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

Example 41 with Expression

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

the class MathModel_SBMLExporter method getFormulaFromExpression.

/**
 * 	getFormulaFromExpression :
 *  Expression infix strings are not handled gracefully by libSBML, esp when ligical or inequality operators are used.
 *  This method
 *		converts the expression into MathML using ExpressionMathMLPrinter;
 *		converts that into libSBMl-readable formula using libSBML utilties.
 *		returns the new formula string.
 */
public static ASTNode getFormulaFromExpression(Expression expression, MathType mathType) {
    // Convert expression into MathML string
    String expMathMLStr = null;
    try {
        // mangling the identifiers in the expression to make them proper SBase ids.
        Expression mangledExpression = new Expression(expression);
        String[] symbols = mangledExpression.getSymbols();
        if (symbols != null) {
            for (String symbol : mangledExpression.getSymbols()) {
                String mangledSymbol = TokenMangler.mangleToSName(symbol);
                if (!mangledSymbol.equals(symbol)) {
                    mangledExpression.substituteInPlace(new Expression(symbol), new Expression(mangledSymbol));
                }
            }
        }
        expMathMLStr = cbit.vcell.parser.ExpressionMathMLPrinter.getMathML(mangledExpression, false, mathType);
    } catch (java.io.IOException e) {
        e.printStackTrace(System.out);
        throw new RuntimeException("Error converting expression to MathML string :" + e.getMessage());
    } catch (cbit.vcell.parser.ExpressionException e1) {
        e1.printStackTrace(System.out);
        throw new RuntimeException("Error converting expression to MathML string :" + e1.getMessage());
    }
    // Use libSBMl routines to convert MathML string to MathML document and a libSBML-readable formula string
    ASTNode mathNode = ASTNode.readMathMLFromString(expMathMLStr);
    return mathNode;
}

Example 42 with Expression

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

the class RbmNetworkGenerator method generateModel.

public static void generateModel(BioModel bioModel, String netfile) throws Exception {
    Model model = bioModel.getModel();
    Map<String, SpeciesContext> speciesMap = new HashMap<String, SpeciesContext>();
    Map<String, ReactionStep> reactionMap = new HashMap<String, ReactionStep>();
    List<ReactionLine> reactionLineList = new ArrayList<ReactionLine>();
    BufferedReader br = new BufferedReader(new StringReader(netfile));
    int reversibleCount = 0;
    int reactionCount = 0;
    while (true) {
        String line = br.readLine();
        if (line == null) {
            break;
        }
        line = line.trim();
        if (line.equals(BEGIN_PARAMETERS)) {
            while (true) {
                String line2 = br.readLine();
                line2 = line2.trim();
                if (line2.length() == 0) {
                    continue;
                }
                if (line2.equals(END_PARAMETERS)) {
                    break;
                }
                StringTokenizer st = new StringTokenizer(line2);
                String token1 = st.nextToken();
                String token2 = st.nextToken();
                String token3 = st.nextToken();
                ModelParameter mp = model.new ModelParameter(token2, new Expression(token3), Model.ROLE_UserDefined, bioModel.getModel().getUnitSystem().getInstance_TBD());
                model.addModelParameter(mp);
            }
        } else if (line.equals(BEGIN_SPECIES)) {
            while (true) {
                String line2 = br.readLine();
                line2 = line2.trim();
                if (line2.length() == 0) {
                    continue;
                }
                if (line2.equals(END_SPECIES)) {
                    break;
                }
                StringTokenizer st = new StringTokenizer(line2);
                // no
                String token1 = st.nextToken();
                // pattern
                String token2 = st.nextToken();
                // initial condition
                String token3 = st.nextToken();
                String newname = token2.replaceAll("\\.", "_");
                newname = newname.replaceAll("[\\(,][a-zA-Z]\\w*", "");
                newname = newname.replaceAll("~|!\\d*", "");
                newname = newname.replaceAll("\\(\\)", "");
                newname = newname.replaceAll("\\)", "");
                SpeciesContext sc = model.createSpeciesContext(model.getStructure(0));
                sc.setName(newname);
                bioModel.getVCMetaData().setFreeTextAnnotation(sc, token2);
                bioModel.getVCMetaData().setFreeTextAnnotation(sc.getSpecies(), token2);
                speciesMap.put(token1, sc);
            }
        } else if (line.equals(BEGIN_REACTIONS)) {
            while (true) {
                String line2 = br.readLine();
                line2 = line2.trim();
                if (line2.length() == 0) {
                    continue;
                }
                if (line2.equals(END_REACTIONS)) {
                    break;
                }
                ++reactionCount;
                StringTokenizer st = new StringTokenizer(line2);
                String token1 = st.nextToken();
                // reactants
                String token2 = st.nextToken();
                // products
                String token3 = st.nextToken();
                // rate
                String token4 = st.nextToken();
                String token5 = st.nextToken();
                boolean bFoundReversible = false;
                Expression rate = new Expression(token4);
                for (ReactionLine rl : reactionLineList) {
                    if (token2.equals(rl.products) && token3.equals(rl.reactants) && token5.equals(rl.ruleLabel + "r")) {
                        ReactionStep rs = reactionMap.get(rl.no);
                        ((MassActionKinetics) rs.getKinetics()).getReverseRateParameter().setExpression(rate);
                        reactionLineList.remove(rl);
                        bFoundReversible = true;
                        break;
                    }
                }
                if (bFoundReversible) {
                    ++reversibleCount;
                    continue;
                }
                ReactionLine rl = new ReactionLine(token1, token2, token3, token5);
                reactionLineList.add(rl);
                SimpleReaction reaction = model.createSimpleReaction(model.getStructure(0));
                reactionMap.put(token1, reaction);
                reaction.setModel(model);
                bioModel.getVCMetaData().setFreeTextAnnotation(reaction, line2);
                MassActionKinetics kinetics = new MassActionKinetics(reaction);
                reaction.setKinetics(kinetics);
                st = new StringTokenizer(token2, ",");
                while (st.hasMoreTokens()) {
                    String t = st.nextToken();
                    SpeciesContext sc = speciesMap.get(t);
                    if (sc != null) {
                        boolean bExists = false;
                        for (ReactionParticipant rp : reaction.getReactionParticipants()) {
                            if (rp instanceof Reactant && rp.getSpeciesContext() == sc) {
                                rp.setStoichiometry(rp.getStoichiometry() + 1);
                                bExists = true;
                                break;
                            }
                        }
                        if (!bExists) {
                            reaction.addReactant(sc, 1);
                        }
                    }
                }
                st = new StringTokenizer(token3, ",");
                while (st.hasMoreTokens()) {
                    String t = st.nextToken();
                    SpeciesContext sc = speciesMap.get(t);
                    if (sc != null) {
                        boolean bExists = false;
                        for (ReactionParticipant rp : reaction.getReactionParticipants()) {
                            if (rp instanceof Product && rp.getSpeciesContext() == sc) {
                                rp.setStoichiometry(rp.getStoichiometry() + 1);
                                bExists = true;
                                break;
                            }
                        }
                        if (!bExists) {
                            reaction.addProduct(sc, 1);
                        }
                    }
                }
                kinetics.getForwardRateParameter().setExpression(rate);
            }
        }
    }
    System.out.println(model.getNumSpecies() + " species added");
    System.out.println(model.getNumReactions() + " reactions added");
    System.out.println(reversibleCount + " reversible reactions found");
    if (reactionCount != model.getNumReactions() + reversibleCount) {
        throw new RuntimeException("Reactions are not imported correctly!");
    }
}

