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jrfaederjrfaeder
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Code that fixes DeleteMolecule bug for multiple Delete ops
1 parent 2f9785b commit 49625c2

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Lines changed: 359 additions & 10 deletions

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‎Issues/parameter_init/parameter_init.py‎

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import bionetgen
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parameter = bionetgen.modelapi.structs.Parameter("A0", "10")
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print(parameter.gen_string())

‎Issues/rule_keywords/run_pybng.ipynb‎

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 1,
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"metadata": {},
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"outputs": [],
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"source": [
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"import bionetgen"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"\n",
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"begin reaction rules\n",
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" R1: Zeta(ITAM1!1).A(State!1,CBL!2).CBL(site!2) -> dead() kdl DeleteMolecules\n",
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" R2: Zeta() -> dead() kdl DeleteMolecules\n",
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"end reaction rules\n",
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"\n"
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]
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}
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],
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"source": [
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"mname=\"test_deleteMolecules\"\n",
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"model= bionetgen.bngmodel(mname+\".bngl\")\n",
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"print(model.rules)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 31,
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"metadata": {},
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"outputs": [],
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"source": [
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"from collections import OrderedDict\n",
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"\n",
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"d = [OrderedDict([('@id', 'RR1_RP1_M1'), ('@DeleteMolecules', '1')]), OrderedDict([('@id', 'RR1_RP1_M2'), ('@DeleteMolecules', '1')]), OrderedDict([('@id', 'RR1_RP1_M3'), ('@DeleteMolecules', '1')])]\n",
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"#d= d + [OrderedDict([('@id', 'RR1_RP1_M1')])]"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Use list comprehension to get an array of values"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 51,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"True\n"
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]
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}
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],
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"source": [
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"vals=[e['@DeleteMolecules'] for e in d]\n",
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"if (all(vals)==1):\n",
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" print(True)\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 58,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"False\n"
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]
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}
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],
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"source": [
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"print(all([0,0,0])==-1)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "base",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.7"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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}

‎Issues/rule_keywords/run_pybng.py‎

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@@ -2,4 +2,4 @@
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mname="test_deleteMolecules"
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model= bionetgen.bngmodel(mname+".bngl")
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print(model.rules)
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print(model)

‎Issues/rule_keywords/test_DeleteMolecules.bngl‎

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@@ -21,4 +21,5 @@ begin reaction rules
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end reaction rules
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end model
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#writeModel({suffix=>"changed",evaluate_expressions=>1,overwrite=>1})
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#writeModel({suffix=>"changed",evaluate_expressions=>1,overwrite=>1})
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writeXML()

