Gapfilling a metabolic model

[1]:

import cobra
#If you have CPLEX, uncomment this
#import cplex
import cobrakbase
#import modelseedpy.fbapkg
from modelseedpy import GapfillingPkg, KBaseMediaPkg
from modelseedpy import FBAHelper, MSBuilder

cobrakbase 0.2.8

[2]:

kbase_api = cobrakbase.KBaseAPI()
model = kbase_api.get_from_ws("test_model",18528)
#If you have CPLEX, uncomment this
#model.solver = 'optlang-cplex'
template = kbase_api.get_from_ws("GramNegModelTemplateV3","NewKBaseModelTemplates")
media = kbase_api.get_from_ws("Carbon-D-Glucose","KBaseMedia")
model = MSBuilder.gapfill_model(model,"bio1",template,media)

kmp = KBaseMediaPkg(model)
kmp.build_package(media)
sol=model.optimize()
model.summary()

[2]:

Objective

1.0 bio1 = 0.8048653841131165

Uptake

Metabolite Reaction Flux C-Number C-Flux
cpd00009_e0 EX_cpd00009_e0 0.9998 0 0.00%
cpd00013_e0 EX_cpd00013_e0 6.037 0 0.00%
cpd00027_e0 EX_cpd00027_e0 5 6 100.00%
cpd00030_e0 EX_cpd00030_e0 0.00639 0 0.00%
cpd00034_e0 EX_cpd00034_e0 0.00639 0 0.00%
cpd00048_e0 EX_cpd00048_e0 0.1755 0 0.00%
cpd00058_e0 EX_cpd00058_e0 0.00639 0 0.00%
cpd00063_e0 EX_cpd00063_e0 0.00639 0 0.00%
cpd00067_e0 EX_cpd00067_e0 61.85 0 0.00%
cpd00099_e0 EX_cpd00099_e0 0.00639 0 0.00%
cpd00149_e0 EX_cpd00149_e0 0.00639 0 0.00%
cpd00205_e0 EX_cpd00205_e0 0.00639 0 0.00%
cpd00254_e0 EX_cpd00254_e0 0.00639 0 0.00%
cpd10516_e0 EX_cpd10516_e0 0.02556 0 0.00%
cpd17041_c0 rxn13782_c0 0.8049 0 0.00%
cpd17042_c0 rxn13783_c0 0.8049 0 0.00%
cpd17043_c0 rxn13784_c0 0.8049 0 0.00%

Secretion

Metabolite Reaction Flux C-Number C-Flux
cpd00001_e0 EX_cpd00001_e0 -82.26 0 0.00%
cpd00007_e0 EX_cpd00007_e0 -2.928 0 0.00%
cpd15378_e0 EX_cpd15378_e0 -0.00639 7 100.00%
cpd11416_c0 SK_cpd11416_c0 -0.8049 0 0.00% 
[85]:

from modelseedpy.helpers import get_template
from modelseedpy.core.mstemplate import MSTemplateBuilder
template_core = get_template('template_core')
template_core = MSTemplateBuilder.from_dict(template_core).build()
template_gramneg = get_template('template_gram_neg')
compcompounds = []
for o in template_gramneg['compcompounds']:
    a, b = o['id'].split('_')
    if b not in ['c', 'e']:
        #print(o)
        pass
    else:
        compcompounds.append(o)
template_gramneg['compcompounds'] = compcompounds
template_gramneg = MSTemplateBuilder.from_dict(template_gramneg).build()

[17]:

for template_reaction in template.reactions:
    template_reaction

[19]:

template_reaction.id.split("_")[0]

[19]:

'rxn09295'

[76]:

template_gramneg = get_template('template_gram_neg')

[52]:

from modelseedpy import MSBuilder
from cobra.core import Model, Reaction, Metabolite
def build_full_model(template, index='0'):
    model = Model('modelo')
    model.add_reactions([r.to_reaction(index=index) for r in template.reactions])
    exchanges = MSBuilder.build_exchanges(model, 'e0')
    #biomasses = MSBuilder.build_biomasses(model, template, '')
    #print(exchanges)
    bio_atp = Reaction('bio2', 'bio2', '', -10000, 10000)
    bio_atp.add_metabolites({
        model.metabolites.cpd00067_c0: 1,
        model.metabolites.cpd00002_c0: -1,
        model.metabolites.cpd00008_c0: 1,
        model.metabolites.cpd00001_c0: -1,
        model.metabolites.cpd00009_c0: 1,
    })
    model.add_reactions(exchanges)
    model.add_reactions([bio_atp])
    model.objective = 'bio2'
    #model.add_reactions(biomasses)
    return model

model_core = build_full_model(template_core)
#model_gramneg = build_full_model(template_gramneg)

