Examples with ElectricalTopology cbit.vcell.model.Model.ElectricalTopology used on opensource projects

Example 6 with ElectricalTopology

use of cbit.vcell.model.Model.ElectricalTopology in project vcell by virtualcell.

the class GHKKinetics method updateGeneratedExpressions.

/**
 * Insert the method's description here.
 * Creation date: (10/19/2003 12:05:14 AM)
 * @exception cbit.vcell.parser.ExpressionException The exception description.
 */
protected void updateGeneratedExpressions() throws ExpressionException, PropertyVetoException {
    KineticsParameter currentParm = getKineticsParameterFromRole(ROLE_CurrentDensity);
    KineticsParameter rateParm = getKineticsParameterFromRole(ROLE_ReactionRate);
    if (currentParm == null && rateParm == null) {
        return;
    }
    Membrane membrane = (Membrane) getReactionStep().getStructure();
    if (!(getReactionStep().getStructure() instanceof Membrane)) {
        return;
    }
    ElectricalTopology electricalTopology = getReactionStep().getModel().getElectricalTopology();
    Membrane.MembraneVoltage V = membrane.getMembraneVoltage();
    Feature negativeFeature = electricalTopology.getNegativeFeature(membrane);
    Feature positiveFeature = electricalTopology.getPositiveFeature(membrane);
    if (negativeFeature == null || positiveFeature == null) {
        return;
    }
    KineticsParameter P = getKineticsParameterFromRole(ROLE_Permeability);
    Model model = getReactionStep().getModel();
    Expression F = getSymbolExpression(model.getFARADAY_CONSTANT());
    Expression K_GHK = getSymbolExpression(model.getK_GHK());
    Expression R = getSymbolExpression(model.getGAS_CONSTANT());
    Expression T = getSymbolExpression(model.getTEMPERATURE());
    ReactionParticipant[] reactionParticipants = getReactionStep().getReactionParticipants();
    ReactionParticipant Neg0 = null;
    ReactionParticipant Pos0 = null;
    for (int i = 0; i < reactionParticipants.length; i++) {
        ReactionParticipant rp = reactionParticipants[i];
        if ((rp instanceof Reactant || rp instanceof Product)) {
            if (rp.getStructure() == negativeFeature) {
                Neg0 = rp;
            } else if (rp.getStructure() == positiveFeature) {
                Pos0 = rp;
            }
        }
    }
    // "-A0*pow("+VALENCE_SYMBOL+",2)*"+VOLTAGE_SYMBOL+"*pow("+F+",2)/("+R+"*"+T+")*(R0-(P0*exp(-"+VALENCE_SYMBOL+"*"+F+"*"+VOLTAGE_SYMBOL+"/("+R+"*"+T+"))))/(1 - exp(-"+VALENCE_SYMBOL+"*"+F+"*"+VOLTAGE_SYMBOL+"/("+R+"*"+T+")))"
    if (Neg0 != null && Pos0 != null && P != null) {
        // PRIMARY CURRENT DENSITY
        // 
        Expression V_exp = getSymbolExpression(V);
        Expression carrier_z = getSymbolExpression(getKineticsParameterFromRole(Kinetics.ROLE_CarrierChargeValence));
        Expression net_z = carrier_z;
        Expression Neg0_exp = getSymbolExpression(Neg0.getSpeciesContext());
        Expression Pos0_exp = getSymbolExpression(Pos0.getSpeciesContext());
        Expression P_exp = getSymbolExpression(P);
        Expression exponentTerm = Expression.div(Expression.mult(Expression.negate(carrier_z), F, V_exp), Expression.mult(R, T));
        Expression expTerm = Expression.exp(exponentTerm);
        Expression term1 = Expression.add(Pos0_exp, Expression.negate(Expression.mult(Neg0_exp, expTerm)));
        Expression numerator = Expression.negate(Expression.mult(P_exp, K_GHK, Expression.power(carrier_z, 2.0), V_exp, Expression.power(F, 2.0), term1));
        Expression denominator = Expression.mult(R, T, Expression.add(new Expression(1.0), Expression.negate(expTerm)));
        Expression newCurrExp = Expression.div(numerator, denominator);
        // Expression newCurrExp = new Expression("-"+P.getName()+"*"+K_GHK.getName()+"*pow("+z+",2)*"+V.getName()+"*pow("+F.getName()+",2)/("+R.getName()+"*"+T.getName()+")*("+R0.getName()+"-("+P0.getName()+"*exp(-"+z+"*"+F.getName()+"*"+V.getName()+"/("+R.getName()+"*"+T.getName()+"))))/(1 - exp(-"+z+"*"+F.getName()+"*"+V.getName()+"/("+R.getName()+"*"+T.getName()+")))");
        currentParm.setExpression(newCurrExp);
        // SECONDARY REACTION RATE
        // update from current density
        updateReactionRatesFromInwardCurrentDensity();
    }
}

Example 7 with ElectricalTopology

use of cbit.vcell.model.Model.ElectricalTopology in project vcell by virtualcell.

the class ModelDbDriver method insertModel.

