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Commit ba0545cb authored by Piotr Gawron's avatar Piotr Gawron
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basic layout for reactions added

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1 merge request!186Resolve "upload of sbml"
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converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
+ 95
− 2
View file @ ba0545cb
package lcsb.mapviewer.converter.model.sbml;
import java.awt.Point;
import java.awt.geom.Point2D;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
......@@ -22,10 +23,20 @@ import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.IConverter;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.AndOperator;
import lcsb.mapviewer.model.map.reaction.Modifier;
import lcsb.mapviewer.model.map.reaction.NodeOperator;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.SplitOperator;
import lcsb.mapviewer.model.map.species.Element;
public class SbmlParser implements IConverter {
......@@ -110,14 +121,18 @@ public class SbmlParser implements IConverter {
}
private void createLayout(Model model, Layout layout) {
for (Element element : model.getElements()) {
if (element.getWidth() == 0 || element.getHeight() == 0) {
element.setWidth(100);
element.setHeight(20);
Point coord = nextCoordinates();
element.setX(coord.x * 120);
element.setX(coord.y * 30);
element.setY(coord.y * 50);
}
}
for (Reaction reaction : model.getReactions()) {
if (!hasLayout(reaction)) {
createLayoutForReaction(reaction);
}
}
......@@ -149,6 +164,83 @@ public class SbmlParser implements IConverter {
model.setHeight(height);
}
private void createLayoutForReaction(Reaction reaction) {
Point2D reactantStartPoint = reaction.getReactants().get(0).getElement().getCenter();
Point2D productEndPoint = reaction.getProducts().get(0).getElement().getCenter();
Point2D center = new Point2D.Double((reactantStartPoint.getX() + productEndPoint.getX()) / 2,
(reactantStartPoint.getY() + productEndPoint.getY()) / 2);
Point2D reactantMergePoint = new Point2D.Double((reactantStartPoint.getX() + center.getX() * 3) / 4,
(reactantStartPoint.getY() + center.getY() * 3) / 4);
Point2D productMergePoint = new Point2D.Double((productEndPoint.getX() + center.getX() * 3) / 4,
(productEndPoint.getY() + center.getY() * 3) / 4);
if (reaction.getReactants().size()==1) {
PolylineData line = new PolylineData();
line.addPoint(reactantStartPoint);
line.addPoint(center);
reaction.getReactants().get(0).setLine(line);
} else {
for (Reactant reactant: reaction.getReactants()) {
PolylineData line = new PolylineData();
line.addPoint(reactantMergePoint);
line.addPoint(reactant.getElement().getCenter());
reactant.setLine(line);
}
NodeOperator operator = new AndOperator();
PolylineData line = new PolylineData();
line.addPoint(reactantMergePoint);
line.addPoint(center);
operator.addInputs(reaction.getReactants());
operator.setLine(line);
reaction.addNode(operator);
}
if (reaction.getProducts().size()==1) {
PolylineData line = new PolylineData();
line.addPoint(productEndPoint);
line.addPoint(center);
reaction.getProducts().get(0).setLine(line);
} else {
for (Product product: reaction.getProducts()) {
PolylineData line = new PolylineData();
line.addPoint(product.getElement().getCenter());
line.addPoint(productMergePoint);
product.setLine(line);
}
NodeOperator operator = new SplitOperator();
PolylineData line = new PolylineData();
line.addPoint(productMergePoint);
line.addPoint(center);
operator.addOutputs(reaction.getProducts());
operator.setLine(line);
reaction.addNode(operator);
}
for (Modifier modifier: reaction.getModifiers()) {
PolylineData line = new PolylineData();
line.addPoint(modifier.getElement().getCenter());
line.addPoint(center);
modifier.setLine(line);
if (modifier.getClass()==Modifier.class) {
line.setEndAtd(ModifierType.MODULATION_STRING.getAtd());
}
}
}
private boolean hasLayout(Reaction reaction) {
for (AbstractNode node : reaction.getNodes()) {
if (node.getLine() == null) {
return false;
} else if (node.getLine().length() == 0) {
return false;
}
}
return true;
}
Point coordinates = null;
int radius = 0;
......@@ -174,6 +266,7 @@ public class SbmlParser implements IConverter {
private Layout getSbmlLayout(org.sbml.jsbml.Model sbmlModel) {
Layout layout = null;
if (sbmlModel.getExtensionCount() > 0) {
for (SBasePlugin plugin : sbmlModel.getExtensionPackages().values()) {
if (plugin.getClass().equals(org.sbml.jsbml.ext.layout.LayoutModelPlugin.class)) {
......