[87]:

def extend_model_with_template_metabolites(model, template, index='0'):
    """
    Add all missing template compartment compounds to the model
    :param template:
    :param index:
    :return:
    """
    new_metabolites = {}
    new_exchange = []
    new_demand = []
    for template_compound in template.compcompounds:
        compartment = template_compound.compartment
        compartment_index = "0" if compartment == 'e' else index
        cobra_metabolite = GapfillingPkg.convert_template_compound(None, template_compound, compartment_index, template)  # TODO: move function out
        if cobra_metabolite.id not in model.metabolites and cobra_metabolite.id not in new_metabolites:
            new_metabolites[cobra_metabolite.id] = cobra_metabolite
            #self.model.add_metabolites([cobra_metabolite])
            msid = FBAHelper.modelseed_id_from_cobra_metabolite(cobra_metabolite)
            if msid in ["cpd02701", "cpd11416", "cpd15302"]:
                if msid != "cpd11416" or cobra_metabolite.compartment == "c0":
                    new_demand.append(cobra_metabolite.id)
            if compartment == "e":
                new_exchange.append(cobra_metabolite.id)
    # Adding all metabolites to model prior to adding reactions
    #self.model.add_metabolites(new_metabolites.values())

    return new_exchange, new_demand, new_metabolites
new_exchange, new_demand, new_metabolites = extend_model_with_template_metabolites(model_core, template_gramneg)

[ ]:

model_gramneg.medium = {
    'EX_cpd00001_e0': 1000,
    'EX_cpd00067_e0': 1000,
    'EX_cpd00009_e0': 1000,
    'EX_cpd00011_e0': 1000,
    'EX_cpd00029_e0': 3,
}

[11]:

model_core.medium = {
    'EX_cpd00001_e0': 1000,
    'EX_cpd00067_e0': 1000,
    'EX_cpd00009_e0': 1000,
    'EX_cpd00011_e0': 1000,
    'EX_cpd00027_e0': 3,
}
model_core.summary()

[11]:

Objective

1.0 bio2 = 10.5

Uptake

Metabolite Reaction Flux C-Number C-Flux
cpd00027_e0 EX_cpd00027_e0 3 6 100.00%

Secretion

Metabolite Reaction Flux C-Number C-Flux
cpd00011_e0 EX_cpd00011_e0 -6 1 33.33%
cpd00363_e0 EX_cpd00363_e0 -6 2 66.67% 
[22]:

model_gramneg.optimize()

[22]:
Optimal solution with objective value 10000.000
fluxes reduced_costs
rxn00594_c 0.0 0.0
rxn01087_c 0.0 0.0
rxn03234_c 0.0 -0.0
rxn01734_c 0.0 0.0
rxn02282_c 0.0 0.0
... ... ...
EX_cpd00561_e -0.0 0.0
EX_cpd03453_e -0.0 0.0
EX_cpd18072_e -0.0 0.0
EX_cpd18074_e -0.0 0.0
bio2 10000.0 2.0

9983 rows × 2 columns

[89]:

from modelseedpy import FBAHelper
from modelseedpy import GapfillingPkg
pkg_gf = GapfillingPkg(model_core)
pkg_gf.build(template_gramneg)

[95]:

model_core.medium = {
    'EX_cpd00001_e0': 1000,
    'EX_cpd00067_e0': 1000,
    'EX_cpd00009_e0': 1000,
    'EX_cpd00011_e0': 1000,
    'EX_cpd00029_e0': 3,
}
sol = model_core.optimize()

[98]:

for r in model_core.reactions:
    r.lower_bound = -1000
    r.upper_bound = 1000

[103]:

model_core.summary()

[103]:

Objective

1.0 bio2 = 0.01

Uptake

Metabolite Reaction Flux C-Number C-Flux

Secretion

Metabolite Reaction Flux C-Number C-Flux 
[102]:

sol = model_core.optimize()
sol

[102]:
Optimal solution with objective value 0.010
fluxes reduced_costs
rxn01975_c0 1000.00000 0.0
rxn00265_c0 93.63949 0.0
rxn00549_c0 1000.00000 -0.0
rxn01123_c0 1000.00000 -0.0
rxn14427_c0 1000.00000 -0.0
... ... ...
EX_cpd00561_e0 -0.00000 0.0
EX_cpd03453_e0 0.00000 0.0
DM_cpd11416_c0 -0.00000 0.0
DM_cpd15302_c0 -0.00000 0.0
DM_cpd02701_c0 -0.00000 0.0

9975 rows × 2 columns

[100]:

model_core.objective = 'bio2'

[48]:

len(model_core.reactions)

[48]:

