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

Example 26 with ReactionRule

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

the class RulebasedTransformer method parseBngOutput.

private void parseBngOutput(SimulationContext simContext, Set<ReactionRule> fromReactions, BNGOutput bngOutput) {
    Model model = simContext.getModel();
    Document bngNFSimXMLDocument = bngOutput.getNFSimXMLDocument();
    bngRootElement = bngNFSimXMLDocument.getRootElement();
    Element modelElement = bngRootElement.getChild("model", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
    Element listOfReactionRulesElement = modelElement.getChild("ListOfReactionRules", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
    List<Element> reactionRuleChildren = new ArrayList<Element>();
    reactionRuleChildren = listOfReactionRulesElement.getChildren("ReactionRule", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
    for (Element reactionRuleElement : reactionRuleChildren) {
        ReactionRuleAnalysisReport rar = new ReactionRuleAnalysisReport();
        boolean bForward = true;
        String rule_id_str = reactionRuleElement.getAttributeValue("id");
        ruleElementMap.put(rule_id_str, reactionRuleElement);
        String rule_name_str = reactionRuleElement.getAttributeValue("name");
        String symmetry_factor_str = reactionRuleElement.getAttributeValue("symmetry_factor");
        Double symmetry_factor_double = Double.parseDouble(symmetry_factor_str);
        ReactionRule rr = null;
        if (rule_name_str.startsWith("_reverse_")) {
            bForward = false;
            rule_name_str = rule_name_str.substring("_reverse_".length());
            rr = model.getRbmModelContainer().getReactionRule(rule_name_str);
            RbmKineticLaw rkl = rr.getKineticLaw();
            try {
                if (symmetry_factor_double != 1.0 && fromReactions.contains(rr)) {
                    Expression expression = rkl.getLocalParameterValue(RbmKineticLawParameterType.MassActionReverseRate);
                    expression = Expression.div(expression, new Expression(symmetry_factor_double));
                    rkl.setLocalParameterValue(RbmKineticLawParameterType.MassActionReverseRate, expression);
                }
            } catch (ExpressionException | PropertyVetoException exc) {
                exc.printStackTrace();
                throw new RuntimeException("Unexpected transform exception: " + exc.getMessage());
            }
            rulesReverseMap.put(rr, rar);
        } else {
            rr = model.getRbmModelContainer().getReactionRule(rule_name_str);
            RbmKineticLaw rkl = rr.getKineticLaw();
            try {
                if (symmetry_factor_double != 1.0 && fromReactions.contains(rr)) {
                    Expression expression = rkl.getLocalParameterValue(RbmKineticLawParameterType.MassActionForwardRate);
                    expression = Expression.div(expression, new Expression(symmetry_factor_double));
                    rkl.setLocalParameterValue(RbmKineticLawParameterType.MassActionForwardRate, expression);
                }
            } catch (ExpressionException | PropertyVetoException exc) {
                exc.printStackTrace();
                throw new RuntimeException("Unexpected transform exception: " + exc.getMessage());
            }
            rulesForwardMap.put(rr, rar);
        }
        rar.symmetryFactor = symmetry_factor_double;
        System.out.println("rule id=" + rule_id_str + ", name=" + rule_name_str + ", symmetry factor=" + symmetry_factor_str);
        keyMap.put(rule_id_str, rr);
        Element listOfReactantPatternsElement = reactionRuleElement.getChild("ListOfReactantPatterns", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        List<Element> reactantPatternChildren = new ArrayList<Element>();
        reactantPatternChildren = listOfReactantPatternsElement.getChildren("ReactantPattern", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        for (int i = 0; i < reactantPatternChildren.size(); i++) {
            Element reactantPatternElement = reactantPatternChildren.get(i);
            String pattern_id_str = reactantPatternElement.getAttributeValue("id");
            ReactionRuleParticipant p = bForward ? rr.getReactantPattern(i) : rr.getProductPattern(i);
            SpeciesPattern sp = p.getSpeciesPattern();
            System.out.println("  reactant id=" + pattern_id_str + ", name=" + sp.toString());
            keyMap.put(pattern_id_str, sp);
            // list of molecules
            extractMolecules(sp, model, reactantPatternElement);
            // list of bonds (not implemented)
            extractBonds(reactantPatternElement);
        }
        Element listOfProductPatternsElement = reactionRuleElement.getChild("ListOfProductPatterns", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        List<Element> productPatternChildren = new ArrayList<Element>();
        productPatternChildren = listOfProductPatternsElement.getChildren("ProductPattern", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        for (int i = 0; i < productPatternChildren.size(); i++) {
            Element productPatternElement = productPatternChildren.get(i);
            String pattern_id_str = productPatternElement.getAttributeValue("id");
            ReactionRuleParticipant p = bForward ? rr.getProductPattern(i) : rr.getReactantPattern(i);
            SpeciesPattern sp = p.getSpeciesPattern();
            System.out.println("  product  id=" + pattern_id_str + ", name=" + sp.toString());
            keyMap.put(pattern_id_str, sp);
            extractMolecules(sp, model, productPatternElement);
            extractBonds(productPatternElement);
        }
        // extract the Map for this rule
        Element listOfMapElement = reactionRuleElement.getChild("Map", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        List<Element> mapChildren = new ArrayList<Element>();
        mapChildren = listOfMapElement.getChildren("MapItem", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        for (Element mapElement : mapChildren) {