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
+ 1
− 1
View file @ ba0545cb
......@@ -227,7 +227,7 @@ public class SbmlReactionParser {
}
protected Reaction parse(org.sbml.jsbml.Reaction sbmlReaction, Model sbmlModel) throws InvalidInputDataExecption {
Reaction reaction = new Reaction();
Reaction reaction = new StateTransitionReaction();
reaction.setIdReaction(sbmlReaction.getId());
if (sbmlReaction.getKineticLaw() != null) {
throw new NotImplementedException("KineticLaw not implemented");
......
converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
+ 22
− 1
View file @ ba0545cb
......@@ -108,7 +108,28 @@ public class SbmlParserTest {
assertNotNull(node.getLine());
assertTrue(node.getLine().length() > 0);
}
// assertEquals(2, reaction.getOperators().size());
assertEquals(2, reaction.getOperators().size());
AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().height(model.getHeight())
.width(model.getWidth()).nested(true).scale(1).level(20).x(0).y(0).model(model);
NormalImageGenerator nig = new PngImageGenerator(params);
nig.saveToFile("tmp.png");
Desktop.getDesktop().open(new File("tmp.png"));
}
@Test
public void testReactionWithoutLayout() throws Exception {
Model model = parser.createModel(new ConverterParams().filename("testFiles/layoutExample/Complete_Example_level2.xml"));
assertNotNull(model);
assertEquals(1, model.getReactions().size());
Reaction reaction = model.getReactions().iterator().next();
for (ReactionNode node : reaction.getReactionNodes()) {
logger.debug(node.getClass()+","+node.getElement());
assertNotNull(node.getLine());
assertTrue(node.getLine().length() > 0);
}
assertEquals(2, reaction.getOperators().size());
AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().height(model.getHeight())
.width(model.getWidth()).nested(true).scale(1).level(20).x(0).y(0).model(model);
......
converter-sbml/testFiles/layoutExample/Complete_Example_level2.xml
+ 238
− 237
View file @ ba0545cb
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
<model id="TestModel_with_modifiers">
<annotation>
<listOfLayouts xmlns="http://projects.eml.org/bcb/sbml/level2"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<layout id="Layout_1">
<dimensions width="400" height="230"/>
<listOfCompartmentGlyphs>
<compartmentGlyph id="CompartmentGlyph_1" compartment="Yeast">
<boundingBox id="bb1">
<position x="5" y="5"/>
<dimensions width="390" height="220"/>
</boundingBox>
</compartmentGlyph>
</listOfCompartmentGlyphs>
<listOfSpeciesGlyphs>
<speciesGlyph id="SpeciesGlyph_Glucose" species="Glucose">
<boundingBox id="bb2">
<position x="105" y="20"/>
<dimensions width="130" height="20"/>
</boundingBox>
</speciesGlyph>
<speciesGlyph id="SpeciesGlyph_G6P" species="G6P">
<boundingBox id="bb5">
<position x="50" y="190"/>
<dimensions width="270" height="20"/>
</boundingBox>
</speciesGlyph>
<speciesGlyph id="SpeciesGlyph_ATP" species="ATP">
<boundingBox id="bb3">
<position x="270" y="70"/>
<dimensions width="80" height="20"/>
</boundingBox>
</speciesGlyph>
<speciesGlyph id="glyph_ADP" species="ADP">
<boundingBox id="bb4">
