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

Example 96 with Structure

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

the class GeneratedSpeciesTableRow method deriveSpecies.

private void deriveSpecies(String inputString, Model tempModel) {
    if (owner != null && owner.getSimulationContext() != null) {
        List<MolecularType> mtList = owner.getSimulationContext().getModel().getRbmModelContainer().getMolecularTypeList();
        try {
            tempModel.getRbmModelContainer().setMolecularTypeList(mtList);
        } catch (PropertyVetoException e1) {
            e1.printStackTrace();
            throw new RuntimeException("Unexpected exception setting " + MolecularType.typeName + " list: " + e1.getMessage(), e1);
        }
    } else {
        System.out.println("something is wrong, we just do nothing rather than crash");
        return;
    }
    try {
        String strStructure = null;
        if (inputString.contains(RbmUtils.SiteStruct)) {
            // we are in the mode where we emulate compartments by adding the compartment name as a fake site
            Pair<List<String>, String> p = RbmUtils.extractCompartment(inputString);
            strStructure = p.one.get(0);
            inputString = p.two;
        } else {
            // should be the normal @comp:expression format - if it's not it will return null
            strStructure = RbmUtils.parseCompartment(inputString, tempModel);
        }
        Structure structure;
        if (strStructure != null) {
            if (tempModel.getStructure(strStructure) == null) {
                tempModel.addFeature(strStructure);
            }
            structure = tempModel.getStructure(strStructure);
        } else {
            structure = tempModel.getStructure(0);
        }
        SpeciesPattern sp = (SpeciesPattern) RbmUtils.parseSpeciesPattern(inputString, tempModel);
        sp.resolveBonds();
        // System.out.println(sp.toString());
        species = new SpeciesContext(new Species("a", ""), structure, sp);
    } catch (ParseException | PropertyVetoException | ModelException e1) {
        e1.printStackTrace();
    }
}

Example 97 with Structure

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

the class ViewGeneratedSpeciesPanel method updateShape.

public void updateShape(int selectedRow) {
    GeneratedSpeciesTableRow speciesTableRow = tableModel.getValueAt(selectedRow);
    String inputString = speciesTableRow.getExpression();
    // System.out.println(selectedRows[0] + ": " + inputString);
    Model tempModel = null;
    try {
        tempModel = new Model("MyTempModel");
        tempModel.addFeature("c0");
    } catch (ModelException | PropertyVetoException e1) {
        e1.printStackTrace();
    }
    if (owner != null && owner.getSimulationContext() != null) {
        List<MolecularType> mtList = owner.getSimulationContext().getModel().getRbmModelContainer().getMolecularTypeList();
        try {
            tempModel.getRbmModelContainer().setMolecularTypeList(mtList);
        } catch (PropertyVetoException e1) {
            e1.printStackTrace();
            throw new RuntimeException("Unexpected exception setting " + MolecularType.typeName + " list: " + e1.getMessage(), e1);
        }
    } else {
        System.out.println("something is wrong, we just do nothing rather than crash");
        return;
    }
    try {
        String strStructure = null;
        if (inputString.contains(RbmUtils.SiteStruct)) {
            // we are in the mode where we emulate compartments by adding the compartment name as a fake site
            Pair<List<String>, String> p = RbmUtils.extractCompartment(inputString);
            // we'll just assume there's only one, may want to throw exception if more
            strStructure = p.one.get(0);
            inputString = p.two;
        } else {
            // should be the normal @comp:expression format - if it's not it will return null
            strStructure = RbmUtils.parseCompartment(inputString, tempModel);
        }
        Structure structure;
        if (strStructure != null) {
            if (tempModel.getStructure(strStructure) == null) {
                if (owner.getSimulationContext().getModel().getStructure(strStructure).getTypeName().equals(Structure.TYPE_NAME_MEMBRANE)) {
                    tempModel.addMembrane(strStructure);
                } else {
                    tempModel.addFeature(strStructure);
                }
            }
            structure = tempModel.getStructure(strStructure);
        } else {
            structure = tempModel.getStructure(0);
        }
        SpeciesPattern sp = (SpeciesPattern) RbmUtils.parseSpeciesPattern(inputString, tempModel);
        sp.resolveBonds();
        SpeciesContext sc = new SpeciesContext(new Species("a", ""), structure, sp);
        spls = new SpeciesPatternLargeShape(20, 20, -1, sp, shapePanel, sc, issueManager);
    } catch (ParseException | PropertyVetoException | ModelException e1) {
        e1.printStackTrace();
        // error (red circle)
        spls = new SpeciesPatternLargeShape(20, 20, -1, shapePanel, true, issueManager);
        shapePanel.repaint();
    }
    int xOffset = spls.getRightEnd() + 45;
    Dimension preferredSize = new Dimension(xOffset + 90, 50);
    shapePanel.setPreferredSize(preferredSize);
    shapePanel.repaint();
}