            String target_id_str = mapElement.getAttributeValue("targetID");
            String source_id_str = mapElement.getAttributeValue("sourceID");
            System.out.println("Map: target=" + target_id_str + " source=" + source_id_str);
            RbmObject target_object = keyMap.get(target_id_str);
            RbmObject source_object = keyMap.get(source_id_str);
            if (target_object == null)
                System.out.println("!!! Missing map target  " + target_id_str);
            if (source_object == null)
                System.out.println("!!! Missing map source " + source_id_str);
            if (source_object != null) {
                // target_object may be null
                System.out.println("      target=" + target_object + " source=" + source_object);
                Pair<RbmObject, RbmObject> mapEntry = new Pair<RbmObject, RbmObject>(target_object, source_object);
                rar.objmappingList.add(mapEntry);
            }
            Pair<String, String> idmapEntry = new Pair<String, String>(target_id_str, source_id_str);
            rar.idmappingList.add(idmapEntry);
        }
        // ListOfOperations
        Element listOfOperationsElement = reactionRuleElement.getChild("ListOfOperations", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        List<Element> operationsChildren = new ArrayList<Element>();
        operationsChildren = listOfOperationsElement.getChildren("StateChange", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        System.out.println("ListOfOperations");
        for (Element operationsElement : operationsChildren) {
            String finalState_str = operationsElement.getAttributeValue("finalState");
            String site_str = operationsElement.getAttributeValue("site");
            RbmObject site_object = keyMap.get(site_str);
            if (site_object == null)
                System.out.println("!!! Missing map object " + site_str);
            if (site_object != null) {
                System.out.println("   finalState=" + finalState_str + " site=" + site_object);
                StateChangeOperation sco = new StateChangeOperation(finalState_str, site_str, site_object);
                rar.operationsList.add(sco);
            }
        }
        operationsChildren = listOfOperationsElement.getChildren("AddBond", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        for (Element operationsElement : operationsChildren) {
            String site1_str = operationsElement.getAttributeValue("site1");
            String site2_str = operationsElement.getAttributeValue("site2");
            RbmObject site1_object = keyMap.get(site1_str);
            RbmObject site2_object = keyMap.get(site2_str);
            if (site1_object == null)
                System.out.println("!!! Missing map object " + site1_str);
            if (site2_object == null)
                System.out.println("!!! Missing map object " + site2_str);
            if (site1_object != null && site2_object != null) {
                System.out.println("   site1=" + site1_object + " site2=" + site2_object);
                AddBondOperation abo = new AddBondOperation(site1_str, site2_str, site1_object, site2_object);
                rar.operationsList.add(abo);
            }
        }
        operationsChildren = listOfOperationsElement.getChildren("DeleteBond", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        for (Element operationsElement : operationsChildren) {
            String site1_str = operationsElement.getAttributeValue("site1");
            String site2_str = operationsElement.getAttributeValue("site2");
            RbmObject site1_object = keyMap.get(site1_str);
            RbmObject site2_object = keyMap.get(site2_str);
            if (site1_object == null)
                System.out.println("!!! Missing map object " + site1_str);
            if (site2_object == null)
                System.out.println("!!! Missing map object " + site2_str);
            if (site1_object != null && site2_object != null) {
                System.out.println("   site1=" + site1_object + " site2=" + site2_object);
                DeleteBondOperation dbo = new DeleteBondOperation(site1_str, site2_str, site1_object, site2_object);
                rar.operationsList.add(dbo);
            }
        }
        operationsChildren = listOfOperationsElement.getChildren("Add", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        for (Element operationsElement : operationsChildren) {
            String id_str = operationsElement.getAttributeValue("id");
            RbmObject id_object = keyMap.get(id_str);
            if (id_object == null)
                System.out.println("!!! Missing map object " + id_str);
            if (id_object != null) {
                System.out.println("   id=" + id_str);
                AddOperation ao = new AddOperation(id_str, id_object);
                rar.operationsList.add(ao);
            }
        }
        operationsChildren = listOfOperationsElement.getChildren("Delete", Namespace.getNamespace("http://www.sbml.org/sbml/level3"));
        for (Element operationsElement : operationsChildren) {
            String id_str = operationsElement.getAttributeValue("id");
            String delete_molecules_str = operationsElement.getAttributeValue("DeleteMolecules");
            RbmObject id_object = keyMap.get(id_str);
            if (id_object == null)
                System.out.println("!!! Missing map object " + id_str);
            int delete_molecules_int = 0;
            if (delete_molecules_str != null) {
                delete_molecules_int = Integer.parseInt(delete_molecules_str);
            }
            if (id_object != null) {
                System.out.println("   id=" + id_str + ", DeleteMolecules=" + delete_molecules_str);
                DeleteOperation dop = new DeleteOperation(id_str, id_object, delete_molecules_int);
                rar.operationsList.add(dop);
            }
        }
    }
    System.out.println("done parsing xml file");
}

