Python e Examples

Example #1

File: Oligopeptide_ABC.py Project: CoreyLeo/isp

from CellScribe import *
from compartments import e, c
from metabolites import *
from genes import SP_1527, SP_1891, SP_0366, SP_1887, SP_1888, SP_1889 , SP_1890



oligopeptide = Metabolite("oligopeptide", kegg="C00098")

oligopeptide_rxn = Reaction(name="oligopeptide_rxn",
                            reactants=e(oligopeptide) + H20 + atp,
                            products=oligopeptide + adp + phosphate)

GeneAssociation(oligopeptide_rxn, SP_1527 or SP_1891 or SP_0366 or SP_1887 or SP_1888 or SP_1889 or SP_1890 )

Example #2

File: AA_ABC.py Project: whittaam/isp

from CellScribe import *
from compartments import e, c
from metabolites import *
from genes import SP_0452, SP_0453, SP_1034, SP_1035, SP_0609, SP_0607, SP_0608, SP_0610, SP_0749, \
    SP_0750, SP_0751, SP_0752, SP_0753, SP_1396, SP_1397, SP_1398, SP_1399, SP_1400

l_lysine_rxn = Reaction(name="l_lysine_rxn",
                    reactants=e(l_lysine) + h2o + atp,
                    products=l_lysine + adp + phosphate,
                    pairs=[(atp, adp)],
                    minors=[atp, adp])

GeneAssociation(lysine_rxn, SP_0452 & SP_0453)


l_glutamate_rxn= Reaction(name="l-glutamate_rxn",
                      reactants=e(l_glutamate) + h2o + atp,
                      products=l_glutamate + adp + phosphate)

GeneAssociation(l_glutamate_rxn, SP_0609 & SP_0607 & SP_0608 & SP_0610)

l_valine_rxn = Reaction(name="l_valine_rxn",
                    reactants=e(l_valine) + h2o + atp,
                    products=l_valine + adp + phosphate,
                    pairs=[(e(l_valine), l_valine)]

GeneAssociation(l_valine_rxn, SP_0749 & SP_0750 & SP_0751 & SP_0752 & SP_0753)


phosphate_rxn= Reaction(name="phosphate_rxn",
                    reactants=e(diphosphate) + H20,

Example #3

from CellScribe import *
from compartments import e
from metabolites import atp, adp, phosphate
from genes import SP_1860, SP_1861

choline_rxn = Reaction(name="choline_rxn",
                       reactants=e(choline) + atp,
                       products=choline + adp + phosphate)

GeneAssociation(choline_rxn, SP_1860 & SP_1861)

choline = Metabolite("choline", kegg="C00114")
choline_rxn = Reaction(name="choline",
                       reactants=e(choline) + atp,
                       products=choline + adp + phosphate,
                       pairs=[(e(choline), choline)])
GeneAssociation(choline_rxn, SP_1860 & SP_1861)

Example #4

from CellScribe import *
from compartments import e, c
from metabolites import *
from genes import SP_2108, SP_2109, SP_2110, SP_2108, SP_2109, SP_2110
from operons import malMP


βmaltose_transport = Reaction(name="βmaltose_transport",
                              reactants=e(βmaltose) + H20+ atp,
                              products=βmaltose + adp + phosphate,
                              pairs=[(atp, adp)],
                              minors=[atp, adp])

GeneAssociation(βmaltose_transport, SP_2108 & SP_2109 & SP_2110)


maltodextrin_transport = Reaction(name="maltodextrin_transport",
                                  reactants=e(maltodextrin) + H20+ atp,
                                  products=maltodextrin + adp + phosphate,
                                  pairs=[(atp, adp)],
                                  minors=[atp, adp])

<<<<<<< HEAD
GeneAssociation(maltodextrin_transport, SP_2108 & SP_2109 & SP_2110)
=======
maltodextrin_GA = GeneAssociation(maltodextrin, SP_2108 & SP_2109 & SP_2110)

# In the absence of maltose, malR binds to the DNA between these two divergent operons to repress them

If (malR & ~maltose, ~malXCD)
If (malR & ~maltose, ~malMP)

Example #5

from CellScribe import *
from compartments import e, c
from metabolites import *
from genes import SP_1527, SP_1891, SP_0366, SP_1887, SP_1888, SP_1889, SP_1890

oligopeptide = Metabolite("oligopeptide", kegg="C00098")

oligopeptide_rxn = Reaction(name="oligopeptide_rxn",
                            reactants=e(oligopeptide) + H20 + atp,
                            products=oligopeptide + adp + phosphate)

GeneAssociation(
    oligopeptide_rxn, SP_1527 or SP_1891 or SP_0366 or SP_1887 or SP_1888
    or SP_1889 or SP_1890)

Example #6

File: AA_ABC.py Project: dmthibault/isp

from CellScribe import *

from compartments import e
from metabolites import *
from genes import SP_0452, SP_0453, SP_1034, SP_1035, SP_0609, SP_0607, SP_0608, SP_0610, SP_0749, \
    SP_0750, SP_0751, SP_0752, SP_0753, SP_1396, SP_1397, SP_1398, SP_1399, SP_1400

l_lysine_rxn = Reaction(name="l_lysine_rxn",
                        reactants=e(l_lysine) + h2o + atp,
                        products=l_lysine + adp + phosphate,
                        pairs=[(atp, adp)],
                        minors=[atp, adp])

GeneAssociation(l_lysine_rxn, SP_0452 & SP_0453)


l_glutamate_rxn = Reaction(name="l-glutamate_rxn",
                           reactants=e(l_glutamate) + h2o + atp,
                           products=l_glutamate + adp + phosphate)

GeneAssociation(l_glutamate_rxn, SP_0609 & SP_0607 & SP_0608 & SP_0610)

l_valine_rxn = Reaction(name="l_valine_rxn",
                        reactants=e(l_valine) + h2o + atp,
                        products=l_valine + adp + phosphate,
                        pairs=[(e(l_valine), l_valine)])

GeneAssociation(l_valine_rxn, SP_0749 & SP_0750 & SP_0751 & SP_0752 & SP_0753)


phosphate_rxn = Reaction(name="phosphate_rxn",