Merge branch 'master' of https://github.com/mauriceling/advancesyntoo…

…lkit
mauriceling · Nov 5, 2021 · 8f9abd4 · 8f9abd4
2 parents 084f5a9 + ac9bfa7
commit 8f9abd4
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Showing 2 changed files with 20 additions and 10 deletions.
diff --git a/ASModeller/gsm_to_km.py b/ASModeller/gsm_to_km.py
@@ -27,7 +27,8 @@
 
 import pandas as pd
 
-def gsm_km_converter(input_model, input_name, outputfile, rxnList):
+def gsm_km_converter(input_model, input_name, outputfile, rxnList, 
+                     metabolite_initial, enzyme_conc, enzyme_kcat, enzyme_km):
     pd.set_option('display.max_colwidth', None)
     filenamedata = []
     filenamedata.append(outputfile)
@@ -88,18 +89,18 @@ def gsm_km_converter(input_model, input_name, outputfile, rxnList):
         ['\n\n']
 
     initialsList = ['[Initials]' + '\n'] + \
-        [row['obj'].strip() + ' : 1e-5' + '\n' 
+        [row['obj'].strip() + ' : ' + str(metabolite_initial) + '\n' 
         for index, row in df4.iterrows()] + \
         ['\n\n']
 
     variable_concList = ['[Variables]' + '\n'] + \
-        [row['rxn_id'].strip() + '_conc : 1e-6' + '\n' 
+        [row['rxn_id'].strip() + '_conc : ' + str(enzyme_conc) + '\n' 
         for index, row in df.iterrows()]
 
-    variable_kcatList = [row['rxn_id'].strip() + '_kcat : 10' + '\n' 
+    variable_kcatList = [row['rxn_id'].strip() + '_kcat : ' + str(enzyme_kcat) + '\n' 
                          for index, row in df.iterrows()]
 
-    variable_kmList = [row['rxn_id'].strip() + '_km : 0.001' + '\n' 
+    variable_kmList = [row['rxn_id'].strip() + '_km : ' + str(enzyme_km) +'\n' 
                        for index, row in df.iterrows()] + ['\n\n']
 
     reactionList = ['[Reactions]' + '\n'] + \

diff --git a/astools.py b/astools.py
@@ -902,20 +902,29 @@ def cameo_mediumpFBA(model, change, result_type='objective',
     else:
         ASExternalTools.mediumFBA(model, change, 'pFBA', result_type)
 
-def GSM_to_ASM(model, name, outputfile):
+def GSM_to_ASM(model, name, outputfile, metabolite_initial=1e-5, 
+               enzyme_conc=1e-6, enzyme_kcat=13.7, enzyme_km=130e-6):
     '''!
     Function to read reactions in Genome-Scale Models (GSM) using 
     Cameo and convert to AdvanceSyn Model (ASM) format.
 
     Usage:
 
-        python astools.py GSM-to-ASM --model=e_coli_core --name=e_coli_core --outputfile=models/asm/e_coli_core.modelspec
+        python astools.py GSM-to-ASM --metabolite_initial=1e-5 --enzyme_conc=1e-6 --enzyme_kcat=13.7 --enzyme_km=130e-6 --model=e_coli_core --name=e_coli_core --outputfile=models/asm/e_coli_core.modelspec 
 
-    @model String: Model acceptable by Cameo (see 
-    http://cameo.bio/02-import-models.html).
+    @param model String: Model acceptable by Cameo (see http://cameo.bio/02-import-models.html).
+    @param name String: Name of model author / creator.
+    @param outputfile String: Relative path to the write out the converted 
+    ASM model.
+    @param metabolite_initial Float: Initial metabolite concentration. Default = 1e-5 (10 uM).
+    @param enzyme_conc Float: Enzyme concentration. Default = 1e-6 (1 uM)
+    @param enzyme_kcat Float: Enzyme kcat / turnover number. Default = 13.7 (13.7 per second).
+    @param enzyme_km Float: Enzyme Km (Michaelis-Menten constant). Default = 130e-6 (130 uM).
     '''
     rxnList = ASExternalTools.get_reaction_compounds(model, False)
-    ASModeller.gsm_km_converter(model, name, outputfile, rxnList)
+    ASModeller.gsm_km_converter(model, name, outputfile, rxnList, 
+                                metabolite_initial, enzyme_conc, 
+                                enzyme_kcat, enzyme_km)
     return rxnList