Example 27 with ReactionRule

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

the class BNGExecutorServiceMultipass method preprocessInput.

// parse the compartmental bngl file and produce the "trick"
// where each molecule has an extra Site with the compartments as possible States
// a reserved name will be used for this Site
// 
private String preprocessInput(String cBngInputString) throws ParseException, PropertyVetoException, ExpressionBindingException {
    // take the cBNGL file (as string), parse it to recover the rules (we'll need them later)
    // and create the bngl string with the extra, fake site for the compartments
    BioModel bioModel = new BioModel(null);
    bioModel.setName("BngBioModel");
    model = new Model("model");
    bioModel.setModel(model);
    model.createFeature();
    simContext = bioModel.addNewSimulationContext("BioNetGen app", SimulationContext.Application.NETWORK_DETERMINISTIC);
    List<SimulationContext> appList = new ArrayList<SimulationContext>();
    appList.add(simContext);
    // set convention for initial conditions in generated application for seed species (concentration or count)
    BngUnitSystem bngUnitSystem = new BngUnitSystem(BngUnitOrigin.DEFAULT);
    InputStream is = new ByteArrayInputStream(cBngInputString.getBytes());
    BufferedReader br = new BufferedReader(new InputStreamReader(is));
    ASTModel astModel = RbmUtils.importBnglFile(br);
    if (astModel.hasCompartments()) {
        Structure struct = model.getStructure(0);
        if (struct != null) {
            try {
                model.removeStructure(struct);
            } catch (PropertyVetoException e) {
                e.printStackTrace();
            }
        }
    }
    BnglObjectConstructionVisitor constructionVisitor = null;
    constructionVisitor = new BnglObjectConstructionVisitor(model, appList, bngUnitSystem, true);
    astModel.jjtAccept(constructionVisitor, model.getRbmModelContainer());
    int numCompartments = model.getStructures().length;
    if (numCompartments == 0) {
        throw new RuntimeException("No structure present in the bngl file.");
    } else if (numCompartments == 1) {
        // for single compartment we don't need the 'trick'
        compartmentMode = CompartmentMode.hide;
    } else {
        compartmentMode = CompartmentMode.asSite;
    }
    // extract all polymer observables for special treatment at the end
    for (RbmObservable oo : model.getRbmModelContainer().getObservableList()) {
        if (oo.getSequence() == RbmObservable.Sequence.PolymerLengthEqual) {
            polymerEqualObservables.add(oo);
        } else if (oo.getSequence() == RbmObservable.Sequence.PolymerLengthGreater) {
            polymerGreaterObservables.add(oo);
        }
    }
    for (RbmObservable oo : polymerEqualObservables) {
        model.getRbmModelContainer().removeObservable(oo);
    }
    for (RbmObservable oo : polymerGreaterObservables) {
        model.getRbmModelContainer().removeObservable(oo);
    }
    // replace all reversible rules with 2 direct rules
    List<ReactionRule> newRRList = new ArrayList<>();
    for (ReactionRule rr : model.getRbmModelContainer().getReactionRuleList()) {
        if (rr.isReversible()) {
            ReactionRule rr1 = ReactionRule.deriveDirectRule(rr);
            newRRList.add(rr1);
            ReactionRule rr2 = ReactionRule.deriveInverseRule(rr);
            newRRList.add(rr2);
        } else {
            newRRList.add(rr);
        }
        model.getRbmModelContainer().removeReactionRule(rr);
    }
    // model.getRbmModelContainer().getReactionRuleList().clear();
    model.getRbmModelContainer().setReactionRules(newRRList);
    StringWriter bnglStringWriter = new StringWriter();
    PrintWriter writer = new PrintWriter(bnglStringWriter);
    writer.println(RbmNetworkGenerator.BEGIN_MODEL);
    writer.println();
    // RbmNetworkGenerator.writeCompartments(writer, model, null);
    RbmNetworkGenerator.writeParameters(writer, model.getRbmModelContainer(), false);
    RbmNetworkGenerator.writeMolecularTypes(writer, model, compartmentMode);
    RbmNetworkGenerator.writeSpeciesSortedAlphabetically(writer, model, simContext, compartmentMode);
    RbmNetworkGenerator.writeObservables(writer, model.getRbmModelContainer(), compartmentMode);
    // RbmNetworkGenerator.writeFunctions(writer, rbmModelContainer, ignoreFunctions);
    RbmNetworkGenerator.writeReactions(writer, model.getRbmModelContainer(), null, false, compartmentMode);
    writer.println(RbmNetworkGenerator.END_MODEL);
    writer.println();
    // we parse the real numbers from the bngl file provided by the caller, the nc in the simContext has the default ones
    NetworkConstraints realNC = extractNetworkConstraints(cBngInputString);
    simContext.getNetworkConstraints().setMaxMoleculesPerSpecies(realNC.getMaxMoleculesPerSpecies());
    simContext.getNetworkConstraints().setMaxIteration(realNC.getMaxIteration());
    RbmNetworkGenerator.generateNetworkEx(1, simContext.getNetworkConstraints().getMaxMoleculesPerSpecies(), writer, model.getRbmModelContainer(), simContext, NetworkGenerationRequirements.AllowTruncatedStandardTimeout);
    String sInputString = bnglStringWriter.toString();
    return sInputString;
}

