Examples with Expression cbit.vcell.parser.Expression used on opensource projects

Example 21 with Expression

use of cbit.vcell.parser.Expression in project vcell by virtualcell.

the class SBMLImporter method addGeometry.

protected void addGeometry() {
    // get a Geometry object via SpatialModelPlugin object.
    org.sbml.jsbml.ext.spatial.Geometry sbmlGeometry = getSbmlGeometry();
    if (sbmlGeometry == null) {
        return;
    }
    int dimension = 0;
    Origin vcOrigin = null;
    Extent vcExtent = null;
    {
        // local code block
        // get a CoordComponent object via the Geometry object.
        ListOf<CoordinateComponent> listOfCoordComps = sbmlGeometry.getListOfCoordinateComponents();
        if (listOfCoordComps == null) {
            throw new RuntimeException("Cannot have 0 coordinate compartments in geometry");
        }
        // coord component
        double ox = 0.0;
        double oy = 0.0;
        double oz = 0.0;
        double ex = 1.0;
        double ey = 1.0;
        double ez = 1.0;
        for (CoordinateComponent coordComponent : listOfCoordComps) {
            double minValue = coordComponent.getBoundaryMinimum().getValue();
            double maxValue = coordComponent.getBoundaryMaximum().getValue();
            switch(coordComponent.getType()) {
                case cartesianX:
                    {
                        ox = minValue;
                        ex = maxValue - minValue;
                        break;
                    }
                case cartesianY:
                    {
                        oy = minValue;
                        ey = maxValue - minValue;
                        break;
                    }
                case cartesianZ:
                    {
                        oz = minValue;
                        ez = maxValue - minValue;
                        break;
                    }
            }
            dimension++;
        }
        vcOrigin = new Origin(ox, oy, oz);
        vcExtent = new Extent(ex, ey, ez);
    }
    // from geometry definition, find out which type of geometry : image or
    // analytic or CSG
    AnalyticGeometry analyticGeometryDefinition = null;
    CSGeometry csGeometry = null;
    SampledFieldGeometry segmentedSampledFieldGeometry = null;
    SampledFieldGeometry distanceMapSampledFieldGeometry = null;
    ParametricGeometry parametricGeometry = null;
    for (int i = 0; i < sbmlGeometry.getListOfGeometryDefinitions().size(); i++) {
        GeometryDefinition gd_temp = sbmlGeometry.getListOfGeometryDefinitions().get(i);
        if (!gd_temp.isSetIsActive()) {
            continue;
        }
        if (gd_temp instanceof AnalyticGeometry) {
            analyticGeometryDefinition = (AnalyticGeometry) gd_temp;
        } else if (gd_temp instanceof SampledFieldGeometry) {
            SampledFieldGeometry sfg = (SampledFieldGeometry) gd_temp;
            String sfn = sfg.getSampledField();
            ListOf<SampledField> sampledFields = sbmlGeometry.getListOfSampledFields();
            if (sampledFields.size() > 1) {
                throw new RuntimeException("only one sampled field supported");
            }
            InterpolationKind ik = sampledFields.get(0).getInterpolationType();
            switch(ik) {
                case linear:
                    distanceMapSampledFieldGeometry = sfg;
                    break;
                case nearestneighbor:
                    segmentedSampledFieldGeometry = sfg;
                    break;
                default:
                    lg.warn("Unsupported " + sampledFields.get(0).getName() + " interpolation type " + ik);
            }
        } else if (gd_temp instanceof CSGeometry) {
            csGeometry = (CSGeometry) gd_temp;
        } else if (gd_temp instanceof ParametricGeometry) {
            parametricGeometry = (ParametricGeometry) gd_temp;
        } else {
            throw new RuntimeException("unsupported geometry definition type " + gd_temp.getClass().getSimpleName());
        }
    }
    if (analyticGeometryDefinition == null && segmentedSampledFieldGeometry == null && distanceMapSampledFieldGeometry == null && csGeometry == null) {
        throw new SBMLImportException("VCell supports only Analytic, Image based (segmentd or distance map) or Constructed Solid Geometry at this time.");
    }
    GeometryDefinition selectedGeometryDefinition = null;
    if (csGeometry != null) {
        selectedGeometryDefinition = csGeometry;
    } else if (analyticGeometryDefinition != null) {
        selectedGeometryDefinition = analyticGeometryDefinition;
    } else if (segmentedSampledFieldGeometry != null) {
        selectedGeometryDefinition = segmentedSampledFieldGeometry;
    } else if (distanceMapSampledFieldGeometry != null) {
        selectedGeometryDefinition = distanceMapSampledFieldGeometry;
    } else if (parametricGeometry != null) {
        selectedGeometryDefinition = parametricGeometry;
    } else {
        throw new SBMLImportException("no geometry definition found");
    }
    Geometry vcGeometry = null;
    if (selectedGeometryDefinition == analyticGeometryDefinition || selectedGeometryDefinition == csGeometry) {
        vcGeometry = new Geometry("spatialGeom", dimension);
    } else if (selectedGeometryDefinition == distanceMapSampledFieldGeometry || selectedGeometryDefinition == segmentedSampledFieldGeometry) {
        SampledFieldGeometry sfg = (SampledFieldGeometry) selectedGeometryDefinition;
        // get image from sampledFieldGeometry
        // get a sampledVol object via the listOfSampledVol (from
        // SampledGeometry) object.
        // gcw gcw gcw
        String sfn = sfg.getSampledField();
        SampledField sf = null;
        for (SampledField sampledField : sbmlGeometry.getListOfSampledFields()) {
            if (sampledField.getSpatialId().equals(sfn)) {
                sf = sampledField;
            }
        }
        int numX = sf.getNumSamples1();
        int numY = sf.getNumSamples2();
        int numZ = sf.getNumSamples3();
        int[] samples = new int[sf.getSamplesLength()];
        StringTokenizer tokens = new StringTokenizer(sf.getSamples(), " ");
        int count = 0;
        while (tokens.hasMoreTokens()) {
            int sample = Integer.parseInt(tokens.nextToken());
            samples[count++] = sample;
        }
        byte[] imageInBytes = new byte[samples.length];
        if (selectedGeometryDefinition == distanceMapSampledFieldGeometry) {
            // 
            for (int i = 0; i < imageInBytes.length; i++) {
                // if (interpolation(samples[i])<0){
                if (samples[i] < 0) {
                    imageInBytes[i] = -1;
                } else {
                    imageInBytes[i] = 1;
                }
            }
        } else {
            for (int i = 0; i < imageInBytes.length; i++) {
                imageInBytes[i] = (byte) samples[i];
            }
        }
        try {
            // System.out.println("ident " + sf.getId() + " " + sf.getName());
            VCImage vcImage = null;
            CompressionKind ck = sf.getCompression();
            DataKind dk = sf.getDataType();
            if (ck == CompressionKind.deflated) {
                vcImage = new VCImageCompressed(null, imageInBytes, vcExtent, numX, numY, numZ);
            } else {
                switch(dk) {
                    case UINT8:
                    case UINT16:
                    case UINT32:
                        vcImage = new VCImageUncompressed(null, imageInBytes, vcExtent, numX, numY, numZ);