Example 43 with Expression

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

the class RbmUtils method getBoundExpression.

public static Expression getBoundExpression(String expressionString, final SymbolTable symbolTable) throws ExpressionException {
    Expression exp = null;
    if (expressionString == null || expressionString.equals("")) {
        exp = new Expression(0);
    } else {
        exp = new Expression(expressionString);
    }
    // 
    // look for function invocations of unsupported but known functions
    // 
    FunctionInvocation[] invocations = exp.getFunctionInvocations(new FunctionFilter() {

        @Override
        public boolean accept(String functionName, FunctionType functionType) {
            if (functionName.equalsIgnoreCase("if")) {
                return true;
            }
            return false;
        }
    });
    if (invocations != null && invocations.length > 0) {
        for (FunctionInvocation invocation : invocations) {
            if (invocation.getFunctionName().equalsIgnoreCase("if")) {
                // build new expression
                // if (testExp, trueExp, falseExp)
                // 
                Expression testExp = invocation.getArguments()[0];
                Expression trueExp = invocation.getArguments()[1];
                Expression falseExp = invocation.getArguments()[2];
                Expression testPassed = Expression.relational("!=", testExp, new Expression(0.0));
                Expression testFailed = Expression.relational("==", testExp, new Expression(0.0));
                Expression newExp = Expression.add(Expression.mult(testPassed, trueExp), Expression.mult(testFailed, falseExp));
                // substitute new expression replacing if()
                exp.substituteInPlace(invocation.getFunctionExpression(), newExp);
            }
        }
        System.out.println(invocations.toString());
    }
    // 
    // "if()" functions are goine ... but lets look for BNGL function invocations
    // 1) if they have no arguments, drop the "()".
    // 2) if they have arguments, have to substitute the arguments in the expression ... flatten it.
    // 
    invocations = exp.getFunctionInvocations(new FunctionFilter() {

