From ba0545cb610eabc646773e425d3137fbe356a581 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 24 Nov 2017 18:05:03 +0100
Subject: [PATCH] basic layout for reactions added
---
.../converter/model/sbml/SbmlParser.java | 97 +++-
.../model/sbml/SbmlReactionParser.java | 2 +-
.../converter/model/sbml/SbmlParserTest.java | 23 +-
.../layoutExample/Complete_Example_level2.xml | 475 +++++++++---------
4 files changed, 356 insertions(+), 241 deletions(-)
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
index 9b92286338..e73ec1dc9d 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
@@ -1,6 +1,7 @@
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)) {
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
index 2acf38c9ff..50be3be76d 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
@@ -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");
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
index 260e80486d..dfa7b80ef1 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
@@ -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);
diff --git a/converter-sbml/testFiles/layoutExample/Complete_Example_level2.xml b/converter-sbml/testFiles/layoutExample/Complete_Example_level2.xml
index ce678f269f..0517a9d2f2 100644
--- a/converter-sbml/testFiles/layoutExample/Complete_Example_level2.xml
+++ b/converter-sbml/testFiles/layoutExample/Complete_Example_level2.xml
@@ -1,240 +1,241 @@
<?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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