Examples with RationalNumberMatrix cbit.vcell.matrix.RationalNumberMatrix used on opensource projects

Example 1 with RationalNumberMatrix

use of cbit.vcell.matrix.RationalNumberMatrix in project vcell by virtualcell.

the class StructureAnalyzer method refreshTotalMatrices.

/**
 * This method was created in VisualAge.
 */
private void refreshTotalMatrices() throws Exception {
    // System.out.println("StructureAnalyzer.refreshTotalMatrices()");
    // 
    // update scheme matrix for full system (slow and fast)
    // 
    ReactionSpec[] reactionSpecs = new ReactionSpec[reactionSteps.length];
    for (int j = 0; j < reactionSteps.length; j++) {
        reactionSpecs[j] = mathMapping.getSimulationContext().getReactionContext().getReactionSpec(reactionSteps[j]);
    }
    // 
    // initialize rate expressions for speciesContext's due to scheme matrix
    // 
    totalSchemeMatrix = new RationalNumberMatrix(speciesContextMappings.length, reactionSteps.length);
    for (int i = 0; i < speciesContextMappings.length; i++) {
        SpeciesContextMapping scm = speciesContextMappings[i];
        SpeciesContext sc = scm.getSpeciesContext();
        // 
        // collect slow rate expression (fast handled by FastSystem)
        // 
        Expression exp = new Expression(0.0);
        for (int j = 0; j < reactionSteps.length; j++) {
            ReactionStep reactionStep = reactionSteps[j];
            int stoichiometry = reactionStep.getStoichiometry(sc);
            totalSchemeMatrix.set_elem(i, j, stoichiometry);
            if (stoichiometry != 0) {
                if (!(reactionStep instanceof DummyReactionStep) && !reactionSpecs[j].isFast() && !reactionSpecs[j].isExcluded()) {
                    ReactionParticipant[] rps1 = reactionStep.getReactionParticipants();
                    ReactionParticipant rp0 = null;
                    for (ReactionParticipant rp : rps1) {
                        if (rp.getSpeciesContext() == sc) {
                            rp0 = rp;
                            break;
                        }
                    }
                    if (rp0 != null) {
                        Expression distributedReactRateExp = getCorrectedRateExpression(reactionStep, rp0, RateType.ConcentrationRate);
                        exp = Expression.add(exp, distributedReactRateExp);
                    }
                }
            }
        }
        // exp.bindExpression(mathMapping);
        scm.setRate(exp.flatten());
    }
    // 
    if (totalSchemeMatrix.getNumRows() > 1) {
        totalNullSpaceMatrix = (RationalMatrix) totalSchemeMatrix.findNullSpace();
    } else {
        totalNullSpaceMatrix = null;
    }
// if (totalNullSpaceMatrix==null){
// System.out.println("total system has full rank");
// }else{
// System.out.println("StructureAnalyzer.refreshTotalMatrices(), nullSpace matrix:");
// totalNullSpaceMatrix.show();
// }
}

Example 2 with RationalNumberMatrix

use of cbit.vcell.matrix.RationalNumberMatrix in project vcell by virtualcell.

the class StructureAnalyzer method refreshFastMatrices.

/**
 * This method was created in VisualAge.
 */
private void refreshFastMatrices() throws Exception {
    // System.out.println("StructureAnalyzer.refreshFastMatrices()");
    // 
    // update scheme matrix for fast system
    // 
    fastSchemeMatrix = new RationalNumberMatrix(fastSpeciesContextMappings.length, fastReactionSteps.length);
    for (int i = 0; i < fastSpeciesContextMappings.length; i++) {
        for (int j = 0; j < fastReactionSteps.length; j++) {
            fastSchemeMatrix.set_elem(i, j, fastReactionSteps[j].getStoichiometry(fastSpeciesContextMappings[i].getSpeciesContext()));
        }
    }
    // 
    for (int i = 0; i < fastSpeciesContextMappings.length; i++) {
        SpeciesContextMapping scm = fastSpeciesContextMappings[i];
        SpeciesContext sc = scm.getSpeciesContext();
        // 
        // collect fast rate expression
        // 
        Expression exp = new Expression(0.0);
        for (int j = 0; j < fastReactionSteps.length; j++) {
            int stoichiometry = fastReactionSteps[j].getStoichiometry(sc);
            ReactionSpec reactionSpec = mathMapping.getSimulationContext().getReactionContext().getReactionSpec(fastReactionSteps[j]);
            if (stoichiometry != 0) {
                if (!reactionSpec.isFast()) {
                    throw new Exception("expected only fast rates");
                }
                if (reactionSpec.isExcluded()) {
                    throw new Exception("expected only included rates");
                }
                ReactionParticipant[] rps = fastReactionSteps[j].getReactionParticipants();
                ReactionParticipant rp0 = null;
                for (ReactionParticipant rp : rps) {
                    if (rp.getSpeciesContext() == sc) {
                        rp0 = rp;
                        break;
                    }
                }
                // 
                if (rp0 != null) {
                    Expression fastRateExpression = getCorrectedRateExpression(fastReactionSteps[j], rp0, RateType.ConcentrationRate).renameBoundSymbols(mathMapping.getNameScope());
                    exp = Expression.add(exp, fastRateExpression);
                }
            }
        }
        // exp.bindExpression(mathMapping);
        scm.setFastRate(exp.flatten());
    }
    // System.out.println("StructureAnalyzer.refreshFastMatrices(), scheme matrix:");
    // fastSchemeMatrix.show();
    // 
    // update null space matrix
    // 
    fastNullSpaceMatrix = fastSchemeMatrix.findNullSpace();
// if (fastNullSpaceMatrix==null){
// System.out.println("fast system has full rank");
// }else{
// System.out.println("StructureAnalyzer.refreshFastMatrices(), nullSpace matrix:");
// fastNullSpaceMatrix.show();
// }
}

