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

Example 31 with FluxReaction

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

the class PathwayMapping method parseReaction.

private ReactionParticipant[] parseReaction(ReactionStep reactionStep, BioModel bioModel, RelationshipObject relationshipObject) throws ExpressionException, PropertyVetoException {
    if (reactionStep == null || bioModel == null || bioModel.getRelationshipModel() == null) {
        return null;
    }
    // create the reaction equation string
    String leftHand = getParticipantsString(((Conversion) relationshipObject.getBioPaxObject()).getLeft());
    String rightHand = getParticipantsString(((Conversion) relationshipObject.getBioPaxObject()).getRight());
    StringTokenizer st = new StringTokenizer(leftHand, "+");
    HashMap<String, SpeciesContext> speciesContextMap = new HashMap<String, SpeciesContext>();
    ArrayList<ReactionParticipant> rplist = new ArrayList<ReactionParticipant>();
    // create and add reaction participants to list for left-hand side of equation
    Model model = bioModel.getModel();
    Structure structure = reactionStep.getStructure();
    while (st.hasMoreElements()) {
        String nextToken = st.nextToken().trim();
        if (nextToken.length() == 0) {
            continue;
        }
        int stoichiIndex = 0;
        while (true) {
            if (Character.isDigit(nextToken.charAt(stoichiIndex))) {
                stoichiIndex++;
            } else {
                break;
            }
        }
        int stoichi = 1;
        String tmp = nextToken.substring(0, stoichiIndex);
        if (tmp.length() > 0) {
            stoichi = Integer.parseInt(tmp);
        }
        String var = nextToken.substring(stoichiIndex).trim();
        // get speciesContext object based on its name
        // if the speciesContext is not existed, create a new one
        SpeciesContext sc = model.getSpeciesContext(var);
        if (sc == null) {
            sc = speciesContextMap.get(var);
            if (sc == null) {
                // get species object based on its name
                // if the species is not existed, create a new one
                Species species = model.getSpecies(var);
                if (species == null) {
                    species = new Species(var, null);
                }
                sc = new SpeciesContext(species, structure);
                sc.setName(var);
                speciesContextMap.put(var, sc);
            }
        }
        // add the existed speciesContext objects or new speciesContext objects to reaction participant list
        if (reactionStep instanceof SimpleReaction || reactionStep instanceof FluxReaction) {
            rplist.add(new Reactant(null, (SimpleReaction) reactionStep, sc, stoichi));
        }
    }
    // create and add reaction participants to list for right-hand side of equation
    st = new StringTokenizer(rightHand, "+");
    while (st.hasMoreElements()) {
        String nextToken = st.nextToken().trim();
        if (nextToken.length() == 0) {
            continue;
        }
        int stoichiIndex = 0;
        while (true) {
            if (Character.isDigit(nextToken.charAt(stoichiIndex))) {
                stoichiIndex++;
            } else {
                break;
            }
        }
        int stoichi = 1;
        String tmp = nextToken.substring(0, stoichiIndex);
        if (tmp.length() > 0) {
            stoichi = Integer.parseInt(tmp);
        }
        String var = nextToken.substring(stoichiIndex);
        SpeciesContext sc = model.getSpeciesContext(var);
        if (sc == null) {
            sc = speciesContextMap.get(var);
            if (sc == null) {
                Species species = model.getSpecies(var);
                if (species == null) {
                    species = new Species(var, null);
                }
                sc = new SpeciesContext(species, structure);
                sc.setName(var);
                speciesContextMap.put(var, sc);
            }
        }
        if (reactionStep instanceof SimpleReaction || reactionStep instanceof FluxReaction) {
            rplist.add(new Product(null, (SimpleReaction) reactionStep, sc, stoichi));
        }
    }
    return rplist.toArray(new ReactionParticipant[0]);
}

Example 32 with FluxReaction

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

the class PathwayMapping method createReactionStep.

