Examples with SpeciesContextSpec cbit.vcell.mapping.SpeciesContextSpec used on opensource projects

Example 41 with SpeciesContextSpec

use of cbit.vcell.mapping.SpeciesContextSpec in project vcell by virtualcell.

the class StructureAnalyzer method refreshTotalDependancies.

/**
 * This method was created by a SmartGuide.
 * @param b cbit.vcell.math.Matrix
 * @param vars java.lang.String[]
 */
static StructureAnalyzer.Dependency[] refreshTotalDependancies(RationalMatrix nullSpaceMatrix, SpeciesContextMapping[] speciesContextMappings, MathMapping_4_8 argMathMapping, boolean bFast) throws Exception {
    // System.out.println("StructureAnalyzer.refreshTotalDependancies()");
    SimulationContext argSimContext = argMathMapping.getSimulationContext();
    if (nullSpaceMatrix == null) {
        // System.out.println("the matrix has full rank, there are no dependencies");
        return new StructureAnalyzer.Dependency[0];
    }
    if (speciesContextMappings.length != nullSpaceMatrix.getNumCols()) {
        // throw new Exception("varName array not same dimension as b matrix");
        System.out.println("varName array not same dimension as b matrix");
        nullSpaceMatrix.show();
        for (int i = 0; i < speciesContextMappings.length; i++) {
            System.out.println("scm[" + i + "] is " + speciesContextMappings[i].getSpeciesContext().getName());
        }
    }
    // System.out.println("there are "+nullSpaceMatrix.rows+" dependencies");
    Vector<Dependency> dependencyList = new Vector<Dependency>();
    for (int i = 0; i < nullSpaceMatrix.getNumRows(); i++) {
        // 
        // find first variable
        // 
        Expression exp = null;
        Expression constantExp = null;
        String constantName = null;
        SpeciesContextMapping firstSCM = null;
        boolean bFirst = true;
        for (int j = 0; j < nullSpaceMatrix.getNumCols(); j++) {
            RationalNumber coeff = nullSpaceMatrix.get_elem(i, j);
            if (coeff.doubleValue() != 0.0) {
                if (bFirst) {
                    if (coeff.doubleValue() != 1.0) {
                        System.out.println("i=" + i + " j=" + j);
                        nullSpaceMatrix.show();
                        throw new Exception("expecting a coefficient of 1.0, instead coeff = " + coeff.infix());
                    }
                    firstSCM = speciesContextMappings[j];
                    // 
                    // first term of dependancy expression   ("K_CalciumCyt")
                    // 
                    SpeciesContext firstSC = firstSCM.getSpeciesContext();
                    constantName = "K_" + firstSC.getName() + "_total";
                    exp = new Expression(constantName);
                    // 
                    // first term of K expression
                    // 
                    StructureMapping firstSM = argSimContext.getGeometryContext().getStructureMapping(firstSC.getStructure());
                    SpeciesContextSpec firstSCS = argSimContext.getReactionContext().getSpeciesContextSpec(firstSC);
                    SymbolTableEntry scSTE = null;
                    if (bFast) {
                        scSTE = firstSCS.getSpeciesContext();
                    } else {
                        scSTE = firstSCS.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
                    }
                    constantExp = Expression.mult(new Expression(coeff), firstSM.getNormalizedConcentrationCorrection(argSimContext, argMathMapping), new Expression(scSTE, argMathMapping.getNameScope()));
                    bFirst = false;
                } else {
                    // 
                    // add term to dependancy expression     (" - 2*IP3Cyt ")
                    // 
                    SpeciesContextMapping scm = speciesContextMappings[j];
                    SpeciesContext sc = scm.getSpeciesContext();
                    StructureMapping sm = argSimContext.getGeometryContext().getStructureMapping(sc.getStructure());
                    SpeciesContextSpec scs = argSimContext.getReactionContext().getSpeciesContextSpec(sc);
                    exp = Expression.add(exp, Expression.negate(Expression.mult(new Expression(coeff), sm.getNormalizedConcentrationCorrection(argSimContext, argMathMapping), new Expression(sc, argMathMapping.getNameScope()))));
                    // 
                    // add term to K expression
                    // 
                    SymbolTableEntry scSTE = null;
                    if (bFast) {
                        scSTE = sc;
                    } else {
                        scSTE = scs.getParameterFromRole(SpeciesContextSpec.ROLE_InitialConcentration);
                    }
                    constantExp = Expression.add(constantExp, Expression.mult(new Expression(coeff), sm.getNormalizedConcentrationCorrection(argSimContext, argMathMapping), new Expression(scSTE, argMathMapping.getNameScope())));
                }
            }
        }
        if (firstSCM != null) {
            // 
            // store totalMass parameter (e.g. K_xyz_total = xyz_init + wzy_init)
            // 
            // MathMapping.MathMappingParameter totalMassParameter = mathMapping.addMathMappingParameter(constantName,constantExp.flatten(),MathMapping.PARAMETER_ROLE_TOTALMASS,cbit.vcell.units.VCUnitDefinition.UNIT_uM);
            // 
            // store dependency parameter (e.g. xyz = K_xyz_total - wzy)
            // 
            StructureMapping sm = argSimContext.getGeometryContext().getStructureMapping(firstSCM.getSpeciesContext().getStructure());
            exp = Expression.mult(exp, Expression.invert(sm.getNormalizedConcentrationCorrection(argSimContext, argMathMapping)));
            exp = exp.flatten();
            // exp.bindExpression(mathMapping_temp);
            // firstSCM.setDependencyExpression(exp);
            Dependency dependency = new Dependency();
            dependency.dependencyExpression = exp;
            dependency.speciesContextMapping = firstSCM;
            dependency.invariantSymbolName = constantName;
            dependency.conservedMoietyExpression = constantExp.flatten();
            dependencyList.add(dependency);
        }
    }
    return (StructureAnalyzer.Dependency[]) BeanUtils.getArray(dependencyList, StructureAnalyzer.Dependency.class);
}