/**
 * This method was created in VisualAge.
 * @param model cbit.vcell.model.Model
 */
private void insertModel(InsertHashtable hash, Connection con, User user, Model model, Version newVersion) throws SQLException, DataAccessException, RecordChangedException {
    // 
    // insert model record
    // 
    insertModelSQL(con, user, model, newVersion);
    hash.put(model, newVersion.getVersionKey());
    // 
    // make sure all species are in the database and the hashtable
    // 
    StructureTopology structureTopology = model.getStructureTopology();
    ElectricalTopology electricalTopology = model.getElectricalTopology();
    Species[] speciesArray = model.getSpecies();
    for (int i = 0; i < speciesArray.length; i++) {
        // speciesArray[i].getKey();
        KeyValue speciesKey = null;
        // if (speciesKey == null) {
        speciesKey = reactStepDB.insertSpecies(hash, con, speciesArray[i], user);
        // throw new DataAccessException("Database error: species "+species.getName()+" has null key");
        // }else if (speciesArray[i].getOwnerKey()!=null && speciesArray[i].getOwnerKey()==user.getID()){
        // reactStepDB.updateSpecies(con,speciesArray[i],user);
        // }
        // if (hash.getDatabaseKey(speciesArray[i])==null){
        hash.put(speciesArray[i], speciesKey);
    // }
    }
    // 
    // make sure all structures are in the database and the hashtable (add entry to link table)
    // this does not populate the parent, negativeFeature, and positiveFeature columns ... done later with updateStructureKeys()
    // 
    Structure[] structures = model.getStructures();
    for (int i = 0; i < structures.length; i++) {
        Structure structure = (Structure) structures[i];
        KeyValue structureKey = null;
        if (hash.getDatabaseKey(structure) == null) {
            structureKey = reactStepDB.insertStructure(hash, con, structure);
        }
        KeyValue linkKey = keyFactory.getNewKey(con);
        insertModelStructLinkSQL(con, linkKey, newVersion.getVersionKey(), /*modelKey*/
        hash.getDatabaseKey(structure));
    }
    // 
    for (Structure structure : structures) {
        KeyValue structKey = hash.getDatabaseKey(structure);
        KeyValue parentKey = null;
        Structure parentStruct = structureTopology.getParentStructure(structure);
        if (parentStruct != null) {
            parentKey = hash.getDatabaseKey(parentStruct);
        }
        KeyValue negKey = null;
        KeyValue posKey = null;
        if (structure instanceof Membrane) {
            Membrane membrane = (Membrane) structure;
            Feature negFeature = electricalTopology.getNegativeFeature(membrane);
            if (negFeature != null) {
                negKey = hash.getDatabaseKey(negFeature);
            }
            Feature posFeature = electricalTopology.getPositiveFeature(membrane);
            if (posFeature != null) {
                posKey = hash.getDatabaseKey(posFeature);
            }
        }
        StructureKeys structureKeys = new StructureKeys(structKey, parentKey, posKey, negKey);
        reactStepDB.updateStructureKeys(con, structureKeys);
    }
    // 
    // make sure all speciesContexts are in database and the hashtable
    // 
    SpeciesContext[] speciesContexts = model.getSpeciesContexts();
    for (int i = 0; i < speciesContexts.length; i++) {
        SpeciesContext sc = speciesContexts[i];
        if (hash.getDatabaseKey(sc) == null) {
            insertSpeciesContextSQL(hash, con, keyFactory.getNewKey(con), sc, newVersion.getVersionKey());
        }
    }
    // 
    // insert all reactionSteps
    // 
    ReactionStep[] reactionSteps = model.getReactionSteps();
    for (int i = 0; i < reactionSteps.length; i++) {
        ReactionStep rs = reactionSteps[i];
        if (hash.getDatabaseKey(rs) == null) {
            reactStepDB.insertReactionStep(hash, con, user, rs, newVersion.getVersionKey());
        }
    }
    // 
    // insert diagrams
    // 
    Diagram[] diagrams = model.getDiagrams();
    for (int i = 0; i < diagrams.length; i++) {
        Diagram diagram = diagrams[i];
        KeyValue key = keyFactory.getNewKey(con);
        KeyValue structKey = hash.getDatabaseKey(diagram.getStructure());
        if (structKey != null) {
            insertDiagramSQL(con, key, diagram, newVersion.getVersionKey(), /*modelKey*/
            hash.getDatabaseKey(diagram.getStructure()));
        } else {
            if (lg.isWarnEnabled())
                lg.warn("ModelDbDriver.insertModel(),  diagram " + diagram.toString() + " is orphaned, check Model logic");
        }
    }
    // 
    // insert GlobalModelParameters
    // 
    // //-----------------testing remove
    // try{
    // Model.ModelParameter testParam = model.new ModelParameter("test",new Expression("1.0"),Model.ROLE_UserDefined,VCUnitDefinition.UNIT_molecules);
    // model.setModelParameters(new Model.ModelParameter[] {testParam});
    // }catch(Exception e){
    // e.printStackTrace();
    // }
    // //-----------------
    GlobalModelParameterTable.table.insertModelParameters(con, keyFactory, model.getModelParameters(), newVersion.getVersionKey());
}