‎Issues/rule_keywords/test_DeleteMolecules.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<!-- Created by BioNetGen 2.9.0 -->
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<sbml xmlns="http://www.sbml.org/sbml/level3" level="3" version="1">
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<model id="test_DeleteMolecules">
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<ListOfParameters>
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<Parameter id="kdl" type="Constant" value="0.03" expr="0.03"/>
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</ListOfParameters>
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<ListOfMoleculeTypes>
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<MoleculeType id="A">
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<ListOfComponentTypes>
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<ComponentType id="State">
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<ListOfAllowedStates>
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<AllowedState id="UZAP"/>
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<AllowedState id="PZAP"/>
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<AllowedState id="SHP"/>
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<AllowedState id="uSYK"/>
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<AllowedState id="pSYK"/>
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</ListOfAllowedStates>
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</ComponentType>
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<ComponentType id="CBL"/>
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</ListOfComponentTypes>
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</MoleculeType>
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<MoleculeType id="CBL">
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<ListOfComponentTypes>
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<ComponentType id="site"/>
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</ListOfComponentTypes>
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</MoleculeType>
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<MoleculeType id="Zeta">
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<ListOfComponentTypes>
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<ComponentType id="receptor"/>
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<ComponentType id="ITAM1">
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<ListOfAllowedStates>
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<AllowedState id="U"/>
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<AllowedState id="PP"/>
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</ListOfAllowedStates>
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</ComponentType>
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<ComponentType id="ITAM2">
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<ListOfAllowedStates>
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<AllowedState id="U"/>
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<AllowedState id="PP"/>
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</ListOfAllowedStates>
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</ComponentType>
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<ComponentType id="ITAM3">
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<ListOfAllowedStates>
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<AllowedState id="U"/>
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<AllowedState id="PP"/>
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</ListOfAllowedStates>
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</ComponentType>
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<ComponentType id="ITAM4">
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<ListOfAllowedStates>
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<AllowedState id="U"/>
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<AllowedState id="PP"/>
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</ListOfAllowedStates>
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</ComponentType>
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<ComponentType id="ITAM5">
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<ListOfAllowedStates>
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<AllowedState id="U"/>
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<AllowedState id="PP"/>
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</ListOfAllowedStates>
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</ComponentType>
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<ComponentType id="ITAM6">
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<ListOfAllowedStates>
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<AllowedState id="U"/>
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<AllowedState id="PP"/>
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</ListOfAllowedStates>
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</ComponentType>
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</ListOfComponentTypes>
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</MoleculeType>
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<MoleculeType id="dead"/>
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</ListOfMoleculeTypes>
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<ListOfCompartments>
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</ListOfCompartments>
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<ListOfSpecies>
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<Species id="S1" concentration="1" name="A(CBL,State~UZAP)">
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<ListOfMolecules>
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<Molecule id="S1_M1" name="A">
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<ListOfComponents>
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<Component id="S1_M1_C1" name="CBL" numberOfBonds="0"/>
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<Component id="S1_M1_C2" name="State" state="UZAP" numberOfBonds="0"/>
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</ListOfComponents>
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</Molecule>
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</ListOfMolecules>
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</Species>
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<Species id="S2" concentration="1" name="Zeta(ITAM1~U,ITAM2~U,ITAM3~U,ITAM4~U,ITAM5~U,ITAM6~U,receptor)">
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<ListOfMolecules>
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<Molecule id="S2_M1" name="Zeta">
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<ListOfComponents>
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<Component id="S2_M1_C1" name="ITAM1" state="U" numberOfBonds="0"/>
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<Component id="S2_M1_C2" name="ITAM2" state="U" numberOfBonds="0"/>
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<Component id="S2_M1_C3" name="ITAM3" state="U" numberOfBonds="0"/>
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<Component id="S2_M1_C4" name="ITAM4" state="U" numberOfBonds="0"/>
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<Component id="S2_M1_C5" name="ITAM5" state="U" numberOfBonds="0"/>
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<Component id="S2_M1_C6" name="ITAM6" state="U" numberOfBonds="0"/>
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<Component id="S2_M1_C7" name="receptor" numberOfBonds="0"/>
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</ListOfComponents>
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</Molecule>
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</ListOfMolecules>
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</Species>
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<Species id="S3" concentration="1" name="CBL(site)">
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<ListOfMolecules>
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<Molecule id="S3_M1" name="CBL">
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<ListOfComponents>
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<Component id="S3_M1_C1" name="site" numberOfBonds="0"/>
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</ListOfComponents>
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</Molecule>
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</ListOfMolecules>
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</Species>
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</ListOfSpecies>
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<ListOfReactionRules>
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<ReactionRule id="RR1" name="R1" symmetry_factor="1">
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<ListOfReactantPatterns>
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<ReactantPattern id="RR1_RP1">
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<ListOfMolecules>
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<Molecule id="RR1_RP1_M1" name="Zeta">
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<ListOfComponents>
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<Component id="RR1_RP1_M1_C1" name="ITAM1" numberOfBonds="1"/>
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</ListOfComponents>
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</Molecule>
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<Molecule id="RR1_RP1_M2" name="A">
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<ListOfComponents>
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<Component id="RR1_RP1_M2_C1" name="State" numberOfBonds="1"/>
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<Component id="RR1_RP1_M2_C2" name="CBL" numberOfBonds="1"/>
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</ListOfComponents>
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</Molecule>
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<Molecule id="RR1_RP1_M3" name="CBL">
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<ListOfComponents>
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<Component id="RR1_RP1_M3_C1" name="site" numberOfBonds="1"/>
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</ListOfComponents>
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</Molecule>
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</ListOfMolecules>
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<ListOfBonds>
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<Bond id="RR1_RP1_B1" site1="RR1_RP1_M1_C1" site2="RR1_RP1_M2_C1"/>
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<Bond id="RR1_RP1_B2" site1="RR1_RP1_M2_C2" site2="RR1_RP1_M3_C1"/>
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</ListOfBonds>
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</ReactantPattern>
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</ListOfReactantPatterns>
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<ListOfProductPatterns>
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<ProductPattern id="RR1_PP1">
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<ListOfMolecules>
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<Molecule id="RR1_PP1_M1" name="dead"/>
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</ListOfMolecules>
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</ProductPattern>
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</ListOfProductPatterns>
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<RateLaw id="RR1_RateLaw" type="Ele" totalrate="0">
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<ListOfRateConstants>
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<RateConstant value="kdl"/>
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</ListOfRateConstants>
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</RateLaw>
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<Map>
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<MapItem sourceID="RR1_RP1_M1"/>
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<MapItem sourceID="RR1_RP1_M1_C1"/>
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<MapItem sourceID="RR1_RP1_M2"/>
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<MapItem sourceID="RR1_RP1_M2_C1"/>
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<MapItem sourceID="RR1_RP1_M2_C2"/>
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<MapItem sourceID="RR1_RP1_M3"/>
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<MapItem sourceID="RR1_RP1_M3_C1"/>
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</Map>
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<ListOfOperations>
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<Add id="RR1_PP1_M1"/>
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<Delete id="RR1_RP1_M1" DeleteMolecules="1"/>
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<Delete id="RR1_RP1_M2" DeleteMolecules="1"/>
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<Delete id="RR1_RP1_M3" DeleteMolecules="1"/>
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</ListOfOperations>
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</ReactionRule>
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<ReactionRule id="RR2" name="R2" symmetry_factor="1">
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<ListOfReactantPatterns>
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<ReactantPattern id="RR2_RP1">
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<ListOfMolecules>
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<Molecule id="RR2_RP1_M1" name="Zeta"/>
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</ListOfMolecules>
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</ReactantPattern>
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</ListOfReactantPatterns>
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<ListOfProductPatterns>
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<ProductPattern id="RR2_PP1">
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<ListOfMolecules>
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<Molecule id="RR2_PP1_M1" name="dead"/>
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</ListOfMolecules>
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</ProductPattern>
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</ListOfProductPatterns>
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<RateLaw id="RR2_RateLaw" type="Ele" totalrate="0">
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<ListOfRateConstants>
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<RateConstant value="kdl"/>
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</ListOfRateConstants>
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</RateLaw>
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<Map>
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<MapItem sourceID="RR2_RP1_M1"/>
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</Map>
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<ListOfOperations>
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<Add id="RR2_PP1_M1"/>
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<Delete id="RR2_RP1_M1" DeleteMolecules="1"/>
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</ListOfOperations>
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</ReactionRule>
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</ListOfReactionRules>
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<ListOfObservables>
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</ListOfObservables>
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<ListOfFunctions>
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</ListOfFunctions>
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</model>
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</sbml>