Example 98 with Structure

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

the class ViewObservablesMapPanel method updateShapeSpecies.

public void updateShapeSpecies(int selectedRow) {
    GeneratedSpeciesTableRow speciesTableRow = speciesTableModel.getValueAt(selectedRow);
    String inputString = speciesTableRow.getExpression();
    // System.out.println(selectedRows[0] + ": " + inputString);
    Model tempModel = null;
    try {
        tempModel = new Model("MyTempModel");
        tempModel.addFeature("c0");
    } catch (ModelException | PropertyVetoException e1) {
        e1.printStackTrace();
    }
    if (owner != null && owner.getSimulationContext() != null) {
        List<MolecularType> mtList = owner.getSimulationContext().getModel().getRbmModelContainer().getMolecularTypeList();
        try {
            tempModel.getRbmModelContainer().setMolecularTypeList(mtList);
        } catch (PropertyVetoException e1) {
            e1.printStackTrace();
            throw new RuntimeException("Unexpected exception setting " + MolecularType.typeName + " list: " + e1.getMessage(), e1);
        }
    } else {
        System.out.println("something is wrong, we just do nothing rather than crash");
        return;
    }
    try {
        String strStructure = null;
        if (inputString.contains(RbmUtils.SiteStruct)) {
            // we are in the mode where we emulate compartments by adding the compartment name as a fake site
            Pair<List<String>, String> p = RbmUtils.extractCompartment(inputString);
            // we'll just assume there's only one, may want to throw exception if more
            strStructure = p.one.get(0);
            inputString = p.two;
        } else {
            // should be the normal @comp:expression format - if it's not it will return null
            strStructure = RbmUtils.parseCompartment(inputString, tempModel);
        }
        Structure structure;
        if (strStructure != null) {
            if (tempModel.getStructure(strStructure) == null) {
                if (owner.getSimulationContext().getModel().getStructure(strStructure).getTypeName().equals(Structure.TYPE_NAME_MEMBRANE)) {
                    tempModel.addMembrane(strStructure);
                } else {
                    tempModel.addFeature(strStructure);
                }
            }
            structure = tempModel.getStructure(strStructure);
        } else {
            structure = tempModel.getStructure(0);
        }
        SpeciesPattern sp = (SpeciesPattern) RbmUtils.parseSpeciesPattern(inputString, tempModel);
        sp.resolveBonds();
        SpeciesContext sc = new SpeciesContext(new Species("a", ""), structure, sp);
        spls = new SpeciesPatternLargeShape(20, 20, -1, sp, shapePanelSpecies, sc, issueManager);
    } catch (ParseException | PropertyVetoException | ModelException e1) {
        e1.printStackTrace();
        // error (red circle)
        spls = new SpeciesPatternLargeShape(20, 20, -1, shapePanelSpecies, true, issueManager);
        shapePanelSpecies.repaint();
    }
    int xOffset = spls.getRightEnd() + 45;
    Dimension preferredSize = new Dimension(xOffset + 90, 50);
    shapePanelSpecies.setPreferredSize(preferredSize);
    shapePanelSpecies.repaint();
}

