Examples with AssignmentRule org.sbml.jsbml.AssignmentRule used on opensource projects

Example 6 with AssignmentRule

use of org.sbml.jsbml.AssignmentRule in project vcell by virtualcell.

the class SBMLExporter method addParameters.

/**
 * addKineticParameterUnits:
 * @throws SbmlException
 */
// private void addKineticAndGlobalParameterUnits() throws SbmlException {
// 
// //
// // Get all kinetic parameters from simple reactions and flux reactions from the Biomodel
// // And all Model (global) parameters from Model.
// // For each parameter,
// //		get its unit (VCunitDefinition)
// //		check if it is part of unitsList - if so, continue
// //		check if it is a base unit - if so, continue
// //		else, get the converted unit (VC -> SBML)
// //		add unit to sbmlModel unit definition
// //
// 
// Vector<Parameter> paramsVector = new Vector<Parameter>();
// // Add globals
// Model vcModel = vcBioModel.getModel();
// ModelParameter[] globalParams = vcModel.getModelParameters();
// for (int i = 0; i < globalParams.length; i++) {
// paramsVector.addElement(globalParams[i]);
// }
// // Add reaction kinetic parameters
// ReactionStep[] vcReactions = vcModel.getReactionSteps();
// for (int i = 0; i < vcReactions.length; i++) {
// Kinetics rxnKinetics = vcReactions[i].getKinetics();
// Parameter[] kineticParams = rxnKinetics.getKineticsParameters();
// for (int j = 0; j < kineticParams.length; j++) {
// paramsVector.addElement(kineticParams[j]);
// }
// }
// 
// for (int i = 0; i < paramsVector.size(); i++){
// Parameter param = (Parameter)paramsVector.elementAt(i);
// VCUnitDefinition paramUnitDefn = param.getUnitDefinition();
// if (paramUnitDefn == null || paramUnitDefn.isTBD()) {
// continue;
// }
// String unitSymbol = org.vcell.util.TokenMangler.mangleToSName(paramUnitDefn.getSymbol());
// if (unitSymbol == null) {
// continue;
// }
// getOrCreateSBMLUnit(paramUnitDefn);
// }
// }
/**
 * At present, the Virtual cell doesn't support global parameters
 * @throws SbmlException
 */
protected void addParameters() throws ExpressionException, SbmlException {
    Model vcModel = getSelectedSimContext().getModel();
    // add VCell global parameters to the SBML listofParameters
    ModelParameter[] vcGlobalParams = vcModel.getModelParameters();
    if (vcGlobalParams != null) {
        for (ModelParameter vcParam : vcGlobalParams) {
            org.sbml.jsbml.Parameter sbmlParam = sbmlModel.createParameter();
            sbmlParam.setId(vcParam.getName());
            sbmlParam.setConstant(vcParam.isConstant());
            Expression paramExpr = new Expression(vcParam.getExpression());
            boolean bParamIsNumeric = true;
            if (paramExpr.isNumeric()) {
                // For a VCell global param, if it is numeric, it has a constant value and is not defined by a rule, hence set Constant = true.
                sbmlParam.setValue(paramExpr.evaluateConstant());
                // the expression for modelParam might be numeric, but modelParam could have a rate rule, if so, set constant attribute to 'false'
                if (getSelectedSimContext().getRateRule(vcParam) != null) {
                    bParamIsNumeric = false;
                }
            } else {
                // non-numeric VCell global parameter will be defined by a (assignment) rule, hence mark Constant = false.
                bParamIsNumeric = false;
                // add assignment rule for param
                ASTNode paramFormulaNode = getFormulaFromExpression(paramExpr);
                AssignmentRule sbmlParamAssignmentRule = sbmlModel.createAssignmentRule();
                sbmlParamAssignmentRule.setVariable(vcParam.getName());
                sbmlParamAssignmentRule.setMath(paramFormulaNode);
            }
            sbmlParam.setConstant(bParamIsNumeric);
            VCUnitDefinition vcParamUnit = vcParam.getUnitDefinition();
            if (!vcParamUnit.isTBD()) {
                sbmlParam.setUnits(getOrCreateSBMLUnit(vcParamUnit));
            }
        }
    }
}

Example 7 with AssignmentRule

use of org.sbml.jsbml.AssignmentRule in project vcell by virtualcell.

the class SBMLExporter method createSBMLParamFromSpeciesParam.