9975

[51]:

for rxn_id in pkg_gf.gapfilling_penalties:
    print(rxn_id, pkg_gf.gapfilling_penalties[rxn_id])

rxn00594_c0 {'forward': 4, 'added': 1}
rxn01087_c0 {'forward': 4, 'added': 1}
rxn03234_c0 {'reverse': 5, 'forward': 5, 'added': 1}
rxn01734_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn02282_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn10561_c0 {'reverse': 7, 'forward': 7, 'added': 1}
rxn02201_c0 {'forward': 2, 'added': 1}
rxn02241_c0 {'forward': 4, 'added': 1}
rxn09471_c0 {'forward': 6, 'added': 1}
rxn05704_c0 {'reverse': 7, 'forward': 7, 'added': 1}
rxn00351_c0 {'forward': 2, 'added': 1}
rxn02637_c0 {'reverse': 6, 'forward': 6, 'added': 1}
rxn10496_c0 {'reverse': 7, 'forward': 7, 'added': 1}
rxn05994_c0 {'reverse': 5, 'forward': 7.654999999999999, 'added': 1}
rxn07431_c0 {'reverse': 2, 'forward': 2, 'added': 1}
rxn11746_c0 {'forward': 5, 'added': 1}
rxn00836_c0 {'reverse': 2, 'added': 1}
rxn03805_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn02209_c0 {'reverse': 5, 'forward': 5, 'added': 1}
rxn08977_c0 {'reversed': 1, 'reverse': 3.2560000000000002}
rxn00390_c0 {'reverse': 4.5237, 'forward': 5, 'added': 1}
rxn11291_c0 {'reverse': 6, 'forward': 6, 'added': 1}
rxn13085_c0 {'forward': 6, 'added': 1}
rxn06636_c0 {'forward': 5, 'added': 1}
rxn03760_c0 {'reverse': 6, 'forward': 10.8895, 'added': 1}
rxn03946_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn08180_c0 {'forward': 4, 'added': 1}
rxn01503_c0 {'reverse': 5, 'forward': 5, 'added': 1}
rxn05318_c0 {'reverse': 5, 'forward': 5, 'added': 1}
rxn04735_c0 {'forward': 4, 'added': 1}
rxn07360_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn03720_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn08230_c0 {'reverse': 6, 'forward': 6, 'added': 1}
rxn09044_c0 {'forward': 6, 'added': 1}
rxn00749_c0 {'reverse': -0.5712999999999999, 'forward': 4, 'added': 1}
rxn14312_c0 {'reverse': 6, 'forward': 6, 'added': 1}
rxn00062_c0 {'forward': 4, 'added': 1}
rxn01094_c0 {'forward': 2, 'added': 1}
rxn06472_c0 {'reverse': 4.686, 'forward': 4, 'added': 1}
rxn10791_c0 {'forward': 6, 'added': 1}
rxn02674_c0 {'forward': 5, 'added': 1}
rxn10568_c0 {'reverse': 6, 'forward': 6, 'added': 1}
rxn11891_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn08709_c0 {'forward': 4, 'added': 1}
rxn11567_c0 {'reverse': 4.6887, 'forward': 4, 'added': 1}
rxn00423_c0 {'forward': 2, 'added': 1}
rxn10298_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn00364_c0 {'reverse': 2, 'forward': 2, 'added': 1}
rxn05521_c0 {'reverse': 7, 'forward': 7, 'added': 1}
rxn12005_c0 {'reverse': 4, 'added': 1}
rxn00877_c0 {'reverse': 5, 'forward': 5, 'added': 1}
rxn11625_c0 {'reverse': 2.987, 'forward': 4, 'added': 1}
rxn00613_c0 {'reverse': 5, 'forward': 5, 'added': 1}
rxn05561_c0 {'reversed': 1, 'reverse': 5}
rxn12564_c0 {'reverse': 7, 'forward': 7, 'added': 1}
rxn09126_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn03505_c0 {'forward': 5, 'added': 1}
rxn01185_c0 {'reverse': 3.998, 'forward': 5, 'added': 1}
rxn02367_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn00603_c0 {'reverse': 5, 'forward': 5, 'added': 1}
rxn13549_c0 {'forward': 7, 'added': 1}
rxn03408_c0 {'reverse': 2, 'forward': 2, 'added': 1}
rxn11807_c0 {'reverse': 5, 'forward': 5, 'added': 1}
rxn06671_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn08866_c0 {'reverse': 7, 'forward': 7, 'added': 1}
rxn05875_c0 {'forward': 5, 'added': 1}
rxn00359_c0 {'reverse': 2.9187000000000003, 'forward': 4, 'added': 1}
rxn02177_c0 {'forward': 2, 'added': 1}
rxn05250_c0 {'forward': 4, 'added': 1}
rxn01177_c0 {'reverse': 4, 'forward': 12.4393, 'added': 1}
rxn02415_c0 {'forward': 4, 'added': 1}
rxn00646_c0 {'forward': 2, 'added': 1}
rxn05440_c0 {'forward': 4, 'added': 1}
rxn01780_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn14087_c0 {'reverse': 6, 'forward': 6, 'added': 1}
rxn13446_c0 {'reverse': 7, 'forward': 7, 'added': 1}
rxn11526_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn00935_c0 {'reversed': 1}
rxn01673_c0 {'reverse': 2, 'forward': 2, 'added': 1}
rxn09959_c0 {'reverse': 7, 'forward': 7, 'added': 1}
rxn03681_c0 {'reverse': 4, 'forward': 15.1793, 'added': 1}
rxn03600_c0 {'forward': 4, 'added': 1}
rxn00247_c0 {}
rxn05625_c0 {'reversed': 1}
rxn03016_c0 {'forward': 4, 'added': 1}
rxn01632_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn01788_c0 {'forward': 4, 'added': 1}
rxn02360_c0 {'reverse': 2, 'forward': 2, 'added': 1}
rxn10115_c0 {'forward': 7, 'added': 1}
rxn02342_c0 {'reversed': 1, 'reverse': 2}
rxn12525_c0 {'reverse': 7, 'forward': 7, 'added': 1}
rxn04933_c0 {'reverse': 5, 'forward': 5, 'added': 1}
rxn02837_c0 {'reverse': 5, 'forward': 5, 'added': 1}
rxn04889_c0 {'reverse': 5, 'forward': 5, 'added': 1}
rxn08191_c0 {'forward': 7, 'added': 1}
rxn10311_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn08836_c0 {'reverse': 6, 'forward': 6, 'added': 1}
rxn05156_c0 {'forward': 5, 'added': 1}
rxn01412_c0 {'reverse': 6, 'forward': 6, 'added': 1}
rxn03576_c0 {'forward': 4, 'added': 1}
