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

Example 1 with ElectricalTopology

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

the class Xmlproducer method getXML.

/**
 * This method identifies if the structure as a parameter is a Feature or a Membrane, and then calls the respective getXML method.
 * Creation date: (2/22/2001 6:31:04 PM)
 * @return Element
 * @param param cbit.vcell.model.Structure
 * @param model cbit.vcell.model.Model
 */
private Element getXML(Structure structure, Model model) throws XmlParseException {
    Element structureElement = null;
    StructureTopology structTopology = model.getStructureTopology();
    if (structure instanceof Feature) {
        // This is a Feature
        structureElement = new Element(XMLTags.FeatureTag);
    } else if (structure instanceof Membrane) {
        // process a Membrane
        structureElement = new Element(XMLTags.MembraneTag);
        // add specific attributes
        Feature insideFeature = structTopology.getInsideFeature((Membrane) structure);
        if (insideFeature != null) {
            structureElement.setAttribute(XMLTags.InsideFeatureTag, mangle(insideFeature.getName()));
        }
        Feature outsideFeature = structTopology.getOutsideFeature((Membrane) structure);
        if (outsideFeature != null) {
            structureElement.setAttribute(XMLTags.OutsideFeatureTag, mangle(outsideFeature.getName()));
        }
        // positive & negative features for electrical topology
        ElectricalTopology electricalTopology = model.getElectricalTopology();
        Feature positiveFeature = electricalTopology.getPositiveFeature((Membrane) structure);
        if (positiveFeature != null) {
            structureElement.setAttribute(XMLTags.PositiveFeatureTag, mangle(positiveFeature.getName()));
        }
        Feature negativeFeature = electricalTopology.getNegativeFeature((Membrane) structure);
        if (negativeFeature != null) {
            structureElement.setAttribute(XMLTags.NegativeFeatureTag, mangle(negativeFeature.getName()));
        }
        structureElement.setAttribute(XMLTags.MemVoltNameTag, mangle(((Membrane) structure).getMembraneVoltage().getName()));
    } else {
        throw new XmlParseException("An unknown type of structure was found:" + structure.getClass().getName());
    }
    // add attributes
    structureElement.setAttribute(XMLTags.NameAttrTag, mangle(structure.getName()));
    // If the keyFlag is on, print Keys
    if (structure.getKey() != null && this.printKeysFlag) {
        structureElement.setAttribute(XMLTags.KeyValueAttrTag, structure.getKey().toString());
    }
    return structureElement;
}

Example 2 with ElectricalTopology

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

the class ElectricalCircuitGraph method getCircuitGraph.

