1 #
   2 ##
   3 ### Identifying how much ATP A. woodii can produce from different combinations of carbon sources
   4 ##
   5 #
   6 
   7 
   8 m = ScrumPy.Model('Awoodii.spy')
   9 
  10 # TASK 1 ----------------------------------- minimise importers of substrate and set ATPase
  11 # load lp object
  12 lp = m.GetLP()
  13 
  14 # set some constraints
  15 
  16 #1) block all transporters
  17 # identify all transporters
  18 for reaction in m.sm.cnames:
  19         if "_tx" in reaction:
  20                 print reaction
  21 
  22 # now block them by setting a fixed flux
  23 for reaction in m.sm.cnames:
  24         if "_tx" in reaction:
  25                 lp.SetFixedFlux({reaction:0})
  26 
  27 
  28 # unblock substrates to be investigated
  29 lp.ClearFluxConstraints(['CO_s_tx','BUTANEDIOL_s_tx'])
  30 
  31 # make a dictionary of all fermentation products
  32 f_product_constraints = {}
  33 for reaction in m.sm.cnames:
  34         if "f_tx" in reaction: # fermentation products have the suffix "f_tx"
  35                 f_product_constraints[reaction] = (None,0) # None, 0 indicates only negative flux (export) is allowed
  36 
  37 # now set the bounds on lp using the dictionary just made
  38 lp.SetFluxBounds(c_constraints)
  39 
  40 
  41 lp.SetFixedFlux({'ADENOSINETRIPHOSPHATASE-RXN':1}) # set a fixed flux of 1 (arbitrary number) on the ATPase reaction
  42 
  43 # set the objective of minimising these two substrate transporters (minimising is default objective)
  44 lp.SetObjective(['CO_s_tx','BUTANEDIOL_s_tx'])
  45 
  46 lp.Solve() # solve
  47 sol_1 = lp.GetPrimSol() # get solution and save to variable
  48 
  49 # now explore what the solution is
  50 
  51 
  52 for reaction in sol_1: # for each reaction in solution
  53        if "tx" in reaction: # if the reaction is a transporter
  54                print reaction, sol_1[reaction] # print the name and flux carried by transporter (can also use round() function here to format value)
  55 
  56 #double check that the ATPase has a flux unit 1
  57 print sol_1['ADENOSINETRIPHOSPHATASE-RXN']
  58 
  59 # calculate the ATP yield per carbon mole
  60 # ATPase_flux / carbon_flux
  61 1 / (0.41*4+1.22)
  62 
  63 # also check that carbon is balanced
  64 # flux x carbon_atoms = carbon_flux
  65 0.41*4+1.22
  66 1.43 * 2