‎bionetgen/modelapi/xmlparsers.py‎

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@@ -700,15 +700,15 @@ def get_rule_mod(self, xml):
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# determine which rule mod is being used, if any
701701
if "Delete" in list_ops:
702702
del_op = list_ops["Delete"]
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# check if modifier was called or automatic
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# for op in del_op:
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# print(op)
706703
if not isinstance(del_op, list):
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mod_call = del_op["@DeleteMolecules"]
708-
if mod_call == "1":
709-
# get mod information & add to string
710-
rule_mod.type = "DeleteMolecules"
711-
rule_mod.id = del_op["@id"]
704+
del_op = [del_op] # Make sure del_op is list
705+
dmvals= [op['@DeleteMolecules'] for op in del_op]
706+
# All Delete operations in rule must have DeleteMolecules attribute or
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# it does not apply to the whole rule
708+
if (all(dmvals)==1):
709+
rule_mod.type = "DeleteMolecules"
710+
# JRF: I don't believe the id of the specific op rule_mod is currently used
711+
#rule_mod.id = op["@id"]
712712
elif "ChangeCompartment" in list_ops:
713713
move_op = list_ops["ChangeCompartment"]
714714
if not isinstance(move_op, list):

‎tests/models/test_DeleteMolecules.bngl‎

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begin model
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begin parameters
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kdl 0.03 #CBL degrades ZAP/SYK
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end parameters
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begin molecule types
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A(State~UZAP~PZAP~SHP~uSYK~pSYK,CBL)
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Zeta(receptor,ITAM1~U~PP,ITAM2~U~PP,ITAM3~U~PP,ITAM4~U~PP,ITAM5~U~PP,ITAM6~U~PP)
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CBL(site)
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dead()
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end molecule types
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begin seed species
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A(State~UZAP,CBL) 1
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Zeta(receptor,ITAM1~U,ITAM2~U,ITAM3~U,ITAM4~U,ITAM5~U,ITAM6~U) 1
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CBL(site) 1
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end seed species
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begin reaction rules
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# Keyword is dropped here by unfixed version
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R1: Zeta(ITAM1!1).A(State!1,CBL!3).CBL(site!3) -> dead() kdl DeleteMolecules
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# Keyword is NOT dropped for this rule because only one molecule is deleted
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R2: Zeta() -> dead() kdl DeleteMolecules
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end reaction rules
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end model
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#writeModel({suffix=>"changed",evaluate_expressions=>1,overwrite=>1})
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writeXML()

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