/*
	 * for reaction:
	 * 1. annotate the selected vcell object using linked pathway conversion
	 * 2. add non-existing speciesContexts from linked pathway conversion
	 * 3. add links between relative vcell objects and pathway objects
	 * Questions:
	 * - how to deal with the case that the reaction is existing in the model?
	 * 		+ add it in no matter what? 
	 * 				(this is the version we have now: 
	 * 					add the duplicated reactions in without name changing, 
	 * 				 	all duplicated reactions share the same participant objects)
	 *      + just modify the existing one?
	 */
private void createReactionStep(BioModel bioModel, Process process, ReactionStep reactionStep, RelationshipObject relationshipObject, ArrayList<ConversionTableRow> participants, boolean addSubunits) throws Exception {
    if (reactionStep == null || bioModel == null || bioModel.getRelationshipModel() == null || participants.size() < 1) {
        return;
    }
    ArrayList<ReactionParticipant> rplist = new ArrayList<ReactionParticipant>();
    // create and add reaction participants to list
    for (ConversionTableRow ctr : participants) {
        if (ctr.getBioPaxObject() instanceof Conversion)
            continue;
        int stoich = ctr.stoich().intValue();
        String safeId = getSafetyName(ctr.id());
        // get speciesContext object based on its name
        // if the speciesContext is not existed, create a new one
        createSpeciesContextFromTableRow(bioModel, (PhysicalEntity) ctr.getBioPaxObject(), ctr.stoich(), ctr.id(), ctr.location(), addSubunits);
        // add the existed speciesContext objects or new speciesContext objects to reaction participant list
        if (ctr.participantType().equals("Reactant")) {
            if (reactionStep instanceof SimpleReaction || reactionStep instanceof FluxReaction) {
                rplist.add(new Reactant(null, reactionStep, bioModel.getModel().getSpeciesContext(safeId), stoich));
            }
        } else if (ctr.participantType().equals("Product")) {
            if (reactionStep instanceof SimpleReaction || reactionStep instanceof FluxReaction) {
                rplist.add(new Product(null, reactionStep, bioModel.getModel().getSpeciesContext(safeId), stoich));
            }
        }
    // we do not add catalysts
    }
    ReactionParticipant[] rpArray = rplist.toArray(new ReactionParticipant[0]);
    reactionStep.setReactionParticipants(rpArray);
    // add Controls to the reaction
    Set<PhysicalEntity> controllers = process.getControllers();
    for (ConversionTableRow ctr : participants) {
        if (controllers.contains(ctr.getBioPaxObject())) {
            if (ctr.participantType().equals("Catalyst")) {
                String safeId = getSafetyName(ctr.id());
                /* 
					 * using addCatalyst() to create catalyst in reaction: 
					 * this function cannot allow an object to be catalyst and (reactant/product) in the same reaction
					 */
                // reactionStep.addCatalyst(bioModel.getModel().getSpeciesContext(safeId));
                /* However, in pathway interaction object, an physicalEntity can be catalyst and (reactant/product) in the same reaction
					 * So we just call create catalyst for the reaction no matter what rolls the object is playing in the reaction
					 * Switch back to the addCatalyst() function when it is necessary, but exceptions make be reported for some reactions
					 */
                reactionStep.addReactionParticipant(new Catalyst(null, reactionStep, bioModel.getModel().getSpeciesContext(safeId)));
            } else if (ctr.participantType().equals("Control")) {
                String safeId = getSafetyName(ctr.id());
                // reactionStep.addCatalyst(bioModel.getModel().getSpeciesContext(safeId));
                reactionStep.addReactionParticipant(new Catalyst(null, reactionStep, bioModel.getModel().getSpeciesContext(safeId)));
            }
        }
    }
}

Example 33 with FluxReaction

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

the class SBMLExporter method getAnnotationElement.

