removed debugging print statements

freiburgermsu · Jul 30, 2024 · 80098e4 · 80098e4
1 parent 1387388
commit 80098e4
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Showing 3 changed files with 12 additions and 4 deletions.
diff --git a/examples/Community Modeling/smetana/BiGG_to_MSID.json b/examples/Community Modeling/smetana/BiGG_to_MSID.json
@@ -353,6 +353,7 @@
    "alltt": "cpd00388",
    "biliverd": "cpd00389",
    "cdpglc": "cpd00390",
+   "meso_Erythritol": "cpd00392",
    "fol": "cpd00393",
    "Lcyst": "cpd00395",
    "rmn": "cpd00396",
@@ -461,6 +462,7 @@
    "dcdp": "cpd00533",
    "i": "cpd00534",
    "ocdcea": "cpd00536",
+   "cis_Oleic acid": "cpd00536",
    "glyb": "cpd00540",
    "lipoate": "cpd00541",
    "crtsl": "cpd00546",
@@ -731,6 +733,7 @@
    "dca": "cpd01107",
    "hxa": "cpd01113",
    "bgly": "cpd01114",
+   "lnlcACP": "cpd01122",
    "malm": "cpd01123",
    "melatn": "cpd01124",
    "nona": "cpd01126",
@@ -994,10 +997,12 @@
    "B_ara1p": "cpd02428",
    "1pyr5c": "cpd02431",
    "5adtststerone": "cpd02435",
+   "dchac": "cpd02733",
    "mcom": "cpd02438",
    "3ddgc": "cpd02441",
    "d5kg": "cpd02446",
    "thdp": "cpd02465",
+   "HC02191": "cpd02475",
    "b124tc": "cpd02483",
    "hacon_C": "cpd02483",
    "hacon_T": "cpd02483",
@@ -1469,6 +1474,7 @@
    "2425dhvitd3": "cpd04848",
    "gmhep7p": "cpd04918",
    "gmhep1p": "cpd04920",
+   "HC02194": "cpd04945",
    "3mb": "cpd05178",
    "djenk": "cpd05190",
    "mtpp": "cpd05191",
@@ -1491,6 +1497,7 @@
    "thfglu": "cpd06227",
    "bzsucc": "cpd06708",
    "bzsuccoa": "cpd06709",
+   "C10164": "cpd07053",
    "phitcoa": "cpd06710",
    "hmpscoa": "cpd06711",
    "6occhcoa": "cpd06713",
@@ -2543,5 +2550,6 @@
    "2dmmq7": "cpd29732",
    "fmnRD": "cpd29733",
    "cu": "cpd30760",
+   "12_Ketolithocholic acid": "cpd35610",
    "hemeC": "cpd37301"
 }
diff --git a/modelseedpy/community/mscommunity.py b/modelseedpy/community/mscommunity.py
@@ -23,7 +23,7 @@
 
 class CommunityMember:
     def __init__(self, community, biomass_cpd, ID=None, index=None, abundance=0):
-        print(biomass_cpd)
+        print("biomass compound:", biomass_cpd)
         self.community, self.biomass_cpd = community, biomass_cpd
         try:     self.index = int(self.biomass_cpd.compartment[1:])
         except:  self.index = index
@@ -101,7 +101,7 @@ def __init__(self, model=None, member_models: list = None, abundances=None, kine
             if "c0" in self.biomass_cpd.id:
                 for rxn in self.util.model.reactions:
                     if self.biomass_cpd not in rxn.metabolites:  continue
-                    print(self.biomass_cpd, rxn, end=";\t")
+                    # print(self.biomass_cpd, rxn, end=";\t")
                     if rxn.metabolites[self.biomass_cpd] == 1 and len(rxn.metabolites) > 1:
                         if self.primary_biomass:  raise ObjectAlreadyDefinedError(
                             f"The primary biomass {self.primary_biomass} is already defined,"
@@ -112,7 +112,7 @@ def __init__(self, model=None, member_models: list = None, abundances=None, kine
             elif 'c' in self.biomass_cpd.compartment:   other_biomass_cpds.append(self.biomass_cpd)
         abundances = abundances or {f"Species{memIndex}": {"biomass_compound": bioCpd, "abundance": 1/len(other_biomass_cpds)}
                                     for memIndex, bioCpd in enumerate(other_biomass_cpds)}
-        print()   # this returns the carriage after the tab-ends in the biomass compound printing 
+        # print()   # this returns the carriage after the tab-ends in the biomass compound printing 
         self.members = DictList(CommunityMember(self, info["biomass_compound"], ID, index, info["abundance"])
                                 for index, (ID, info) in enumerate(abundances.items()))
         # assign the MSCommunity constraints and objective

diff --git a/modelseedpy/core/msminimalmedia.py b/modelseedpy/core/msminimalmedia.py
@@ -49,7 +49,7 @@ def bioFlux_check(model, sol=None, sol_dict=None, min_growth=0.1):
     sol_dict = sol_dict or FBAHelper.solution_to_variables_dict(sol, model)
     # print({k:v for k,v in sol_dict.items() if v > 1E-8})
     simulated_growth = max(sum([flux for var, flux in sol_dict.items() if re.search(r"(^bio\d+$)", var.name)]), sol.objective_value)
-    if simulated_growth < min_growth*0.9999:
+    if simulated_growth < min_growth*0.9999 and simulated_growth+min_growth > 1e-8:
         raise ObjectiveError(f"The assigned minimal_growth of {min_growth} was not maintained during the simulation,"
                              f" where the observed growth value was {simulated_growth}.")
     if sol.status != "optimal":