Example 99 with Structure

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

the class ModelUnitConverter method createBioModelWithNewUnitSystem.

public static BioModel createBioModelWithNewUnitSystem(BioModel oldBioModel, ModelUnitSystem newUnitSystem) throws ExpressionException, XmlParseException {
    // new BioModel has new unit system applied to all built-in units ... but expressions still need to be corrected (see below).
    BioModel newBioModel = XmlHelper.cloneBioModelWithNewUnitSystem(oldBioModel, newUnitSystem);
    Model newModel = newBioModel.getModel();
    Model oldModel = oldBioModel.getModel();
    for (Parameter p : newBioModel.getModel().getModelParameters()) {
        convertVarsWithUnitFactors(oldBioModel.getModel(), newBioModel.getModel(), p);
    }
    for (ReactionStep reactionStep : newBioModel.getModel().getReactionSteps()) {
        SymbolTable oldSymbolTable = oldBioModel.getModel().getReactionStep(reactionStep.getName());
        SymbolTable newSymbolTable = reactionStep;
        for (Parameter p : reactionStep.getKinetics().getUnresolvedParameters()) {
            convertVarsWithUnitFactors(oldSymbolTable, newSymbolTable, p);
        }
        for (Parameter p : reactionStep.getKinetics().getKineticsParameters()) {
            convertVarsWithUnitFactors(oldSymbolTable, newSymbolTable, p);
        }
    }
    for (ReactionRule reactionRule : newBioModel.getModel().getRbmModelContainer().getReactionRuleList()) {
        SymbolTable oldSymbolTable = oldBioModel.getModel().getRbmModelContainer().getReactionRule(reactionRule.getName()).getKineticLaw().getScopedSymbolTable();
        SymbolTable newSymbolTable = reactionRule.getKineticLaw().getScopedSymbolTable();
        for (Parameter p : reactionRule.getKineticLaw().getUnresolvedParameters()) {
            convertVarsWithUnitFactors(oldSymbolTable, newSymbolTable, p);
        }
        for (Parameter p : reactionRule.getKineticLaw().getLocalParameters()) {
            convertVarsWithUnitFactors(oldSymbolTable, newSymbolTable, p);
        }
    }
    for (SimulationContext simContext : newBioModel.getSimulationContexts()) {
        SimulationContext oldSimContext = oldBioModel.getSimulationContext(simContext.getName());
        // ArrayList<Parameter> parameterList = new ArrayList<Parameter>();
        for (StructureMapping mapping : simContext.getGeometryContext().getStructureMappings()) {
            Structure oldStructure = oldModel.getStructure(mapping.getStructure().getName());
            StructureMapping oldMapping = oldSimContext.getGeometryContext().getStructureMapping(oldStructure);
            for (Parameter p : mapping.computeApplicableParameterList()) {
                convertVarsWithUnitFactors(oldMapping, mapping, p);
            }
        }
        for (SpeciesContextSpec spec : simContext.getReactionContext().getSpeciesContextSpecs()) {
            SpeciesContext oldSpeciesContext = oldModel.getSpeciesContext(spec.getSpeciesContext().getName());
            SpeciesContextSpec oldSpec = oldSimContext.getReactionContext().getSpeciesContextSpec(oldSpeciesContext);
            for (Parameter p : spec.computeApplicableParameterList()) {
                convertVarsWithUnitFactors(oldSpec, spec, p);
            }
        }
        for (int i = 0; i < simContext.getElectricalStimuli().length; i++) {
            ElectricalStimulus newElectricalStimulus = simContext.getElectricalStimuli()[i];
            ElectricalStimulus oldElectricalStimulus = oldSimContext.getElectricalStimuli()[i];
            for (Parameter p : newElectricalStimulus.getParameters()) {
                convertVarsWithUnitFactors(oldElectricalStimulus.getNameScope().getScopedSymbolTable(), newElectricalStimulus.getNameScope().getScopedSymbolTable(), p);