                    default:
                }
            }
            if (vcImage == null) {
                throw new SbmlException("Unsupported type combination " + ck + ", " + dk + " for sampled field " + sf.getName());
            }
            vcImage.setName(sf.getId());
            ListOf<SampledVolume> sampledVolumes = sfg.getListOfSampledVolumes();
            final int numSampledVols = sampledVolumes.size();
            if (numSampledVols == 0) {
                throw new RuntimeException("Cannot have 0 sampled volumes in sampledField (image_based) geometry");
            }
            // check to see if values are uniquely integer , add set up scaling if necessary
            double scaleFactor = checkPixelScaling(sampledVolumes, 1);
            if (scaleFactor != 1) {
                double checkScaleFactor = checkPixelScaling(sampledVolumes, scaleFactor);
                VCAssert.assertTrue(checkScaleFactor != scaleFactor, "Scale factor check failed");
            }
            VCPixelClass[] vcpixelClasses = new VCPixelClass[numSampledVols];
            // get pixel classes for geometry
            for (int i = 0; i < numSampledVols; i++) {
                SampledVolume sVol = sampledVolumes.get(i);
                // from subVolume, get pixelClass?
                final int scaled = (int) (scaleFactor * sVol.getSampledValue());
                vcpixelClasses[i] = new VCPixelClass(null, sVol.getDomainType(), scaled);
            }
            vcImage.setPixelClasses(vcpixelClasses);
            // now create image geometry
            vcGeometry = new Geometry("spatialGeom", vcImage);
        } catch (Exception e) {
            e.printStackTrace(System.out);
            throw new RuntimeException("Unable to create image from SampledFieldGeometry : " + e.getMessage());
        }
    }
    GeometrySpec vcGeometrySpec = vcGeometry.getGeometrySpec();
    vcGeometrySpec.setOrigin(vcOrigin);
    try {
        vcGeometrySpec.setExtent(vcExtent);
    } catch (PropertyVetoException e) {
        e.printStackTrace(System.out);
        throw new SBMLImportException("Unable to set extent on VC geometry : " + e.getMessage(), e);
    }
    // get listOfDomainTypes via the Geometry object.
    ListOf<DomainType> listOfDomainTypes = sbmlGeometry.getListOfDomainTypes();
    if (listOfDomainTypes == null || listOfDomainTypes.size() < 1) {
        throw new SBMLImportException("Cannot have 0 domainTypes in geometry");
    }
    // get a listOfDomains via the Geometry object.
    ListOf<Domain> listOfDomains = sbmlGeometry.getListOfDomains();
    if (listOfDomains == null || listOfDomains.size() < 1) {
        throw new SBMLImportException("Cannot have 0 domains in geometry");
    }
    // ListOfGeometryDefinitions listOfGeomDefns =
    // sbmlGeometry.getListOfGeometryDefinitions();
    // if ((listOfGeomDefns == null) ||
    // (sbmlGeometry.getNumGeometryDefinitions() > 1)) {
    // throw new
    // RuntimeException("Can have only 1 geometry definition in geometry");
    // }
    // use the boolean bAnalytic to create the right kind of subvolume.
    // First match the somVol=domainTypes for spDim=3. Deal witl spDim=2
    // afterwards.
    GeometrySurfaceDescription vcGsd = vcGeometry.getGeometrySurfaceDescription();
    Vector<DomainType> surfaceClassDomainTypesVector = new Vector<DomainType>();
    try {
        for (DomainType dt : listOfDomainTypes) {
            if (dt.getSpatialDimensions() == 3) {
                // subvolume
                if (selectedGeometryDefinition == analyticGeometryDefinition) {
                    // will set expression later - when reading in Analytic
                    // Volumes in GeometryDefinition
                    vcGeometrySpec.addSubVolume(new AnalyticSubVolume(dt.getId(), new Expression(1.0)));
                } else {
                // add SubVolumes later for CSG and Image-based
                }
            } else if (dt.getSpatialDimensions() == 2) {
                surfaceClassDomainTypesVector.add(dt);
            }
        }
        // analytic vol is needed to get the expression for subVols
        if (selectedGeometryDefinition == analyticGeometryDefinition) {
            // get an analyticVol object via the listOfAnalyticVol (from
            // AnalyticGeometry) object.
            ListOf<AnalyticVolume> aVolumes = analyticGeometryDefinition.getListOfAnalyticVolumes();
            if (aVolumes.size() < 1) {
                throw new SBMLImportException("Cannot have 0 Analytic volumes in analytic geometry");
            }
            for (AnalyticVolume analyticVol : aVolumes) {
                // get subVol from VC geometry using analyticVol spatialId;
                // set its expr using analyticVol's math.
                SubVolume vcSubvolume = vcGeometrySpec.getSubVolume(analyticVol.getDomainType());
                CastInfo<AnalyticSubVolume> ci = BeanUtils.attemptCast(AnalyticSubVolume.class, vcSubvolume);
                if (!ci.isGood()) {
                    throw new RuntimeException("analytic volume '" + analyticVol.getId() + "' does not map to any VC subvolume.");
                }
                AnalyticSubVolume asv = ci.get();
                try {
                    Expression subVolExpr = getExpressionFromFormula(analyticVol.getMath());
                    asv.setExpression(subVolExpr);
                } catch (ExpressionException e) {
                    e.printStackTrace(System.out);
                    throw new SBMLImportException("Unable to set expression on subVolume '" + asv.getName() + "'. " + e.getMessage(), e);
                }
            }
        }
        SampledFieldGeometry sfg = BeanUtils.downcast(SampledFieldGeometry.class, selectedGeometryDefinition);
        if (sfg != null) {
            ListOf<SampledVolume> sampledVolumes = sfg.getListOfSampledVolumes();
            int numSampledVols = sampledVolumes.size();
            if (numSampledVols == 0) {
                throw new SBMLImportException("Cannot have 0 sampled volumes in sampledField (image_based) geometry");
            }
            VCPixelClass[] vcpixelClasses = new VCPixelClass[numSampledVols];
            ImageSubVolume[] vcImageSubVols = new ImageSubVolume[numSampledVols];
            // get pixel classes for geometry
            int idx = 0;
            for (SampledVolume sVol : sampledVolumes) {
                // from subVolume, get pixelClass?
                final String name = sVol.getDomainType();
                final int pixelValue = SBMLUtils.ignoreZeroFraction(sVol.getSampledValue());
                VCPixelClass pc = new VCPixelClass(null, name, pixelValue);
                vcpixelClasses[idx] = pc;
                // Create the new Image SubVolume - use index of this for
                // loop as 'handle' for ImageSubVol?
                ImageSubVolume isv = new ImageSubVolume(null, pc, idx);
                isv.setName(name);
                vcImageSubVols[idx++] = isv;
            }
            vcGeometry.getGeometrySpec().setSubVolumes(vcImageSubVols);
        }
        if (selectedGeometryDefinition == csGeometry) {
            ListOf<org.sbml.jsbml.ext.spatial.CSGObject> listOfcsgObjs = csGeometry.getListOfCSGObjects();
            ArrayList<org.sbml.jsbml.ext.spatial.CSGObject> sbmlCSGs = new ArrayList<org.sbml.jsbml.ext.spatial.CSGObject>(listOfcsgObjs);
            // we want the CSGObj with highest ordinal to be the first
            // element in the CSG subvols array.
            Collections.sort(sbmlCSGs, new Comparator<org.sbml.jsbml.ext.spatial.CSGObject>() {

