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

Example 51 with ReactionParticipant

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

the class SBMLImporter method addReactionParticipants.

/**
 * addReactionParticipant : Adds reactants and products and modifiers to a
 * reaction. Input args are the sbml reaction, vc reaction This method was
 * created mainly to handle reactions where there are reactants and/or
 * products that appear multiple times in a reaction. Virtual Cell now
 * allows the import of such reactions.
 */
private void addReactionParticipants(org.sbml.jsbml.Reaction sbmlRxn, ReactionStep vcRxn) throws Exception {
    Model vcModel = vcBioModel.getSimulationContext(0).getModel();
    // if (!(vcRxn instanceof FluxReaction)) {
    if (true) {
        // reactants in sbmlRxn
        HashMap<String, Integer> sbmlReactantsHash = new HashMap<String, Integer>();
        for (int j = 0; j < (int) sbmlRxn.getNumReactants(); j++) {
            SpeciesReference spRef = sbmlRxn.getReactant(j);
            String sbmlReactantSpId = spRef.getSpecies();
            if (sbmlModel.getSpecies(sbmlReactantSpId) != null) {
                // check
                // if
                // spRef
                // is in
                // sbml
                // model
                // If stoichiometry of speciesRef is not an integer, it is
                // not handled in the VCell at this time; no point going
                // further
                double stoichiometry = 0.0;
                if (level < 3) {
                    // for SBML models < L3, default
                    // stoichiometry is 1, if field is not
                    // set.
                    // default value of stoichiometry,
                    stoichiometry = 1.0;
                    // if not set.
                    if (spRef.isSetStoichiometry()) {
                        stoichiometry = spRef.getStoichiometry();
                        if (((int) stoichiometry != stoichiometry) || spRef.isSetStoichiometryMath()) {
                            throw new SBMLImportException("Non-integer stoichiometry ('" + stoichiometry + "' for reactant '" + sbmlReactantSpId + "' in reaction '" + sbmlRxn.getId() + "') or stoichiometryMath not handled in VCell at this time.", Category.NON_INTEGER_STOICH);
                        // logger.sendMessage(VCLogger.Priority.HighPriority,
                        // VCLogger.ErrorType.ReactionError,
                        // "Non-integer stoichiometry or stoichiometryMath not handled in VCell at this time.");
                        }
                    }
                } else {
                    if (spRef.isSetStoichiometry()) {
                        stoichiometry = spRef.getStoichiometry();
                        if (((int) stoichiometry != stoichiometry) || spRef.isSetStoichiometryMath()) {
                            throw new SBMLImportException("Non-integer stoichiometry ('" + stoichiometry + "' for reactant '" + sbmlReactantSpId + "' in reaction '" + sbmlRxn.getId() + "') or stoichiometryMath not handled in VCell at this time.", Category.NON_INTEGER_STOICH);
                        // logger.sendMessage(VCLogger.Priority.HighPriority,
                        // VCLogger.ErrorType.ReactionError,
                        // "Non-integer stoichiometry or stoichiometryMath not handled in VCell at this time.");
                        // logger.sendMessage(VCLogger.Priority.HighPriority,
                        // VCLogger.ErrorType.ReactionError,
                        // "Non-integer stoichiometry or stoichiometryMath not handled in VCell at this time.");
                        }
                    } else {
                        throw new SBMLImportException("This is a SBML level 3 model, stoichiometry is not set for the reactant '" + sbmlReactantSpId + "' and no default value can be assumed.");
                    // logger.sendMessage(VCLogger.Priority.HighPriority,
                    // VCLogger.ErrorType.ReactionError,
                    // "This is a SBML level 3 model, stoichiometry is not set for the reactant '"
                    // + spRef.getSpecies() +
                    // "' and no default value can be assumed.");
                    }
                }
                if (sbmlReactantsHash.get(sbmlReactantSpId) == null) {
                    // if sbmlReactantSpId is NOT in sbmlReactantsHash, add
                    // it with its stoichiometry
                    sbmlReactantsHash.put(sbmlReactantSpId, Integer.valueOf((int) stoichiometry));
                } else {
                    // if sbmlReactantSpId IS in sbmlReactantsHash, update
                    // its stoichiometry value to (existing-from-hash +
                    // stoichiometry) and put it back in hash
                    int intStoich = sbmlReactantsHash.get(sbmlReactantSpId).intValue();
                    intStoich += (int) stoichiometry;
                    sbmlReactantsHash.put(sbmlReactantSpId, Integer.valueOf(intStoich));
                }
            } else {
                // spRef is not in model, throw exception
                throw new SBMLImportException("Reactant '" + sbmlReactantSpId + "' in reaction '" + sbmlRxn.getId() + "' not found as species in SBML model.");
            }
        // end - if (spRef is species in model)
        }
        // sbmlReactionParticipantsHash as reactants to vcRxn
        for (Entry<String, Integer> es : sbmlReactantsHash.entrySet()) {
            SpeciesContext speciesContext = vcModel.getSpeciesContext(es.getKey());
            int stoich = es.getValue();
            vcRxn.addReactant(speciesContext, stoich);
        }
        /*
			Iterator<String> sbmlReactantsIter = sbmlReactantsHash.keySet()
					.iterator();
			while (sbmlReactantsIter.hasNext()) {
				String sbmlReactantStr = sbmlReactantsIter.next();
				SpeciesContext speciesContext = vcModel
						.getSpeciesContext(sbmlReactantStr);
				int stoich = sbmlReactantsHash.get(sbmlReactantStr).intValue();
				((SimpleReaction) vcRxn).addReactant(speciesContext, stoich);
			}
			*/
        // products in sbmlRxn
        HashMap<String, Integer> sbmlProductsHash = new HashMap<String, Integer>();
        for (int j = 0; j < (int) sbmlRxn.getNumProducts(); j++) {
            SpeciesReference spRef = sbmlRxn.getProduct(j);
            String sbmlProductSpId = spRef.getSpecies();
            if (sbmlModel.getSpecies(sbmlProductSpId) != null) {