/**
 * Insert the method's description here.
 * Creation date: (2/19/2002 11:24:04 AM)
 * @return cbit.vcell.mapping.potential.Graph
 * @param simContext cbit.vcell.mapping.SimulationContext
 */
public static Graph getCircuitGraph(SimulationContext simContext, AbstractMathMapping mathMapping) throws ExpressionException {
    Graph graph = new Graph();
    Model model = simContext.getModel();
    // 
    // add nodes to the graph (one for each Feature)
    // 
    Structure[] structures = model.getStructures();
    for (int i = 0; i < structures.length; i++) {
        if (structures[i] instanceof Feature) {
            graph.addNode(new Node(structures[i].getName(), structures[i]));
        }
    }
    // 
    // add edges for all current clamp electrodes (always have dependent voltages)
    // 
    ElectricalStimulus[] stimuli = simContext.getElectricalStimuli();
    Electrode groundElectrode = simContext.getGroundElectrode();
    for (int i = 0; i < stimuli.length; i++) {
        ElectricalStimulus stimulus = stimuli[i];
        // 
        // get electrodes
        // 
        Electrode probeElectrode = stimulus.getElectrode();
        if (probeElectrode == null) {
            throw new RuntimeException("null electrode for electrical stimulus");
        }
        if (groundElectrode == null) {
            throw new RuntimeException("null ground electrode for electrical stimulus");
        }
        // if (!membraneMapping.getResolved()){
        Node groundNode = graph.getNode(groundElectrode.getFeature().getName());
        Node probeNode = graph.getNode(probeElectrode.getFeature().getName());
        if (stimulus instanceof CurrentDensityClampStimulus) {
            CurrentDensityClampStimulus ccStimulus = (CurrentDensityClampStimulus) stimulus;
            ElectricalDevice device = new CurrentClampElectricalDevice(ccStimulus, mathMapping);
            Edge edge = new Edge(probeNode, groundNode, device);
            graph.addEdge(edge);
        } else if (stimulus instanceof TotalCurrentClampStimulus) {
            TotalCurrentClampStimulus ccStimulus = (TotalCurrentClampStimulus) stimulus;
            ElectricalDevice device = new CurrentClampElectricalDevice(ccStimulus, mathMapping);
            Edge edge = new Edge(probeNode, groundNode, device);
            graph.addEdge(edge);
        }
    // }
    }
    // 
    // add edges for all membranes
    // 
    ElectricalTopology electricalTopology = simContext.getModel().getElectricalTopology();
    for (int i = 0; i < structures.length; i++) {
        if (structures[i] instanceof Membrane) {
            Membrane membrane = (Membrane) structures[i];
            MembraneMapping membraneMapping = (MembraneMapping) simContext.getGeometryContext().getStructureMapping(membrane);
            Feature positiveFeature = electricalTopology.getPositiveFeature(membrane);
            Feature negativeFeature = electricalTopology.getNegativeFeature(membrane);
            if (positiveFeature != null && negativeFeature != null) {
                Node insideNode = graph.getNode(positiveFeature.getName());
                Node outsideNode = graph.getNode(negativeFeature.getName());
                // 
                // getTotalMembraneCurrent() already converts to "outwardCurrent" so that same convention as voltage
                // 
                Expression currentSource = getTotalMembraneCurrent(simContext, membrane, mathMapping);
                MembraneElectricalDevice device = new MembraneElectricalDevice(membraneMapping, mathMapping);
                device.getParameterFromRole(ElectricalDevice.ROLE_TransmembraneCurrent).setExpression(currentSource);
                Edge edge = new Edge(insideNode, outsideNode, device);
                graph.addEdge(edge);
            }
        }
    }
    // 
    for (int i = 0; i < stimuli.length; i++) {
        ElectricalStimulus stimulus = stimuli[i];
        // 
        // get electrodes
        // 
        Electrode probeElectrode = stimulus.getElectrode();
        if (probeElectrode == null) {
            throw new RuntimeException("null electrode for electrical stimulus");
        }
        if (groundElectrode == null) {
            throw new RuntimeException("null ground electrode for electrical stimulus");
        }
        // if (!membraneMapping.getResolved()){
        Node groundNode = graph.getNode(groundElectrode.getFeature().getName());
        Node probeNode = graph.getNode(probeElectrode.getFeature().getName());
        if (stimulus instanceof VoltageClampStimulus) {
            VoltageClampStimulus vcStimulus = (VoltageClampStimulus) stimulus;
            ElectricalDevice device = new VoltageClampElectricalDevice(vcStimulus, mathMapping);
            Edge edge = new Edge(probeNode, groundNode, device);
            graph.addEdge(edge);
        }
    // }
    }
    // System.out.println(graph);
    return graph;
}

Example 3 with ElectricalTopology

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

the class PotentialMapping method getEdges.

/**
 * Insert the method's description here.
 * Creation date: (3/2/2002 11:10:22 PM)
 * @return cbit.vcell.mapping.potential.Edge[]
 */
private Edge[] getEdges(Membrane membrane) {
    java.util.Vector<Edge> edgeList = new java.util.Vector<Edge>();
    ElectricalTopology electricalTopology = fieldSimContext.getModel().getElectricalTopology();
    for (int i = 0; i < fieldEdges.length; i++) {
        boolean a1 = ((Feature) fieldEdges[i].getNode1().getData()).compareEqual(electricalTopology.getPositiveFeature(membrane));
        boolean a2 = ((Feature) fieldEdges[i].getNode2().getData()).compareEqual(electricalTopology.getNegativeFeature(membrane));
        if (a1 && a2) {
            edgeList.add(fieldEdges[i]);
        }
        boolean b1 = ((Feature) fieldEdges[i].getNode2().getData()).compareEqual(electricalTopology.getPositiveFeature(membrane));
        boolean b2 = ((Feature) fieldEdges[i].getNode1().getData()).compareEqual(electricalTopology.getNegativeFeature(membrane));
        if (b1 && b2) {
            edgeList.add(fieldEdges[i]);
        }
    }
    Edge[] edgesForMembrane = new Edge[edgeList.size()];
    edgeList.copyInto(edgesForMembrane);
    return edgesForMembrane;
}

Example 4 with ElectricalTopology

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

the class StructurePropertiesPanel method updateInterface.

