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

Example 1 with ReactantPattern

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

the class ViewGeneratedReactionsPanel method updateShape.

public void updateShape(int selectedRow) {
    GeneratedReactionTableRow reactionTableRow = tableModel.getValueAt(selectedRow);
    String inputString = reactionTableRow.getExpression();
    System.out.println(selectedRow + ": " + inputString);
    // ReactionRule newReactionRule = (ReactionRule)RbmUtils.parseReactionRule(inputString, bioModel);
    Model tempModel = null;
    try {
        tempModel = new Model("MyTempModel");
        tempModel.addFeature("c0");
    } catch (ModelException | PropertyVetoException e1) {
        e1.printStackTrace();
    }
    if (owner != null && owner.getSimulationContext() != null) {
        List<MolecularType> mtList = owner.getSimulationContext().getModel().getRbmModelContainer().getMolecularTypeList();
        try {
            tempModel.getRbmModelContainer().setMolecularTypeList(mtList);
        } catch (PropertyVetoException e1) {
            e1.printStackTrace();
            throw new RuntimeException("Unexpected exception setting " + MolecularType.typeName + " list: " + e1.getMessage(), e1);
        }
    } else {
        // This should not be possible
        throw new RuntimeException("Owner or SimulationContext are null.");
    }
    int arrowIndex = inputString.indexOf("<->");
    boolean bReversible = true;
    if (arrowIndex < 0) {
        arrowIndex = inputString.indexOf("->");
        bReversible = false;
    }
    String left = inputString.substring(0, arrowIndex).trim();
    String right = inputString.substring(arrowIndex + (bReversible ? 3 : 2)).trim();
    if (left.length() == 0 && right.length() == 0) {
        return;
    }
    // we recover the original rule that generated the flattened reaction we now try to transform back into a fake rule
    BNGReaction reactionObject = reactionTableRow.getReactionObject();
    String name = reactionObject.getRuleName();
    if (name.contains(GeneratedReactionTableModel.reverse)) {
        name = name.substring(GeneratedReactionTableModel.reverse.length());
    }
    if (name.endsWith(ReactionRule.DirectHalf)) {
        name = name.substring(0, name.indexOf(ReactionRule.DirectHalf));
    }
    if (name.endsWith(ReactionRule.InverseHalf)) {
        name = name.substring(0, name.indexOf(ReactionRule.InverseHalf));
    }
    // get the name of the original structure from the original rule and make here another structure with the same name
    String strStructure = null;
    Structure ruleStructure;
    SimulationContext sc = owner.getSimulationContext();
    ReactionRule rr = sc.getModel().getRbmModelContainer().getReactionRule(name);
    if (rr != null && rr.getStructure() != null) {
        strStructure = rr.getStructure().getName();
    }
    if (strStructure != null) {
        if (tempModel.getStructure(strStructure) == null) {
            try {
                if (rr.getStructure().getTypeName().equals(Structure.TYPE_NAME_MEMBRANE)) {
                    tempModel.addMembrane(strStructure);
                } else {
                    tempModel.addFeature(strStructure);
                }
            } catch (ModelException | PropertyVetoException e) {
                e.printStackTrace();
            }
        }
        ruleStructure = tempModel.getStructure(strStructure);
    } else {
        throw new RuntimeException("Failed to recover a Structure name from the Reaction Rule: " + name);
    }
    // making the fake rules just for display purpose, actually they are the flattened reactions resulted from bngl
    // the name is probably not unique, it's likely that many flattened reactions are derived from the same rule
    ReactionRule reactionRule = tempModel.getRbmModelContainer().createReactionRule(name, ruleStructure, bReversible);
    String regex = "[^!]\\+";
    String[] patterns = left.split(regex);
    for (String spString : patterns) {
        try {
            spString = spString.trim();
            // if compartments are present, we're cheating big time making some fake compartments just for compartment name display purposes
            SpeciesPattern speciesPattern = (SpeciesPattern) RbmUtils.parseSpeciesPattern(spString, tempModel);
            strStructure = RbmUtils.parseCompartment(spString, tempModel);
            speciesPattern.resolveBonds();
            Structure structure;
            if (strStructure != null) {
                if (tempModel.getStructure(strStructure) == null) {
                    if (sc.getModel().getStructure(strStructure).getTypeName().equals(Structure.TYPE_NAME_MEMBRANE)) {
                        tempModel.addMembrane(strStructure);
                    } else {
                        tempModel.addFeature(strStructure);
                    }
                }
                structure = tempModel.getStructure(strStructure);
            } else {
                // if nothing explicit for a participant, we use by default the structure of the rule
