Examples with DBNonFormalUnboundSpecies cbit.vcell.dictionary.DBNonFormalUnboundSpecies used on opensource projects

Example 1 with DBNonFormalUnboundSpecies

use of cbit.vcell.dictionary.DBNonFormalUnboundSpecies in project vcell by virtualcell.

the class BiomodelVCMLModelInfoResource method createReactionDescription.

// Copied from DBReactionWizrdPanel and altered to display speciescontext names in ReactionStep text representation
public static ReactionDescription createReactionDescription(ReactionStep rxStep, KeyValue bmid, KeyValue structRef) {
    ReactionType rxType = null;
    if (rxStep instanceof FluxReaction) {
        if (rxStep.isReversible()) {
            rxType = ReactionType.REACTTYPE_FLUX_REVERSIBLE;
        } else {
            rxType = ReactionType.REACTTYPE_FLUX_IRREVERSIBLE;
        }
    } else {
        if (rxStep.isReversible()) {
            rxType = ReactionType.REACTTYPE_SIMPLE_REVERSIBLE;
        } else {
            rxType = ReactionType.REACTTYPE_SIMPLE_IRREVERSIBLE;
        }
    }
    ReactionDescription dbfr = new ReactionDescription(rxStep.getName(), rxType, rxStep.getKey(), bmid, structRef);
    // 
    ReactionParticipant[] rpArr = rxStep.getReactionParticipants();
    for (int i = 0; i < rpArr.length; i += 1) {
        DBNonFormalUnboundSpecies dbnfu = new DBNonFormalUnboundSpecies(rpArr[i].getSpeciesContext().getName());
        char role;
        if (rpArr[i] instanceof Reactant) {
            role = ReactionDescription.RX_ELEMENT_REACTANT;
        } else if (rpArr[i] instanceof Product) {
            role = ReactionDescription.RX_ELEMENT_PRODUCT;
        } else if (rpArr[i] instanceof Catalyst) {
            role = ReactionDescription.RX_ELEMENT_CATALYST;
        } else {
            throw new RuntimeException("Unsupported ReationParticiapnt=" + rpArr[i].getClass().getName());
        }
        dbfr.addReactionElement(dbnfu, rpArr[i].getSpeciesContext().getName(), rpArr[i].getSpeciesContext().getStructure().getName(), rpArr[i].getStoichiometry(), role);
    }
    if (dbfr.isFluxReaction()) {
        // make sure flux is in right direction
        Structure outsideStruct = rxStep.getModel().getStructureTopology().getOutsideFeature((Membrane) rxStep.getStructure());
        String defaultOutsideSCName = dbfr.getOrigSpeciesContextName(dbfr.getFluxIndexOutside());
        for (int i = 0; i < rpArr.length; i += 1) {
            if (rpArr[i].getSpeciesContext().getName().equals(defaultOutsideSCName)) {
                if (!rpArr[i].getStructure().equals(outsideStruct)) {
                    dbfr.swapFluxSCNames();
                }
                break;
            }
        }
    }
    return dbfr;
}

Example 2 with DBNonFormalUnboundSpecies

use of cbit.vcell.dictionary.DBNonFormalUnboundSpecies in project vcell by virtualcell.

the class ReactStepTable method getUserReactionList.