                /* check if spRef is in sbml model
					If stoichiometry of speciesRef is not an integer, it is
					not handled in the VCell at this time; no point going
					further */
                double stoichiometry = 0.0;
                if (level < 3) {
                    // for sBML models < L3, default
                    // stoichiometry is 1, if field is not
                    // set.
                    // default value of stoichiometry,
                    stoichiometry = 1.0;
                    // if not set.
                    if (spRef.isSetStoichiometry()) {
                        stoichiometry = spRef.getStoichiometry();
                        if (((int) stoichiometry != stoichiometry) || spRef.isSetStoichiometryMath()) {
                            throw new SBMLImportException("Non-integer stoichiometry ('" + stoichiometry + "' for product '" + sbmlProductSpId + "' in reaction '" + sbmlRxn.getId() + "') or stoichiometryMath not handled in VCell at this time.", Category.NON_INTEGER_STOICH);
                        // logger.sendMessage(VCLogger.Priority.HighPriority,
                        // VCLogger.ErrorType.ReactionError,
                        // "Non-integer stoichiometry or stoichiometryMath not handled in VCell at this time.");
                        }
                    }
                } else {
                    if (spRef.isSetStoichiometry()) {
                        stoichiometry = spRef.getStoichiometry();
                        if (((int) stoichiometry != stoichiometry) || spRef.isSetStoichiometryMath()) {
                            throw new SBMLImportException("Non-integer stoichiometry ('" + stoichiometry + "' for product '" + sbmlProductSpId + "' in reaction '" + sbmlRxn.getId() + "') or stoichiometryMath not handled in VCell at this time.", Category.NON_INTEGER_STOICH);
                        // logger.sendMessage(VCLogger.Priority.HighPriority,
                        // VCLogger.ErrorType.ReactionError,
                        // "Non-integer stoichiometry or stoichiometryMath not handled in VCell at this time.");
                        }
                    } else {
                        throw new SBMLImportException("This is a SBML level 3 model, stoichiometry is not set for the product '" + sbmlProductSpId + "' and no default value can be assumed.");
                    // logger.sendMessage(VCLogger.Priority.HighPriority,
                    // VCLogger.ErrorType.ReactionError,
                    // "This is a SBML level 3 model, stoichiometry is not set for the product '"
                    // + spRef.getSpecies() +
                    // "' and no default value can be assumed.");
                    }
                }
                if (sbmlProductsHash.get(sbmlProductSpId) == null) {
                    // if sbmlProductSpId is NOT in sbmlProductsHash, add it
                    // with its stoichiometry
                    sbmlProductsHash.put(sbmlProductSpId, Integer.valueOf((int) stoichiometry));
                } else {
                    // if sbmlProductSpId IS in sbmlProductsHash, update its
                    // stoichiometry value to (existing-value-from-hash +
                    // stoichiometry) and put it back in hash
                    int intStoich = sbmlProductsHash.get(sbmlProductSpId).intValue();
                    intStoich += (int) stoichiometry;
                    sbmlProductsHash.put(sbmlProductSpId, Integer.valueOf(intStoich));
                }
            } else {
                // spRef is not in model, throw exception
                throw new SBMLImportException("Product '" + sbmlProductSpId + "' in reaction '" + sbmlRxn.getId() + "' not found as species in SBML model.");
            }
        // end - if (spRef is species in model)
        }
        // as products to vcRxn
        for (Entry<String, Integer> es : sbmlProductsHash.entrySet()) {
            SpeciesContext speciesContext = vcModel.getSpeciesContext(es.getKey());
            int stoich = es.getValue();
            vcRxn.addProduct(speciesContext, stoich);
        }
    /*
			Iterator<String> sbmlProductsIter = sbmlProductsHash.keySet()
					.iterator();
			while (sbmlProductsIter.hasNext()) {
				String sbmlProductStr = sbmlProductsIter.next();
				SpeciesContext speciesContext = vcModel
						.getSpeciesContext(sbmlProductStr);
				int stoich = sbmlProductsHash.get(sbmlProductStr).intValue();
				((SimpleReaction) vcRxn).addProduct(speciesContext, stoich);
			}
			*/
    // proxy.addProducts(sbmlProductsHash);
    }
    // modifiers
    for (int j = 0; j < (int) sbmlRxn.getNumModifiers(); j++) {
        ModifierSpeciesReference spRef = sbmlRxn.getModifier(j);
        String sbmlSpId = spRef.getSpecies();
        if (sbmlModel.getSpecies(sbmlSpId) != null) {
            // check if this modifier species is preesent in vcRxn (could
            // have been added as reactamt/product/catalyst).
            // If alreay a catalyst in vcRxn, do nothing
            ArrayList<ReactionParticipant> vcRxnParticipants = getVCReactionParticipantsFromSymbol(vcRxn, sbmlSpId);
            SpeciesContext speciesContext = vcModel.getSpeciesContext(sbmlSpId);
            if (vcRxnParticipants == null || vcRxnParticipants.size() == 0) {
                // If not in reactionParticipantList of vcRxn, add as
                // catalyst.
                vcRxn.addCatalyst(speciesContext);
            } else {
                for (ReactionParticipant rp : vcRxnParticipants) {
                    if (rp instanceof Reactant || rp instanceof Product) {
                        // If already a reactant or product in vcRxn, add
                        // warning to localIssuesList, don't do anything
                        localIssueList.add(new Issue(speciesContext, issueContext, IssueCategory.SBMLImport_Reaction, "Species " + speciesContext.getName() + " was already added as a reactant and/or product to " + vcRxn.getName() + "; Cannot add it as a catalyst also.", Issue.SEVERITY_INFO));
                        break;
                    }
                }
            }
        } else {
            // spRef is not in model, throw exception
            throw new SBMLImportException("Modifier '" + sbmlSpId + "' in reaction '" + sbmlRxn.getId() + "' not found as species in SBML model.");
        }
    // end - if (spRef is species in model)
    }
// end - for modifiers
}