rxn10803_c0 {'reverse': 6.5443, 'forward': 6, 'added': 1}
rxn05529_c0 {'reverse': 7, 'forward': 7, 'added': 1}
rxn01452_c0 {'reversed': 1, 'forward': 2}
rxn07116_c0 {'forward': 4, 'added': 1}
rxn13524_c0 {'reverse': 7, 'forward': 7, 'added': 1}
rxn00642_c0 {'forward': 2, 'added': 1}
rxn00022_c0 {'forward': 2, 'added': 1}
rxn02733_c0 {'forward': 13, 'added': 1}
rxn01903_c0 {'forward': 4, 'added': 1}
rxn10297_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn14009_c0 {'forward': 6, 'added': 1}
rxn02454_c0 {'reverse': 5.2267, 'forward': 5, 'added': 1}
rxn01772_c0 {'reverse': 5, 'forward': 5, 'added': 1}
rxn09956_c0 {'reverse': 6.0197, 'forward': 6, 'added': 1}
rxn08435_c0 {'forward': 6, 'added': 1}
rxn00096_c0 {'forward': 4, 'added': 1}
rxn12169_c0 {'forward': 5, 'added': 1}
rxn08968_c0 {'reverse': 6, 'forward': 6, 'added': 1}
rxn02772_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn10091_c0 {'forward': 7, 'added': 1}
rxn10406_c0 {'forward': 6, 'added': 1}
rxn14271_c0 {'reverse': 6, 'forward': 6, 'added': 1}
rxn00973_c0 {'reversed': 1, 'reverse': 3}
rxn03863_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn05667_c0 {'reverse': 6, 'forward': 6, 'added': 1}
rxn07671_c0 {'forward': 4, 'added': 1}
rxn05483_c0 {'reverse': 8, 'forward': 8, 'added': 1}
rxn11411_c0 {'reverse': 3.3967, 'forward': 6, 'added': 1}
rxn04031_c0 {'reverse': 6, 'forward': 6, 'added': 1}
rxn07137_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn02000_c0 {'reverse': 2, 'forward': 2, 'added': 1}
rxn03239_c0 {'reverse': 2, 'forward': 2, 'added': 1}
rxn01419_c0 {'forward': 5, 'added': 1}
rxn12225_c0 {'forward': 6, 'added': 1}
rxn03534_c0 {'reverse': 3, 'forward': 3, 'added': 1}
rxn06434_c0 {'forward': 4, 'added': 1}
rxn10835_c0 {'reverse': 8, 'forward': 8, 'added': 1}
rxn02512_c0 {'reverse': 4.3687000000000005, 'forward': 5, 'added': 1}
rxn03939_c0 {'forward': 6, 'added': 1}
rxn03120_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn05111_c0 {'forward': 4, 'added': 1}
rxn00144_c0 {'reverse': 5.6197, 'forward': 5, 'added': 1}
rxn01038_c0 {'reverse': 5, 'forward': 5, 'added': 1}
rxn04974_c0 {'forward': 4, 'added': 1}
rxn00944_c0 {'reverse': 5, 'forward': 5, 'added': 1}
rxn02043_c0 {'reverse': 5, 'forward': 5, 'added': 1}
rxn09466_c0 {'forward': 6, 'added': 1}
rxn10480_c0 {'reverse': 8, 'forward': 8, 'added': 1}
rxn09917_c0 {'forward': 7, 'added': 1}
rxn02632_c0 {'reverse': 2, 'forward': 2, 'added': 1}
rxn07764_c0 {'forward': 4, 'added': 1}
rxn11962_c0 {'forward': 4, 'added': 1}
rxn01577_c0 {'reverse': 5, 'forward': 5, 'added': 1}
rxn00322_c0 {'forward': 2, 'added': 1}
rxn03883_c0 {'reverse': 2, 'forward': 2, 'added': 1}
rxn00654_c0 {'forward': 2, 'added': 1}
rxn04466_c0 {'reverse': 3.7413, 'forward': 4, 'added': 1}
rxn05212_c0 {'reverse': 9, 'forward': 9, 'added': 1}
rxn08111_c0 {'reverse': 6.0197, 'forward': 6, 'added': 1}
rxn10488_c0 {'forward': 7, 'added': 1}
rxn05063_c0 {'forward': 3, 'added': 1}
rxn00889_c0 {'reverse': 5.5187, 'forward': 5, 'added': 1}
rxn14019_c0 {'reverse': 6, 'forward': 6, 'added': 1}
rxn10700_c0 {'reverse': 6, 'forward': 6, 'added': 1}
rxn06991_c0 {'reverse': 2.3891, 'forward': 6, 'added': 1}
rxn13496_c0 {'reverse': 7, 'forward': 7, 'added': 1}
rxn01988_c0 {'forward': 6, 'added': 1}
rxn01357_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn08143_c0 {'forward': 7, 'added': 1}
rxn04426_c0 {'forward': 4, 'added': 1}
rxn03303_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn05457_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn02559_c0 {'reverse': 5, 'forward': 5, 'added': 1}
rxn00107_c0 {'forward': 5, 'added': 1}
rxn09560_c0 {'reverse': 6.0707, 'forward': 6, 'added': 1}
rxn10278_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn06276_c0 {'reverse': 7, 'forward': 7, 'added': 1}
rxn02089_c0 {'forward': 4, 'added': 1}
rxn04271_c0 {'reverse': 4.0197, 'forward': 4, 'added': 1}
rxn13783_c0 {'forward': 5, 'added': 1}
rxn08734_c0 {}
rxn07782_c0 {'reverse': 4.163, 'forward': 4, 'added': 1}
rxn00557_c0 {'reverse': 5, 'forward': 5, 'added': 1}
rxn05392_c0 {'forward': 4, 'added': 1}
rxn08934_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn07678_c0 {'reverse': 4, 'forward': 6.2, 'added': 1}
rxn12008_c0 {'reverse': 2, 'added': 1}
rxn04641_c0 {'reverse': 5, 'forward': 5, 'added': 1}
rxn03474_c0 {'reverse': 5, 'forward': 5, 'added': 1}
rxn05431_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn05353_c0 {'reverse': 2, 'added': 1}
rxn09412_c0 {'forward': 6, 'added': 1}
rxn04600_c0 {'reverse': 2, 'forward': 2, 'added': 1}
rxn04681_c0 {'reverse': 3.689, 'forward': 4, 'added': 1}
rxn07966_c0 {'forward': 6, 'added': 1}
rxn06096_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn04070_c0 {'forward': 2, 'added': 1}
rxn00199_c0 {}
rxn01536_c0 {'forward': 5, 'added': 1}
rxn01358_c0 {'reverse': 2, 'forward': 2, 'added': 1}
rxn00099_c0 {'forward': 5, 'added': 1}
rxn03433_c0 {'forward': 2, 'added': 1}
rxn02997_c0 {'reverse': 3.6233, 'forward': 4, 'added': 1}
rxn03009_c0 {'reverse': 5, 'forward': 5, 'added': 1}
rxn05057_c0 {'forward': 5, 'added': 1}