<position x="270" y="140"/>
<dimensions width="80" height="20"/>
</boundingBox>
</speciesGlyph>
<speciesGlyph id="SpeciesGlyph_Pi" species="Pi">
<boundingBox id="bb6">
<position x="50" y="100"/>
<dimensions width="60" height="20"/>
</boundingBox>
</speciesGlyph>
</listOfSpeciesGlyphs>
<listOfReactionGlyphs>
<reactionGlyph id="glyph_Hexokinase" reaction="Hexokinase">
<curve>
<listOfCurveSegments>
<curveSegment xsi:type="LineSegment">
<start x="170" y="100"/>
<end x="170" y="130"/>
</curveSegment>
</listOfCurveSegments>
</curve>
<listOfSpeciesReferenceGlyphs>
<speciesReferenceGlyph id="SpeciesReferenceGlyph_Glucose"
speciesReference="SpeciesReference_Glucose"
speciesGlyph="SpeciesGlyph_Glucose" role="substrate">
<curve>
<listOfCurveSegments>
<curveSegment xsi:type="LineSegment">
<start x="170" y="100"/>
<end x="170" y="50"/>
</curveSegment>
</listOfCurveSegments>
</curve>
</speciesReferenceGlyph>
<speciesReferenceGlyph id="SpeciesReferenceGlyph_ATP"
speciesReference="SpeciesReference_ATP"
speciesGlyph="SpeciesGlyph_ATP" role="sidesubstrate">
<curve>
<listOfCurveSegments>
<curveSegment xsi:type="CubicBezier">
<start x="170" y="100"/>
<end x="260" y="80"/>
<basePoint1 x="170" y="80"/>
<basePoint2 x="170" y="80"/>
</curveSegment>
</listOfCurveSegments>
</curve>
</speciesReferenceGlyph>
<speciesReferenceGlyph id="SpeciesReferenceGlyph_G6P_1"
speciesReference="SpeciesReference_G6P"
speciesGlyph="SpeciesGlyph_G6P" role="product">
<curve>
<listOfCurveSegments>
<curveSegment xsi:type="LineSegment">
<start x="170" y="130"/>
<end x="170" y="180"/>
</curveSegment>
</listOfCurveSegments>
</curve>
</speciesReferenceGlyph>
<speciesReferenceGlyph id="SpeciesReferenceGlyph_ADP"
speciesReference="SpeciesReference_ADP"
speciesGlyph="glyph_ADP" role="sideproduct">
<curve>
<listOfCurveSegments>
<curveSegment xsi:type="CubicBezier">
<start x="170" y="130"/>
<end x="260" y="150"/>
<basePoint1 x="170" y="150"/>
<basePoint2 x="170" y="150"/>
</curveSegment>
</listOfCurveSegments>
</curve>
</speciesReferenceGlyph>
<speciesReferenceGlyph id="SpeciesReferenceGlyph_G6P_2"
speciesReference="ModifierSpeciesReference_G6P"
speciesGlyph="SpeciesGlyph_G6P" role="inhibitor">
<curve>
<listOfCurveSegments>
<curveSegment xsi:type="CubicBezier">
<start x="45" y="200"/>
<end x="165" y="120"/>
<basePoint1 x="0" y="200"/>
<basePoint2 x="0" y="120"/>
</curveSegment>
</listOfCurveSegments>
</curve>
</speciesReferenceGlyph>
<speciesReferenceGlyph id="SpeciesReferenceGlyph_PI"
speciesReference="ModifierSpeciesReference_Pi"
speciesGlyph="SpeciesGlyph_Pi" role="activator">
<curve>
<listOfCurveSegments>
<curveSegment xsi:type="CubicBezier">
<start x="115" y="110"/>
<end x="165" y="110"/>
<basePoint1 x="140" y="110"/>
<basePoint2 x="140" y="110"/>
</curveSegment>
</listOfCurveSegments>
</curve>
</speciesReferenceGlyph>
</listOfSpeciesReferenceGlyphs>
</reactionGlyph>
</listOfReactionGlyphs>
<listOfTextGlyphs>
<textGlyph id="TextGlyph_Glucose" graphicalObject="SpeciesGlyph_Glucose"
originOfText="Glucose">
<boundingBox id="bbA">
<position x="115" y="20"/>