/**
 * Insert the method's description here.
 * Creation date: (7/12/2003 2:59:27 PM)
 * @return java.lang.String
 * @param likeString java.lang.String
 */
public ReactionDescription[] getUserReactionList(java.sql.ResultSet rset) throws java.sql.SQLException {
    java.util.Vector resultV = new java.util.Vector();
    ReactionDescription[] result = null;
    java.util.Vector rxidV = null;
    // 
    java.math.BigDecimal rxid = null;
    java.math.BigDecimal bmid = null;
    ReactionDescription dbfr = null;
    // 
    while (rset.next()) {
        java.math.BigDecimal currRXID = rset.getBigDecimal(ReactStepTable.table.id.toString());
        java.math.BigDecimal currBMID = rset.getBigDecimal(BMID_NAME);
        if (rset.isFirst()) {
            rxid = currRXID;
            bmid = currBMID;
        }
        if (!rxid.equals(currRXID) || !bmid.equals(currBMID)) {
            rxid = currRXID;
            bmid = currBMID;
            dbfr = null;
        }
        // 
        if (dbfr == null) {
            ReactionType rxType = ReactionType.fromDatabaseName(rset.getString(ReactStepTable.table.reactType.toString()));
            String rxName = rset.getString(ReactStepTable.table.name.toString());
            java.math.BigDecimal currStructID = rset.getBigDecimal(ReactStepTable.table.structRef.toString());
            dbfr = new ReactionDescription(rxName, rxType, new KeyValue(rxid), new KeyValue(bmid), new KeyValue(currStructID));
            resultV.add(dbfr);
        }
        String name = rset.getString(SPECCONT_NAME);
        DBNonFormalUnboundSpecies dbnfu = new DBNonFormalUnboundSpecies(name);
        // 
        String partRole = rset.getString(ReactPartTable.table.role.toString());
        char partRoleType;
        if (partRole.equals("reactant")) {
            partRoleType = ReactionDescription.RX_ELEMENT_REACTANT;
        } else if (partRole.equals("flux")) {
            partRoleType = ReactionDescription.RX_ELEMENT_FLUX;
        } else if (partRole.equals("catalyst")) {
            partRoleType = ReactionDescription.RX_ELEMENT_CATALYST;
        } else if (partRole.equals("product")) {
            partRoleType = ReactionDescription.RX_ELEMENT_PRODUCT;
        } else {
            throw new RuntimeException("Unknown role in UserList Query results");
        }
        // 
        int stoich = rset.getInt(ReactPartTable.table.stoich.toString());
        dbfr.addReactionElement(dbnfu, stoich, partRoleType);
        if (partRole.equals("flux")) {
            dbfr.addReactionElement(new DBNonFormalUnboundSpecies(name), stoich, partRoleType);
        }
    }
    // 
    if (resultV.size() > 0) {
        result = new ReactionDescription[resultV.size()];
        resultV.copyInto(result);
    }
    return result;
}

Example 3 with DBNonFormalUnboundSpecies

use of cbit.vcell.dictionary.DBNonFormalUnboundSpecies in project vcell by virtualcell.

the class DBReactionWizardPanel method createReactionDescription.

public static ReactionDescription createReactionDescription(ReactionStep rxStep, KeyValue bmid, KeyValue structRef) {
    ReactionType rxType = null;
    if (rxStep instanceof FluxReaction) {
        if (rxStep.isReversible()) {
            rxType = ReactionType.REACTTYPE_FLUX_REVERSIBLE;
        } else {
            rxType = ReactionType.REACTTYPE_FLUX_IRREVERSIBLE;
        }
    } else {
        if (rxStep.isReversible()) {
            rxType = ReactionType.REACTTYPE_SIMPLE_REVERSIBLE;
        } else {
            rxType = ReactionType.REACTTYPE_SIMPLE_IRREVERSIBLE;
        }
    }
    ReactionDescription dbfr = new ReactionDescription(rxStep.getName(), rxType, rxStep.getKey(), bmid, structRef);
    // 
    ReactionParticipant[] rpArr = rxStep.getReactionParticipants();
    for (int i = 0; i < rpArr.length; i += 1) {
        DBNonFormalUnboundSpecies dbnfu = new DBNonFormalUnboundSpecies(rpArr[i].getSpecies().getCommonName());
        char role;
        if (rpArr[i] instanceof Reactant) {
            role = ReactionDescription.RX_ELEMENT_REACTANT;
        } else if (rpArr[i] instanceof Product) {
            role = ReactionDescription.RX_ELEMENT_PRODUCT;
        } else if (rpArr[i] instanceof Catalyst) {
            role = ReactionDescription.RX_ELEMENT_CATALYST;
        } else {
            throw new RuntimeException("Unsupported ReationParticiapnt=" + rpArr[i].getClass().getName());
        }
        dbfr.addReactionElement(dbnfu, rpArr[i].getSpeciesContext().getName(), rpArr[i].getSpeciesContext().getStructure().getName(), rpArr[i].getStoichiometry(), role);
    }
    if (dbfr.isFluxReaction()) {
        // make sure flux is in right direction
        Structure outsideStruct = rxStep.getModel().getStructureTopology().getOutsideFeature((Membrane) rxStep.getStructure());
        String defaultOutsideSCName = dbfr.getOrigSpeciesContextName(dbfr.getFluxIndexOutside());
        for (int i = 0; i < rpArr.length; i += 1) {
            if (rpArr[i].getSpeciesContext().getName().equals(defaultOutsideSCName)) {
                if (!rpArr[i].getStructure().equals(outsideStruct)) {
                    dbfr.swapFluxSCNames();
                }
                break;
            }
        }
    }
    return dbfr;
}