rxn04761_c0 {'forward': 4, 'added': 1}
rxn09567_c0 {'reverse': 6, 'forward': 6, 'added': 1}
rxn10231_c0 {'forward': 4, 'added': 1}
rxn00511_c0 {'reverse': 2, 'forward': 2, 'added': 1}
rxn07800_c0 {'forward': 4, 'added': 1}
rxn04176_c0 {'forward': 4, 'added': 1}
rxn03284_c0 {'forward': 4, 'added': 1}
rxn12679_c0 {'reverse': 7, 'forward': 7, 'added': 1}
rxn09235_c0 {'forward': 7, 'added': 1}
rxn02944_c0 {'reverse': 2, 'forward': 2, 'added': 1}
rxn01867_c0 {'forward': 2, 'added': 1}
rxn04648_c0 {'forward': 4, 'added': 1}
rxn03086_c0 {'reverse': 2, 'forward': 2, 'added': 1}
rxn03473_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn07266_c0 {'reverse': 4, 'forward': 4, 'added': 1}
rxn01317_c0 {'forward': 4, 'added': 1}
rxn08002_c0 {'forward': 6, 'added': 1}
rxn06602_c0 {'reverse': 4.58, 'forward': 5, 'added': 1}
rxn07969_c0 {'reverse': 6, 'forward': 6, 'added': 1}
rxn00218_c0 {'reverse': 5, 'forward': 5, 'added': 1}
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EX_cpd00109_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00599_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd01107_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00060_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00668_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00028_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00249_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00581_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd10114_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00069_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00870_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00242_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00655_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00308_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00155_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd01741_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd01701_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00204_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd01048_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00448_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd02305_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00099_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd11576_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd16658_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00560_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd11685_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00700_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd04181_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00441_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd15378_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00239_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd10516_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00379_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd11582_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00122_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00165_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00091_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd01308_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd05158_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00307_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00186_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd15269_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00224_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd11593_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00386_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00417_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd01399_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd15141_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd01307_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd15606_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd11590_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00179_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd11640_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00138_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd01262_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd16877_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd15352_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00418_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd02241_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd13391_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd01572_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00322_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd03805_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00591_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00247_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd08306_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd04761_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00492_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00