<dimensions width="110" height="20"/>
</boundingBox>
</textGlyph>
<textGlyph id="TextGlyph_G6P" graphicalObject="SpeciesGlyph_G6P"
originOfText="G6P">
<boundingBox id="bbD">
<position x="60" y="190"/>
<dimensions width="250" height="20"/>
</boundingBox>
</textGlyph>
<textGlyph id="TextGlyph_ATP" graphicalObject="SpeciesGlyph_ATP"
originOfText="ATP">
<boundingBox id="bbB">
<position x="280" y="70"/>
<dimensions width="60" height="20"/>
</boundingBox>
</textGlyph>
<textGlyph id="TextGlyph_ADP" graphicalObject="glyph_ADP"
originOfText="ADP">
<boundingBox id="bbC">
<position x="280" y="140"/>
<dimensions width="60" height="20"/>
</boundingBox>
</textGlyph>
<textGlyph id="TextGlyph_PI" graphicalObject="SpeciesGlyph_Pi"
originOfText="Pi">
<boundingBox id="bbE">
<position x="60" y="100"/>
<dimensions width="40" height="20"/>
</boundingBox>
</textGlyph>
</listOfTextGlyphs>
</layout>
</listOfLayouts>
</annotation>
<listOfCompartments>
<compartment id="Yeast"/>
</listOfCompartments>
<listOfSpecies>
<species id="Glucose" compartment="Yeast"/>
<species id="G6P" name="Glucose-6-phosphate" compartment="Yeast"/>
<species id="ATP" compartment="Yeast"/>
<species id="ADP" compartment="Yeast"/>
<species id="Pi" compartment="Yeast"/>
</listOfSpecies>
<listOfReactions>
<reaction id="Hexokinase" reversible="false">
<listOfReactants>
<speciesReference species="Glucose">
<annotation>
<layoutId xmlns="http://projects.eml.org/bcb/sbml/level2"
id="SpeciesReference_Glucose"/>
</annotation>
</speciesReference>
<speciesReference species="ATP">
<annotation>
<layoutId xmlns="http://projects.eml.org/bcb/sbml/level2"
id="SpeciesReference_ATP"/>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference species="G6P">
<annotation>
<layoutId xmlns="http://projects.eml.org/bcb/sbml/level2"
id="SpeciesReference_G6P"/>
</annotation>
</speciesReference>
<speciesReference species="ADP">
<annotation>
<layoutId xmlns="http://projects.eml.org/bcb/sbml/level2"
id="SpeciesReference_ADP"/>
</annotation>
</speciesReference>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="G6P">
<annotation>
<layoutId xmlns="http://projects.eml.org/bcb/sbml/level2"
id="ModifierSpeciesReference_G6P"/>
</annotation>
</modifierSpeciesReference>
<modifierSpeciesReference species="Pi">
<annotation>
<layoutId xmlns="http://projects.eml.org/bcb/sbml/level2"
id="ModifierSpeciesReference_Pi"/>
</annotation>
</modifierSpeciesReference>
</listOfModifiers>
</reaction>
</listOfReactions>
</model>
<model id="TestModel_with_modifiers">
<annotation>
<listOfLayouts xmlns="http://projects.eml.org/bcb/sbml/level2"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<layout id="Layout_1">
<dimensions width="400" height="230" />
<listOfCompartmentGlyphs>
<compartmentGlyph id="CompartmentGlyph_1"
compartment="Yeast">
<boundingBox id="bb1">
<position x="5" y="5" />
<dimensions width="390" height="220" />
</boundingBox>
</compartmentGlyph>
</listOfCompartmentGlyphs>
<listOfSpeciesGlyphs>
<speciesGlyph id="SpeciesGlyph_Glucose" species="Glucose">
<boundingBox id="bb2">
<position x="105" y="20" />