                structure = ruleStructure;
            }
            reactionRule.addReactant(new ReactantPattern(speciesPattern, structure));
        } catch (Throwable ex) {
            ex.printStackTrace();
            // error (red circle)
            SpeciesPatternLargeShape spls = new SpeciesPatternLargeShape(20, 20, -1, shapePanel, true, issueManager);
            reactantPatternShapeList.clear();
            productPatternShapeList.clear();
            reactantPatternShapeList.add(spls);
            shapePanel.repaint();
            return;
        }
    }
    patterns = right.split(regex);
    for (String spString : patterns) {
        try {
            spString = spString.trim();
            SpeciesPattern speciesPattern = (SpeciesPattern) RbmUtils.parseSpeciesPattern(spString, tempModel);
            strStructure = RbmUtils.parseCompartment(spString, tempModel);
            speciesPattern.resolveBonds();
            Structure structure;
            if (strStructure != null) {
                if (tempModel.getStructure(strStructure) == null) {
                    if (sc.getModel().getStructure(strStructure).getTypeName().equals(Structure.TYPE_NAME_MEMBRANE)) {
                        tempModel.addMembrane(strStructure);
                    } else {
                        tempModel.addFeature(strStructure);
                    }
                }
                structure = tempModel.getStructure(strStructure);
            } else {
                structure = ruleStructure;
            }
            // BNGLParser parser = new BNGLParser(new StringReader(sp));
            // ASTSpeciesPattern astSpeciesPattern = parser.SpeciesPattern();
            // BnglObjectConstructionVisitor constructionVisitor = new BnglObjectConstructionVisitor(tempModel, null, false);
            // SpeciesPattern speciesPattern = (SpeciesPattern) astSpeciesPattern.jjtAccept(constructionVisitor, null);
            // for(MolecularTypePattern mtp : speciesPattern.getMolecularTypePatterns()) {
            // mtp.setParticipantMatchLabel("*");
            // }
            // System.out.println(speciesPattern.toString());
            reactionRule.addProduct(new ProductPattern(speciesPattern, structure));
        } catch (Throwable ex) {
            ex.printStackTrace();
            // error (red circle)
            SpeciesPatternLargeShape spls = new SpeciesPatternLargeShape(20, 20, -1, shapePanel, true, issueManager);
            reactantPatternShapeList.clear();
            productPatternShapeList.clear();
            reactantPatternShapeList.add(spls);
            shapePanel.repaint();
            return;
        }
    }
    // ----------------------------------------------------------------------------------------------------
    List<ReactantPattern> rpList = reactionRule.getReactantPatterns();
    reactantPatternShapeList.clear();
    int xOffset = 20;
    int xOffsetRound = 20;
    if (rpList != null && rpList.size() > 0) {
        for (int i = 0; i < rpList.size(); i++) {
            SpeciesPattern sp = rpList.get(i).getSpeciesPattern();
            for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
                mtp.setParticipantMatchLabel("*");
            }
            SpeciesPatternLargeShape sps = new SpeciesPatternLargeShape(xOffset, 20, -1, sp, shapePanel, reactionRule, issueManager);
            // SpeciesPatternRoundShape sps = new SpeciesPatternRoundShape(xOffsetRound, 20, -1, sp, shapePanel, reactionRule);
            if (i < rpList.size() - 1) {
                sps.addEndText("+");
            } else {
                if (reactionRule.isReversible()) {
                    sps.addEndText("<->");
                } else {
                    sps.addEndText("->");
                }
            }
            xOffset = sps.getRightEnd() + 45;
            xOffsetRound = sps.getRightEnd() + 45;
            reactantPatternShapeList.add(sps);
        }
    }
    // space for the <-> sign
    xOffset += 15;
    List<ProductPattern> ppList = reactionRule.getProductPatterns();
    productPatternShapeList.clear();
    if (ppList != null && ppList.size() > 0) {
        for (int i = 0; i < ppList.size(); i++) {
            SpeciesPattern sp = ppList.get(i).getSpeciesPattern();
            for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
                mtp.setParticipantMatchLabel("*");
            }
            SpeciesPatternLargeShape sps = new SpeciesPatternLargeShape(xOffset, 20, -1, sp, shapePanel, reactionRule, issueManager);
            // SpeciesPatternRoundShape sps = new SpeciesPatternRoundShape(xOffset, 20, -1, sp, shapePanel, reactionRule);
            if (i < ppList.size() - 1) {
                sps.addEndText("+");
            }
            xOffset = sps.getRightEnd() + 45;
            productPatternShapeList.add(sps);
        }
    }
    Dimension preferredSize = new Dimension(xOffset + 90, 50);
    shapePanel.setPreferredSize(preferredSize);
    shapePanel.repaint();
}