108_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd03884_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00053_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd09068_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00020_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00061_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd09457_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd11573_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd01991_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00094_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00280_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd04534_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00654_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00156_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd10515_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00146_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00277_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd05240_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00059_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00051_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd01293_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00480_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00902_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00248_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd16062_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd11581_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd03454_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd15270_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00041_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd11617_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd15139_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00467_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00017_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd03385_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00547_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd03776_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00572_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00164_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00507_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00876_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd11595_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00066_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd15603_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd09075_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd05192_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd16873_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00339_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd03279_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd11598_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd13392_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd08023_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd01098_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00139_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00380_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd15353_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00136_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00644_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd05267_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00312_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd04349_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00104_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00214_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00396_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd03535_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00453_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00832_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00092_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00367_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd11579_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd15311_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd15574_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00381_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd01157_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00166_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00731_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd01757_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd08374_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd15559_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd15466_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd27384_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd00561_e0 {'added': 1, 'reverse': 1, 'forward': 1}
EX_cpd03453_e0 {'added': 1, 'reverse': 1, 'forward': 1}
DM_cpd11416_c0 {'added': 1, 'reverse': 1, 'forward': 1}
DM_cpd15302_c0 {'added': 1, 'reverse': 1, 'forward': 1}
DM_cpd02701_c0 {'added': 1, 'reverse': 1, 'forward': 1}

