File changes on NFsim issue

Issues/nfsim_indrani/.gitignore

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+!*.gdat
+!*.net
+BioModel*

Issues/nfsim_indrani/deleteMolecules.bngl

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+begin parameters
+    d 1
+    kdeg_Ste2_PO4 1
+end parameters
+
+begin molecule types
+    CELL()
+    Ste2(Pheromone_site,Gpa1_site,Sst2_site,Yck_site,S338_S339~none~PO4)
+    Pheromone(Ste2_site)
+end molecule types
+
+begin seed species
+    Pheromone(Ste2_site!1).Ste2(Pheromone_site!1,Gpa1_site,Sst2_site,Yck_site,S338_S339~PO4) 1
+end seed species
+
+begin reaction rules
+#    Ste2(S338_S339~PO4) -> CELL() kdeg_Ste2_PO4 DeleteMolecules
+    Ste2(S338_S339~PO4) -> CELL() 100 DeleteMolecules
+end reaction rules
+
+#writeModel({suffix=>"test",evaluate_expressions=>1})
+generate_network({overwrite=>1})

Issues/nfsim_indrani/deleteMolecules/2024_02_07__16_11_07/deleteMolecules.bngl

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+begin parameters
+    d 1
+    kdeg_Ste2_PO4 1
+end parameters
+
+begin molecule types
+    CELL()
+    Ste2(Pheromone_site,Gpa1_site,Sst2_site,Yck_site,S338_S339~none~PO4)
+    Pheromone(Ste2_site)
+end molecule types
+
+begin seed species
+    Pheromone(Ste2_site!1).Ste2(Pheromone_site!1,Gpa1_site,Sst2_site,Yck_site,S338_S339~PO4) 1
+end seed species
+
+begin reaction rules
+#    Ste2(S338_S339~PO4) -> CELL() kdeg_Ste2_PO4 DeleteMolecules
+    Ste2(S338_S339~PO4) -> CELL() 100 DeleteMolecules
+end reaction rules
+
+writeModel({suffix=>"test",evaluate_expressions=>1})
+generate_network({overwrite=>1})

Issues/nfsim_indrani/deleteMolecules/2024_02_07__16_11_07/deleteMolecules/2024_02_07__16_11_47/deleteMolecules.bngl

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+begin parameters
+    d 1
+    kdeg_Ste2_PO4 1
+end parameters
+
+begin molecule types
+    CELL()
+    Ste2(Pheromone_site,Gpa1_site,Sst2_site,Yck_site,S338_S339~none~PO4)
+    Pheromone(Ste2_site)
+end molecule types
+
+begin seed species
+    Pheromone(Ste2_site!1).Ste2(Pheromone_site!1,Gpa1_site,Sst2_site,Yck_site,S338_S339~PO4) 1
+end seed species
+
+begin reaction rules
+#    Ste2(S338_S339~PO4) -> CELL() kdeg_Ste2_PO4 DeleteMolecules
+    Ste2(S338_S339~PO4) -> CELL() 100 DeleteMolecules
+end reaction rules
+
+writeModel({suffix=>"test",evaluate_expressions=>1})
+generate_network({overwrite=>1})

Issues/nfsim_indrani/deleteMolecules/2024_02_07__16_11_07/deleteMolecules/2024_02_07__16_11_47/deleteMolecules.net

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+# Created by BioNetGen 2.9.0
+begin parameters
+    1 d              1  # Constant
+    2 kdeg_Ste2_PO4  1  # Constant
+    3 _rateLaw1      100  # Constant
+end parameters
+begin species
+    1 Pheromone(Ste2_site!1).Ste2(Gpa1_site,Pheromone_site!1,S338_S339~PO4,Sst2_site,Yck_site) 1
+    2 CELL() 0
+    3 Pheromone(Ste2_site) 0
+end species
+begin reactions
+    1 1 2,3 _rateLaw1 #_R1
+end reactions

Issues/nfsim_indrani/deleteMolecules/2024_02_07__16_11_07/deleteMolecules/2024_02_07__16_11_47/deleteMolecules_test.bngl