Example 28 with ReactionRule

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

the class RbmReactionParticipantTreeCellRenderer method getTreeCellRendererComponent.

@Override
public Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) {
    super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus);
    setBorder(null);
    if (value instanceof BioModelNode) {
        BioModelNode node = (BioModelNode) value;
        Object userObject = node.getUserObject();
        obj = userObject;
        String text = null;
        Icon icon = null;
        String toolTip = null;
        if (userObject instanceof ReactionRule) {
            ReactionRule rr = (ReactionRule) userObject;
            text = toHtml(rr);
            toolTip = toHtmlWithTip(rr);
            icon = rr.isReversible() ? VCellIcons.rbmReactRuleReversIcon : VCellIcons.rbmReactRuleDirectIcon;
        } else if (userObject instanceof ReactionRuleParticipantLocal) {
            ReactionRuleParticipantLocal rrp = (ReactionRuleParticipantLocal) userObject;
            text = toHtml(rrp, true);
            toolTip = toHtmlWithTip(rrp, true);
            icon = rrp.type == ReactionRuleParticipantType.Reactant ? VCellIcons.rbmReactantIcon : VCellIcons.rbmProductIcon;
        } else if (userObject instanceof MolecularTypePattern) {
            MolecularTypePattern molecularTypePattern = (MolecularTypePattern) userObject;
            text = toHtml(molecularTypePattern, true);
            toolTip = toHtmlWithTip(molecularTypePattern, true);
            if (owner == null) {
                icon = VCellIcons.rbmMolecularTypeSimpleIcon;
                ;
            } else {
                Graphics gc = owner.getGraphics();
                icon = new MolecularTypeSmallShape(1, 5, molecularTypePattern.getMolecularType(), null, gc, molecularTypePattern.getMolecularType(), null, issueManager);
            }
        } else if (userObject instanceof MolecularComponentPattern) {
            MolecularComponentPattern mcp = (MolecularComponentPattern) userObject;
            text = toHtml(mcp, true);
            toolTip = toHtmlWithTip(mcp, true);
            icon = VCellIcons.rbmComponentGrayIcon;
            if (mcp.getMolecularComponent().getComponentStateDefinitions().size() > 0) {
                icon = VCellIcons.rbmComponentGrayStateIcon;
            }
            if (mcp.isbVisible()) {
                icon = VCellIcons.rbmComponentGreenIcon;
                if (mcp.getMolecularComponent().getComponentStateDefinitions().size() > 0) {
                    icon = VCellIcons.rbmComponentGreenStateIcon;
                }
            }
            ComponentStatePattern csp = mcp.getComponentStatePattern();
            if (csp != null && !csp.isAny()) {
                icon = VCellIcons.rbmComponentGreenIcon;
                if (mcp.getMolecularComponent().getComponentStateDefinitions().size() > 0) {
                    icon = VCellIcons.rbmComponentGreenStateIcon;
                }
            }
            BioModelNode parent = (BioModelNode) ((BioModelNode) value).getParent().getParent().getParent();
            if (parent == null) {
                icon = VCellIcons.rbmComponentErrorIcon;
                return this;
            }
        } else if (userObject instanceof StateLocal) {
            StateLocal sl = (StateLocal) userObject;
            text = toHtml(sl, true);
            toolTip = toHtmlWithTip(sl, true);
            icon = VCellIcons.rbmComponentStateIcon;
        } else if (userObject instanceof BondLocal) {
            BondLocal bl = (BondLocal) userObject;
            text = toHtml(bl, sel);
            toolTip = toHtmlWithTip(bl, true);
            icon = VCellIcons.rbmBondIcon;
        } else if (userObject instanceof ParticipantMatchLabelLocal) {
            ParticipantMatchLabelLocal pmll = (ParticipantMatchLabelLocal) userObject;
            text = toHtml(pmll, sel);
            toolTip = toHtmlWithTip(pmll, true);
            icon = VCellIcons.rbmBondIcon;
        } else {
            if (userObject != null) {
                System.out.println(userObject.toString());
                text = userObject.toString();
            } else {
                text = "null user object";
            }
        }
        setText(text);
        setIcon(icon);
        setToolTipText(toolTip == null ? text : toolTip);
    }
    return this;
}