Example 42 with SpeciesContextSpec

use of cbit.vcell.mapping.SpeciesContextSpec in project vcell by virtualcell.

the class BioModelParametersTableModel method getApplicationEditableSymbolTableEntryList.

private List<EditableSymbolTableEntry> getApplicationEditableSymbolTableEntryList(SimulationContext simulationContext) {
    ArrayList<EditableSymbolTableEntry> parameterList = new ArrayList<EditableSymbolTableEntry>();
    Map<String, SymbolTableEntry> entryMap = new HashMap<String, SymbolTableEntry>();
    simulationContext.getEntries(entryMap);
    for (SymbolTableEntry ste : entryMap.values()) {
        if (ste instanceof EditableSymbolTableEntry && ste.getNameScope() == simulationContext.getNameScope()) {
            parameterList.add((EditableSymbolTableEntry) ste);
        }
    }
    for (StructureMapping mapping : simulationContext.getGeometryContext().getStructureMappings()) {
        parameterList.addAll(mapping.computeApplicableParameterList());
    }
    for (SpeciesContextSpec spec : simulationContext.getReactionContext().getSpeciesContextSpecs()) {
        parameterList.addAll(spec.computeApplicableParameterList());
    }
    for (ElectricalStimulus elect : simulationContext.getElectricalStimuli()) {
        parameterList.addAll(Arrays.asList(elect.getParameters()));
    }
    for (SpatialProcess sp : simulationContext.getSpatialProcesses()) {
        parameterList.addAll(Arrays.asList(sp.getParameters()));
    }
    return parameterList;
}

Example 43 with SpeciesContextSpec

use of cbit.vcell.mapping.SpeciesContextSpec in project vcell by virtualcell.

the class BioModelParametersTableModel method bioModelChange.

