Examples with Membrane cbit.vcell.model.Membrane used on opensource projects

Example 21 with Membrane

use of cbit.vcell.model.Membrane in project vcell by virtualcell.

the class DiffEquMathMapping method computeBoundaryConditionSource.

// determine membrane inside and outside subvolume
public static Pair<SubVolume, SubVolume> computeBoundaryConditionSource(Model model, SimulationContext simContext, SurfaceClass surfaceClass) {
    SubVolume outerSubVolume = null;
    SubVolume innerSubVolume = null;
    Structure[] mappedStructures = simContext.getGeometryContext().getStructuresFromGeometryClass(surfaceClass);
    // inside and outside correspond to structure hierarchy when present
    for (Structure s : mappedStructures) {
        if (s instanceof Membrane) {
            Membrane m = (Membrane) s;
            Feature infeature = model.getStructureTopology().getInsideFeature(m);
            if (infeature != null) {
                FeatureMapping insm = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(infeature);
                if (insm.getGeometryClass() instanceof SubVolume) {
                    innerSubVolume = (SubVolume) insm.getGeometryClass();
                }
            }
            Feature outfeature = model.getStructureTopology().getOutsideFeature(m);
            if (outfeature != null) {
                FeatureMapping outsm = (FeatureMapping) simContext.getGeometryContext().getStructureMapping(outfeature);
                if (outsm.getGeometryClass() instanceof SubVolume) {
                    outerSubVolume = (SubVolume) outsm.getGeometryClass();
                }
            }
        }
    }
    // make the choice deterministic
    if (innerSubVolume == null || outerSubVolume == null || innerSubVolume == outerSubVolume) {
        Set<SubVolume> sv = surfaceClass.getAdjacentSubvolumes();
        Iterator<SubVolume> iterator = sv.iterator();
        innerSubVolume = iterator.next();
        outerSubVolume = iterator.next();
        if (innerSubVolume.getName().compareTo(outerSubVolume.getName()) > 0) {
            SubVolume temp = innerSubVolume;
            innerSubVolume = outerSubVolume;
            outerSubVolume = temp;
        }
    }
    Pair<SubVolume, SubVolume> ret = new Pair<>(innerSubVolume, outerSubVolume);
    return ret;
}

Example 22 with Membrane

use of cbit.vcell.model.Membrane in project vcell by virtualcell.

the class DiffEquMathMapping method refreshVariables.

/**
 * This method was created in VisualAge.
 */
private void refreshVariables() throws MappingException {
    // System.out.println("MathMapping.refreshVariables()");
    // 
    // non-constant dependent variables require a function
    // 
    Enumeration<SpeciesContextMapping> enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = enum1.nextElement();
        SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(scm.getSpeciesContext());
        if (scm.getDependencyExpression() != null && !scs.isConstant()) {
            // scm.setVariable(new Function(scm.getSpeciesContext().getName(),scm.getDependencyExpression()));
            scm.setVariable(null);
        }
        if (getSimulationContext().hasEventAssignment(scs.getSpeciesContext())) {
            scm.setDependencyExpression(null);
        }
    }
    // 
    // non-constant independent variables require either a membrane or volume variable
    // 
    enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
        SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(scm.getSpeciesContext());
        if (scm.getDependencyExpression() == null && (!scs.isConstant() || getSimulationContext().hasEventAssignment(scs.getSpeciesContext()))) {
            StructureMapping sm = simContext.getGeometryContext().getStructureMapping(scm.getSpeciesContext().getStructure());
            Structure struct = scm.getSpeciesContext().getStructure();
            Domain domain = null;
            if (sm.getGeometryClass() != null) {
                domain = new Domain(sm.getGeometryClass());
            }
            if (struct instanceof Feature || struct instanceof Membrane) {
                if (sm.getGeometryClass() instanceof SurfaceClass) {
                    if (scs.isWellMixed()) {
                        scm.setVariable(new MembraneRegionVariable(scm.getSpeciesContext().getName(), domain));
                    } else if (getSimulationContext().isStoch() && getSimulationContext().getGeometry().getDimension() > 0 && !scs.isForceContinuous()) {
                        scm.setVariable(new MemVariable(scm.getSpeciesContext().getName() + "_conc", domain));
                    } else {
                        scm.setVariable(new MemVariable(scm.getSpeciesContext().getName(), domain));
                    }
                } else {
                    if (scs.isWellMixed()) {
                        scm.setVariable(new VolumeRegionVariable(scm.getSpeciesContext().getName(), domain));
                    } else if (getSimulationContext().isStoch() && getSimulationContext().getGeometry().getDimension() > 0 && !scs.isForceContinuous()) {
                        scm.setVariable(new VolVariable(scm.getSpeciesContext().getName() + "_conc", domain));
                    } else {
                        scm.setVariable(new VolVariable(scm.getSpeciesContext().getName(), domain));
                    }
                }
            } else {
                throw new MappingException("class " + scm.getSpeciesContext().getStructure().getClass() + " not supported");
            }
            mathSymbolMapping.put(scm.getSpeciesContext(), scm.getVariable().getName());
        }
    }
}