        @Override
        public boolean accept(String functionName, FunctionType functionType) {
            return true;
        }
    });
    if (invocations != null && invocations.length > 0) {
        for (FunctionInvocation invocation : invocations) {
            if (invocation.getArguments().length == 0) {
                // 
                // no arguments, look for existing parameter by name (parameter name is function name).
                // 
                // look up "identifier()" as "identifier" to find a model parameter generated earlier when processing functions (or prior functions)
                // 
                SymbolTableEntry parameter = symbolTable.getEntry(invocation.getFunctionName());
                if (parameter != null) {
                    exp.substituteInPlace(invocation.getFunctionExpression(), new Expression(parameter, parameter.getNameScope()));
                } else {
                    // 
                    // didn't find a parameter, may be a built-in function with zero arguments built into VCell. (none exists right now).
                    // 
                    SymbolTableFunctionEntry vcellFunction = (SymbolTableFunctionEntry) symbolTable.getEntry(invocation.getFormalDefinition());
                    if (vcellFunction != null) {
                    // 
                    // nothing to do, vcell will parse and interpret this correctly
                    // 
                    } else {
                        throw new RuntimeException("function \"" + invocation.getFunctionExpression().infix() + "\" not found as a bngl function or as a vcell built-in function");
                    }
                }
            } else {
                // 
                // should be a build-in vcell function with arguments ... user defined functions with arguments not supported yet in bngl import.
                // 
                FunctionType builtinFunctionType = cbit.vcell.parser.ASTFuncNode.FunctionType.fromFunctionName(invocation.getFunctionName());
                if (builtinFunctionType == null) {
                    throw new RuntimeException("function \"" + invocation.getFunctionExpression().infix() + "\" not found as a built-in VCell function (and bngl functions with arguments are not yet supported");
                } else {
                    if (invocation.getArguments().length != builtinFunctionType.getArgTypes().length) {
                        throw new RuntimeException("built-in function \"" + invocation.getFunctionExpression().infix() + "\" expects " + builtinFunctionType.getArgTypes().length + " arguments");
                    }
                }
            }
            System.out.println(invocations.toString());
        }
    }
    exp.bindExpression(symbolTable);
    return exp;
}

Example 44 with Expression

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

the class RbmUtils method toBnglStringSortedAlphabetically.

public static String toBnglStringSortedAlphabetically(SimulationContext sc, SpeciesContext speciesContext, CompartmentMode compartmentMode) {
    SpeciesContextSpec scs = sc.getReactionContext().getSpeciesContextSpec(speciesContext);
    Expression expression = scs.getParameter(SpeciesContextSpec.ROLE_InitialConcentration).getExpression();
    SpeciesPattern sp = speciesContext.getSpeciesPattern();
    // nothing to sort here, sorting done within the species pattern
    String s = "";
    if (compartmentMode == CompartmentMode.show) {
        s += "@" + speciesContext.getStructure().getName() + ":";
        s += toBnglStringSortedAlphabetically(sp, null, CompartmentMode.hide, 0) + "";
    } else if (compartmentMode == CompartmentMode.asSite) {
        s += toBnglStringSortedAlphabetically(sp, speciesContext.getStructure(), CompartmentMode.asSite, 0) + "";
    } else {
        s += toBnglStringSortedAlphabetically(sp, null, CompartmentMode.hide, 0) + "";
    }
    s += " " + expression.infix();
    return s;
}

Example 45 with Expression

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

the class ParameterEstimationTaskSimulatorIDA method getRowColumnRestultSetByBestEstimations.

public RowColumnResultSet getRowColumnRestultSetByBestEstimations(ParameterEstimationTask parameterEstimationTask, String[] paramNames, double[] paramValues) throws Exception {
    // create a temp simulation based on math description
    KeyValue key = new KeyValue("" + Math.abs(new Random().nextLong()));
    SimulationVersion dummyVersion = new SimulationVersion(key, "name", new User("temp", new KeyValue("1")), null, null, null, null, null, null, null);
    Simulation simulation = new Simulation(dummyVersion, parameterEstimationTask.getSimulationContext().getMathDescription());
    ReferenceData refData = parameterEstimationTask.getModelOptimizationSpec().getReferenceData();
    double[] times = refData.getDataByColumn(0);
    double endTime = times[times.length - 1];
    ExplicitOutputTimeSpec exTimeSpec = new ExplicitOutputTimeSpec(times);
    // set simulation ending time and output interval
    simulation.getSolverTaskDescription().setTimeBounds(new TimeBounds(0, endTime));
    simulation.getSolverTaskDescription().setOutputTimeSpec(exTimeSpec);
    // set parameters as math overrides
    MathOverrides mathOverrides = simulation.getMathOverrides();
    for (int i = 0; i < paramNames.length; i++) {
        mathOverrides.putConstant(new Constant(paramNames[i], new Expression(paramValues[i])));
    }
    SimulationTask simTask = new SimulationTask(new SimulationJob(simulation, 0, null), 0);
    IDASolverStandalone idaSolver = new IDASolverStandalone(simTask, ResourceUtil.getLocalSimDir("temp"), false);
    // startSolver();
    idaSolver.runSolver();
    Thread.sleep(1000);
    long startTimeMS = System.currentTimeMillis();
    while (idaSolver.getSolverStatus().isRunning() && System.currentTimeMillis() < (startTimeMS + 10000L)) {
        Thread.sleep(500);
    }
    ODESolverResultSet resultset = idaSolver.getODESolverResultSet();
    return resultset;
}