biochem

Author: Fxe

modelseedpy/biochem/modelseed_biochem.py

@@ -194,19 +194,21 @@ def load_reactions_from_df(df: pd.DataFrame, database_metabolites: dict, names:
             reactions.append(rxn)
         except Exception as e:
             logger.error('failed to read reaction at Index: %s. %s', t[0], e)
-    return reactions
+    return reactions, list(metabolites_indexed.values())
 
 
 class ModelSEEDDatabase:
     """
     ModelSEED database instance.
     """
 
-    def __init__(self, compounds, reactions):
+    def __init__(self, compounds, reactions, compound_tokens):
         self.compounds = DictList()
+        self.compound_tokens = DictList()
         self.reactions = DictList()
         self.compounds += compounds
         self.reactions += reactions
+        self.reactions += compound_tokens
         self.inchi_key_lookup = {}
         self.metabolite_reactions = {}
 
@@ -403,8 +405,9 @@ def load_database(compounds_url, reactions_url,
     reaction_ecs = get_aliases_from_df(pd.read_csv(reactions_ec_url, sep='\t'))
 
     df_reactions = pd.read_csv(reactions_url, sep='\t', low_memory=False)
-    reactions = load_reactions_from_df(df_reactions, dict(map(lambda x: (x.id, x), compounds)), reaction_names,
-                                       reaction_aliases, reaction_ecs)
+    reactions, metabolites_indexed = load_reactions_from_df(
+        df_reactions, dict(map(lambda x: (x.id, x), compounds)), reaction_names,
+        reaction_aliases, reaction_ecs)
 
     database = ModelSEEDDatabase(compounds, reactions)
     return database

modelseedpy/biochem/modelseed_reaction.py

@@ -158,9 +158,7 @@ def to_template_reaction(self, compartment_setup=None):
                 raise ValueError(f'invalid compartment setup missing key [{m.compartment}] in {compartment_setup}')
             cpd = m.to_template_compartment_compound(compartment_setup[m.compartment])
             metabolites[cpd] = v
-            print(m.id, m.compartment, cpd)
-
-            print(v)
+            # print(m.id, m.compartment, cpd, v)
 
         # if len(str(index)) > 0:
         #    name = f'{self.name} [{compartment}]'

modelseedpy/core/msatpcorrection.py

@@ -37,7 +37,7 @@ def __init__(self, model, core_template, atp_medias,compartment="c0",
         self.max_gapfilling = max_gapfilling
         self.gapfilling_delta = gapfilling_delta
         self.coretemplate = core_template
-        self.msgapfill = MSGapfill(model,default_gapfill_templates=core_template)
+        self.msgapfill = MSGapfill(model, default_gapfill_templates=core_template)
         self.original_bounds = {}
         self.noncore_reactions = []
         self.other_compartments = []
@@ -126,7 +126,7 @@ def evaluate_growth_media(self):
                 logger.debug('evaluate media %s - %f (%s)', media.id, solution.objective_value, solution.status)
                 self.media_gapfill_stats[media] = None
                 if solution.objective_value == 0 or solution.status != 'optimal':
-                    self.media_gapfill_stats[media] = self.msgapfill.run_gapfilling(media, self.atp_hydrolysis.id)  
+                    self.media_gapfill_stats[media] = self.msgapfill.run_gapfilling(media, self.atp_hydrolysis.id)
                     #IF gapfilling fails - need to activate and penalize the noncore and try again
                 elif solution.objective_value > 0 or solution.status == 'optimal':
                     self.media_gapfill_stats[media] = {'reversed': {}, 'new': {}}

modelseedpy/core/msgapfill.py

@@ -56,7 +56,7 @@ def run_gapfilling(self, media=None, target="bio1", minimum_obj=0.01, binary_che
             "gapfill_all_indecies_with_default_models": self.gapfill_all_indecies_with_default_models,
             "default_excretion":100,
             "default_uptake":100,
-            "minimum_obj":minimum_obj,
+            "minimum_obj": minimum_obj,
             "blacklist": self.blacklist,
             "reaction_scores": self.reaction_scores,
             "set_objective": 1