Example 4 with DBNonFormalUnboundSpecies

use of cbit.vcell.dictionary.DBNonFormalUnboundSpecies in project vcell by virtualcell.

the class EnzymeReactionTable method getReactions.

/**
 * returns a Compound object from the ResultSet
 * @return cbit.vcell.dictionary.Compound
 * @param rset java.sql.ResultSet
 */
public ReactionDescription[] getReactions(java.sql.ResultSet rset) throws java.sql.SQLException {
    Vector reactions = new Vector();
    String currentReactionID = null;
    String currentEnzymeFID = null;
    ReactionDescription current_dbfr = null;
    while (rset.next()) {
        String reactionID = null;
        String enzymeFID = null;
        if (!rset.isAfterLast()) {
            reactionID = rset.getString(EnzymeReactionTable.table.reactionId.toString());
            enzymeFID = rset.getString(RXQ_ENZYMEFID_ALIAS);
        }
        if (!reactionID.equals(currentReactionID) || !org.vcell.util.Compare.isEqualOrNull(enzymeFID, currentEnzymeFID)) {
            java.math.BigDecimal enzymeID = rset.getBigDecimal(RXQ_ENZYMEID_ALIAS);
            if (enzymeID != null) {
                String enzymeName = rset.getString(RXQ_ENZYMENAME_ALIAS);
                current_dbfr = new ReactionDescription(reactionID);
                current_dbfr.addReactionElement(new FormalEnzyme(new KeyValue(enzymeID), new EnzymeInfo(enzymeFID, new String[] { enzymeName }, null, null, null)), 0, ReactionDescription.RX_ELEMENT_CATALYST);
            } else if (enzymeFID != null) {
                current_dbfr = new ReactionDescription(reactionID);
                current_dbfr.addReactionElement(new DBNonFormalUnboundSpecies(enzymeFID), /*FormalUnknown(enzymeFID,null)*/
                0, ReactionDescription.RX_ELEMENT_CATALYST);
            } else {
                current_dbfr = new ReactionDescription(reactionID);
            }
            reactions.add(current_dbfr);
        }
        currentReactionID = reactionID;
        currentEnzymeFID = enzymeFID;
        // 
        FormalCompound formalCompound = new FormalCompound(new KeyValue(rset.getBigDecimal(RXQ_CMPNDID_ALIAS)), new CompoundInfo(rset.getString(CompoundTable.table.keggID.toString()), new String[] { rset.getString(RXQ_CMPDNDNAME_ALIAS) }, null, null, null));
        current_dbfr.addReactionElement(formalCompound, rset.getInt(EnzymeReactionTable.table.stoich.toString()), rset.getString(EnzymeReactionTable.table.type.toString()).charAt(0));
    }
    ReactionDescription[] reactionsArr = null;
    if (reactions.size() > 0) {
        reactionsArr = new ReactionDescription[reactions.size()];
        reactions.copyInto(reactionsArr);
    }
    return reactionsArr;
}