Example 2 with ReactantPattern

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

the class XmlReader method getRbmReactantPatternsList.

private void getRbmReactantPatternsList(Element e, ReactionRule r, Model newModel) {
    if (e != null) {
        List<Element> rpChildren = e.getChildren(XMLTags.RbmReactantPatternTag, vcNamespace);
        for (Element rpElement : rpChildren) {
            Structure structure = null;
            String structureName = rpElement.getAttributeValue(XMLTags.StructureAttrTag);
            if (structureName == null || structureName.isEmpty()) {
                // the tag is missing
                throw new RuntimeException("XMLReader: structure missing for reaction rule pattern.");
            } else {
                structure = newModel.getStructure(structureName);
            }
            Element spe = rpElement.getChild(XMLTags.RbmSpeciesPatternTag, vcNamespace);
            SpeciesPattern s = getSpeciesPattern(spe, newModel);
            if (s != null) {
                r.addReactant(new ReactantPattern(s, structure), false);
            }
        }
        // older models have the species pattern saved directly and using the structure or the rule
        List<Element> spChildren = e.getChildren(XMLTags.RbmSpeciesPatternTag, vcNamespace);
        for (Element element : spChildren) {
            SpeciesPattern s = getSpeciesPattern(element, newModel);
            if (s != null) {
                r.addReactant(new ReactantPattern(s, r.getStructure()), false);
            }
        }
    }
}

Example 3 with ReactantPattern

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

the class Xmlproducer method getXML.

private Element getXML(ReactionRule param) {
    Element e = new Element(XMLTags.RbmReactionRuleTag);
    e.setAttribute(XMLTags.NameAttrTag, mangle(param.getName()));
    e.setAttribute(XMLTags.StructureAttrTag, mangle(param.getStructure().getName()));
    e.setAttribute(XMLTags.RbmReactionRuleLabelTag, mangle(param.getName()));
    boolean reversible = param.isReversible();
    e.setAttribute(XMLTags.RbmReactionRuleReversibleTag, String.valueOf(reversible));
    // if (param.getKineticLaw().getLocalParameterValue(RbmKineticLawParameterType.MassActionForwardRate)!=null){
    // e.setAttribute(XMLTags.RbmMassActionKfTag, mangleExpression(param.getKineticLaw().getLocalParameterValue(RbmKineticLawParameterType.MassActionForwardRate)));
    // }
    // if (param.getKineticLaw().getLocalParameterValue(RbmKineticLawParameterType.MassActionReverseRate)!=null){
    // e.setAttribute(XMLTags.RbmMassActionKrTag, mangleExpression(param.getKineticLaw().getLocalParameterValue(RbmKineticLawParameterType.MassActionReverseRate)));
    // }
    // if (param.getKineticLaw().getLocalParameterValue(RbmKineticLawParameterType.MichaelisMentenKcat)!=null){
    // e.setAttribute(XMLTags.RbmMichaelisMentenKcatTag, mangleExpression(param.getKineticLaw().getLocalParameterValue(RbmKineticLawParameterType.MichaelisMentenKcat)));
    // }
    // if (param.getKineticLaw().getLocalParameterValue(RbmKineticLawParameterType.MichaelisMentenKm)!=null){
    // e.setAttribute(XMLTags.RbmMichaelisMentenKmTag, mangleExpression(param.getKineticLaw().getLocalParameterValue(RbmKineticLawParameterType.MichaelisMentenKm)));
    // }
    // if (param.getKineticLaw().getLocalParameterValue(RbmKineticLawParameterType.SaturableKs)!=null){
    // e.setAttribute(XMLTags.RbmSaturableKsTag, mangleExpression(param.getKineticLaw().getLocalParameterValue(RbmKineticLawParameterType.SaturableKs)));
    // }
    // if (param.getKineticLaw().getLocalParameterValue(RbmKineticLawParameterType.SaturableVmax)!=null){
    // e.setAttribute(XMLTags.RbmSaturableVmaxTag, mangleExpression(param.getKineticLaw().getLocalParameterValue(RbmKineticLawParameterType.SaturableVmax)));
    // }
    List<ReactantPattern> reactantPatterns = param.getReactantPatterns();
    if (!reactantPatterns.isEmpty()) {
        Element reactantPatternsListElement = new Element(XMLTags.RbmReactantPatternsListTag);
        for (ReactantPattern rp : reactantPatterns) {
            reactantPatternsListElement.addContent(getXML(rp));
        }
        e.addContent(reactantPatternsListElement);
    }
    List<ProductPattern> productPatterns = param.getProductPatterns();
    if (!productPatterns.isEmpty()) {
        Element productPatternsListElement = new Element(XMLTags.RbmProductPatternsListTag);
        for (ProductPattern pp : productPatterns) {
            productPatternsListElement.addContent(getXML(pp));
        }
        e.addContent(productPatternsListElement);
    }
    // apparently the molecularTypeMapping list is not being used
    // Add kinetics
    e.addContent(getXML(param.getKineticLaw()));
    return e;
}

Example 4 with ReactantPattern

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

the class RbmUtils method toBnglStringShort.