Example 29 with ReactionRule

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

the class ReactionRuleParticipantSignaturePropertiesPanel method updateShape.

private void updateShape() {
    int maxXOffset = 0;
    ruleShapeList.clear();
    // all the reactants go in one single ReactionRulePatternLargeShape, all the products the other
    int yOffset = yOffsetReactantInitial + GraphConstants.ReactionRuleParticipantDisplay_ReservedSpaceForNameOnYAxis;
    for (Map.Entry<String, ReactionRule> entry : reactionRuleMap.entrySet()) {
        ReactionRule rr = entry.getValue();
        ReactionRulePatternLargeShape reactantShape = new ReactionRulePatternLargeShape(xOffsetInitial, yOffset, -1, shapePanel, rr, true, issueManager);
        reactantShape.setWriteName(true);
        int xOffset = reactantShape.getRightEnd() + 70;
        ReactionRulePatternLargeShape productShape = new ReactionRulePatternLargeShape(xOffset, yOffset, -1, shapePanel, rr, false, issueManager);
        xOffset += productShape.getRightEnd();
        yOffset += SpeciesPatternLargeShape.defaultHeight + GraphConstants.ReactionRuleParticipantDisplay_ReservedSpaceForNameOnYAxis;
        maxXOffset = Math.max(maxXOffset, xOffset);
        Pair<ReactionRulePatternLargeShape, ReactionRulePatternLargeShape> p = new Pair<>(reactantShape, productShape);
        ruleShapeList.add(p);
    }
    int maxYOffset = Math.max(yOffsetReactantInitial + SpeciesPatternLargeShape.defaultHeight + GraphConstants.ReactionRuleParticipantDisplay_ReservedSpaceForNameOnYAxis, yOffsetReactantInitial + (SpeciesPatternLargeShape.defaultHeight + GraphConstants.ReactionRuleParticipantDisplay_ReservedSpaceForNameOnYAxis) * ruleShapeList.size());
    Dimension preferredSize = new Dimension(maxXOffset, maxYOffset);
    shapePanel.setPreferredSize(preferredSize);
    containerOfScrollPanel.repaint();
}

Example 30 with ReactionRule

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

the class ReactionRulePropertiesPanel method setReactionRule.

private void setReactionRule(ReactionRule newValue) {
    kpp.setReactionRule(reactionRule);
    epp.setReactionRule(reactionRule);
    if (reactionRule == newValue) {
        return;
    }
    ReactionRule oldValue = reactionRule;
    if (oldValue != null) {
        oldValue.removePropertyChangeListener(eventHandler);
    }
    reactionRule = newValue;
    if (newValue != null) {
        newValue.addPropertyChangeListener(eventHandler);
    }
    refreshInterface();
}