added format emit data method

process_bigraph/emitter.py

@@ -205,6 +205,21 @@ def __init__(self, config: Dict[str, Any]) -> None:
 
         self.fallback_serializer = make_fallback_serializer_function()
 
+    @staticmethod
+    def format_emit_data(
+            table_id: str,
+            times: Union[Tuple, List, Dict, np.ndarray],
+            values: Union[Tuple, List, Dict, np.ndarray]
+            ) -> Dict[str, Union[Tuple, List, Dict, np.ndarray]]:
+        """Format the given data for mongo db emit."""
+        return {
+            'table': {
+                'id': table_id
+            },
+            'time': times,
+            'values': values
+        }
+
     def emit(self, data: Dict[str, Any]) -> None:
         """Emit data to the Mongo instance.
 

process_bigraph/experiments/model.txt

@@ -0,0 +1,115 @@
+# File Min1.txt, by Steve Andrews, 11/2009.
+# E. coli Min system, based on Huang, Meir, Wingreen (HMW)
+# This file is HMW system exactly, plus surface diffusion
+# units are micron, second
+
+define D_D		2.5	# MinD diffusion coefficient (um^2/s)
+define D_E		2.5	# MinE diffusion coefficient (um^2/s)
+define D_d		0.01	# MinD_ATP(front) diff. coeff. (um^2/s)
+define D_de		0.01	# MinDMinE(front) diff. coeff. (um^2/s)
+define SIGMA_D_D2T	1	# MinD phosphorylation rate (s^-1)
+define SIGMA_D		0.025	# MinD_ATP adsorption coeff. (um/s)
+define SIGMA_dD		0.0015	# cooperative adsorption coeff. (um^3/s)
+define SIGMA_de		0.7	# desorption rate of MinDMinE (s^-1)
+define SIGMA_E		0.093	# MinE binding to surface-bound MinD (um^3/s)
+
+define UNBINDRAD	0.01	# MinD separation on surface (um)
+
+define R		0.5	# cell radius
+define L_PARAM		2	# half of cell length
+define L_PARAM2		1.5	# half of cell length minus radius
+
+define NUMBER_MIND	4000	# number of MinD in cell
+define NUMBER_MINE	1400	# number of MinE in cell
+
+define TIME_STOP	500	# stopping time
+
+#define KICK_START	1	# start with MinD_ATP at an end
+
+random_seed 1
+
+#graphics opengl
+#graphic_iter 100
+
+#tiff_name movie/MinMovie
+#tiff_iter 200
+#tiff_min 1
+#tiff_max 200
+
+dim 3
+boundaries 0 -L_PARAM L_PARAM
+boundaries 1 -R R
+boundaries 2 -R R
+frame_thickness 0
+time_start 0
+time_stop TIME_STOP
+time_step 0.002			# 2 millisecond time step
+
+accuracy 5
+molperbox 4
+
+species MinD_ATP
+species MinD_ADP
+species MinE
+species MinDMinE
+
+molecule_lists list1 list2 list3 list4 list5
+mol_list MinD_ATP(soln) list1
+mol_list MinD_ATP(front) list2
+mol_list MinD_ADP(all) list3
+mol_list MinE(all) list4
+mol_list MinDMinE(all) list5
+
+difc MinD_ATP(solution) D_D
+difc MinD_ATP(front) D_d
+difc MinD_ADP(solution) D_D
+difc MinE(solution) D_E
+difc MinDMinE(front) D_de
+
+color MinD_ATP(soln) 0 0 0.6	# MinD_ATP(solution) is dark blue
+color MinD_ATP(front) 0 0.6 0	# MinD_ATP(front) is dark green
+color MinD_ADP(soln) 0.4 0.6 1	# MinD_ADP is light blue
+color MinE(soln) 1 0 0		# MinE is red
+color MinDMinE(front) 0.2 1 0.2	# MinDMinE is bright green
+display_size all(solution) 2
+display_size all(front) 4
+
+start_surface membrane
+action both all reflect
+rate MinD_ATP fsoln front SIGMA_D	# reaction 1a
+polygon both edge
+panel cylinder -L_PARAM2 0 0 L_PARAM2 0 0 -R 20 10 cyl0
+panel hemi -L_PARAM2 0 0 -R 1 0 0 20 5 hemi0
+panel hemi L_PARAM2 0 0 -R -1 0 0 20 5 hemi1
+neighbors cyl0 hemi0 hemi1
+neighbors hemi0 cyl0
+neighbors hemi1 cyl0
+end_surface
+
+start_compartment cell
+surface membrane
+point 0 0 0
+end_compartment
+
+reaction rxn1b MinD_ATP(fsoln) + MinD_ATP(front) -> MinD_ATP(front) + MinD_ATP(front) SIGMA_dD
+product_placement rxn1b unbindrad UNBINDRAD
+reaction rxn1c MinD_ATP(fsoln) + MinDMinE(front) -> MinD_ATP(front) + MinDMinE(front) SIGMA_dD
+product_placement rxn1c unbindrad UNBINDRAD
+reaction rxn2 MinE(fsoln) + MinD_ATP(front) -> MinDMinE(front) SIGMA_E
+reaction rxn3 MinDMinE(front) -> MinD_ADP(fsoln) + MinE(fsoln) SIGMA_de
+reaction rxn4 MinD_ADP -> MinD_ATP SIGMA_D_D2T
+
+ifundefine KICK_START
+  surface_mol NUMBER_MIND MinD_ATP(front) membrane all all
+else
+  surface_mol NUMBER_MIND MinD_ATP(front) membrane hemi hemi1
+endif
+compartment_mol NUMBER_MINE MinE cell
+
+
+#output_files FILEROOTout.txt
+#cmd i 0 TIME_STOP 1 executiontime FILEROOTout.txt
+#cmd i 0 TIME_STOP 1 listmols FILEROOTout.txt
+
+end_file
+

process_bigraph/experiments/smoldyn_database.py

@@ -16,3 +16,27 @@
 """
 
 
+import os
+from typing import *
+from smoldyn import Simulation
+from process_bigraph.emitter import MongoDatabaseEmitter
+
+
+def run_smoldyn_simulation():
+    model_fp = 'process_bigraph/experiments/model.txt'
+    simulation = Simulation.fromFile(model_fp)
+    simulation.addOutputData('time')
+    simulation.addOutputData('molecules')
+    simulation.addCommand(cmd='executiontime time', cmd_type='E')
+    simulation.addCommand(cmd='listmols molecules', cmd_type='E')
+
+    interval = 10
+    simulation.run(interval, simulation.dt)
+
+    time_output = simulation.getOutputData('time')
+    mol_output = simulation.getOutputData('molecules')
+
+
+
+
+