<jupyter_start><jupyter_text>IntroductionAs a last step of checking nucleotide metabolism, I will now visit the (d)NTP nodes and check that they are properly formed, and consumed.N.B.: I will not look into ATP, as this is a very long list of reactions that requires seperate investigation<jupyter_code>import cameo
import pandas as pd
import cobra.io
import escher
from escher import Builder
from cobra import Reaction, Metabolite
model = cobra.io.read_sbml_model('../model/p-thermo.xml')
model_e_coli = cameo.load_model ('iML1515')
model_b_sub = cameo.load_model('iYO844')<jupyter_output><empty_output><jupyter_text>__CTP__<jupyter_code>model.reactions.CMS.id = 'MEPCT'
#remove reaction
model.remove_reactions(model.reactions.CTPT)<jupyter_output><empty_output><jupyter_text>__GTP__<jupyter_code>#remove reaction GTPT
model.remove_reactions(model.reactions.GTPT)<jupyter_output><empty_output><jupyter_text>__UTP__<jupyter_code>#i will not remove this yet, it will come with the RNA/DNA node
with model:
    model.remove_reactions(model.reactions.UTPT)
    print (model.optimize().objective_value)
model.reactions.GALT.bounds = (0,1000)
model.reactions.GALUi.bounds = (0,1000)
#save & commit
cobra.io.write_sbml_model(model,'../model/p-thermo.xml')<jupyter_output><empty_output><jupyter_text>__dCTP__ Should remove DCTPT reaction, but cannot right now. It will come back in this DNA/RNA node, so I will leave it for now.  __dGTP__ Seems fine, except this DGTPT reaction. Also this becomes a dead end now.  __DTTP__<jupyter_code>#remove reaction
model.remove_reactions(model.reactions.DTTPT)<jupyter_output><empty_output><jupyter_text>__DATP__<jupyter_code>model.remove_reactions(model.reactions.DATPT)
#save&commit
cobra.io.write_sbml_model(model,'../model/p-thermo.xml')<jupyter_output><empty_output>
StarcoderdataJupyterStructuredCleanDedup