Example 52 with ReactionParticipant

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

the class SBPAXKineticsExtractor method setVMForwardParamAsExpression.

private static void setVMForwardParamAsExpression(ReactionStep reaction, SBOParam kCat, Kinetics kinetics) throws ExpressionException, PropertyVetoException {
    if (kCat != null) {
        KineticsParameter Vmax = ((HMM_IRRKinetics) kinetics).getVmaxParameter();
        String unitF = SBOParam.formatUnit(kCat.getUnit());
        VCUnitDefinition kCatUnit = reaction.getModel().getUnitSystem().getInstance(unitF);
        Double numberKCat = 0.0;
        if (kCat.hasNumber()) {
            numberKCat = kCat.getNumber();
        }
        Expression KCatExpression = new Expression(numberKCat);
        KineticsParameter Kcat = kinetics.addUserDefinedKineticsParameter("Kcat", KCatExpression, kCatUnit);
        String enzymeName = "";
        ReactionParticipant[] participants = reaction.getReactionParticipants();
        for (int i = 0; i < participants.length; i++) {
            ReactionParticipant rp = participants[i];
            if (rp instanceof Catalyst) {
                enzymeName = rp.getName();
            }
        }
        SpeciesContext enzyme = reaction.getModel().getSpeciesContext(enzymeName);
        Vmax.setExpression(Expression.mult(new Expression(Kcat, reaction.getNameScope()), new Expression(enzyme, reaction.getNameScope())));
    }
}