            }
        }
        // convert events : trigger and delay parameters and event assignments
        for (int i = 0; simContext.getBioEvents() != null && oldSimContext.getBioEvents() != null && i < simContext.getBioEvents().length; i++) {
            BioEvent newBioEvent = simContext.getBioEvents()[i];
            BioEvent oldBioEvent = oldSimContext.getBioEvent(newBioEvent.getName());
            for (Parameter p : newBioEvent.getEventParameters()) {
                convertVarsWithUnitFactors(oldBioEvent.getNameScope().getScopedSymbolTable(), newBioEvent.getNameScope().getScopedSymbolTable(), p);
            }
            // for each event assignment expression
            for (int e = 0; e < newBioEvent.getEventAssignments().size(); e++) {
                ScopedSymbolTable newSymbolTable = newBioEvent.getNameScope().getScopedSymbolTable();
                ScopedSymbolTable oldSymbolTable = oldBioEvent.getNameScope().getScopedSymbolTable();
                EventAssignment newEventAssignment = newBioEvent.getEventAssignments().get(e);
                EventAssignment oldEventAssignment = oldBioEvent.getEventAssignments().get(e);
                VCUnitDefinition oldTargetUnit = oldEventAssignment.getTarget().getUnitDefinition();
                VCUnitDefinition newTargetUnit = newEventAssignment.getTarget().getUnitDefinition();
                Expression eventAssgnExpr = newEventAssignment.getAssignmentExpression();
                convertExprWithUnitFactors(oldSymbolTable, newSymbolTable, oldTargetUnit, newTargetUnit, eventAssgnExpr);
            }
        }
        /**
         * @TODO: If rate rule variable unit is TBD, we still need to handle the rate expression unit.
         */
        // convert rate rules
        RateRule[] rateRules = simContext.getRateRules();
        if (rateRules != null && rateRules.length > 0) {
            for (RateRule rateRule : rateRules) {
                RateRule oldRateRule = oldSimContext.getRateRule(rateRule.getName());
                ScopedSymbolTable oldSymbolTable = oldRateRule.getSimulationContext();
                ScopedSymbolTable newSymbolTable = rateRule.getSimulationContext();
                VCUnitDefinition oldTargetUnit = oldRateRule.getRateRuleVar().getUnitDefinition();
                VCUnitDefinition newTargetUnit = rateRule.getRateRuleVar().getUnitDefinition();
                Expression rateRuleExpr = rateRule.getRateRuleExpression();
                convertExprWithUnitFactors(oldSymbolTable, newSymbolTable, oldTargetUnit, newTargetUnit, rateRuleExpr);
            }
        }
    }
    // end  for - simulationContext
    return newBioModel;
}

Example 100 with Structure

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

the class GraphContainerLayoutVCellClassical method refreshLayoutChildrenContainerContainerShape.

public void refreshLayoutChildrenContainerContainerShape(ContainerContainerShape shape) {
    List<ReactionContainerShape> structureContainers = shape.getStructureContainers();
    int currentX = 4;
    int currentY = 0;
    for (int i = 0; i < structureContainers.size(); i++) {
        structureContainers.get(i).getSpaceManager().setRelPos(currentX, currentY);
        currentX += structureContainers.get(i).getSpaceManager().getSize().width;
        int padding = 8;
        if (i < structureContainers.size() - 1) {
            Structure structure1 = structureContainers.get(i).getStructure();
            Structure structure2 = structureContainers.get(i + 1).getStructure();
            if (StructureUtil.areAdjacent(structure1, structure2)) {
                padding = 0;
            }
        }
        currentX += padding;
    }
}