<dimensions width="130" height="20" />
</boundingBox>
</speciesGlyph>
<speciesGlyph id="SpeciesGlyph_G6P" species="G6P">
<boundingBox id="bb5">
<position x="50" y="190" />
<dimensions width="270" height="20" />
</boundingBox>
</speciesGlyph>
<speciesGlyph id="SpeciesGlyph_ATP" species="ATP">
<boundingBox id="bb3">
<position x="270" y="70" />
<dimensions width="80" height="20" />
</boundingBox>
</speciesGlyph>
<speciesGlyph id="glyph_ADP" species="ADP">
<boundingBox id="bb4">
<position x="270" y="140" />
<dimensions width="80" height="20" />
</boundingBox>
</speciesGlyph>
<speciesGlyph id="SpeciesGlyph_Pi" species="Pi">
<boundingBox id="bb6">
<position x="50" y="100" />
<dimensions width="60" height="20" />
</boundingBox>
</speciesGlyph>
</listOfSpeciesGlyphs>
<listOfReactionGlyphs>
<reactionGlyph id="glyph_Hexokinase" reaction="Hexokinase">
<curve>
<listOfCurveSegments>
<curveSegment xsi:type="LineSegment">
<start x="170" y="100" />
<end x="170" y="130" />
</curveSegment>
</listOfCurveSegments>
</curve>
<listOfSpeciesReferenceGlyphs>
<speciesReferenceGlyph id="SpeciesReferenceGlyph_Glucose"
speciesReference="SpeciesReference_Glucose" speciesGlyph="SpeciesGlyph_Glucose"
role="substrate">
<curve>
<listOfCurveSegments>
<curveSegment xsi:type="LineSegment">
<start x="170" y="100" />
<end x="170" y="50" />
</curveSegment>
</listOfCurveSegments>
</curve>
</speciesReferenceGlyph>
<speciesReferenceGlyph id="SpeciesReferenceGlyph_ATP"
speciesReference="SpeciesReference_ATP" speciesGlyph="SpeciesGlyph_ATP"
role="sidesubstrate">
<curve>
<listOfCurveSegments>
<curveSegment xsi:type="CubicBezier">
<start x="170" y="100" />
<end x="260" y="80" />
<basePoint1 x="170" y="80" />
<basePoint2 x="170" y="80" />
</curveSegment>
</listOfCurveSegments>
</curve>
</speciesReferenceGlyph>
<speciesReferenceGlyph id="SpeciesReferenceGlyph_G6P_1"
speciesReference="SpeciesReference_G6P" speciesGlyph="SpeciesGlyph_G6P"
role="product">
<curve>
<listOfCurveSegments>
<curveSegment xsi:type="LineSegment">
<start x="170" y="130" />
<end x="170" y="180" />
</curveSegment>
</listOfCurveSegments>
</curve>
</speciesReferenceGlyph>
<speciesReferenceGlyph id="SpeciesReferenceGlyph_ADP"
speciesReference="SpeciesReference_ADP" speciesGlyph="glyph_ADP"
role="sideproduct">
<curve>
<listOfCurveSegments>
<curveSegment xsi:type="CubicBezier">
<start x="170" y="130" />
<end x="260" y="150" />
<basePoint1 x="170" y="150" />
<basePoint2 x="170" y="150" />
</curveSegment>
</listOfCurveSegments>
</curve>
</speciesReferenceGlyph>
<speciesReferenceGlyph id="SpeciesReferenceGlyph_G6P_2"
speciesReference="ModifierSpeciesReference_G6P" speciesGlyph="SpeciesGlyph_G6P"
role="inhibitor">
<curve>
<listOfCurveSegments>
<curveSegment xsi:type="CubicBezier">
<start x="45" y="200" />
<end x="165" y="120" />
<basePoint1 x="0" y="200" />
<basePoint2 x="0" y="120" />
</curveSegment>
</listOfCurveSegments>
</curve>
</speciesReferenceGlyph>
<speciesReferenceGlyph id="SpeciesReferenceGlyph_PI"
speciesReference="ModifierSpeciesReference_Pi" speciesGlyph="SpeciesGlyph_Pi"
role="activator">
<curve>
