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

Example 36 with Reactant

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

the class ReactionSpec method gatherIssues.

/**
 * Insert the method's description here.
 * Creation date: (11/1/2005 10:06:04 AM)
 * @param issueList java.util.Vector
 */
public void gatherIssues(IssueContext issueContext, List<Issue> issueList, ReactionContext rc) {
    ReactionCombo r = new ReactionCombo(this, rc);
    ReactionStep step = getReactionStep();
    if (!isExcluded() && rc.getSimulationContext().isStoch() && (rc.getSimulationContext().getGeometry().getDimension() > 0)) {
        boolean haveParticle = false;
        boolean haveContinuous = false;
        for (ReactionParticipant p : step.getReactionParticipants()) {
            if (p instanceof Product || p instanceof Reactant) {
                SpeciesContextSpec candidate = rc.getSpeciesContextSpec(p.getSpeciesContext());
                if (candidate.isForceContinuous() && !candidate.isConstant()) {
                    haveParticle = true;
                } else if (!candidate.isForceContinuous() && !candidate.isConstant()) {
                    haveContinuous = true;
                }
            }
        }
        if (haveParticle && haveContinuous) {
            String msg = "Reaction " + step.getName() + " has both continuous and particle Participants.";
            String tip = "Mass conservation for reactions of binding between discrete and continuous species is handled approximately. <br>" + "To avoid any algorithmic approximation, which may produce undesired results, the user is advised to indicate <br>" + "the continuous species in those reactions as modifiers (i.e. 'catalysts') in the physiology.";
            issueList.add(new Issue(r, issueContext, IssueCategory.Identifiers, msg, tip, Issue.SEVERITY_WARNING));
        }
    }
}

Example 37 with Reactant

use of cbit.vcell.model.Reactant 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;
}