Example 3 with RationalNumberMatrix

use of cbit.vcell.matrix.RationalNumberMatrix in project vcell by virtualcell.

the class StructureAnalyzer method refreshFastMatrices.

/**
 * This method was created in VisualAge.
 */
private void refreshFastMatrices() throws Exception {
    // System.out.println("StructureAnalyzer.refreshFastMatrices()");
    // 
    // update scheme matrix for fast system
    // 
    fastSchemeMatrix = new RationalNumberMatrix(fastSpeciesContextMappings.length, fastReactionSteps.length);
    for (int i = 0; i < fastSpeciesContextMappings.length; i++) {
        for (int j = 0; j < fastReactionSteps.length; j++) {
            fastSchemeMatrix.set_elem(i, j, fastReactionSteps[j].getStoichiometry(fastSpeciesContextMappings[i].getSpeciesContext()));
        }
    }
    // 
    for (int i = 0; i < fastSpeciesContextMappings.length; i++) {
        SpeciesContextMapping scm = fastSpeciesContextMappings[i];
        SpeciesContext sc = scm.getSpeciesContext();
        // 
        // collect fast rate expression
        // 
        Expression exp = new Expression(0.0);
        for (int j = 0; j < fastReactionSteps.length; j++) {
            int stoichiometry = fastReactionSteps[j].getStoichiometry(sc);
            ReactionSpec reactionSpec = mathMapping_4_8.getSimulationContext().getReactionContext().getReactionSpec(fastReactionSteps[j]);
            if (stoichiometry != 0) {
                if (!reactionSpec.isFast()) {
                    throw new Exception("expected only fast rates");
                }
                if (reactionSpec.isExcluded()) {
                    throw new Exception("expected only included rates");
                }
                ReactionParticipant[] rps = fastReactionSteps[j].getReactionParticipants();
                ReactionParticipant rp0 = null;
                for (ReactionParticipant rp : rps) {
                    if (rp.getSpeciesContext() == sc) {
                        rp0 = rp;
                        break;
                    }
                }
                // 
                if (rp0 != null) {
                    Structure structure = fastReactionSteps[j].getStructure();
                    Expression fastRateExpression = getReactionRateExpression(fastReactionSteps[j], rp0).renameBoundSymbols(mathMapping_4_8.getNameScope());
                    if ((structure instanceof Membrane) && (rp0.getStructure() != structure)) {
                        Membrane membrane = (Membrane) structure;
                        MembraneMapping membraneMapping = (MembraneMapping) mathMapping_4_8.getSimulationContext().getGeometryContext().getStructureMapping(membrane);
                        Expression fluxCorrection = new Expression(mathMapping_4_8.getFluxCorrectionParameter(membraneMapping, (Feature) rp0.getStructure()), mathMapping_4_8.getNameScope());
                        exp = Expression.add(exp, Expression.mult(fluxCorrection, fastRateExpression));
                    } else {
                        exp = Expression.add(exp, new Expression(fastRateExpression));
                    }
                }
            }
        }
        // exp.bindExpression(mathMapping);
        scm.setFastRate(exp.flatten());
    }
    // System.out.println("StructureAnalyzer.refreshFastMatrices(), scheme matrix:");
    // fastSchemeMatrix.show();
    // 
    // update null space matrix
    // 
    fastNullSpaceMatrix = fastSchemeMatrix.findNullSpace();
// if (fastNullSpaceMatrix==null){
// System.out.println("fast system has full rank");
// }else{
// System.out.println("StructureAnalyzer.refreshFastMatrices(), nullSpace matrix:");
// fastNullSpaceMatrix.show();
// }
}

Example 4 with RationalNumberMatrix

use of cbit.vcell.matrix.RationalNumberMatrix in project vcell by virtualcell.

the class StructureAnalyzer method refreshTotalMatrices.