<listOfCurveSegments>
<curveSegment xsi:type="CubicBezier">
<start x="115" y="110" />
<end x="165" y="110" />
<basePoint1 x="140" y="110" />
<basePoint2 x="140" y="110" />
</curveSegment>
</listOfCurveSegments>
</curve>
</speciesReferenceGlyph>
</listOfSpeciesReferenceGlyphs>
</reactionGlyph>
</listOfReactionGlyphs>
<listOfTextGlyphs>
<textGlyph id="TextGlyph_Glucose" graphicalObject="SpeciesGlyph_Glucose"
originOfText="Glucose">
<boundingBox id="bbA">
<position x="115" y="20" />
<dimensions width="110" height="20" />
</boundingBox>
</textGlyph>
<textGlyph id="TextGlyph_G6P" graphicalObject="SpeciesGlyph_G6P"
originOfText="G6P">
<boundingBox id="bbD">
<position x="60" y="190" />
<dimensions width="250" height="20" />
</boundingBox>
</textGlyph>
<textGlyph id="TextGlyph_ATP" graphicalObject="SpeciesGlyph_ATP"
originOfText="ATP">
<boundingBox id="bbB">
<position x="280" y="70" />
<dimensions width="60" height="20" />
</boundingBox>
</textGlyph>
<textGlyph id="TextGlyph_ADP" graphicalObject="glyph_ADP"
originOfText="ADP">
<boundingBox id="bbC">
<position x="280" y="140" />
<dimensions width="60" height="20" />
</boundingBox>
</textGlyph>
<textGlyph id="TextGlyph_PI" graphicalObject="SpeciesGlyph_Pi"
originOfText="Pi">
<boundingBox id="bbE">
<position x="60" y="100" />
<dimensions width="40" height="20" />
</boundingBox>
</textGlyph>
</listOfTextGlyphs>
</layout>
</listOfLayouts>
</annotation>
<listOfCompartments>
<compartment id="Yeast" />
</listOfCompartments>
<listOfSpecies>
<species id="Glucose" compartment="Yeast" />
<species id="G6P" name="Glucose-6-phosphate" compartment="Yeast" />
<species id="ATP" compartment="Yeast" />
<species id="ADP" compartment="Yeast" />
<species id="Pi" compartment="Yeast" />
</listOfSpecies>
<listOfReactions>
<reaction id="Hexokinase" reversible="false">
<listOfReactants>
<speciesReference species="Glucose">
<annotation>
<layoutId xmlns="http://projects.eml.org/bcb/sbml/level2"
id="SpeciesReference_Glucose" />
</annotation>
</speciesReference>
<speciesReference species="ATP">
<annotation>
<layoutId xmlns="http://projects.eml.org/bcb/sbml/level2"
id="SpeciesReference_ATP" />
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference species="G6P">
<annotation>
<layoutId xmlns="http://projects.eml.org/bcb/sbml/level2"
id="SpeciesReference_G6P" />
</annotation>
</speciesReference>
<speciesReference species="ADP">
<annotation>
<layoutId xmlns="http://projects.eml.org/bcb/sbml/level2"
id="SpeciesReference_ADP" />
</annotation>
</speciesReference>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="G6P">
<annotation>
<layoutId xmlns="http://projects.eml.org/bcb/sbml/level2"
id="ModifierSpeciesReference_G6P" />
</annotation>
</modifierSpeciesReference>
<modifierSpeciesReference species="Pi">
<annotation>
<layoutId xmlns="http://projects.eml.org/bcb/sbml/level2"
id="ModifierSpeciesReference_Pi" />
</annotation>
</modifierSpeciesReference>
</listOfModifiers>
</reaction>
</listOfReactions>
</model>
</sbml>
\ No newline at end of file
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