[47]:

model_core.metabolites.cpd00006_0

[47]:
Metabolite identifiercpd00006_0
NameNADP
Memory address 0x07f5224dfb2b0
FormulaC21H25N7O17P3
Compartment0
In 0 reaction(s) 
[44]:

import re
index_hash = {"none": 0}
for metabolite in model_core.metabolites:
    print(metabolite.id)
    if re.search('_[a-z]\d+$', metabolite.id) is not None:
        m = re.search('_([a-z])(\d+)$', metabolite.id)
        if m[1] != "e":
            if m[2] not in index_hash:
                index_hash[m[2]] = 0
            index_hash[m[2]] += 1
    else:
        index_hash["none":0]
        # Iterating over all indecies with more than 10 intracellular compounds:

cpd00006_c0
cpd00863_c0
cpd00005_c0
cpd00067_c0
cpd00911_c0
cpd00137_c0
cpd00029_c0
cpd00032_c0
cpd00001_c0
cpd00290_c0
cpd00009_c0
cpd00072_c0
cpd00002_c0
cpd00176_c0
cpd00008_c0
cpd02711_c0
cpd00209_c0
cpd18074_c0
cpd00067_e0
cpd00075_c0
cpd18072_c0
cpd00024_c0
cpd00056_c0
cpd00011_c0
cpd03189_c0
cpd00079_c0
cpd00106_e0
cpd00106_c0
cpd00171_c0
cpd00047_c0
cpd11225_c0
cpd00007_c0
cpd00100_c0
cpd00100_e0
cpd00139_c0
cpd00040_c0
cpd00013_c0
cpd15560_c0
cpd15561_c0
cpd00022_c0
cpd00120_c0
cpd00010_c0
cpd03123_c0
cpd00891_c0
cpd00519_c0
cpd00102_c0
cpd00238_c0
cpd00236_c0
cpd00011_e0
cpd01476_c0
cpd10515_c0
cpd00028_c0
cpd00003_c0
cpd01947_c0
cpd00004_c0
cpd00361_c0
cpd00055_c0
cpd03583_c0
cpd00203_c0
cpd03049_c0
cpd00020_c0
cpd00260_c0
cpd00036_c0
cpd00078_c0
cpd00095_c0
cpd00159_e0
cpd00159_c0
cpd00876_c0
cpd00287_c0
cpd11620_c0
cpd11621_c0
cpd00198_c0
cpd00331_c0
cpd00130_c0
cpd15414_c0
cpd00104_c0
cpd00029_e0
cpd00971_e0
cpd00971_c0
cpd00027_c0
cpd00027_e0
cpd00169_c0
cpd00080_c0
cpd00015_c0
cpd00851_c0
cpd00982_c0
cpd02625_c0
cpd00142_c0
cpd00178_c0
cpd18080_c0
cpd18079_c0
cpd00101_c0
cpd00284_c0
cpd01662_c0
cpd00018_c0
cpd00061_c0
cpd00012_c0
cpd00141_c0
cpd00141_e0
cpd00449_c0
cpd00213_c0
cpd00196_c0
cpd00528_c0
cpd00659_c0
cpd00050_c0
cpd00094_c0
cpd00086_c0
cpd00363_c0
cpd00071_c0
cpd00009_e0
cpd00482_c0
cpd00349_c0
cpd18081_c0
cpd18082_c0
cpd11640_c0
cpd00211_c0
cpd00279_c0
cpd00668_c0
cpd15500_c0
cpd15499_c0
cpd01011_c0
cpd00209_e0
cpd00058_c0
cpd00058_e0
cpd01947_e0
cpd09818_c0
cpd09819_c0
cpd03662_c0
cpd00836_c0
cpd00860_c0
cpd03187_c0
cpd00220_c0
cpd08021_c0
cpd15499_e0
cpd00450_c0
cpd15500_e0
cpd18072_e0
cpd18074_e0
cpd00190_c0
cpd01844_c0
cpd02234_c0
cpd00650_c0
cpd03113_c0
cpd03126_c0
cpd03115_c0
cpd12689_c0
cpd03122_c0
cpd03125_c0
cpd18075_c0
cpd18076_c0
cpd18078_c0
cpd18077_c0
cpd00448_c0
cpd00075_e0
cpd01269_c0
cpd00036_e0
cpd00418_c0
cpd12225_c0
cpd12005_c0
cpd00842_c0
cpd00109_c0
cpd00110_c0
cpd00242_c0
cpd00221_c0
cpd00222_c0
cpd00802_c0
cpd00386_c0
cpd00007_e0
cpd00038_c0
cpd00031_c0
cpd00239_c0
cpd00081_c0
cpd00363_e0
cpd00811_c0
cpd00441_c0
cpd00805_c0
cpd02371_c0
cpd00047_e0
cpd00103_c0
cpd12072_c0
cpd12139_c0
cpd00211_e0
cpd15561_e0
cpd15560_e0
cpd00157_c0
cpd00001_e0
cpd00797_c0
cpd00797_e0
cpd01217_c0
cpd01217_e0
cpd03707_c0
cpd14870_c0
cpd02782_c0
cpd03194_c0
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cpd16920_c0
cpd03117_c0
cpd16897_c0
cpd03400_c0
cpd00202_c0
cpd15951_c0
cpd02037_c0
cpd01560_c0
cpd15911_c0
cpd00112_c0