Example 23 with Membrane

use of cbit.vcell.model.Membrane in project vcell by virtualcell.

the class StructureAnalyzer method refreshFastMatrices.

/**
 * This method was created in VisualAge.
 */
private void refreshFastMatrices() throws Exception {
    // System.out.println("StructureAnalyzer.refreshFastMatrices()");
    // 
    // update scheme matrix for fast system
    // 
    fastSchemeMatrix = new RationalNumberMatrix(fastSpeciesContextMappings.length, fastReactionSteps.length);
    for (int i = 0; i < fastSpeciesContextMappings.length; i++) {
        for (int j = 0; j < fastReactionSteps.length; j++) {
            fastSchemeMatrix.set_elem(i, j, fastReactionSteps[j].getStoichiometry(fastSpeciesContextMappings[i].getSpeciesContext()));
        }
    }
    // 
    for (int i = 0; i < fastSpeciesContextMappings.length; i++) {
        SpeciesContextMapping scm = fastSpeciesContextMappings[i];
        SpeciesContext sc = scm.getSpeciesContext();
        // 
        // collect fast rate expression
        // 
        Expression exp = new Expression(0.0);
        for (int j = 0; j < fastReactionSteps.length; j++) {
            int stoichiometry = fastReactionSteps[j].getStoichiometry(sc);
            ReactionSpec reactionSpec = mathMapping_4_8.getSimulationContext().getReactionContext().getReactionSpec(fastReactionSteps[j]);
            if (stoichiometry != 0) {
                if (!reactionSpec.isFast()) {
                    throw new Exception("expected only fast rates");
                }
                if (reactionSpec.isExcluded()) {
                    throw new Exception("expected only included rates");
                }
                ReactionParticipant[] rps = fastReactionSteps[j].getReactionParticipants();
                ReactionParticipant rp0 = null;
                for (ReactionParticipant rp : rps) {
                    if (rp.getSpeciesContext() == sc) {
                        rp0 = rp;
                        break;
                    }
                }
                // 
                if (rp0 != null) {
                    Structure structure = fastReactionSteps[j].getStructure();
                    Expression fastRateExpression = getReactionRateExpression(fastReactionSteps[j], rp0).renameBoundSymbols(mathMapping_4_8.getNameScope());
                    if ((structure instanceof Membrane) && (rp0.getStructure() != structure)) {
                        Membrane membrane = (Membrane) structure;
                        MembraneMapping membraneMapping = (MembraneMapping) mathMapping_4_8.getSimulationContext().getGeometryContext().getStructureMapping(membrane);
                        Expression fluxCorrection = new Expression(mathMapping_4_8.getFluxCorrectionParameter(membraneMapping, (Feature) rp0.getStructure()), mathMapping_4_8.getNameScope());
                        exp = Expression.add(exp, Expression.mult(fluxCorrection, fastRateExpression));
                    } else {
                        exp = Expression.add(exp, new Expression(fastRateExpression));
                    }
                }
            }
        }
        // exp.bindExpression(mathMapping);
        scm.setFastRate(exp.flatten());
    }
    // System.out.println("StructureAnalyzer.refreshFastMatrices(), scheme matrix:");
    // fastSchemeMatrix.show();
    // 
    // update null space matrix
    // 
    fastNullSpaceMatrix = fastSchemeMatrix.findNullSpace();
// if (fastNullSpaceMatrix==null){
// System.out.println("fast system has full rank");
// }else{
// System.out.println("StructureAnalyzer.refreshFastMatrices(), nullSpace matrix:");
// fastNullSpaceMatrix.show();
// }
}

Example 24 with Membrane

use of cbit.vcell.model.Membrane in project vcell by virtualcell.

the class StructureAnalyzer method getReactionRateExpression.