/**
 * Comment
 */
private void updateInterface() {
    boolean bNonNullStructure = structure != null && fieldModel != null;
    nameTextField.setEditable(bNonNullStructure);
    annotationTextArea.setEditable(bNonNullStructure);
    boolean bMembrane = bNonNullStructure && structure instanceof Membrane;
    voltageLabel.setVisible(bMembrane);
    voltageTextField.setVisible(bMembrane);
    electrophysiologyLabel.setVisible(bMembrane);
    positiveFeatureLabel.setVisible(bMembrane);
    positiveFeatureComboBox.setVisible(bMembrane);
    negativeFeatureLabel.setVisible(bMembrane);
    negativeFeatureComboBox.setVisible(bMembrane);
    electrophysiologyExplanationLabel.setVisible(bMembrane);
    if (bNonNullStructure) {
        nameTextField.setText(structure.getName());
        annotationTextArea.setText(fieldModel.getVcMetaData().getFreeTextAnnotation(structure));
        StructureSize structureSize = structure.getStructureSize();
        sizeTextField.setText(structureSize.getName() + " [" + structureSize.getUnitDefinition().getSymbolUnicode() + "]");
        if (bMembrane) {
            Membrane membrane = (Membrane) structure;
            MembraneVoltage memVoltage = membrane.getMembraneVoltage();
            voltageTextField.setText(memVoltage.getName() + " [" + memVoltage.getUnitDefinition().getSymbolUnicode() + "]");
            // if membrane has +ve/-ve feature set, set the comboBox with that selection.
            ElectricalTopology electricalTopology = fieldModel.getElectricalTopology();
            Feature positiveFeature = electricalTopology.getPositiveFeature(membrane);
            if (positiveFeature != null) {
                positiveFeatureComboBox.setSelectedItem(positiveFeature.getName());
            }
            Feature negativeFeature = electricalTopology.getNegativeFeature(membrane);
            if (negativeFeature != null) {
                negativeFeatureComboBox.setSelectedItem(negativeFeature.getName());
            }
            this.electrophysiologyExplanationLabel.setText(getExplanationText());
        }
    } else {
        annotationTextArea.setText(null);
        nameTextField.setText(null);
        sizeTextField.setText(null);
        voltageTextField.setText(null);
    }
}

Example 5 with ElectricalTopology

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

the class NernstKinetics 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 cbit.vcell.parser.ExpressionException, java.beans.PropertyVetoException {
    KineticsParameter rateParm = getKineticsParameterFromRole(ROLE_ReactionRate);
    KineticsParameter currentParm = getKineticsParameterFromRole(ROLE_CurrentDensity);
    KineticsParameter conductivity = getKineticsParameterFromRole(ROLE_Conductivity);
    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;
    }
    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;
            }
        }
    }
    if (Neg0 != null && Pos0 != null) {
        Model model = getReactionStep().getModel();
        Expression carrier_z = getSymbolExpression(getKineticsParameterFromRole(ROLE_CarrierChargeValence));
        Expression net_z = carrier_z;
        Expression F = getSymbolExpression(model.getFARADAY_CONSTANT());
        Expression R = getSymbolExpression(model.getGAS_CONSTANT());
        Expression T = getSymbolExpression(model.getTEMPERATURE());
        Expression Pos0_exp = getSymbolExpression(Pos0.getSpeciesContext());
        Expression Neg0_exp = getSymbolExpression(Neg0.getSpeciesContext());
        Expression V_exp = getSymbolExpression(V);
        Expression conductivity_exp = getSymbolExpression(conductivity);
        // new Expression("A0*(("+R+"*"+T+"/("+VALENCE_SYMBOL+"*"+F+"))*log(P0/R0)-"+VOLTAGE_SYMBOL+")"),
        // Expression newCurrExp = new Expression(conductivity.getName()+"*(("+R.getName()+"*"+T.getName()+"/("+z+"*"+F.getName()+"))*log("+P0.getName()+"/"+R0.getName()+") - "+V.getName()+")");
        // log(P/R)
        Expression logterm = Expression.log(Expression.div(Neg0_exp, Pos0_exp));
        // (R * T / (z * F))
        Expression term1 = Expression.div(Expression.mult(R, T), Expression.mult(carrier_z, F));
        // C * (term1 * logterm - V)
        Expression newCurrExp = Expression.mult(conductivity_exp, Expression.add(Expression.mult(term1, logterm), Expression.negate(V_exp)));
        currentParm.setExpression(newCurrExp);
        // SECONDARY REACTION RATE
        // update from current density
        updateReactionRatesFromInwardCurrentDensity();
    }
}