original_docstring:  
      Plots the amounts of ListOfSpeciesToPlot in the given SBML files 
      starting at initialTime and for the timepoints given. 
      The other arguments for axes labels and sizes are optional.
      If a list of files is given, then corresponding list of list of species is 
      used to plot the corresponding list of species for each SBML model. 
      The same initialTime, timepoints and other arguments are used for all SBML files 
      
docstring: Plots the amounts of ListOfSpeciesToPlot in the given SBML files
  starting at initialTime and for the timepoints given.
  The other arguments for axes labels and sizes are optional.
  If a list of files is given, then corresponding list of list of species is
  used to plot the corresponding list of species for each SBML model.
  The same initialTime, timepoints and other arguments are used for all SBML files
docstring_tokens: Plots the amounts of ListOfSpeciesToPlot in the given SBML files starting at initialTime and for the timepoints given . The other arguments for axes labels and sizes are optional . If a list of files is given then corresponding list of list of species is used to plot the corresponding list of species for each SBML model . The same initialTime timepoints and other arguments are used for all SBML files
code: def plotSbmlWithBioscrape(ListOfFiles, initialTime, timepoints, ListOfListOfSpeciesToPlot, xlabel = 'Time', ylabel = 'Concentration (AU)', sizeOfXLabels = 14, sizeOfYLabels = 14):
      ''' 
      Plots the amounts of ListOfSpeciesToPlot in the given SBML files 
      starting at initialTime and for the timepoints given. 
      The other arguments for axes labels and sizes are optional.
      If a list of files is given, then corresponding list of list of species is 
      used to plot the corresponding list of species for each SBML model. 
      The same initialTime, timepoints and other arguments are used for all SBML files 
      '''
      mpl.rc('axes', prop_cycle=(mpl.cycler('color', ['r', 'k', 'b','g','y','m','c']) ))
      mpl.rc('xtick', labelsize=sizeOfXLabels) 
      mpl.rc('ytick', labelsize=sizeOfYLabels)
      if type(ListOfFiles) is str:
          filename = ListOfFiles
          ListOfSpeciesToPlot = ListOfListOfSpeciesToPlot[:]
          doc = getFromXML(filename)
          model = doc.getModel()
          mod_obj = SimpleModel(model)
          m = bioscrape.types.read_model_from_sbml(filename)
          s = bioscrape.simulator.ModelCSimInterface(m)
          s.py_prep_deterministic_simulation()
          s.py_set_initial_time(initialTime)
          species_ind = []
          SpeciesToPlot = ListOfSpeciesToPlot[:]
          for i in range(len(ListOfSpeciesToPlot)):
              species_name = ListOfSpeciesToPlot[i]
              species = mod_obj.getSpeciesByName(species_name)
              if type(species) is list:
                  print('WARNING -- There are multiple species with the name ' + species_name + ' in plot function. Suffixed species will be plotted ')
                  for species_i in species:
                      species_ind.append(m.get_species_index(species_i.getId()))
                  key_ind = ListOfSpeciesToPlot.index(species_name)
                  insert_new = []
                  for j in range(len(species)-1):
                      insert_new.append(species_name + str(j+1))
                  SpeciesToPlot[key_ind+1:key_ind+1] = insert_new 
              else:
                  species_ind.append(m.get_species_index(species.getId()))
          sim = bioscrape.simulator.DeterministicSimulator()
          result = sim.py_simulate(s, timepoints)
          plt.xlabel(xlabel)
          plt.ylabel(ylabel)
          for i in range(len(species_ind)):
              plt.plot(timepoints, result.py_get_result()[:, species_ind[i]])
          plt.legend(SpeciesToPlot)
          plt.show()
          return
  