                @Override
                public int compare(org.sbml.jsbml.ext.spatial.CSGObject lhs, org.sbml.jsbml.ext.spatial.CSGObject rhs) {
                    // minus one to reverse sort
                    return -1 * Integer.compare(lhs.getOrdinal(), rhs.getOrdinal());
                }
            });
            int n = sbmlCSGs.size();
            CSGObject[] vcCSGSubVolumes = new CSGObject[n];
            for (int i = 0; i < n; i++) {
                org.sbml.jsbml.ext.spatial.CSGObject sbmlCSGObject = sbmlCSGs.get(i);
                CSGObject vcellCSGObject = new CSGObject(null, sbmlCSGObject.getDomainType(), i);
                vcellCSGObject.setRoot(getVCellCSGNode(sbmlCSGObject.getCSGNode()));
            }
            vcGeometry.getGeometrySpec().setSubVolumes(vcCSGSubVolumes);
        }
        // Call geom.geomSurfDesc.updateAll() to automatically generate
        // surface classes.
        // vcGsd.updateAll();
        vcGeometry.precomputeAll(new GeometryThumbnailImageFactoryAWT(), true, true);
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new SBMLImportException("Unable to create VC subVolumes from SBML domainTypes : " + e.getMessage(), e);
    }
    // should now map each SBML domain to right VC geometric region.
    GeometricRegion[] vcGeomRegions = vcGsd.getGeometricRegions();
    ISize sampleSize = vcGsd.getVolumeSampleSize();
    RegionInfo[] regionInfos = vcGsd.getRegionImage().getRegionInfos();
    int numX = sampleSize.getX();
    int numY = sampleSize.getY();
    int numZ = sampleSize.getZ();
    double ox = vcOrigin.getX();
    double oy = vcOrigin.getY();
    double oz = vcOrigin.getZ();
    for (Domain domain : listOfDomains) {
        String domainType = domain.getDomainType();
        InteriorPoint interiorPt = domain.getListOfInteriorPoints().get(0);
        if (interiorPt == null) {
            DomainType currDomainType = null;
            for (DomainType dt : sbmlGeometry.getListOfDomainTypes()) {
                if (dt.getSpatialId().equals(domainType)) {
                    currDomainType = dt;
                }
            }
            if (currDomainType.getSpatialDimensions() == 2) {
                continue;
            }
        }
        Coordinate sbmlInteriorPtCoord = new Coordinate(interiorPt.getCoord1(), interiorPt.getCoord2(), interiorPt.getCoord3());
        for (int j = 0; j < vcGeomRegions.length; j++) {
            if (vcGeomRegions[j] instanceof VolumeGeometricRegion) {
                int regionID = ((VolumeGeometricRegion) vcGeomRegions[j]).getRegionID();
                for (int k = 0; k < regionInfos.length; k++) {
                    // (using gemoRegion regionID).
                    if (regionInfos[k].getRegionIndex() == regionID) {
                        int volIndx = 0;
                        Coordinate nearestPtCoord = null;
                        double minDistance = Double.MAX_VALUE;
                        // represented by SBML 'domain[i]'.
                        for (int z = 0; z < numZ; z++) {
                            for (int y = 0; y < numY; y++) {
                                for (int x = 0; x < numX; x++) {
                                    if (regionInfos[k].isIndexInRegion(volIndx)) {
                                        double unit_z = (numZ > 1) ? ((double) z) / (numZ - 1) : 0.5;
                                        double coordZ = oz + vcExtent.getZ() * unit_z;
                                        double unit_y = (numY > 1) ? ((double) y) / (numY - 1) : 0.5;
                                        double coordY = oy + vcExtent.getY() * unit_y;
                                        double unit_x = (numX > 1) ? ((double) x) / (numX - 1) : 0.5;
                                        double coordX = ox + vcExtent.getX() * unit_x;
                                        // for now, find the shortest dist
                                        // coord. Can refine algo later.
                                        Coordinate vcCoord = new Coordinate(coordX, coordY, coordZ);
                                        double distance = sbmlInteriorPtCoord.distanceTo(vcCoord);
                                        if (distance < minDistance) {
                                            minDistance = distance;
                                            nearestPtCoord = vcCoord;
                                        }
                                    }
                                    volIndx++;
                                }
                            // end - for x
                            }
                        // end - for y
                        }
                        // with domain name
                        if (nearestPtCoord != null) {
                            GeometryClass geomClassSBML = vcGeometry.getGeometryClass(domainType);
                            // we know vcGeometryReg[j] is a VolGeomRegion
                            GeometryClass geomClassVC = ((VolumeGeometricRegion) vcGeomRegions[j]).getSubVolume();
                            if (geomClassSBML.compareEqual(geomClassVC)) {
                                vcGeomRegions[j].setName(domain.getId());
                            }
                        }
                    }
                // end if (regInfoIndx = regId)
                }
            // end - for regInfo
            }
        }
    // end for - vcGeomRegions
    }
    // deal with surfaceClass:spDim2-domainTypes
    for (int i = 0; i < surfaceClassDomainTypesVector.size(); i++) {
        DomainType surfaceClassDomainType = surfaceClassDomainTypesVector.elementAt(i);
        // 'surfaceClassDomainType'
        for (Domain d : listOfDomains) {
            if (d.getDomainType().equals(surfaceClassDomainType.getId())) {
                // get the adjacent domains of this 'surface' domain
                // (surface domain + its 2 adj vol domains)
                Set<Domain> adjacentDomainsSet = getAssociatedAdjacentDomains(sbmlGeometry, d);
                // get the domain types of the adjacent domains in SBML and
                // store the corresponding subVol counterparts from VC for
                // adj vol domains
                Vector<SubVolume> adjacentSubVolumesVector = new Vector<SubVolume>();
                Vector<VolumeGeometricRegion> adjVolGeomRegionsVector = new Vector<VolumeGeometricRegion>();
                Iterator<Domain> iterator = adjacentDomainsSet.iterator();
                while (iterator.hasNext()) {
                    Domain dom = iterator.next();
                    DomainType dt = getBySpatialID(sbmlGeometry.getListOfDomainTypes(), dom.getDomainType());
                    if (dt.getSpatialDimensions() == 3) {
                        // for domain type with sp. dim = 3, get
                        // correspoinding subVol from VC geometry.
                        GeometryClass gc = vcGeometry.getGeometryClass(dt.getId());
                        adjacentSubVolumesVector.add((SubVolume) gc);
                        // store volGeomRegions corresponding to this (vol)
                        // geomClass in adjVolGeomRegionsVector : this
                        // should return ONLY 1 region for subVol.
                        GeometricRegion[] geomRegion = vcGsd.getGeometricRegions(gc);
                        adjVolGeomRegionsVector.add((VolumeGeometricRegion) geomRegion[0]);
                    }
                }
                // there should be only 2 subVols in this vector
                if (adjacentSubVolumesVector.size() != 2) {
                    throw new RuntimeException("Cannot have more or less than 2 subvolumes that are adjacent to surface (membrane) '" + d.getId() + "'");
                }
                // get the surface class with these 2 adj subVols. Set its
                // name to that of 'surfaceClassDomainType'
                SurfaceClass surfacClass = vcGsd.getSurfaceClass(adjacentSubVolumesVector.get(0), adjacentSubVolumesVector.get(1));
                surfacClass.setName(surfaceClassDomainType.getSpatialId());
                // get surfaceGeometricRegion that has adjVolGeomRegions as
                // its adjacent vol geom regions and set its name from
                // domain 'd'
                SurfaceGeometricRegion surfaceGeomRegion = getAssociatedSurfaceGeometricRegion(vcGsd, adjVolGeomRegionsVector);
                if (surfaceGeomRegion != null) {
                    surfaceGeomRegion.setName(d.getId());
                }
            }