/**
 * 	getAnnotationElement :
 *	For a flux reaction, we need to add an annotation specifying the structure, flux carrier, carrier valence and fluxOption.
 *  For a simple reaction, we need to add a annotation specifying the structure (useful for import)
 *  Using XML JDOM elements, so that it is convenient for libSBML setAnnotation (requires the annotation to be provided as an xml string).
 */
private Element getAnnotationElement(ReactionStep reactionStep) throws cbit.vcell.xml.XmlParseException {
    Element sbmlImportRelatedElement = new Element(XMLTags.VCellRelatedInfoTag, sbml_vcml_ns);
    Element rxnElement = null;
    if (reactionStep instanceof FluxReaction) {
        FluxReaction fluxRxn = (FluxReaction) reactionStep;
        // Element for flux reaction. Write out the structure and flux carrier name.
        rxnElement = new Element(XMLTags.FluxStepTag, sbml_vcml_ns);
        rxnElement.setAttribute(XMLTags.StructureAttrTag, fluxRxn.getStructure().getName());
        // Get the physics option value.
        if (fluxRxn.getPhysicsOptions() == ReactionStep.PHYSICS_ELECTRICAL_ONLY) {
            rxnElement.setAttribute(XMLTags.FluxOptionAttrTag, XMLTags.FluxOptionElectricalOnly);
        } else if (fluxRxn.getPhysicsOptions() == ReactionStep.PHYSICS_MOLECULAR_AND_ELECTRICAL) {
            rxnElement.setAttribute(XMLTags.FluxOptionAttrTag, XMLTags.FluxOptionMolecularAndElectrical);
        } else if (fluxRxn.getPhysicsOptions() == ReactionStep.PHYSICS_MOLECULAR_ONLY) {
            rxnElement.setAttribute(XMLTags.FluxOptionAttrTag, XMLTags.FluxOptionMolecularOnly);
        }
    } else if (reactionStep instanceof cbit.vcell.model.SimpleReaction) {
        // Element for a simple reaction - just store structure name - will be useful while importing.
        cbit.vcell.model.SimpleReaction simpleRxn = (cbit.vcell.model.SimpleReaction) reactionStep;
        rxnElement = new org.jdom.Element(cbit.vcell.xml.XMLTags.SimpleReactionTag, sbml_vcml_ns);
        rxnElement.setAttribute(cbit.vcell.xml.XMLTags.StructureAttrTag, simpleRxn.getStructure().getName());
    }
    // Add rate name as an element of annotation - this is especially useful when roundtripping VCell models, when the reaction
    // rate parameters have been renamed by user.
    Element rateElement = new Element(XMLTags.ReactionRateTag, sbml_vcml_ns);
    if (reactionStep.getKinetics() instanceof DistributedKinetics) {
        rateElement.setAttribute(XMLTags.NameAttrTag, ((DistributedKinetics) reactionStep.getKinetics()).getReactionRateParameter().getName());
    } else if (reactionStep.getKinetics() instanceof LumpedKinetics) {
        rateElement.setAttribute(XMLTags.NameAttrTag, ((LumpedKinetics) reactionStep.getKinetics()).getLumpedReactionRateParameter().getName());
    } else {
        throw new RuntimeException("unexpected kinetic type " + reactionStep.getKinetics().getClass().getName());
    }
    sbmlImportRelatedElement.addContent(rxnElement);
    sbmlImportRelatedElement.addContent(rateElement);
    return sbmlImportRelatedElement;
}

Example 34 with FluxReaction

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

the class VCReactionProxy method factory.

/**
 * get proxy for Reaction type
 * @param reaction not null
 * @return proxy
 * @throws ProgrammingException unknown type
 */
public static VCReactionProxy factory(ReactionStep reaction) {
    VCAssert.assertValid(reaction);
    SimpleReaction sr = BeanUtils.downcast(SimpleReaction.class, reaction);
    if (sr != null) {
        return new Simple(sr);
    }
    FluxReaction fr = BeanUtils.downcast(FluxReaction.class, reaction);
    if (fr != null) {
        return new Flux(fr);
    }
    throw new ProgrammingException("Unknown reaction type " + ExecutionTrace.justClassName(reaction));
}