/**
 * This method was created in VisualAge.
 */
private void refreshTotalMatrices() throws Exception {
    // System.out.println("StructureAnalyzer.refreshTotalMatrices()");
    // 
    // update scheme matrix for full system (slow and fast)
    // 
    ReactionSpec[] reactionSpecs = new ReactionSpec[reactionSteps.length];
    for (int j = 0; j < reactionSteps.length; j++) {
        reactionSpecs[j] = mathMapping_4_8.getSimulationContext().getReactionContext().getReactionSpec(reactionSteps[j]);
    }
    // 
    // initialize rate expressions for speciesContext's due to scheme matrix
    // 
    totalSchemeMatrix = new RationalNumberMatrix(speciesContextMappings.length, reactionSteps.length);
    for (int i = 0; i < speciesContextMappings.length; i++) {
        SpeciesContextMapping scm = speciesContextMappings[i];
        SpeciesContext sc = scm.getSpeciesContext();
        // 
        // collect slow rate expression (fast handled by FastSystem)
        // 
        Expression exp = new Expression(0.0);
        for (int j = 0; j < reactionSteps.length; j++) {
            int stoichiometry = reactionSteps[j].getStoichiometry(sc);
            totalSchemeMatrix.set_elem(i, j, stoichiometry);
            if (stoichiometry != 0) {
                if (!(reactionSteps[j] instanceof DummyReactionStep) && !reactionSpecs[j].isFast() && !reactionSpecs[j].isExcluded()) {
                    ReactionParticipant[] rps1 = reactionSteps[j].getReactionParticipants();
                    ReactionParticipant rp0 = null;
                    for (ReactionParticipant rp : rps1) {
                        if (rp.getSpeciesContext() == sc) {
                            rp0 = rp;
                            break;
                        }
                    }
                    Structure structure = reactionSteps[j].getStructure();
                    // 
                    if (rp0 != null) {
                        Expression reactRateExp = getReactionRateExpression(reactionSteps[j], rp0).renameBoundSymbols(mathMapping_4_8.getNameScope());
                        if ((structure instanceof Membrane) && (sc.getStructure() != structure)) {
                            Membrane membrane = (Membrane) structure;
                            MembraneMapping membraneMapping = (MembraneMapping) mathMapping_4_8.getSimulationContext().getGeometryContext().getStructureMapping(membrane);
                            Parameter fluxCorrectionParameter = mathMapping_4_8.getFluxCorrectionParameter(membraneMapping, (Feature) sc.getStructure());
                            Expression fluxCorrection = new Expression(fluxCorrectionParameter, mathMapping_4_8.getNameScope());
                            if (reactionSteps[j] instanceof FluxReaction) {
                                exp = Expression.add(exp, Expression.mult(fluxCorrection, reactRateExp));
                            // Expression.add(exp,new Expression(fluxCorrectionParameterSymbolName+"*"+expInfix));
                            } else if (reactionSteps[j] instanceof SimpleReaction) {
                                ModelUnitSystem unitSystem = mathMapping_4_8.getSimulationContext().getModel().getUnitSystem();
                                Expression unitFactor = mathMapping_4_8.getUnitFactor(unitSystem.getVolumeSubstanceUnit().divideBy(unitSystem.getMembraneSubstanceUnit()));
                                exp = Expression.add(exp, Expression.mult(fluxCorrection, unitFactor, reactRateExp));
                            // exp = Expression.add(exp,new Expression(fluxCorrectionParameterSymbolName+"*"+ReservedSymbol.KMOLE.getName()+"*"+expInfix));
                            } else {
                                throw new RuntimeException("Internal Error: expected ReactionStep " + reactionSteps[j] + " to be of type SimpleReaction or FluxReaction");
                            }
                        } else {
                            exp = Expression.add(exp, reactRateExp);
                        }
                    }
                }
            }
        }
        // exp.bindExpression(mathMapping);
        scm.setRate(exp.flatten());
    }
    // 
    if (totalSchemeMatrix.getNumRows() > 1) {
        totalNullSpaceMatrix = (RationalMatrix) totalSchemeMatrix.findNullSpace();
    } else {
        totalNullSpaceMatrix = null;
    }
// if (totalNullSpaceMatrix==null){
// System.out.println("total system has full rank");
// }else{
// System.out.println("StructureAnalyzer.refreshTotalMatrices(), nullSpace matrix:");
// totalNullSpaceMatrix.show();
// }
}