        // end if - domain.domainType == surfaceClassDomainType
        }
    // end for - numDomains
    }
    // structureMappings in VC from compartmentMappings in SBML
    try {
        // set geometry first and then set structureMappings?
        vcBioModel.getSimulationContext(0).setGeometry(vcGeometry);
        // update simContextName ...
        vcBioModel.getSimulationContext(0).setName(vcBioModel.getSimulationContext(0).getName() + "_" + vcGeometry.getName());
        Model vcModel = vcBioModel.getSimulationContext(0).getModel();
        ModelUnitSystem vcModelUnitSystem = vcModel.getUnitSystem();
        Vector<StructureMapping> structMappingsVector = new Vector<StructureMapping>();
        SpatialCompartmentPlugin cplugin = null;
        for (int i = 0; i < sbmlModel.getNumCompartments(); i++) {
            Compartment c = sbmlModel.getCompartment(i);
            String cname = c.getName();
            cplugin = (SpatialCompartmentPlugin) c.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
            CompartmentMapping compMapping = cplugin.getCompartmentMapping();
            if (compMapping != null) {
                // final String id = compMapping.getId();
                // final String name = compMapping.getName();
                CastInfo<Structure> ci = SBMLHelper.getTypedStructure(Structure.class, vcModel, cname);
                if (ci.isGood()) {
                    Structure struct = ci.get();
                    String domainType = compMapping.getDomainType();
                    GeometryClass geometryClass = vcGeometry.getGeometryClass(domainType);
                    double unitSize = compMapping.getUnitSize();
                    Feature feat = BeanUtils.downcast(Feature.class, struct);
                    if (feat != null) {
                        FeatureMapping featureMapping = new FeatureMapping(feat, vcBioModel.getSimulationContext(0), vcModelUnitSystem);
                        featureMapping.setGeometryClass(geometryClass);
                        if (geometryClass instanceof SubVolume) {
                            featureMapping.getVolumePerUnitVolumeParameter().setExpression(new Expression(unitSize));
                        } else if (geometryClass instanceof SurfaceClass) {
                            featureMapping.getVolumePerUnitAreaParameter().setExpression(new Expression(unitSize));
                        }
                        structMappingsVector.add(featureMapping);
                    } else if (struct instanceof Membrane) {
                        MembraneMapping membraneMapping = new MembraneMapping((Membrane) struct, vcBioModel.getSimulationContext(0), vcModelUnitSystem);
                        membraneMapping.setGeometryClass(geometryClass);
                        if (geometryClass instanceof SubVolume) {
                            membraneMapping.getAreaPerUnitVolumeParameter().setExpression(new Expression(unitSize));
                        } else if (geometryClass instanceof SurfaceClass) {
                            membraneMapping.getAreaPerUnitAreaParameter().setExpression(new Expression(unitSize));
                        }
                        structMappingsVector.add(membraneMapping);
                    }
                }
            }
        }
        StructureMapping[] structMappings = structMappingsVector.toArray(new StructureMapping[0]);
        vcBioModel.getSimulationContext(0).getGeometryContext().setStructureMappings(structMappings);
        // if type from SBML parameter Boundary Condn is not the same as the
        // boundary type of the
        // structureMapping of structure of paramSpContext, set the boundary
        // condn type of the structureMapping
        // to the value of 'type' from SBML parameter Boundary Condn.
        ListOf<Parameter> listOfGlobalParams = sbmlModel.getListOfParameters();
        for (Parameter sbmlGlobalParam : sbmlModel.getListOfParameters()) {
            SpatialParameterPlugin spplugin = (SpatialParameterPlugin) sbmlGlobalParam.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
            ParameterType paramType = spplugin.getParamType();
            if (!(paramType instanceof BoundaryCondition)) {
                continue;
            }
            BoundaryCondition bCondn = (BoundaryCondition) paramType;
            if (bCondn.isSetVariable()) {
                // get the var of boundaryCondn; find appropriate spContext
                // in vcell;
                SpeciesContext paramSpContext = vcBioModel.getSimulationContext(0).getModel().getSpeciesContext(bCondn.getVariable());
                if (paramSpContext != null) {
                    Structure s = paramSpContext.getStructure();
                    StructureMapping sm = vcBioModel.getSimulationContext(0).getGeometryContext().getStructureMapping(s);
                    if (sm != null) {
                        BoundaryConditionType bct = null;
                        switch(bCondn.getType()) {
                            case Dirichlet:
                                {
                                    bct = BoundaryConditionType.DIRICHLET;
                                    break;
                                }
                            case Neumann:
                                {
                                    bct = BoundaryConditionType.NEUMANN;
                                    break;
                                }
                            case Robin_inwardNormalGradientCoefficient:
                            case Robin_sum:
                            case Robin_valueCoefficient:
                            default:
                                throw new RuntimeException("boundary condition type " + bCondn.getType().name() + " not supported");
                        }
                        for (CoordinateComponent coordComp : getSbmlGeometry().getListOfCoordinateComponents()) {
                            if (bCondn.getSpatialRef().equals(coordComp.getBoundaryMinimum().getSpatialId())) {
                                switch(coordComp.getType()) {
                                    case cartesianX:
                                        {
                                            sm.setBoundaryConditionTypeXm(bct);
                                        }
                                    case cartesianY:
                                        {
                                            sm.setBoundaryConditionTypeYm(bct);
                                        }
                                    case cartesianZ:
                                        {
                                            sm.setBoundaryConditionTypeZm(bct);
                                        }
                                }
                            }
                            if (bCondn.getSpatialRef().equals(coordComp.getBoundaryMaximum().getSpatialId())) {
                                switch(coordComp.getType()) {
                                    case cartesianX:
                                        {
                                            sm.setBoundaryConditionTypeXm(bct);
                                        }
                                    case cartesianY:
                                        {
                                            sm.setBoundaryConditionTypeYm(bct);
                                        }
                                    case cartesianZ:
                                        {
                                            sm.setBoundaryConditionTypeZm(bct);
                                        }
                                }
                            }
                        }
                    } else // sm != null
                    {
                        logger.sendMessage(VCLogger.Priority.MediumPriority, VCLogger.ErrorType.OverallWarning, "No structure " + s.getName() + " requested by species context " + paramSpContext.getName());
                    }
                }
            // end if (paramSpContext != null)
            }
        // end if (bCondn.isSetVar())
        }
        // end for (sbmlModel.numParams)
        vcBioModel.getSimulationContext(0).getGeometryContext().refreshStructureMappings();
        vcBioModel.getSimulationContext(0).refreshSpatialObjects();
    } catch (Exception e) {
        e.printStackTrace(System.out);
        throw new SBMLImportException("Unable to create VC structureMappings from SBML compartment mappings : " + e.getMessage(), e);
    }
}

