved_media = self.parameters['saved_media']
 
     def ports_schema(self):
         return {
@@ -38,7 +37,6 @@ def ports_schema(self):
                 }
             },
             'environment': {
-                'media_id': {'_default': ''},
                 'exchange_data': {
                     'constrained': {'_default': {}, '_updater': 'set'},
                     'unconstrained': {'_default': set(), '_updater': 'set'}
@@ -54,22 +52,14 @@ def ports_schema(self):
     def next_update(self, timestep, states):
         if states['first_update']:
             return {'first_update': False}
-
-        env_concs = self.saved_media[states['environment']['media_id']]
-        conc_update = {}
-        # Calculate concentration delta to get from environment specified
-        # by old media ID to the one specified by the current media ID
-        for mol, conc in env_concs.items():
-            conc_update[mol] = conc * units.mM - states['boundary']['external'][mol]
-
+
         # Set exchange constraints for metabolism
+        env_concs = {mol: states['boundary']['external'][mol].to('mM').magnitude
+            for mol in self.environment_molecules}
         exchange_data = self.exchange_data_from_concentrations(env_concs)
         unconstrained = exchange_data['importUnconstrainedExchangeMolecules']
         constrained = exchange_data['importConstrainedExchangeMolecules']
         return {
-            'boundary': {
-                'external': conc_update
-            },
             'environment': {
                 'exchange_data': {
                     'constrained': constrained,

ecoli/processes/environment/media_update.py

@@ -0,0 +1,60 @@
+from ecoli.processes.registries import topology_registry
+from vivarium.core.process import Step
+from vivarium.library.units import units
+
+NAME = 'media_update'
+TOPOLOGY = {
+    'boundary': ('boundary',),
+    'environment': ('environment',),
+    'first_update': ('first_update', 'media_update')
+}
+topology_registry.register(NAME, TOPOLOGY)
+
+class MediaUpdate(Step):
+    """
+    Update environment concentrations according to current media ID.
+    """
+    name = NAME
+    topology = TOPOLOGY
+    defaults = {
+        'saved_media': {},
+        'time_step': 1,
+    }
+
+    def __init__(self, parameters=None):
+        super().__init__(parameters)
+        self.saved_media = self.parameters['saved_media']
+
+    def ports_schema(self):
+        return {
+            'boundary': {
+                'external': {
+                    '*': {'_default': 0 * units.mM}
+                }
+            },
+            'environment': {
+                'media_id': {'_default': ''}
+            },
+            'first_update': {
+                '_default': True,
+                '_updater': 'set',
+                '_divider': {'divider': 'set_value',
+                    'config': {'value': True}}},
+        }
+
+    def next_update(self, timestep, states):
+        if states['first_update']:
+            return {'first_update': False}
+
+        env_concs = self.saved_media[states['environment']['media_id']]
+        conc_update = {}
+        # Calculate concentration delta to get from environment specified
+        # by old media ID to the one specified by the current media ID
+        for mol, conc in env_concs.items():
+            conc_update[mol] = conc * units.mM - states['boundary']['external'][mol]
+
+        return {
+            'boundary': {
+                'external': conc_update
+            }
+        }

ecoli/processes/metabolism.py

@@ -842,7 +842,7 @@ def set_molecule_levels(self, metabolite_counts, counts_to_molar,
             current_media_id, unconstrained, constrained, conc_updates,
         )
         self.fba.update_homeostatic_targets(objective)
-        self.homeostatic_objective = objective
+        self.homeostatic_objective = {**self.homeostatic_objective, **objective}
 
         # Internal concentrations
         metabolite_conc = counts_to_molar * metabolite_counts