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+# Created by BioNetGen 2.9.0
+
+begin model
+begin parameters
+  d              1
+  kdeg_Ste2_PO4  1
+  _rateLaw1      100
+end parameters
+begin molecule types
+  CELL()                                                              
+  Pheromone(Ste2_site)                                                
+  Ste2(Pheromone_site,Gpa1_site,Sst2_site,Yck_site,S338_S339~none~PO4)
+end molecule types
+begin species
+  Pheromone(Ste2_site!1).Ste2(Gpa1_site,Pheromone_site!1,S338_S339~PO4,Sst2_site,Yck_site) 1
+end species
+begin reaction rules
+  _R1:  Ste2(S338_S339~PO4) -> CELL()  _rateLaw1 DeleteMolecules
+end reaction rules
+end model

Issues/nfsim_indrani/deleteMolecules_changed.bngl

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+begin model
+
+begin parameters
+  d 1
+  kdeg_Ste2_PO4 1
+  _rateLaw1 100
+end parameters
+
+begin molecule types
+  CELL()
+  Pheromone(Ste2_site)
+  Ste2(Pheromone_site,Gpa1_site,Sst2_site,Yck_site,S338_S339~none~PO4)
+end molecule types
+
+begin species
+  Pheromone(Ste2_site!1).Ste2(Gpa1_site,Pheromone_site!1,S338_S339~PO4,Sst2_site,Yck_site) 1
+end species
+
+begin reaction rules
+  _R1: Ste2(S338_S339~PO4) -> CELL() _rateLaw1 DeleteMolecules
+end reaction rules
+
+end model
+
+generate_network({overwrite=>1})

Issues/nfsim_indrani/run_pybng.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import bionetgen"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 34,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "begin reaction rules\n",
+      "  dZeta: Zeta() -> dead() kdl DeleteMolecules\n",
+      "end reaction rules\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "#mname=\"deleteMolecules\"\n",
+    "#mname=\"test_deleteMolecules\"\n",
+    "mname= \"test_deleteMolecules_simple\"\n",
+    "model= bionetgen.bngmodel(mname+\".bngl\")\n",
+    "#with open(mname+\"_pybng.bngl\", \"w\") as f:\n",
+    "#    f.write(str(model)) # writes the changed model to new_model file\n",
+    "print(model.rules)\n",
+    "#ret = bionetgen.run(\"Model_ZAP70_SYK.bngl\", out=\"HPC\",suppress=False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 35,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "DeleteMolecules\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(model.rules[model.rules[0]].rule_mod.type)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "base",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.7"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

Issues/nfsim_indrani/run_pybng.py

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+import bionetgen
+
+#mname="deleteMolecules"
+mname="test_deleteMolecules"
+model= bionetgen.bngmodel(mname+".bngl")
+#with open(mname+"_pybng.bngl", "w") as f:
+#    f.write(str(model)) # writes the changed model to new_model file
+print(model.rules)

Issues/nfsim_indrani/test_deleteMolecules.bngl

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+begin model
+
+
+
+begin parameters
+  kdl 0.03 #CBL degrades ZAP/SYK
+end parameters
+
+begin molecule types
+  A(State~UZAP~PZAP~SHP~uSYK~pSYK,CBL)
+  Zeta(receptor,ITAM1~U~PP,ITAM2~U~PP,ITAM3~U~PP,ITAM4~U~PP,ITAM5~U~PP,ITAM6~U~PP)
+  CBL(site)
+  dead()
+end molecule types
+
+begin seed species
+  A(State~UZAP,CBL) 1
+  Zeta(receptor,ITAM1~U,ITAM2~U,ITAM3~U,ITAM4~U,ITAM5~U,ITAM6~U) 1
+  CBL(site) 1
+end seed species
+
+begin reaction rules
+  CBL_degrade_ITAM1:	Zeta(ITAM1!1).A(State!1,CBL!3).CBL(site!3) -> dead()	kdl DeleteMolecules
+end reaction rules
+
+end model
+
+writeModel({suffix=>"changed",evaluate_expressions=>1,overwrite=>1})
+writeXML()
+#simulate_nf({t_end=>270,n_steps=>1000})
+