Example 22 with Expression

use of cbit.vcell.parser.Expression in project vcell by virtualcell.

the class RationalExp method getTermExpression.

private cbit.vcell.parser.Expression getTermExpression(Term term) throws ExpressionException {
    cbit.vcell.parser.Expression exp = new cbit.vcell.parser.Expression(term.getCoefficient().doubleValue());
    while (!term.symbolList.isEmpty()) {
        String symbol = term.symbolList.remove(0);
        int count = 1;
        while (term.symbolList.remove(symbol)) {
            count++;
        }
        cbit.vcell.parser.Expression tempExp = null;
        if (count == 1) {
            exp = cbit.vcell.parser.Expression.mult(exp, new cbit.vcell.parser.Expression(symbol));
        } else {
            exp = cbit.vcell.parser.Expression.mult(exp, cbit.vcell.parser.Expression.power(new Expression(symbol), count));
        }
    }
    return exp;
}

Example 23 with Expression

use of cbit.vcell.parser.Expression in project vcell by virtualcell.

the class ModelTest method getExample_Bound.

/**
 * This method was created by a SmartGuide.
 */
public static Model getExample_Bound() throws Exception {
    double FRACTIONAL_VOLUME_ER = 0.15;
    double SURFACE_TO_VOLUME_ER = 6;
    double FRACTIONAL_VOLUME_CYTOSOL = 0.15;
    double SURFACE_TO_VOLUME_CYTOSOL = 0.25;
    org.vcell.util.document.Version version = new org.vcell.util.document.Version("boundModel", new org.vcell.util.document.User("frm", new org.vcell.util.document.KeyValue("227")));
    Model model = new Model(version);
    FormalSpeciesInfo fsi = null;
    DBFormalSpecies dbfs = null;
    DBSpecies dbs = null;
    String[] names1 = new String[1];
    names1[0] = "IP3";
    fsi = new CompoundInfo(names1[0] + "_KeggID", names1, names1[0] + "_Formula", names1[0] + "_casID", null);
    dbfs = new FormalCompound(new org.vcell.util.document.KeyValue("0"), (CompoundInfo) fsi);
    dbs = new BoundCompound(new org.vcell.util.document.KeyValue("1"), (FormalCompound) dbfs);
    model.addSpecies(new Species(names1[0], null, dbs));
    String[] names2 = new String[1];
    names2[0] = "Calcium";
    fsi = new CompoundInfo(names2[0] + "_KeggID", names2, names2[0] + "_Formula", names2[0] + "_casID", null);
    dbfs = new FormalCompound(new org.vcell.util.document.KeyValue("2"), (CompoundInfo) fsi);
    dbs = new BoundCompound(new org.vcell.util.document.KeyValue("3"), (FormalCompound) dbfs);
    model.addSpecies(new Species(names2[0], null, dbs));
    String keywords = "keword1,keyword2";
    String descr = "Decription Text";
    String[] names3 = new String[1];
    names3[0] = "IP3_Receptor";
    fsi = new ProteinInfo(names3[0] + "_SwissProtID", names3, names3[0] + "_Organism", names3[0] + "_Accession", keywords, descr);
    dbfs = new FormalProtein(new org.vcell.util.document.KeyValue("4"), (ProteinInfo) fsi);
    dbs = new BoundProtein(new org.vcell.util.document.KeyValue("5"), (FormalProtein) dbfs);
    model.addSpecies(new Species(names3[0], null, dbs));
    // names[0] = "IP3_Receptor_Activated";
    // fsi = new ProteinInfo(names[0]+"_SwissProtID",names,names[0]+"_Organism",names[0]+"_Accession",keywords,descr);
    // dbfs = new FormalProtein(new cbit.sql.KeyValue("6"),(ProteinInfo)fsi);
    // dbs = new BoundProtein(new cbit.sql.KeyValue("7"),(FormalProtein)dbfs);
    // make 1 unbound
    model.addSpecies(new Species("IP3_Receptor_Activated", null));
    model.addFeature("Extracellular");
    Feature extracellular = (Feature) model.getStructure("Extracellular");
    model.addFeature("Cytosol");
    Feature cytosol = (Feature) model.getStructure("Cytosol");
    Membrane plasmaMembrane = (Membrane) model.getStructure("PlasmaMembrane");
    model.addFeature("ER");
    Feature er = (Feature) model.getStructure("ER");
    Membrane erMembrane = (Membrane) model.getStructure("ER_Membrane");
    Species calcium = model.getSpecies("Calcium");
    Species ip3 = model.getSpecies("IP3");
    Species r = model.getSpecies("IP3_Receptor");
    Species ri = model.getSpecies("IP3_Receptor_Activated");
    model.addSpeciesContext(calcium, er);
    model.addSpeciesContext(calcium, cytosol);
    model.addSpeciesContext(calcium, extracellular);
    model.addSpeciesContext(ip3, cytosol);
    model.addSpeciesContext(ip3, extracellular);
    model.addSpeciesContext(r, erMembrane);
    model.addSpeciesContext(ri, erMembrane);
    SpeciesContext ip3_cytosol = model.getSpeciesContext(ip3, cytosol);
    SpeciesContext ip3_extracellular = model.getSpeciesContext(ip3, extracellular);
    SpeciesContext calcium_cytosol = model.getSpeciesContext(calcium, cytosol);
    SpeciesContext calcium_extracellular = model.getSpeciesContext(calcium, extracellular);
    SpeciesContext calcium_er = model.getSpeciesContext(calcium, er);
    SpeciesContext r_erMembrane = model.getSpeciesContext(r, erMembrane);
    SpeciesContext ri_erMembrane = model.getSpeciesContext(ri, erMembrane);
    SimpleReaction sr;
    SimpleReaction sr1;
    FluxReaction fr;
    // 
    // CYTOSOL REACTIONS
    // 
    // 1.0/12.0;
    double IP3_DEGRADATION = 0.5;
    double IP3_DESIRED_INITIAL = 0.01;
    double IP3_DESIRED_FINAL = 0.03;
    double PLASMA_MEM_SURFACE_TO_VOLUME_ER = 0.25;
    double IP3_FLUX_TIME_CONSTANT = 0.050;
    double IP3_FLUX_FINAL = IP3_DEGRADATION * (IP3_DESIRED_FINAL - IP3_DESIRED_INITIAL) * (1 - FRACTIONAL_VOLUME_ER) / PLASMA_MEM_SURFACE_TO_VOLUME_ER;
    // 
    // IP3_DEGRADATION
    // IP3 ----------------->
    // 
    // 
    // source(IP3) = IP3_DEGRADATION * IP3_DESIRED_INITIAL
    // 
    // model.addReaction("IP3_Volume");
    // reaction = model.getReaction("IP3_Volume");
    sr = new SimpleReaction(model, cytosol, "IP3_DEGRADATION", true);
    sr.addReactant(ip3_cytosol, 1);
    sr.setKinetics(new MassActionKinetics(sr));
    MassActionKinetics massAct = (MassActionKinetics) sr.getKinetics();