Example 35 with FluxReaction

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

the class ReactStepTable method getReactionStep.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.model.ReactionParticipant
 * @param rset java.sql.ResultSet
 */
public ReactionStep getReactionStep(Structure structure, Model model, KeyValue rsKey, java.sql.ResultSet rset, DatabaseSyntax dbSyntax) throws java.sql.SQLException, DataAccessException {
    KeyValue key = rsKey;
    if (rset.wasNull()) {
        key = null;
    }
    String reactType = rset.getString(ReactStepTable.table.reactType.toString());
    String reactionStepName = null;
    String nameString = rset.getString(ReactStepTable.table.name.toString());
    if (rset.wasNull()) {
        nameString = null;
    }
    if (nameString != null) {
        reactionStepName = TokenMangler.getSQLRestoredString(nameString);
    }
    ReactionStep rs = null;
    try {
        if (reactType.equals(ReactStepTable.REACTTYPE_FLUX_REVERSIBLE)) {
            rs = new FluxReaction(model, (Membrane) structure, key, reactionStepName, true);
        } else if (reactType.equals(ReactStepTable.REACTTYPE_FLUX_IRREVERSIBLE)) {
            rs = new FluxReaction(model, (Membrane) structure, key, reactionStepName, false);
        } else if (reactType.equals(ReactStepTable.REACTTYPE_SIMPLE_REVERSIBLE)) {
            rs = new SimpleReaction(model, structure, key, reactionStepName, true);
        } else if (reactType.equals(ReactStepTable.REACTTYPE_SIMPLE_IRREVERSIBLE)) {
            rs = new SimpleReaction(model, structure, key, reactionStepName, false);
        }
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException(e.getMessage());
    }
    // 
    // if valence is stored as a 'null', it was an error (previous models were updated administratively).
    // 
    int valenceValue = rset.getInt(ReactStepTable.table.chargeValence.toString());
    if (rset.wasNull()) {
        throw new DataAccessException("unexpected null for chargeValence");
    }
    // 
    // New procedure for getting kinetics
    // 
    String kinetics_vcml = DbDriver.varchar2_CLOB_get(rset, ReactStepTable.table.kineticsSmall, ReactStepTable.table.kineticsLarge, dbSyntax);
    if (kinetics_vcml == null || kinetics_vcml.length() == 0) {
        throw new DataAccessException("no data stored for kinetics");
    }
    // This isn't needed?
    // if (kinetics_vcml.endsWith(";}\n")){
    // StringBuffer buffer = new StringBuffer(kinetics_vcml.substring(0,kinetics_vcml.length()-2));
    // buffer.append("\n}\n");
    // kinetics_vcml = buffer.toString();
    // }
    org.vcell.util.CommentStringTokenizer tokens = new org.vcell.util.CommentStringTokenizer(kinetics_vcml);
    Kinetics kinetics = null;
    try {
        String token = tokens.nextToken();
        if (!token.equalsIgnoreCase(VCMODL.Kinetics)) {
            throw new DataAccessException("expected " + VCMODL.Kinetics);
        }
        token = tokens.nextToken();
        KineticsDescription kineticsDescription = KineticsDescription.fromVCMLKineticsName(token);
        if (kineticsDescription != null) {
            kinetics = kineticsDescription.createKinetics(rs);
        } else {
            throw new DataAccessException("expected valid kinetics type, read '" + token + "'");
        }
        kinetics.fromTokens(kinetics_vcml);
        // 
        // for debug purposes only, remove when unresolvedParameters are ok ... when globals exist
        // 
        // if (kinetics.getUnresolvedParameters().length!=0){
        // System.out.println("<<<WARNING>>> ReactStepTable.getReactionStep(key="+rsKey+") has "+kinetics.getUnresolvedParameters().length+" UnresolvedParameters");
        // for (int i = 0; i < kinetics.getUnresolvedParameters().length; i++){
        // System.out.println(">>>>>>>>>>>>> UnresolvedParameter["+i+"] = "+kinetics.getUnresolvedParameters()[i].toString());
        // }
        // }
        KineticsParameter chargeValenceParameter = kinetics.getChargeValenceParameter();
        if (chargeValenceParameter != null) {
            chargeValenceParameter.setExpression(new cbit.vcell.parser.Expression(valenceValue));
        }
    } catch (Exception e) {
        lg.error(e.getMessage(), e);
        throw new DataAccessException(e.getMessage());
    }
    rs.setKinetics(kinetics);
    // 
    // if physicsOptions is stored as a 'null', it was an error (previous models were updated administratively).
    // 
    int physicsOptionsValue = rset.getInt(ReactStepTable.table.physicsOptions.toString());
    if (rset.wasNull()) {
        throw new DataAccessException("unexpected null for physicsOptions");
    }
    try {
        rs.setPhysicsOptions(physicsOptionsValue);
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace(System.out);
    }
    String annot = rset.getString(ReactStepTable.table.annotation.getUnqualifiedColName());
    if (!rset.wasNull()) {
    // annot = TokenMangler.getSQLRestoredString(annot);
    // rs.setAnnotation(annot);
    }
    return rs;
}