first commit wcm with violacein and MM metabolism

Author: Ioana Gherman

models/ecoli/processes/metabolism_new_pathway.py

@@ -29,7 +29,7 @@ def initialize(self, sim, sim_data):
         # Get constants
         self.nAvogadro = sim_data.constants.n_avogadro.asNumber(1 / units.mmol)
         self.cellDensity = sim_data.constants.cell_density.asNumber(units.g / units.L)
-
+        print(sim_data.process.metabolism_new_pathway.__dir__())
         #check if there is a new metabolic pathway to be added
         if hasattr(sim_data.process.metabolism_new_pathway, 'molecule_names'):
             self.new_pathway = True
@@ -49,6 +49,7 @@ def initialize(self, sim, sim_data):
             self.bulkMoleculesRequestPriorityIs(REQUEST_PRIORITY_METABOLISM_NEW)
         else:
             self.new_pathway = False
+            print('External pathway not included')
 
 
     def calculateRequest(self):
@@ -58,6 +59,7 @@ def calculateRequest(self):
             enzymeCounts = self.enzymes.total_counts()
             EnzymesDict = dict(zip(self.cleanEnzyme, enzymeCounts))
 
+            print('Total molec counts ', moleculeCounts)
             # Get cell mass and volume
             cellMass = (self.readFromListener("Mass", "cellMass") * units.fg).asNumber(units.g)
             self.cellVolume = cellMass / self.cellDensity
@@ -68,8 +70,8 @@ def calculateRequest(self):
             # solver for this setting among the list of solvers that can be used
             # by the scipy ODE suite.
             self.molecules_required, self.all_molecule_changes = self.moleculesToNextTimeStep(
-            	moleculeCounts, self.moleculeNames, self.enzymeNames, EnzymesDict, self.cellVolume, self.nAvogadro,
-            	self.timeStepSec(), method="LSODA", jit=self.jit)
+                moleculeCounts, self.moleculeNames, self.enzymeNames, EnzymesDict, self.cellVolume, self.nAvogadro,
+                self.timeStepSec(), self.randomState, method="LSODA", jit=self.jit)
 
             # Request counts of molecules needed
             self.molecules.requestIs(self.molecules_required)
@@ -82,20 +84,21 @@ def evolveState(self):
             enzymeCounts = self.enzymes.total_counts()
             EnzymesDict = dict(zip(self.cleanEnzyme, enzymeCounts))
 
-
+            print('Molec counts ', moleculeCounts)
             # Check if any molecules were allocated fewer counts than requested
             if (self.molecules_required > moleculeCounts).any():
-                # Solve ODEs to a large time step using the the counts of molecules
+                # Solve ODEs to a large time step using the counts of molecules
                 # allocated to this process using the BDF solver for stable integration.
                 # The number of reactions has already been determined in calculateRequest
                 # and rates will be much lower with a fraction of total counts allocated
                 # so a much longer time scale is needed.
 
                 _, self.all_molecule_changes = self.moleculesToNextTimeStep(
                     moleculeCounts, self.moleculeNames, self.enzymeNames, EnzymesDict, self.cellVolume, self.nAvogadro,
-                    10000, method="BDF", jit=self.jit
+                    10000, self.randomState, method="BDF",  min_time_step = self.timeStepSec(), jit=self.jit
                     )
 
+
             # Increment changes in molecule counts
             self.molecules.countsInc(self.all_molecule_changes)
 

models/ecoli/sim/simulation.py

@@ -1,5 +1,4 @@
 from wholecell.sim.simulation import Simulation
-import os
 
 # States
 from wholecell.states.bulk_molecules import BulkMolecules