Create cinnm.py

added_reactions/cinnm.py

@@ -0,0 +1,20 @@
+# trans-Cinnamate (cinnm) reaction
+
+# EC Number 4.3.1.25 https://biocyc.org/META/NEW-IMAGE?type=REACTION&object=PHENYLALANINE-AMMONIA-LYASE-RXN
+
+phe__L = model.metabolites.get_by_id("phe__L_c")
+cinnm = model.metabolites.get_by_id("cinnm_c")
+nh4 = model.metabolites.get_by_id("nh4_c")
+
+phenylalanine_ammonia_lyase = Reaction("PAL")
+phenylalanine_ammonia_lyase.name = "Phenylalanine Ammonia Lyase Reaction"
+phenylalanine_ammonia_lyase.add_metabolites(
+    {
+        phe__L: -1.0,
+        cinnm: 1.0,
+        nh4: 1.0
+    }
+)
+model.add_reactions([phenylalanine_ammonia_lyase])
+cobra.io.save_json_model(model, "./models/iML1515_cinnm.json")
+model.optimize().objective_value