    massAct.setParameterValue(massAct.getForwardRateParameter(), new Expression("Kdegr1;"));
    massAct.setParameterValue(massAct.getKineticsParameter("Kdegr1"), new Expression(IP3_DEGRADATION));
    model.addReactionStep(sr);
    sr = new SimpleReaction(model, cytosol, "IP3_BASAL_CREATION", true);
    sr.addProduct(ip3_cytosol, 1);
    massAct = new MassActionKinetics(sr);
    sr.setKinetics(massAct);
    massAct.setParameterValue(massAct.getForwardRateParameter(), new Expression("Kdegr2 * IP3i;"));
    massAct.setParameterValue(massAct.getKineticsParameter("Kdegr2"), new Expression(IP3_DEGRADATION));
    massAct.setParameterValue(massAct.getKineticsParameter("IP3i"), new Expression(IP3_DESIRED_INITIAL));
    model.addReactionStep(sr);
    sr1 = new SimpleReaction(model, cytosol, "IP3_DEGRADATION2", true);
    sr1.addReactant(ip3_cytosol, 1);
    sr1.setKinetics(new HMM_IRRKinetics(sr1));
    HMM_IRRKinetics hmmKinetics = (HMM_IRRKinetics) sr1.getKinetics();
    hmmKinetics.setParameterValue(hmmKinetics.getVmaxParameter(), new Expression("10.0"));
    hmmKinetics.setParameterValue(hmmKinetics.getKmParameter(), new Expression("12.0"));
    model.addReactionStep(sr1);
    // 
    // flux(IP3) = IP3_FLUX_FINAL * (1 - exp(-t/IP3_FLUX_TIME_CONSTANT))
    // 
    // model.addReaction("IP3_generation");
    // reaction = model.getReaction("IP3_generation");
    fr = new FluxReaction(model, plasmaMembrane, null, "IP3_FLUX", true);
    GeneralKinetics genKinetics = new GeneralKinetics(fr);
    fr.setKinetics(genKinetics);
    genKinetics.setParameterValue(genKinetics.getReactionRateParameter(), new Expression("Jfinal * (1 - exp(-t/TAU));"));
    genKinetics.setParameterValue(genKinetics.getKineticsParameter("Jfinal"), new Expression(0.034));
    genKinetics.setParameterValue(genKinetics.getKineticsParameter("TAU"), new Expression(IP3_FLUX_TIME_CONSTANT));
    model.addReactionStep(fr);
    // 
    // ER REACTIONS
    // 
    // 
    // IP3 Receptor
    // 
    double I1 = 3.33333333;
    double ii1 = 100;
    double i1 = ii1 / I1;
    double channel_density = 25;
    // channel_density / (1 + IP3_DESIRED_INITIAL * I1);
    double R = 19.35;
    // channel_density * IP3_DESIRED_INITIAL * I1 * R;
    double RI = 0.65;
    double TOTAL_CHANNEL = R + RI;
    double channel_flux = 143.7;
    double CALCIUM_DIFFUSION = 180.0;
    double IP3_DIFFUSION = 250;
    double CALCIUM_CYTOSOL = 0.050;
    double CALCIUM_ER = 2500.0;
    double CALCIUM_EXTRACELLULAR_INITIAL = 1000;
    double IP3_EXTRACELLULAR_INITIAL = 10;
    // model.addReaction("IP3_Receptor");
    // reaction = model.getReaction("IP3_Receptor");
    sr = new SimpleReaction(model, erMembrane, "IP3_BINDING", true);
    sr.addReactant(r_erMembrane, 2);
    sr.addReactant(ip3_cytosol, 3);
    sr.addProduct(ri_erMembrane, 1);
    massAct = new MassActionKinetics(sr);
    sr.setKinetics(massAct);
    massAct.setParameterValue(massAct.getForwardRateParameter(), new Expression("ii1;"));
    massAct.setParameterValue(massAct.getReverseRateParameter(), new Expression("i1;"));
    massAct.setParameterValue(massAct.getKineticsParameter("ii1"), new Expression(ii1));
    massAct.setParameterValue(massAct.getKineticsParameter("i1"), new Expression("ii1/I1"));
    massAct.setParameterValue(massAct.getKineticsParameter("I1"), new Expression(I1));
    model.addReactionStep(sr);
    fr = new FluxReaction(model, erMembrane, null, "IP3R_FLUX", true);
    fr.addCatalyst(ri_erMembrane);
    // fr.addCatalyst(calcium_cytosol);
    // fr.addCatalyst(calcium_er);
    // fr.setInwardFlux(-channel_flux+" * "+ (4/(channel_density*channel_density))+" * pow(RI,3);");
    genKinetics = (GeneralKinetics) fr.getKinetics();
    genKinetics.setParameterValue(genKinetics.getReactionRateParameter(), new Expression("Jchan * (" + calcium_cytosol.getName() + " - " + calcium_er.getName() + ") * pow(" + ri_erMembrane.getName() + "/Rtotal,3);"));
    genKinetics.setParameterValue(genKinetics.getKineticsParameter("Rtotal"), new Expression(TOTAL_CHANNEL));
    genKinetics.setParameterValue(genKinetics.getKineticsParameter("Jchan"), new Expression(4.6));
    model.addReactionStep(fr);
    // 
    // SERCA pump
    // 
    double K_serca = 0.270;
    double pump_coef = (K_serca * K_serca + CALCIUM_CYTOSOL * CALCIUM_CYTOSOL) * channel_flux * 4 * RI * RI * RI / (channel_density * channel_density * CALCIUM_CYTOSOL * CALCIUM_CYTOSOL);
    // model.addReaction("Serca_Pump");
    // reaction = model.getReaction("Serca_Pump");
    fr = new FluxReaction(model, erMembrane, null, "SERCA_FLUX", true);
    genKinetics = (GeneralKinetics) fr.getKinetics();
    genKinetics.setParameterValue(genKinetics.getReactionRateParameter(), new Expression("Vmax * pow(" + calcium_cytosol.getName() + ",2) / (pow(Kd,2) + pow(" + calcium_er.getName() + ",2));"));
    genKinetics.setParameterValue(genKinetics.getKineticsParameter("Kd"), new Expression(0.7));
    genKinetics.setParameterValue(genKinetics.getKineticsParameter("Vmax"), new Expression(77.77));
    model.addReactionStep(fr);
    SpeciesContext sc = model.getSpeciesContext(r, erMembrane);
    // sc.setInitialValue(R);
    sc = model.getSpeciesContext(ri, erMembrane);
    // sc.setInitialValue(RI);
    sc = model.getSpeciesContext(calcium, er);
    // sc.setInitialValue(CALCIUM_ER);
    sc = model.getSpeciesContext(calcium, cytosol);
    // sc.setInitialValue(CALCIUM_CYTOSOL);
    // sc.setDiffusionRate(CALCIUM_DIFFUSION);
    sc = model.getSpeciesContext(calcium, extracellular);
    // sc.setDiffusionRate(CALCIUM_DIFFUSION);
    // sc.setInitialValue(CALCIUM_EXTRACELLULAR_INITIAL);
    sc = model.getSpeciesContext(ip3, cytosol);
    // sc.setInitialValue(IP3_DESIRED_INITIAL);
    // sc.setDiffusionRate(IP3_DIFFUSION);
    sc = model.getSpeciesContext(ip3, extracellular);
    return model;
}