@Override
protected void bioModelChange(PropertyChangeEvent evt) {
    super.bioModelChange(evt);
    BioModel oldValue = (BioModel) evt.getOldValue();
    if (oldValue != null) {
        for (EditableSymbolTableEntry parameter : oldValue.getModel().getModelParameters()) {
            parameter.removePropertyChangeListener(this);
        }
        for (SpeciesContext sc : oldValue.getModel().getSpeciesContexts()) {
            sc.removePropertyChangeListener(this);
        }
        for (ReactionStep reactionStep : oldValue.getModel().getReactionSteps()) {
            reactionStep.removePropertyChangeListener(this);
            Kinetics kinetics = reactionStep.getKinetics();
            kinetics.removePropertyChangeListener(this);
            for (KineticsParameter kineticsEditableSymbolTableEntry : kinetics.getKineticsParameters()) {
                kineticsEditableSymbolTableEntry.removePropertyChangeListener(this);
            }
            for (ProxyParameter proxyEditableSymbolTableEntry : kinetics.getProxyParameters()) {
                proxyEditableSymbolTableEntry.removePropertyChangeListener(this);
            }
            for (UnresolvedParameter unresolvedEditableSymbolTableEntry : kinetics.getUnresolvedParameters()) {
                unresolvedEditableSymbolTableEntry.removePropertyChangeListener(this);
            }
        }
        for (SimulationContext simulationContext : oldValue.getSimulationContexts()) {
            simulationContext.removePropertyChangeListener(this);
            simulationContext.getGeometryContext().removePropertyChangeListener(this);
            for (StructureMapping mapping : simulationContext.getGeometryContext().getStructureMappings()) {
                mapping.removePropertyChangeListener(this);
                for (EditableSymbolTableEntry parameter : mapping.getParameters()) {
                    parameter.removePropertyChangeListener(this);
                }
            }
            simulationContext.getReactionContext().removePropertyChangeListener(this);
            for (SpeciesContextSpec spec : simulationContext.getReactionContext().getSpeciesContextSpecs()) {
                spec.removePropertyChangeListener(this);
                for (EditableSymbolTableEntry parameter : spec.getParameters()) {
                    parameter.removePropertyChangeListener(this);
                }
            }
            for (ElectricalStimulus elect : simulationContext.getElectricalStimuli()) {
                elect.removePropertyChangeListener(this);
                for (EditableSymbolTableEntry parameter : elect.getParameters()) {
                    parameter.removePropertyChangeListener(this);
                }
            }
            for (SpatialObject spatialObject : simulationContext.getSpatialObjects()) {
                spatialObject.removePropertyChangeListener(this);
            }
            for (SpatialProcess spatialProcess : simulationContext.getSpatialProcesses()) {
                spatialProcess.removePropertyChangeListener(this);
                for (LocalParameter p : spatialProcess.getParameters()) {
                    p.removePropertyChangeListener(this);
                }
            }
            for (SimulationContextParameter p : simulationContext.getSimulationContextParameters()) {
                p.removePropertyChangeListener(this);
            }
        }
    }
    BioModel newValue = (BioModel) evt.getNewValue();
    if (newValue != null) {
        for (ModelParameter modelEditableSymbolTableEntry : newValue.getModel().getModelParameters()) {
            modelEditableSymbolTableEntry.addPropertyChangeListener(this);
        }
        for (SpeciesContext sc : newValue.getModel().getSpeciesContexts()) {
            sc.addPropertyChangeListener(this);
        }
        for (ReactionStep reactionStep : newValue.getModel().getReactionSteps()) {
            reactionStep.addPropertyChangeListener(this);
            Kinetics kinetics = reactionStep.getKinetics();
            kinetics.addPropertyChangeListener(this);
            for (KineticsParameter kineticsEditableSymbolTableEntry : kinetics.getKineticsParameters()) {
                kineticsEditableSymbolTableEntry.addPropertyChangeListener(this);
            }
            for (ProxyParameter proxyEditableSymbolTableEntry : kinetics.getProxyParameters()) {
                proxyEditableSymbolTableEntry.addPropertyChangeListener(this);
            }
            for (UnresolvedParameter unresolvedEditableSymbolTableEntry : kinetics.getUnresolvedParameters()) {
                unresolvedEditableSymbolTableEntry.addPropertyChangeListener(this);
            }
        }
        for (SimulationContext simulationContext : newValue.getSimulationContexts()) {
            simulationContext.addPropertyChangeListener(this);
            simulationContext.getGeometryContext().addPropertyChangeListener(this);
            for (StructureMapping mapping : simulationContext.getGeometryContext().getStructureMappings()) {
                mapping.addPropertyChangeListener(this);
                for (EditableSymbolTableEntry parameter : mapping.getParameters()) {
                    parameter.addPropertyChangeListener(this);
                }
            }
            simulationContext.getReactionContext().addPropertyChangeListener(this);
            for (SpeciesContextSpec spec : simulationContext.getReactionContext().getSpeciesContextSpecs()) {
                spec.addPropertyChangeListener(this);
                for (EditableSymbolTableEntry parameter : spec.getParameters()) {
                    parameter.addPropertyChangeListener(this);
                }
            }
            for (ElectricalStimulus elect : simulationContext.getElectricalStimuli()) {
                elect.addPropertyChangeListener(this);
                for (EditableSymbolTableEntry parameter : elect.getParameters()) {
                    parameter.addPropertyChangeListener(this);
                }
            }
            for (SpatialObject spatialObject : simulationContext.getSpatialObjects()) {
                spatialObject.addPropertyChangeListener(this);
            }
            for (SpatialProcess spatialProcess : simulationContext.getSpatialProcesses()) {
                spatialProcess.addPropertyChangeListener(this);
                for (LocalParameter p : spatialProcess.getParameters()) {
                    p.addPropertyChangeListener(this);
                }
            }
            for (SimulationContextParameter p : simulationContext.getSimulationContextParameters()) {
                p.addPropertyChangeListener(this);
            }
        }
    }
}