Example 53 with ReactionParticipant

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

the class ReactPartTable method getReactionParticipant.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.model.ReactionParticipant
 * @param rset java.sql.ResultSet
 */
public ReactionParticipant getReactionParticipant(KeyValue rpKey, java.sql.ResultSet rset) throws java.sql.SQLException, DataAccessException {
    ReactionParticipant rp = null;
    KeyValue key = rpKey;
    String role = rset.getString(ReactPartTable.table.role.toString());
    int stoichiometry = rset.getInt(ReactPartTable.table.stoich.toString());
    if (role.equals(ROLE_CATALYST)) {
        rp = new Catalyst(key, null, null);
    } else if (role.equals(ROLE_PRODUCT)) {
        rp = new Product(key, null, null, stoichiometry);
    } else if (role.equals(ROLE_REACTANT)) {
        rp = new Reactant(key, null, null, stoichiometry);
    } else if (role.equals(ROLE_FLUX)) {
        rp = new FluxReaction.Flux(key, null, null);
    } else {
        throw new DataAccessException("unexpected value of " + ReactPartTable.table.role.toString() + "'" + role + "'");
    }
    rp.setStoichiometry(stoichiometry);
    return rp;
}

Example 54 with ReactionParticipant

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

the class ReactStepDbDriver method getReactionStep.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.model.ReactionStep
 * @param rset java.sql.ResultSet
 * @exception java.sql.SQLException The exception description.
 */
private ReactionStep getReactionStep(QueryHashtable dbc, Connection con, ResultSet rset, Model model) throws SQLException, DataAccessException, PropertyVetoException {
    // 
    // try to get ReactionStep from the object cache
    // 
    KeyValue rsKey = new KeyValue(rset.getBigDecimal(ReactStepTable.table.id.toString()));
    ReactionStep rs = (ReactionStep) dbc.get(rsKey);
    if (rs != null) {
        return rs;
    }
    // 
    // construct reactionStep (from ReactStepTable results)
    // 
    KeyValue structKey = new KeyValue(rset.getBigDecimal(ReactStepTable.table.structRef.toString()));
    Structure structure = getStructure(dbc, con, structKey);
    rs = reactStepTable.getReactionStep(structure, model, rsKey, rset, dbSyntax);
    // 
    // add reaction participants for this reactionStep
    // 
    ReactionParticipant[] rp_Array = getReactionParticipants(dbc, con, rsKey, rs);
    rs.setReactionParticipantsFromDatabase(model, rp_Array);
    try {
        rs.getKinetics().bind(rs);
    } catch (cbit.vcell.parser.ExpressionException e) {
        e.printStackTrace(System.out);
        throw new DataAccessException("ExpressionException: " + e.getMessage());
    }
    dbc.put(rsKey, rs);
    // MIRIAMTable.table.setMIRIAMAnnotation(con, rs, rs.getKey());
    return rs;
}

Example 55 with ReactionParticipant

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

the class ReactStepDbDriver method insertReactionStep.

/**
 * addModel method comment.
 */
KeyValue insertReactionStep(InsertHashtable hash, Connection con, User user, ReactionStep reactionStep, KeyValue modelKey) throws SQLException, DataAccessException {
    // log.print("ReactStepDbDriver.insertReactionStep(user="+user+", reacitonStep="+reactionStep+")");
    // 
    // make sure all species and structures are in the database
    // 
    ReactionParticipant[] rp_Array = reactionStep.getReactionParticipants();
    for (int i = 0; i < rp_Array.length; i++) {
        // 
        // insert/update species for this reactionParticipant
        // 
        Species species = rp_Array[i].getSpecies();
        KeyValue speciesKey = hash.getDatabaseKey(species);
        if (speciesKey == null) {
            speciesKey = insertSpecies(hash, con, species, user);
        // throw new DataAccessException("Database error: species "+species.getName()+" has null key");
        }
        // }
        if (hash.getDatabaseKey(species) == null) {
            hash.put(species, speciesKey);
        }
        // 
        // may insert structure for this reactionParicipant
        // 
        Structure structure = rp_Array[i].getStructure();
        if (structure != null && hash.getDatabaseKey(structure) == null) {
            throw new DataAccessException("ReactionParticipant '" + rp_Array[i].getName() + "' for reaction '" + reactionStep.getName() + "' refers to structure '" + structure.getName() + "' which is not found in database");
        }
    }
    // 
    // make sure structure holding reactionStep is also in database
    // 
    Structure structure = reactionStep.getStructure();
    if (hash.getDatabaseKey(structure) == null) {
        throw new DataAccessException("Structure '" + structure.getName() + "' for reaction '" + reactionStep.getName() + "' not found in database");
    }
    // 
    // insert reactionStep
    // 
    KeyValue rsKey = keyFactory.getNewKey(con);
    insertReactionStepSQL(con, modelKey, hash.getDatabaseKey(structure), reactionStep, rsKey);
    // 
    // insert reactionParticipants
    // 
    ReactionParticipant[] react_participants = reactionStep.getReactionParticipants();
    for (int i = 0; i < react_participants.length; i++) {
        KeyValue rpKey = keyFactory.getNewKey(con);
        insertReactionParticipantSQL(hash, con, rpKey, react_participants[i], rsKey);
    }
    return rsKey;
}