Example 24 with Expression

use of cbit.vcell.parser.Expression in project vcell by virtualcell.

the class ModelTest method getExample2_Fast.

/**
 * This method was created by a SmartGuide.
 */
public static Model getExample2_Fast() throws Exception {
    double A_init = 10.0;
    double B_init = 20.0;
    double C_init = 30.0;
    double D_init = 40.0;
    double E_init = 50.0;
    double F_init = 60.0;
    double A_diff = 11.0;
    double B_diff = 22.0;
    double C_diff = 33.0;
    double D_diff = 44.0;
    double E_diff = 55.0;
    double F_diff = 66.0;
    Model model = new Model("model1");
    model.addSpecies(new Species("A", "A"));
    Species A = model.getSpecies("A");
    model.addSpecies(new Species("B", "B"));
    Species B = model.getSpecies("B");
    model.addSpecies(new Species("C", "C"));
    Species C = model.getSpecies("C");
    model.addSpecies(new Species("D", "D"));
    Species D = model.getSpecies("D");
    model.addSpecies(new Species("E", "E"));
    Species E = model.getSpecies("E");
    model.addSpecies(new Species("F", "F"));
    Species F = model.getSpecies("F");
    model.addFeature("Cytosol");
    Feature cytosol = (Feature) model.getStructure("Cytosol");
    model.addSpeciesContext(F, cytosol);
    SpeciesContext F_cyt = model.getSpeciesContext(F, cytosol);
    // F_cyt.setInitialValue(F_init);
    // F_cyt.setDiffusionRate(F_diff);
    model.addSpeciesContext(A, cytosol);
    SpeciesContext A_cyt = model.getSpeciesContext(A, cytosol);
    // A_cyt.setInitialValue(A_init);
    // A_cyt.setDiffusionRate(A_diff);
    model.addSpeciesContext(B, cytosol);
    SpeciesContext B_cyt = model.getSpeciesContext(B, cytosol);
    // B_cyt.setInitialValue(B_init);
    // B_cyt.setDiffusionRate(B_diff);
    model.addSpeciesContext(D, cytosol);
    SpeciesContext D_cyt = model.getSpeciesContext(D, cytosol);
    // D_cyt.setInitialValue(D_init);
    // D_cyt.setDiffusionRate(D_diff);
    model.addSpeciesContext(E, cytosol);
    SpeciesContext E_cyt = model.getSpeciesContext(E, cytosol);
    // E_cyt.setInitialValue(E_init);
    // E_cyt.setDiffusionRate(E_diff);
    model.addSpeciesContext(C, cytosol);
    SpeciesContext C_cyt = model.getSpeciesContext(C, cytosol);
    // C_cyt.setInitialValue(C_init);
    // C_cyt.setDiffusionRate(C_diff);
    SimpleReaction sr;
    // 
    // CYTOSOL REACTIONS
    // 
    double K1f = 1.0;
    double K1r = 1.0;
    double K2f = 200.0;
    double K2r = 300.0;
    double K3f = 4.0;
    double K3r = 4.0;
    sr = new SimpleReaction(model, cytosol, "SIMPLE_REACTION_ABC", true);
    sr.addReactant(A_cyt, 1);
    sr.addReactant(B_cyt, 1);
    sr.addProduct(C_cyt, 1);
    MassActionKinetics massAct = new MassActionKinetics(sr);
    massAct.setParameterValue(massAct.getForwardRateParameter(), new Expression(K1f));
    massAct.setParameterValue(massAct.getReverseRateParameter(), new Expression(K1r));
    massAct.getForwardRateParameter().setName("K1f");
    massAct.getReverseRateParameter().setName("K1r");
    // massAct.setFast(false);
    sr.setKinetics(massAct);
    model.addReactionStep(sr);
    sr = new SimpleReaction(model, cytosol, "SIMPLE_REACTION_CDE", true);
    sr.addReactant(C_cyt, 1);
    sr.addReactant(D_cyt, 1);
    sr.addProduct(E_cyt, 1);
    massAct = new MassActionKinetics(sr);
    massAct.setParameterValue(massAct.getForwardRateParameter(), new Expression(K2f));
    massAct.setParameterValue(massAct.getReverseRateParameter(), new Expression(K2r));
    massAct.getForwardRateParameter().setName("K2f");
    massAct.getReverseRateParameter().setName("K2r");
    // massAct.setFast(true);
    sr.setKinetics(massAct);
    model.addReactionStep(sr);
    sr = new SimpleReaction(model, cytosol, "SIMPLE_REACTION_EAF", true);
    sr.addReactant(E_cyt, 1);
    sr.addReactant(A_cyt, 1);
    sr.addProduct(F_cyt, 1);
    massAct = new MassActionKinetics(sr);
    massAct.setParameterValue(massAct.getForwardRateParameter(), new Expression(K3f));
    massAct.setParameterValue(massAct.getReverseRateParameter(), new Expression(K3r));
    massAct.getForwardRateParameter().setName("K3f");
    massAct.getReverseRateParameter().setName("K3r");
    // massAct.setFast(false);
    sr.setKinetics(massAct);
    model.addReactionStep(sr);
    return model;
}

Example 25 with Expression

use of cbit.vcell.parser.Expression in project vcell by virtualcell.

the class ModelTest method getExample.