public static String toBnglStringShort(ReactionRule reactionRule, CompartmentMode compartmentMode) {
    StringBuilder buffer = new StringBuilder();
    List<ReactantPattern> reactants = reactionRule.getReactantPatterns();
    for (int i = 0; i < reactants.size(); ++i) {
        if (i > 0) {
            buffer.append(" + ");
        }
        ReactantPattern rp = reactants.get(i);
        if (compartmentMode == CompartmentMode.show) {
            buffer.append("@" + rp.getStructure().getName() + ":");
            buffer.append(toBnglString(rp.getSpeciesPattern(), null, CompartmentMode.hide, 0));
        } else if (compartmentMode == CompartmentMode.asSite) {
            buffer.append(toBnglString(rp.getSpeciesPattern(), rp.getStructure(), CompartmentMode.asSite, 0));
        } else {
            buffer.append(toBnglString(rp.getSpeciesPattern(), null, CompartmentMode.hide, 0));
        }
    }
    buffer.append(reactionRule.isReversible() ? " <-> " : " -> ");
    List<ProductPattern> products = reactionRule.getProductPatterns();
    for (int i = 0; i < products.size(); ++i) {
        if (i > 0) {
            buffer.append(" + ");
        }
        ProductPattern pp = products.get(i);
        if (compartmentMode == CompartmentMode.show) {
            buffer.append("@" + pp.getStructure().getName() + ":");
            // because we already set the compartment
            buffer.append(toBnglString(pp.getSpeciesPattern(), null, CompartmentMode.hide, 0));
        } else if (compartmentMode == CompartmentMode.asSite) {
            // last arg is index of product
            buffer.append(toBnglString(pp.getSpeciesPattern(), pp.getStructure(), CompartmentMode.asSite, i + 1));
        } else {
            buffer.append(toBnglString(pp.getSpeciesPattern(), null, CompartmentMode.hide, 0));
        }
    }
    return buffer.toString();
}

Example 5 with ReactantPattern

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

the class SpeciesPatternRoundShape method paintCompartment.

public void paintCompartment(Graphics g) {
    Color structureColor = Color.black;
    Structure structure = null;
    if (owner instanceof ReactionRule && !speciesShapes.isEmpty()) {
        ReactionRule rr = (ReactionRule) owner;
        ReactantPattern rp = rr.getReactantPattern(sp);
        ProductPattern pp = rr.getProductPattern(sp);
        if (rp != null) {
            structure = rp.getStructure();
        } else if (pp != null) {
            structure = pp.getStructure();
        } else {
            structure = ((ReactionRule) owner).getStructure();
        }
    } else if (owner instanceof SpeciesContext && ((SpeciesContext) owner).hasSpeciesPattern()) {
        structure = ((SpeciesContext) owner).getStructure();
        structureColor = Color.gray;
    } else if (owner instanceof RbmObservable && !speciesShapes.isEmpty()) {
        structure = ((RbmObservable) owner).getStructure();
    } else {
        // other things don't have structure
        return;
    }
    if (structure == null) {
        return;
    }
    // don't have a real structure, so we show them structureless (for now)
    if (structure.getName() == null) {
        return;
    }
    Graphics2D g2 = (Graphics2D) g;
    Color colorOld = g2.getColor();
    Paint paintOld = g2.getPaint();
    Font fontOld = g2.getFont();
    Font font;
    // width of compartment shape, adjusted continuously based on zoom factor
    int w;
    String name = structure.getName();
    int z = shapePanel.getZoomFactor();
    if (z > -3) {
        font = fontOld.deriveFont(Font.BOLD);
        g.setFont(font);
        w = 46 + 3 * z;
        name = buildCompartmentName(g, name, "..", w);
    } else if (z < LargeShapeCanvas.SmallestZoomFactorWithText) {
        font = fontOld.deriveFont(fontOld.getSize2D() * 0.8f);
        g.setFont(font);
        w = 20;
        name = buildCompartmentName(g, name, ".", w);
    } else {
        font = fontOld;
        g.setFont(font);
        w = 44 + 3 * z;
        name = buildCompartmentName(g, name, "..", w);
    }
    // a bit darker for border
    Color darker = Color.gray;
    Rectangle2D border = new Rectangle2D.Double(xPos - 9, yPos - 4, w, 58);
    g2.setColor(darker);
    g2.draw(border);
    Color lighter = new Color(224, 224, 224);
    Rectangle2D filling = new Rectangle2D.Double(xPos - 9, yPos - 3, w, 57);
    g2.setPaint(lighter);
    g2.fill(filling);
    g.setColor(structureColor);
    g2.drawString(name, xPos - 4, yPos + 48);
    g2.setFont(fontOld);
    g2.setPaint(paintOld);
    g2.setColor(colorOld);
}