      # If a list of files is given
      
      species_ind = []
      speciesLegend = []
      for i in range(len(ListOfFiles)):
          filename = ListOfFiles[i]
          ListOfSpeciesToPlot = ListOfListOfSpeciesToPlot[i]
          doc = getFromXML(filename)
          model = doc.getModel()
          mod_obj = SimpleModel(model)
          m = bioscrape.types.read_model_from_sbml(filename)
          s = bioscrape.simulator.ModelCSimInterface(m)
          s.py_prep_deterministic_simulation()
          s.py_set_initial_time(initialTime)
          SpeciesToPlot = ListOfSpeciesToPlot[:]
          for i in range(len(ListOfSpeciesToPlot)):
              species_name = ListOfSpeciesToPlot[i]
              speciesLegend.append(species_name)
              species = mod_obj.getSpeciesByName(species_name)
              if type(species) is list:
                  print('WARNING -- There are multiple species with the name ' + species_name + ' in plot function. Suffixed species will be plotted ')
                  for species_i in species:
                      species_ind.append(m.get_species_index(species_i.getId()))
                  key_ind = ListOfSpeciesToPlot.index(species_name)
                  insert_new = []
                  for i in range(len(species)-1):
                      insert_new.append(species_name + str(i+1))
                      speciesLegend.append(species_name + str(i+1))
                  SpeciesToPlot[key_ind+1:key_ind+1] = insert_new 
              else:
                  species_ind.append(m.get_species_index(species.getId()))
          sim = bioscrape.simulator.DeterministicSimulator()
          result = sim.py_simulate(s, timepoints)
          for i in range(len(species_ind)):
              plt.plot(timepoints, result.py_get_result()[:, species_ind[i]])
          species_ind = []
      plt.legend(speciesLegend) # add the extra species to this list
      plt.xlabel(xlabel)
      plt.ylabel(ylabel)
      plt.show()
code_tokens: def plotSbmlWithBioscrape ( ListOfFiles , initialTime , timepoints , ListOfListOfSpeciesToPlot , xlabel = 'Time' , ylabel = 'Concentration (AU)' , sizeOfXLabels = 14 , sizeOfYLabels = 14 ) : mpl . rc ( 'axes' , prop_cycle = ( mpl . cycler ( 'color' , [ 'r' , 'k' , 'b' , 'g' , 'y' , 'm' , 'c' ] ) ) ) mpl . rc ( 'xtick' , labelsize = sizeOfXLabels ) mpl . rc ( 'ytick' , labelsize = sizeOfYLabels ) if type ( ListOfFiles ) is str : filename = ListOfFiles ListOfSpeciesToPlot = ListOfListOfSpeciesToPlot [ : ] doc = getFromXML ( filename ) model = doc . getModel ( ) mod_obj = SimpleModel ( model ) m = bioscrape . types . read_model_from_sbml ( filename ) s = bioscrape . simulator . ModelCSimInterface ( m ) s . py_prep_deterministic_simulation ( ) s . py_set_initial_time ( initialTime ) species_ind = [ ] SpeciesToPlot = ListOfSpeciesToPlot [ : ] for i in range ( len ( ListOfSpeciesToPlot ) ) : species_name = ListOfSpeciesToPlot [ i ] species = mod_obj . getSpeciesByName ( species_name ) if type ( species ) is list : print ( 'WARNING -- There are multiple species with the name ' + species_name + ' in plot function. Suffixed species will be plotted ' ) for species_i in species : species_ind . append ( m . get_species_index ( species_i . getId ( ) ) ) key_ind = ListOfSpeciesToPlot . index ( species_name ) insert_new = [ ] for j in range ( len ( species ) - 1 ) : insert_new . append ( species_name + str ( j + 1 ) ) SpeciesToPlot [ key_ind + 1 : key_ind + 1 ] = insert_new else : species_ind . append ( m . get_species_index ( species . getId ( ) ) ) sim = bioscrape . simulator . DeterministicSimulator ( ) result = sim . py_simulate ( s , timepoints ) plt . xlabel ( xlabel ) plt . ylabel ( ylabel ) for i in range ( len ( species_ind ) ) : plt . plot ( timepoints , result . py_get_result ( ) [ : , species_ind [ i ] ] ) plt . legend ( SpeciesToPlot ) plt . show ( ) return species_ind = [ ] speciesLegend = [ ] for i in range ( len ( ListOfFiles ) ) : filename = ListOfFiles [ i ] ListOfSpeciesToPlot = ListOfListOfSpeciesToPlot [ i ] doc = getFromXML ( filename ) model = doc . getModel ( ) mod_obj = SimpleModel ( model ) m = bioscrape . types . read_model_from_sbml ( filename ) s = bioscrape . simulator . ModelCSimInterface ( m ) s . py_prep_deterministic_simulation ( ) s . py_set_initial_time ( initialTime ) SpeciesToPlot = ListOfSpeciesToPlot [ : ] for i in range ( len ( ListOfSpeciesToPlot ) ) : species_name = ListOfSpeciesToPlot [ i ] speciesLegend . append ( species_name ) species = mod_obj . getSpeciesByName ( species_name ) if type ( species ) is list : print ( 'WARNING -- There are multiple species with the name ' + species_name + ' in plot function. Suffixed species will be plotted ' ) for species_i in species : species_ind . append ( m . get_species_index ( species_i . getId ( ) ) ) key_ind = ListOfSpeciesToPlot . index ( species_name ) insert_new = [ ] for i in range ( len ( species ) - 1 ) : insert_new . append ( species_name + str ( i + 1 ) ) speciesLegend . append ( species_name + str ( i + 1 ) ) SpeciesToPlot [ key_ind + 1 : key_ind + 1 ] = insert_new else : species_ind . append ( m . get_species_index ( species . getId ( ) ) ) sim = bioscrape . simulator . DeterministicSimulator ( ) result = sim . py_simulate ( s , timepoints ) for i in range ( len ( species_ind ) ) : plt . plot ( timepoints , result . py_get_result ( ) [ : , species_ind [ i ] ] ) species_ind = [ ] plt . legend ( speciesLegend ) plt . xlabel ( xlabel ) plt . ylabel ( ylabel ) plt . show ( )
short_docstring: Plots the amounts of ListOfSpeciesToPlot in the given SBML files
  starting at initialTime and for the timepoints given.
short_docstring_tokens: Plots the amounts of ListOfSpeciesToPlot in the given SBML files starting at initialTime and for the timepoints given .
comment: ''' 
      Plots the amounts of ListOfSpeciesToPlot in the given SBML files 
      starting at initialTime and for the timepoints given. 
      The other arguments for axes labels and sizes are optional.
      If a list of files is given, then corresponding list of list of species is 
      used to plot the corresponding list of species for each SBML model. 
      The same initialTime, timepoints and other arguments are used for all SBML files 
      '''$SEP$# If a list of files is given$SEP$# add the extra species to this list