cpd15577_c0
cpd15911_e0
cpd14936_c0
cpd16656_c0
cpd03445_c0
cpd12451_c0
cpd16278_c0
cpd03448_c0
cpd00054_c0
cpd00054_e0
cpd16414_c0
cpd02241_c0
cpd00906_c0
cpd00477_c0
cpd00477_e0
cpd15832_c0
cpd02307_c0
cpd10898_c0
cpd06698_c0
cpd03680_c0
cpd15478_c0
cpd00531_e0
cpd06996_c0
cpd00531_c0
cpd09265_c0
cpd03215_c0
cpd14977_c0
cpd16994_c0
cpd16058_c0
cpd00014_c0
cpd08746_c0
cpd08490_c0
cpd00485_c0
cpd12190_c0
cpd00485_e0
cpd00281_e0
cpd00945_c0
cpd00281_c0
cpd11631_c0
cpd12736_c0
cpd12801_c0
cpd01569_c0
cpd00442_c0
cpd11574_e0
cpd04002_c0
cpd15716_c0
cpd11574_c0
cpd17043_c0
cpd03560_c0
cpd01172_c0
cpd02346_c0
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cpd15377_c0
cpd01135_c0
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cpd02183_c0
cpd00039_e0
cpd02717_c0
cpd11987_c0
cpd03293_c0
cpd04878_c0
cpd04360_c0
cpd15502_c0
cpd12597_c0
cpd03749_c0
cpd11495_c0
cpd11791_c0
cpd16937_c0
cpd03998_c0
cpd00215_e0
cpd01251_c0
cpd02911_c0
cpd02777_c0
cpd16916_c0
cpd06702_c0
cpd11799_c0
cpd03255_c0
cpd11533_c0
cpd12698_c0
cpd11255_c0
cpd07333_c0
cpd07333_e0
cpd08790_c0
cpd00504_c0
cpd02882_c0
cpd03359_c0
cpd08877_c0
cpd02414_c0
cpd15687_c0
cpd12105_c0
cpd00234_c0
cpd00824_c0
cpd08343_c0
cpd01482_c0
cpd02734_c0
cpd01282_c0
cpd06003_c0
cpd03603_c0
cpd17036_c0
cpd01637_c0
cpd14505_c0
cpd04123_c0
cpd01989_c0
cpd08878_c0
cpd00864_c0
cpd01680_c0
cpd03990_c0
cpd15044_c0
cpd03642_c0
cpd02919_c0
cpd16954_c0
cpd15619_c0
cpd15719_c0
cpd08799_c0
cpd03802_c0
cpd01006_c0
cpd15955_c0
cpd15724_c0
cpd01006_e0
cpd02816_c0
cpd01674_c0
cpd15176_c0
cpd17077_c0
cpd01903_c0
cpd01982_c0
cpd12165_c0
cpd16051_c0
cpd14890_c0
cpd01059_c0
cpd04328_c0
cpd05337_c0
cpd09433_c0
cpd12365_c0
cpd00425_e0
cpd01289_c0
cpd00425_c0
cpd00647_c0
cpd02855_c0
cpd03852_c0
cpd01415_c0
cpd14484_c0
cpd01415_e0
cpd12422_c0
cpd12494_c0
cpd00276_e0
cpd00276_c0
cpd04547_c0
cpd16399_c0
cpd10554_c0
cpd02673_c0
cpd15711_c0
cpd11589_c0
cpd11589_e0
cpd00162_c0
cpd02632_c0
cpd02914_c0
cpd11451_e0
cpd01973_c0
cpd16741_c0
cpd00163_c0
cpd15863_c0
cpd15862_c0
cpd09848_c0
cpd01067_e0
cpd03801_c0
cpd01845_c0
cpd00542_c0
cpd09162_c0
cpd11217_c0
cpd15823_c0
cpd15036_c0
cpd17422_c0
cpd01733_c0
cpd01454_c0
cpd02142_c0
cpd00080_e0
cpd04049_c0
cpd16359_c0
cpd01772_c0
cpd03588_c0
cpd01054_c0
cpd00128_c0
cpd02708_c0
cpd16745_c0
cpd02027_c0
cpd02027_e0
cpd02536_c0
cpd12547_c0
cpd15483_c0
cpd11805_c0
cpd04137_c0
cpd02419_c0
cpd02794_c0
cpd11748_c0
cpd12601_c0
cpd11748_e0
cpd01512_c0
cpd01301_c0
cpd12640_c0
cpd03144_c0
cpd15553_c0
cpd16398_c0
cpd11923_c0
cpd09489_c0
cpd00609_c0
cpd04046_c0
cpd11580_e0
cpd03654_c0
cpd15523_c0
cpd01720_c0
cpd02317_c0
cpd15828_c0
cpd00918_c0
cpd09271_c0
cpd00549_c0
cpd15346_c0
cpd00549_e0
cpd01594_c0
cpd12392_c0
cpd02459_c0
cpd15980_c0
cpd12608_c0
cpd14537_c0
cpd01227_c0
cpd02813_c0
cpd03455_c0
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---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-44-538ef6420f0a> in <module>
     10             index_hash[m[2]] += 1
     11     else:
---> 12         index_hash["none":0]
     13         # Iterating over all indecies with more than 10 intracellular compounds:

TypeError: unhashable type: 'slice'