Example 44 with SpeciesContextSpec

use of cbit.vcell.mapping.SpeciesContextSpec in project vcell by virtualcell.

the class RbmNetworkGenerator method writeBngl_internal.

public static void writeBngl_internal(SimulationContext simulationContext, PrintWriter writer, Map<FakeReactionRuleRateParameter, LocalParameter> kineticsParameterMap, Map<FakeSeedSpeciesInitialConditionsParameter, Pair<SpeciesContext, Expression>> speciesEquivalenceMap, NetworkGenerationRequirements networkGenerationRequirements, CompartmentMode compartmentMode) {
    String callerClassName = new Exception().getStackTrace()[1].getClassName();
    String networkTransformerClassName = NetworkTransformer.class.getName();
    String rulebasedTransformerClassName = RulebasedTransformer.class.getName();
    if (!callerClassName.equals(networkTransformerClassName) && !callerClassName.equals(rulebasedTransformerClassName)) {
        throw new UnsupportedOperationException("This method may only be called from within a " + networkTransformerClassName + " or " + rulebasedTransformerClassName + " instance.");
    }
    Model model = simulationContext.getModel();
    RbmModelContainer rbmModelContainer = model.getRbmModelContainer();
    checkConsistency(model);
    // first we prepare the fake parameters we need to maintain the relationship between the species context and the seed species
    List<FakeSeedSpeciesInitialConditionsParameter> fakeParameterList = new ArrayList<FakeSeedSpeciesInitialConditionsParameter>();
    List<String> seedSpeciesList = new ArrayList<String>();
    SpeciesContext[] speciesContexts = model.getSpeciesContexts();
    for (int i = 0; i < speciesContexts.length; i++) {
        SpeciesContext sc = speciesContexts[i];
        if (!sc.hasSpeciesPattern()) {
            continue;
        }
        SpeciesContextSpec scs = simulationContext.getReactionContext().getSpeciesContextSpec(sc);
        Expression initialConcentration = scs.getParameter(SpeciesContextSpec.ROLE_InitialConcentration).getExpression();
        // fake initial values for the seed species, we need to present them to bngl as parameters
        FakeSeedSpeciesInitialConditionsParameter fakeSeedSpeciesParam = new FakeSeedSpeciesInitialConditionsParameter(sc.getName());
        Pair<SpeciesContext, Expression> p = new Pair<SpeciesContext, Expression>(sc, initialConcentration);
        speciesEquivalenceMap.put(fakeSeedSpeciesParam, p);
        String modified;
        if (compartmentMode == CompartmentMode.show) {
            modified = RbmUtils.toBnglString(sc.getSpeciesPattern(), null, CompartmentMode.hide, 0);
            modified = "@" + sc.getStructure().getName() + ":" + modified;
        } else if (compartmentMode == CompartmentMode.asSite) {
            modified = RbmUtils.toBnglString(sc.getSpeciesPattern(), sc.getStructure(), CompartmentMode.asSite, 0);
        } else {
            // CompartmentMode.hide
            modified = RbmUtils.toBnglString(sc.getSpeciesPattern(), null, CompartmentMode.hide, 0);
        }
        modified += " " + fakeSeedSpeciesParam.fakeParameterName;
        // we label the seed species with the index
        modified = (i + 1) + " " + modified;
        // we build the seed species list now, we write it later (in the BEGIN SPECIES block)
        seedSpeciesList.add(modified);
        fakeParameterList.add(fakeSeedSpeciesParam);
    }
    // second we produce the bngl file
    writer.println(BEGIN_MODEL);
    writer.println();
    for (ReactionRuleSpec rrs : simulationContext.getReactionContext().getReactionRuleSpecs()) {
        if (!rrs.isExcluded()) {
            ReactionRule reactionRule = rrs.getReactionRule();
            RbmKineticLaw kineticLaw = reactionRule.getKineticLaw();
            switch(kineticLaw.getRateLawType()) {
                case MassAction:
                    {