/**
 * createSBMLParamFromSpeciesParam : creates an SBML parameter for each speciesContextSpecParameter (diffusion coefficient,
 * advection coeffs, boundary conditions (X,Y,Z).
 *
 * @param spContext
 * @param scsParam
 * @return
 * @throws SbmlException
 */
org.sbml.jsbml.Parameter createSBMLParamFromSpeciesParam(SpeciesContext spContext, SpeciesContextSpecParameter scsParam) throws SbmlException {
    try {
        Expression paramExpr = scsParam.getExpression();
        // if scsParam is diff, Vel X, Y, Z parameter and if its expression is null or 0.0, don't create parameter.
        int role = scsParam.getRole();
        if (((role == SpeciesContextSpec.ROLE_DiffusionRate) || (role == SpeciesContextSpec.ROLE_VelocityX) || (role == SpeciesContextSpec.ROLE_VelocityY) || (role == SpeciesContextSpec.ROLE_VelocityZ)) && ((paramExpr == null) || (paramExpr.isNumeric() && (scsParam.getConstantValue() == 0.0)))) {
            return null;
        }
        // if scsParam is a BoundaryCondition, and paramExpr is null, values are set based on boundary condition type.
        if (((role == SpeciesContextSpec.ROLE_BoundaryValueXm) || (role == SpeciesContextSpec.ROLE_BoundaryValueXp) || (role == SpeciesContextSpec.ROLE_BoundaryValueYm) || (role == SpeciesContextSpec.ROLE_BoundaryValueYp) || (role == SpeciesContextSpec.ROLE_BoundaryValueZm) || (role == SpeciesContextSpec.ROLE_BoundaryValueZp)) && (paramExpr == null)) {
            StructureMapping sm = getSelectedSimContext().getGeometryContext().getStructureMapping(spContext.getStructure());
            Expression initCondnExpr = getSelectedSimContext().getReactionContext().getSpeciesContextSpec(spContext).getInitialConditionParameter().getExpression();
            // if BC type is Neumann (flux), its value is 0.0
            if ((role == SpeciesContextSpec.ROLE_BoundaryValueXm)) {
                if (sm.getBoundaryConditionTypeXm().isDIRICHLET()) {
                    paramExpr = new Expression(initCondnExpr);
                } else if (sm.getBoundaryConditionTypeXm().isNEUMANN()) {
                    paramExpr = new Expression(0.0);
                }
            }
            if ((role == SpeciesContextSpec.ROLE_BoundaryValueXp)) {
                if (sm.getBoundaryConditionTypeXp().isDIRICHLET()) {
                    paramExpr = new Expression(initCondnExpr);
                } else if (sm.getBoundaryConditionTypeXp().isNEUMANN()) {
                    paramExpr = new Expression(0.0);
                }
            }
            if ((role == SpeciesContextSpec.ROLE_BoundaryValueYm)) {
                if (sm.getBoundaryConditionTypeYm().isDIRICHLET()) {
                    paramExpr = new Expression(initCondnExpr);
                } else if (sm.getBoundaryConditionTypeYm().isNEUMANN()) {
                    paramExpr = new Expression(0.0);
                }
            }
            if ((role == SpeciesContextSpec.ROLE_BoundaryValueYp)) {
                if (sm.getBoundaryConditionTypeYp().isDIRICHLET()) {
                    paramExpr = new Expression(initCondnExpr);
                } else if (sm.getBoundaryConditionTypeYp().isNEUMANN()) {
                    paramExpr = new Expression(0.0);
                }
            }
            if ((role == SpeciesContextSpec.ROLE_BoundaryValueZm)) {
                if (sm.getBoundaryConditionTypeZm().isDIRICHLET()) {
                    paramExpr = new Expression(initCondnExpr);
                } else if (sm.getBoundaryConditionTypeZm().isNEUMANN()) {
                    paramExpr = new Expression(0.0);
                }
            }
            if ((role == SpeciesContextSpec.ROLE_BoundaryValueZp)) {
                if (sm.getBoundaryConditionTypeZp().isDIRICHLET()) {
                    paramExpr = new Expression(initCondnExpr);
                } else if (sm.getBoundaryConditionTypeZp().isNEUMANN()) {
                    paramExpr = new Expression(0.0);
                }
            }
        }
        // create SBML parameter
        org.sbml.jsbml.Parameter param = sbmlModel.createParameter();
        param.setId(TokenMangler.mangleToSName(spContext.getName() + "_" + scsParam.getName()));
        UnitDefinition unitDefn = getOrCreateSBMLUnit(scsParam.getUnitDefinition());
        param.setUnits(unitDefn);
        param.setConstant(scsParam.isConstant());
        if (paramExpr.isNumeric()) {
            param.setValue(paramExpr.evaluateConstant());
            param.setConstant(true);
        } else {
            // we need to create a parameter and a rule for the non-numeric expr of diffParam
            param.setValue(0.0);
            param.setConstant(false);
            // now add assignment rule in SBML for the diff param
            ASTNode assgnRuleMathNode = getFormulaFromExpression(paramExpr);
            AssignmentRule assgnRule = sbmlModel.createAssignmentRule();
            assgnRule.setVariable(param.getId());
            assgnRule.setMath(assgnRuleMathNode);
        }
        return param;
    } catch (ExpressionException e) {
        e.printStackTrace(System.out);
        throw new RuntimeException("Unable to interpret parameter '" + scsParam.getName() + "' of species : " + spContext.getName());
    }
}