Examples with ParticleSpeciesPattern cbit.vcell.math.ParticleSpeciesPattern used on opensource projects

Example 1 with ParticleSpeciesPattern

use of cbit.vcell.math.ParticleSpeciesPattern in project vcell by virtualcell.

the class NFsimXMLWriter method getParticleSpeciesPatternList.

private static Element getParticleSpeciesPatternList(String prefix0, ParticleObservable particleObservable) {
    Element listOfPatternsElement = new Element("ListOfPatterns");
    for (int molecularPatternIndex = 0; molecularPatternIndex < particleObservable.getParticleSpeciesPatterns().size(); molecularPatternIndex++) {
        ParticleSpeciesPattern pattern = particleObservable.getParticleSpeciesPatterns().get(molecularPatternIndex);
        if (pattern instanceof VolumeParticleSpeciesPattern) {
            Element patternElement;
            try {
                String molecularPatternID = "P" + (molecularPatternIndex + 1);
                patternElement = getObservableParticipantPattern(prefix0, molecularPatternID, (VolumeParticleSpeciesPattern) pattern, "Pattern", particleObservable.getSequence(), particleObservable.getQuantity());
                listOfPatternsElement.addContent(patternElement);
            } catch (SolverException e) {
                e.printStackTrace();
            }
        }
    }
    return listOfPatternsElement;
}

Example 2 with ParticleSpeciesPattern

use of cbit.vcell.math.ParticleSpeciesPattern in project vcell by virtualcell.

the class NFsimXMLWriter method getListOfSpecies.

private static Element getListOfSpecies(MathDescription mathDesc, SimulationSymbolTable simulationSymbolTable) throws SolverException {
    CompartmentSubDomain compartmentSubDomain = (CompartmentSubDomain) mathDesc.getSubDomains().nextElement();
    // 
    // NFsim expects a list of seed species.  These are concrete species patterns that have a "ParticleProperties" element defined (for initial conditions).
    // 
    Element listOfSpeciesElement = new Element("ListOfSpecies");
    for (int speciesIndex = 0; speciesIndex < compartmentSubDomain.getParticleProperties().size(); speciesIndex++) {
        // seedSpecies.getSpeciesPattern().resolveBonds();
        ParticleProperties particleProperties = compartmentSubDomain.getParticleProperties().get(speciesIndex);
        Element speciesElement = new Element("Species");
        String speciesID = "S" + (speciesIndex + 1);
        ParticleSpeciesPattern seedSpecies = (ParticleSpeciesPattern) particleProperties.getVariable();
        speciesElement.setAttribute("id", speciesID);
        speciesElement.setAttribute("name", seedSpecies.getName());
        List<ParticleInitialCondition> particleInitialConditions = particleProperties.getParticleInitialConditions();
        if (particleInitialConditions.size() != 1) {
            throw new SolverException("multiple particle initial conditions not expected for " + ParticleSpeciesPattern.class.getSimpleName() + " " + seedSpecies.getName());
        }
        // the initial conditions must be a count in math (ParticleInitialConditionCount)
        if (!(particleInitialConditions.get(0) instanceof ParticleInitialConditionCount)) {
            throw new SolverException("expecting initial count for " + ParticleSpeciesPattern.class.getSimpleName() + " " + seedSpecies.getName());
        }
        ParticleInitialConditionCount initialCount = (ParticleInitialConditionCount) particleInitialConditions.get(0);
        try {
            double value = evaluateConstant(initialCount.getCount(), simulationSymbolTable);
            Integer maxMoleculesPerType = simulationSymbolTable.getSimulation().getSolverTaskDescription().getNFSimSimulationOptions().getMaxMoleculesPerType();
            if (maxMoleculesPerType == null) {
                maxMoleculesPerType = NFsimSimulationOptions.DefaultMaxMoleculesPerSpecies;
            }
            if (maxMoleculesPerType.doubleValue() < value) {
                String eMessage = "The Initial count for Species '" + seedSpecies.getName() + "' is " + BigDecimal.valueOf(value).toBigInteger();
                eMessage += ", which is higher than the limit of " + maxMoleculesPerType + ".\n";
                eMessage += "Please do one of the following: \n- reduce the Initial Condition value for this Species or reduce the compartment size\n";
                eMessage += "- increase the maximal number of Molecules per Molecular Type in the Advanced Solver Options panel.";
                throw new RuntimeException(eMessage);
            }
            speciesElement.setAttribute("concentration", Double.toString(value));
        } catch (ExpressionException | MathException e) {
            e.printStackTrace();
            throw new SolverException("error processing initial count of " + ParticleSpeciesPattern.class.getSimpleName() + " " + seedSpecies.getName() + ": " + e.getMessage());
        }
        HashMap<Bond, BondSites> bondSiteMapping = new HashMap<Bond, BondSites>();
        Element listOfMoleculesElement = getListOfMolecules(speciesID, seedSpecies, bondSiteMapping);
        speciesElement.addContent(listOfMoleculesElement);
        if (bondSiteMapping.size() > 0) {
            Element listOfBondsElement = getListOfBonds(bondSiteMapping);
            speciesElement.addContent(listOfBondsElement);
        }
        listOfSpeciesElement.addContent(speciesElement);
    }
    return listOfSpeciesElement;
}