                        FakeReactionRuleRateParameter fakeRateParameterForward = new FakeReactionRuleRateParameter(reactionRule, RbmKineticLawParameterType.MassActionForwardRate);
                        LocalParameter origForwardRateParameter = kineticLaw.getLocalParameter(RbmKineticLawParameterType.MassActionForwardRate);
                        kineticsParameterMap.put(fakeRateParameterForward, origForwardRateParameter);
                        if (reactionRule.isReversible()) {
                            FakeReactionRuleRateParameter fakeRateParameterReverse = new FakeReactionRuleRateParameter(reactionRule, RbmKineticLawParameterType.MassActionReverseRate);
                            LocalParameter origReverseRateParameter = kineticLaw.getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate);
                            kineticsParameterMap.put(fakeRateParameterReverse, origReverseRateParameter);
                        }
                        break;
                    }
                default:
                    {
                        throw new RuntimeException("kinetic law type " + kineticLaw.getRateLawType().name() + " not yet implemented");
                    }
            }
        }
    }
    if (compartmentMode == CompartmentMode.show) {
        RbmNetworkGenerator.writeCompartments(writer, model, simulationContext);
    }
    writer.println(BEGIN_PARAMETERS);
    // the fake parameters used for reaction rule kinetics
    for (FakeReactionRuleRateParameter p : kineticsParameterMap.keySet()) {
        writer.println(p.fakeParameterName + "\t\t1");
    }
    // the fake parameters used at initial values for the seed species
    for (FakeSeedSpeciesInitialConditionsParameter s : fakeParameterList) {
        writer.println(s.fakeParameterName + "\t\t1");
    }
    writer.println(END_PARAMETERS);
    writer.println();
    RbmNetworkGenerator.writeMolecularTypes(writer, model, compartmentMode);
    // write modified version of seed species while maintaining the connection between the species context and the real seed species
    writer.println(BEGIN_SPECIES);
    for (String s : seedSpeciesList) {
        writer.println(s);
    }
    writer.println(END_SPECIES);
    writer.println();
    RbmNetworkGenerator.writeObservables(writer, rbmModelContainer, compartmentMode);
    RbmNetworkGenerator.writeReactions_internal(writer, simulationContext, compartmentMode);
    writer.println(END_MODEL);
    writer.println();
    if (callerClassName.equals(networkTransformerClassName)) {
        RbmNetworkGenerator.writeNetworkConstraints(writer, rbmModelContainer, simulationContext, networkGenerationRequirements);
    } else if (callerClassName.equals(rulebasedTransformerClassName)) {
        writer.println();
        writer.println("writeXML()");
    }
    writer.println();
}

Example 45 with SpeciesContextSpec

use of cbit.vcell.mapping.SpeciesContextSpec in project vcell by virtualcell.

the class RbmUtils method toBnglString.

public static String toBnglString(SimulationContext sc, SpeciesContext speciesContext, CompartmentMode compartmentMode) {
    SpeciesContextSpec scs = sc.getReactionContext().getSpeciesContextSpec(speciesContext);
    Expression expression = scs.getParameter(SpeciesContextSpec.ROLE_InitialConcentration).getExpression();
    SpeciesPattern sp = speciesContext.getSpeciesPattern();
    String s = "";
    if (compartmentMode == CompartmentMode.show) {
        s += "@" + speciesContext.getStructure().getName() + ":";
        s += toBnglString(sp, null, CompartmentMode.hide, 0) + "";
    } else if (compartmentMode == CompartmentMode.asSite) {
        s += toBnglString(sp, speciesContext.getStructure(), CompartmentMode.asSite, 0) + "";
    } else {
        s += toBnglString(sp, null, CompartmentMode.hide, 0) + "";
    }
    s += " " + expression.infix();
    return s;
}