/**
 * This method was created by a SmartGuide.
 */
public static Model getExample() throws Exception {
    double FRACTIONAL_VOLUME_ER = 0.15;
    double SURFACE_TO_VOLUME_ER = 6;
    double FRACTIONAL_VOLUME_CYTOSOL = 0.15;
    double SURFACE_TO_VOLUME_CYTOSOL = 0.25;
    Model model = new Model("model1");
    model.addSpecies(new Species("IP3", "Inositol-trisphosphate(1,4,5)"));
    model.addSpecies(new Species("Ca", "Calcium"));
    model.addSpecies(new Species("R", "IP3-Receptor"));
    model.addSpecies(new Species("RI", "IP3-Receptor-Activated"));
    model.addFeature("Extracellular");
    Feature extracellular = (Feature) model.getStructure("Extracellular");
    model.addFeature("Cytosol");
    Feature cytosol = (Feature) model.getStructure("Cytosol");
    Membrane plasmaMembrane = (Membrane) model.getStructure("PlasmaMembrane");
    model.addFeature("ER");
    Feature er = (Feature) model.getStructure("ER");
    Membrane erMembrane = (Membrane) model.getStructure("ER_Membrane");
    Species calcium = model.getSpecies("Ca");
    Species ip3 = model.getSpecies("IP3");
    Species r = model.getSpecies("R");
    Species ri = model.getSpecies("RI");
    model.addSpeciesContext(calcium, er);
    model.addSpeciesContext(calcium, cytosol);
    model.addSpeciesContext(calcium, extracellular);
    model.addSpeciesContext(ip3, cytosol);
    model.addSpeciesContext(ip3, extracellular);
    model.addSpeciesContext(r, erMembrane);
    model.addSpeciesContext(ri, erMembrane);
    SpeciesContext ip3_cytosol = model.getSpeciesContext(ip3, cytosol);
    SpeciesContext ip3_extracellular = model.getSpeciesContext(ip3, extracellular);
    SpeciesContext calcium_cytosol = model.getSpeciesContext(calcium, cytosol);
    SpeciesContext calcium_extracellular = model.getSpeciesContext(calcium, extracellular);
    SpeciesContext calcium_er = model.getSpeciesContext(calcium, er);
    SpeciesContext r_erMembrane = model.getSpeciesContext(r, erMembrane);
    SpeciesContext ri_erMembrane = model.getSpeciesContext(ri, erMembrane);
    SimpleReaction sr;
    SimpleReaction sr1;
    FluxReaction fr;
    // 
    // CYTOSOL REACTIONS
    // 
    // 1.0/12.0;
    double IP3_DEGRADATION = 0.5;
    double IP3_DESIRED_INITIAL = 0.01;
    double IP3_DESIRED_FINAL = 0.03;
    double PLASMA_MEM_SURFACE_TO_VOLUME_ER = 0.25;
    double IP3_FLUX_TIME_CONSTANT = 0.050;
    double IP3_FLUX_FINAL = IP3_DEGRADATION * (IP3_DESIRED_FINAL - IP3_DESIRED_INITIAL) * (1 - FRACTIONAL_VOLUME_ER) / PLASMA_MEM_SURFACE_TO_VOLUME_ER;
    // 
    // IP3_DEGRADATION
    // IP3 ----------------->
    // 
    // 
    // source(IP3) = IP3_DEGRADATION * IP3_DESIRED_INITIAL
    // 
    // model.addReaction("IP3_Volume");
    // reaction = model.getReaction("IP3_Volume");
    sr = new SimpleReaction(model, cytosol, "IP3_DEGRADATION", true);
    sr.setModel(model);
    sr.addReactant(ip3_cytosol, 1);
    sr.setKinetics(new MassActionKinetics(sr));
    MassActionKinetics massAct = (MassActionKinetics) sr.getKinetics();
    massAct.setParameterValue(massAct.getForwardRateParameter(), new Expression("Kdegr1;"));
    massAct.setParameterValue(massAct.getKineticsParameter("Kdegr1"), new Expression(IP3_DEGRADATION));
    model.addReactionStep(sr);
    sr = new SimpleReaction(model, cytosol, "IP3_BASAL_CREATION", true);
    sr.setModel(model);
    sr.addProduct(ip3_cytosol, 1);
    massAct = new MassActionKinetics(sr);
    sr.setKinetics(massAct);
    massAct.setParameterValue(massAct.getForwardRateParameter(), new Expression("Kdegr2 * IP3i;"));
    massAct.setParameterValue(massAct.getKineticsParameter("Kdegr2"), new Expression(IP3_DEGRADATION));
    massAct.setParameterValue(massAct.getKineticsParameter("IP3i"), new Expression(IP3_DESIRED_INITIAL));
    model.addReactionStep(sr);
    sr1 = new SimpleReaction(model, cytosol, "IP3_DEGRADATION1", true);
    sr1.setModel(model);
    sr1.addReactant(ip3_cytosol, 1);
    sr1.setKinetics(new HMM_IRRKinetics(sr1));
    HMM_IRRKinetics hmmKinetics = (HMM_IRRKinetics) sr1.getKinetics();
    hmmKinetics.setParameterValue(hmmKinetics.getVmaxParameter(), new Expression("10.0"));
    hmmKinetics.setParameterValue(hmmKinetics.getKmParameter(), new Expression("12.0"));
    model.addReactionStep(sr1);
    // 
    // flux(IP3) = IP3_FLUX_FINAL * (1 - exp(-t/IP3_FLUX_TIME_CONSTANT))
    // 
    // model.addReaction("IP3_generation");
    // reaction = model.getReaction("IP3_generation");
    fr = new FluxReaction(model, plasmaMembrane, null, "IP3_FLUX", true);
    fr.setModel(model);
    GeneralKinetics genKinetics = new GeneralKinetics(fr);
    fr.setKinetics(genKinetics);
    genKinetics.setParameterValue(genKinetics.getReactionRateParameter(), new Expression("Jfinal * (1 - exp(-t/TAU));"));
    genKinetics.setParameterValue(massAct.getKineticsParameter("Jfinal"), new Expression(0.034));
    genKinetics.setParameterValue(massAct.getKineticsParameter("TAU"), new Expression(IP3_FLUX_TIME_CONSTANT));
    model.addReactionStep(fr);
    // 
    // ER REACTIONS
    // 
    // 
    // IP3 Receptor
    // 
    double I1 = 3.33333333;
    double ii1 = 100;
    double i1 = ii1 / I1;
    double channel_density = 25;
    // channel_density / (1 + IP3_DESIRED_INITIAL * I1);
    double R = 19.35;
    // channel_density * IP3_DESIRED_INITIAL * I1 * R;
    double RI = 0.65;
    double TOTAL_CHANNEL = R + RI;
    double channel_flux = 143.7;
    double CALCIUM_DIFFUSION = 180.0;
    double IP3_DIFFUSION = 250;
    double CALCIUM_CYTOSOL = 0.050;
    double CALCIUM_ER = 2500.0;
    double CALCIUM_EXTRACELLULAR_INITIAL = 1000;
    double IP3_EXTRACELLULAR_INITIAL = 10;
    // model.addReaction("IP3_Receptor");
    // reaction = model.getReaction("IP3_Receptor");
    sr = new SimpleReaction(model, erMembrane, "IP3_BINDING", true);
    sr.setModel(model);
    sr.addReactant(r_erMembrane, 2);
    sr.addReactant(ip3_cytosol, 3);
    sr.addProduct(ri_erMembrane, 1);
    massAct = new MassActionKinetics(sr);
    sr.setKinetics(massAct);
    massAct.setParameterValue(massAct.getForwardRateParameter(), new Expression("ii1;"));
    massAct.setParameterValue(massAct.getReverseRateParameter(), new Expression("i1;"));
    massAct.setParameterValue(massAct.getKineticsParameter("ii1"), new Expression(ii1));
    massAct.setParameterValue(massAct.getKineticsParameter("i1"), new Expression("ii1/I1"));
    massAct.setParameterValue(massAct.getKineticsParameter("I1"), new Expression(I1));
    model.addReactionStep(sr);
    fr = new FluxReaction(model, erMembrane, null, "IP3R_FLUX", true);
    fr.setModel(model);
    fr.addCatalyst(ri_erMembrane);
    // fr.addCatalyst(calcium_cytosol);
    // fr.addCatalyst(calcium_er);
    // fr.setInwardFlux(-channel_flux+" * "+ (4/(channel_density*channel_density))+" * pow(RI,3);");
    genKinetics = (GeneralKinetics) fr.getKinetics();
    genKinetics.setParameterValue(genKinetics.getReactionRateParameter(), new Expression("Jchan * (" + calcium_cytosol.getName() + " - " + calcium_er.getName() + ") * pow(" + ri_erMembrane.getName() + "/Rtotal,3);"));
    genKinetics.setParameterValue(genKinetics.getKineticsParameter("Rtotal"), new Expression(TOTAL_CHANNEL));
    genKinetics.setParameterValue(genKinetics.getKineticsParameter("Jchan"), new Expression(4.6));
    model.addReactionStep(fr);
    // 
    // SERCA pump
    // 
    double K_serca = 0.270;
    double pump_coef = (K_serca * K_serca + CALCIUM_CYTOSOL * CALCIUM_CYTOSOL) * channel_flux * 4 * RI * RI * RI / (channel_density * channel_density * CALCIUM_CYTOSOL * CALCIUM_CYTOSOL);
    // model.addReaction("Serca_Pump");
    // reaction = model.getReaction("Serca_Pump");
    fr = new FluxReaction(model, erMembrane, null, "SERCA_FLUX", true);
    fr.setModel(model);
    genKinetics = (GeneralKinetics) fr.getKinetics();
    genKinetics.setParameterValue(genKinetics.getReactionRateParameter(), new Expression("Vmax * pow(" + calcium_cytosol.getName() + ",2) / (pow(Kd,2) + pow(" + calcium_er.getName() + ",2));"));
    genKinetics.setParameterValue(genKinetics.getKineticsParameter("Kd"), new Expression(0.7));
    genKinetics.setParameterValue(genKinetics.getKineticsParameter("Vmax"), new Expression(77.77));
    model.addReactionStep(fr);
    SpeciesContext sc = model.getSpeciesContext(r, erMembrane);
    // sc.setInitialValue(R);
    sc = model.getSpeciesContext(ri, erMembrane);
    // sc.setInitialValue(RI);
    sc = model.getSpeciesContext(calcium, er);
    // sc.setInitialValue(CALCIUM_ER);
    sc = model.getSpeciesContext(calcium, cytosol);
    // sc.setInitialValue(CALCIUM_CYTOSOL);
    // sc.setDiffusionRate(CALCIUM_DIFFUSION);
    sc = model.getSpeciesContext(calcium, extracellular);
    // sc.setDiffusionRate(CALCIUM_DIFFUSION);
    // sc.setInitialValue(CALCIUM_EXTRACELLULAR_INITIAL);
    sc = model.getSpeciesContext(ip3, cytosol);
    // sc.setInitialValue(IP3_DESIRED_INITIAL);
    // sc.setDiffusionRate(IP3_DIFFUSION);
    sc = model.getSpeciesContext(ip3, extracellular);
    return model;
}