Example 3 with ParticleSpeciesPattern

use of cbit.vcell.math.ParticleSpeciesPattern in project vcell by virtualcell.

the class XmlReader method getVolumeParticleObservable.

private VolumeParticleObservable getVolumeParticleObservable(Element param, VariableHash varHash) throws XmlParseException {
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag));
    Domain domain = null;
    if (domainStr != null) {
        domain = new Domain(domainStr);
    }
    String molecularTypeString = unMangle(param.getAttributeValue(XMLTags.ParticleMolecularTypePatternTag));
    ObservableType observableType = ObservableType.fromString(molecularTypeString);
    VolumeParticleObservable var = new VolumeParticleObservable(name, domain, observableType);
    String sequenceAttr = param.getAttributeValue(XMLTags.ParticleObservableSequenceTypeAttrTag);
    if (sequenceAttr != null) {
        Sequence sequence = Sequence.fromString(sequenceAttr);
        String sequenceLength = param.getAttributeValue(XMLTags.ParticleObservableSequenceLengthAttrTag);
        var.setSequence(sequence);
        if (sequence != Sequence.Multimolecular) {
            var.setQuantity(Integer.parseInt(sequenceLength));
        }
    } else {
        var.setSequence(Sequence.Multimolecular);
    }
    Element volumeParticleSpeciesPatternsElement = param.getChild(XMLTags.VolumeParticleSpeciesPatternsTag, vcNamespace);
    List<Element> volumeParticleSpeciesPatternList = volumeParticleSpeciesPatternsElement.getChildren(XMLTags.VolumeParticleSpeciesPatternTag, vcNamespace);
    for (Element volumeParticleSpeciesPattern : volumeParticleSpeciesPatternList) {
        String volumeParticleSpeciesPatternName = unMangle(volumeParticleSpeciesPattern.getAttributeValue(XMLTags.NameAttrTag));
        Variable v = varHash.getVariable(volumeParticleSpeciesPatternName);
        if (v == null) {
            throw new XmlParseException("failed to find VolumeParticleSpeciesPattern named " + volumeParticleSpeciesPatternName);
        }
        if (v instanceof ParticleSpeciesPattern) {
            var.addParticleSpeciesPattern((ParticleSpeciesPattern) v);
        } else {
            throw new XmlParseException("Variable " + volumeParticleSpeciesPatternName + " is not a ParticleSpeciesPattern");
        }
    }
    return var;
}

Example 4 with ParticleSpeciesPattern

use of cbit.vcell.math.ParticleSpeciesPattern in project vcell by virtualcell.

the class RbmUtils method toBnglStringShort.

public static String toBnglStringShort(ParticleJumpProcess particleJumpProcess, List<ParticleSpeciesPattern> reactantSpeciesPatterns, List<ParticleSpeciesPattern> productSpeciesPatterns) {
    StringBuilder buffer = new StringBuilder();
    for (int i = 0; i < reactantSpeciesPatterns.size(); i++) {
        ParticleSpeciesPattern reactantSpeciesPattern = reactantSpeciesPatterns.get(i);
        if (i > 0) {
            buffer.append(" + ");
        }
        buffer.append(toBnglString(reactantSpeciesPattern));
    }
    // particleJumpProcesses are not reversible
    boolean bReversible = false;
    buffer.append(bReversible ? " <-> " : " -> ");
    for (int i = 0; i < productSpeciesPatterns.size(); i++) {
        ParticleSpeciesPattern productSpeciesPattern = productSpeciesPatterns.get(i);
        if (i > 0) {
            buffer.append(" + ");
        }
        buffer.append(toBnglString(productSpeciesPattern));
    }
    return buffer.toString();
}

Example 5 with ParticleSpeciesPattern

use of cbit.vcell.math.ParticleSpeciesPattern in project vcell by virtualcell.

the class Xmlproducer method getVolumeParticleSpeciesPatternList.

private Element getVolumeParticleSpeciesPatternList(ParticleObservable param) {
    org.jdom.Element e = null;
    e = new org.jdom.Element(XMLTags.VolumeParticleSpeciesPatternsTag);
    for (ParticleSpeciesPattern pp : param.getParticleSpeciesPatterns()) {
        org.jdom.Element e1 = new org.jdom.Element(XMLTags.VolumeParticleSpeciesPatternTag);
        e1.setAttribute(XMLTags.NameAttrTag, mangle(pp.getName()));
        e.addContent(e1);
    }
    return e;
}