Adding flux_visualizations.py for addition of source carbon reaction

binary_models/flux_visualizations.py

@@ -0,0 +1,88 @@
+import cobra
+import pandas as pd
+import binary_models.helpers as helpers
+from binary_models.load_ternary import load_community_model, model_folder
+from cobra import Metabolite, Reaction
+
+def create_explicit_carbon(community_model):
+
+    source_carbon = Metabolite('co2_source_m',
+                               name='Source CO2',
+                               compartment='m'
+                               )
+
+    co2_source2Azoto = Reaction('EX_co2_source_e__Azotobacter',
+                                name='co2 source2Azoto'
+                                )
+    co2_source2Rhodo = Reaction('EX_co2_source_e__Rhodosporidium',
+                                name='co2 source2Rhodo'
+                                )
+    co2_source2Synec = Reaction('EX_co2_source_e__Synechococcus',
+                                name='co2 source2Synec'
+                                )
+
+    community_model.add_metabolites([source_carbon])
+    community_model.add_boundary(
+        community_model.metabolites.get_by_id("co2_source_m"), type="exchange"
+    )
+    co2_source_m = community_model.metabolites.co2_source_m
+    co2_m = community_model.metabolites.co2_m
+    co2_e__Azotobacter = community_model.metabolites.co2_e__Azotobacter
+    co2_e__Rhodosporidium = community_model.metabolites.co2_e__Rhodosporidium
+    co2_e__Synechococcus = community_model.metabolites.co2_e__Synechococcus
+
+    co2_source2Azoto.add_metabolites({
+        co2_source_m: -1.0,
+        co2_e__Azotobacter: 1.0
+    })
+
+    co2_source2Rhodo.add_metabolites({
+        co2_source_m: -1.0,
+        co2_e__Rhodosporidium: 1.0
+    })
+
+    co2_source2Synec.add_metabolites({
+        co2_source_m: -1.0,
+        co2_e__Synechococcus: 1.0
+    })
+
+    community_model.add_reactions([co2_source2Azoto,co2_source2Rhodo,co2_source2Synec])
+
+    # Set Micom Global IDs and Community IDs
+    community_model.metabolites.co2_source_m.global_id = 'co2_source_m'
+    community_model.metabolites.co2_source_m.community_id = 'medium'
+    community_model.reactions.EX_co2_source_e__Azotobacter.global_id = 'EX_co2_source_e'
+    community_model.reactions.EX_co2_source_e__Azotobacter.community_id = 'Azotobacter'
+    community_model.reactions.EX_co2_source_e__Rhodosporidium.global_id = 'EX_co2_source_e'
+    community_model.reactions.EX_co2_source_e__Rhodosporidium.community_id = 'Rhodosporidium'
+    community_model.reactions.EX_co2_source_e__Synechococcus.global_id = 'EX_co2_source_e'
+    community_model.reactions.EX_co2_source_e__Synechococcus.community_id = 'Synechococcus'
+    community_model.reactions.EX_co2_source_m.global_id = 'EX_co2_source_m'
+    community_model.reactions.EX_co2_source_m.community_id = 'medium'
+
+    # Force EX_co2_source_m to push only and EX_co2_m to pull only
+    community_model.reactions.EX_co2_source_m.lower_bound = -1.9
+    community_model.reactions.EX_co2_source_m.upper_bound = 0
+    community_model.reactions.EX_co2_m.lower_bound = 0
+    # 
+
+    return community_model
+
+
+def remove_hco3_to_co2(community_model):
+    """Removes the the hco3 to co2 reaction in Rhodosporidium"""
+
+    HCO3E = community_model.reactions.HCO3E__Rhodosporidium
+    community_model.remove_reactions([HCO3E])
+
+    return community_model
+
+
+if __name__ == '__main__':
+    community, manifest = load_community_model(prep_files=False)
+
+    source_carbon_community = create_explicit_carbon(community)
+
+
+
+