public Expression getReactionRateExpression(ReactionStep reactionStep, ReactionParticipant reactionParticipant) throws Exception {
    if (reactionParticipant instanceof Catalyst) {
        throw new Exception("Catalyst " + reactionParticipant + " doesn't have a rate for this reaction");
    // return new Expression(0.0);
    }
    double stoich = reactionStep.getStoichiometry(reactionParticipant.getSpeciesContext());
    if (stoich == 0.0) {
        return new Expression(0.0);
    }
    if (reactionStep.getKinetics() instanceof DistributedKinetics) {
        DistributedKinetics distributedKinetics = (DistributedKinetics) reactionStep.getKinetics();
        if (stoich != 1) {
            Expression exp = Expression.mult(new Expression(stoich), new Expression(distributedKinetics.getReactionRateParameter(), mathMapping_4_8.getNameScope()));
            return exp;
        } else {
            Expression exp = new Expression(distributedKinetics.getReactionRateParameter(), mathMapping_4_8.getNameScope());
            return exp;
        }
    } else if (reactionStep.getKinetics() instanceof LumpedKinetics) {
        Structure.StructureSize structureSize = reactionStep.getStructure().getStructureSize();
        // 
        // need to put this into concentration/time with respect to structure for reaction.
        // 
        LumpedKinetics lumpedKinetics = (LumpedKinetics) reactionStep.getKinetics();
        Expression factor = null;
        ModelUnitSystem unitSystem = mathMapping_4_8.getSimulationContext().getModel().getUnitSystem();
        if (reactionStep.getStructure() instanceof Feature || ((reactionStep.getStructure() instanceof Membrane) && reactionStep instanceof FluxReaction)) {
            VCUnitDefinition lumpedToVolumeSubstance = unitSystem.getVolumeSubstanceUnit().divideBy(unitSystem.getLumpedReactionSubstanceUnit());
            factor = Expression.div(new Expression(lumpedToVolumeSubstance.getDimensionlessScale()), new Expression(structureSize, mathMapping_4_8.getNameScope()));
        } else if (reactionStep.getStructure() instanceof Membrane && reactionStep instanceof SimpleReaction) {
            VCUnitDefinition lumpedToVolumeSubstance = unitSystem.getMembraneSubstanceUnit().divideBy(unitSystem.getLumpedReactionSubstanceUnit());
            factor = Expression.div(new Expression(lumpedToVolumeSubstance.getDimensionlessScale()), new Expression(structureSize, mathMapping_4_8.getNameScope()));
        } else {
            throw new RuntimeException("failed to create reaction rate expression for reaction " + reactionStep.getName() + ", with kinetic type of " + reactionStep.getKinetics().getClass().getName());
        }
        if (stoich != 1) {
            Expression exp = Expression.mult(new Expression(stoich), Expression.mult(new Expression(lumpedKinetics.getLumpedReactionRateParameter(), mathMapping_4_8.getNameScope()), factor));
            return exp;
        } else {
            Expression exp = Expression.mult(new Expression(lumpedKinetics.getLumpedReactionRateParameter(), mathMapping_4_8.getNameScope()), factor);
            return exp;
        }
    } else {
        throw new RuntimeException("unexpected kinetic type " + reactionStep.getKinetics().getClass().getName());
    }
}

Example 25 with Membrane

use of cbit.vcell.model.Membrane in project vcell by virtualcell.

the class VolumeStructureAnalyzer method refreshStructures.

/**
 * Build list of structures that are mapped to this volume subdomain
 */
protected void refreshStructures() {
    // 
    // get all structures that are mapped to this subvolume (subdomain)
    // 
    Structure[] structs = mathMapping_4_8.getStructures(subVolume);
    Vector<Structure> structList = new Vector<Structure>();
    if (structs != null) {
        for (int i = 0; i < structs.length; i++) {
            // 
            if (structs[i] instanceof Membrane) {
                Membrane membrane = (Membrane) structs[i];
                MembraneMapping membraneMapping = (MembraneMapping) mathMapping_4_8.getSimulationContext().getGeometryContext().getStructureMapping(membrane);
                if (mathMapping_4_8.getResolved(membraneMapping)) {
                    continue;
                }
            }
            // 
            // add all others to the structure list
            // 
            structList.addElement(structs[i]);
        }
    }
    // 
    if (structList.size() > 0) {
        structures = new Structure[structList.size()];
        structList.copyInto(structures);
    } else {
        structures = null;
    }
}