Merge branch '812-wrong-start-and-end-of-reaction-lines' into 'master'

Resolve "wrong start and end of reaction lines"

Closes #812

See merge request !771

CHANGELOG

@@ -68,6 +68,8 @@ minerva (13.1.0~alpha.0) unstable; urgency=low
   * Bug fix: plugin contect element width is adjusted when link to tabs are
     wrapped in more than one line (#758)
   * Bug fix: export to CellDesigner preserve font size (#803)
+  * Bug fix: layout data was ignored for some reactions when improting from 
+    SBML (#812)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 7 May 2019 15:00:00 +0200
 

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/compartment/CompartmentConverter.java

@@ -179,12 +179,9 @@ public abstract class CompartmentConverter<T extends Compartment> extends Elemen
 
 	@Override
 	public void draw(T alias, Graphics2D graphics, ConverterParams params, List<ColorSchema> visualizedLayoutsColorSchemas) throws DrawingException {
-	  logger.debug("Draw: "+alias.getElementId());
 	    if (alias.getGlyph() != null) {
-	      logger.debug("as glyph");
 	      drawGlyph(alias, graphics);
 	    } else {
-          logger.debug("without glyph");
 	      drawImpl(alias, graphics, params);
 	    }
 

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverter.java

@@ -498,12 +498,9 @@ public abstract class SpeciesConverter<T extends Species> extends ElementConvert
   @Override
   public final void draw(T species, Graphics2D graphics, ConverterParams params,
       List<ColorSchema> visualizedLayoutsColorSchemas) throws DrawingException {
-    logger.debug("Draw: "+species.getElementId());
     if (species.getGlyph() != null) {
-      logger.debug("as glyph");
       drawGlyph(species, graphics);
     } else {
-      logger.debug("without glyph");
       drawImpl(species, graphics, params);
     }
 

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java

@@ -21,6 +21,7 @@ import org.sbml.jsbml.SpeciesReference;
 import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
 import org.sbml.jsbml.ext.layout.BoundingBox;
 import org.sbml.jsbml.ext.layout.Curve;
+import org.sbml.jsbml.ext.layout.CurveSegment;
 import org.sbml.jsbml.ext.layout.LineSegment;
 import org.sbml.jsbml.ext.layout.Point;
 import org.sbml.jsbml.ext.layout.ReactionGlyph;
@@ -35,8 +36,10 @@ import org.w3c.dom.Node;
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.PolylineDataFactory;
 import lcsb.mapviewer.converter.model.sbml.SbmlBioEntityExporter;
 import lcsb.mapviewer.converter.model.sbml.SbmlExtension;
+import lcsb.mapviewer.model.graphics.PolylineData;
 import lcsb.mapviewer.model.map.InconsistentModelException;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
@@ -295,14 +298,38 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
     if (isExtensionEnabled(SbmlExtension.RENDER)) {
       assignStyleToGlyph(reactionGlyph, createStyle(reaction));
     }
-    if (reactionGlyph.getBoundingBox()==null) {
+    if (reactionGlyph.getBoundingBox() == null) {
       reactionGlyph.setBoundingBox(new BoundingBox());
     }
-    if (reactionGlyph.getBoundingBox().getPosition()==null) {
+    if (reactionGlyph.getBoundingBox().getPosition() == null) {
       reactionGlyph.getBoundingBox().setPosition(new Point());
     }
     reactionGlyph.getBoundingBox().getPosition().setZ(reaction.getZ());
 
+    removeColinearPoints(reactionGlyph);
+  }
+
+  private void removeColinearPoints(ReactionGlyph glyph) {
+    PolylineData line = createLine(glyph.getCurve());
+    logger.debug(line);
+    line = PolylineDataFactory.removeCollinearPoints(line);
+    logger.debug(line);
+    Curve curve = createCurve(line, false);
+    glyph.setCurve(curve);
+  }
+
+  private PolylineData createLine(Curve curve) {
+    PolylineData result = new PolylineData();
+    if (curve.getCurveSegmentCount() > 0) {
+      CurveSegment segment = curve.getCurveSegment(0);
+      result.addPoint(new Point2D.Double(segment.getStart().getX(), segment.getStart().getY()));
+    }
+    for (int i = 0; i < curve.getCurveSegmentCount(); i++) {
+      CurveSegment segment = curve.getCurveSegment(i);
+      result.addPoint(new Point2D.Double(segment.getEnd().getX(), segment.getEnd().getY()));
+
+    }
+    return result;
   }
 
   private LocalStyle createStyle(ReactionNode node) {
@@ -358,16 +385,20 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
   private SpeciesReferenceGlyph createNodeGlyph(ReactionGlyph reactionGlyph, ReactionNode node) {
     SpeciesReferenceGlyph reactantGlyph = reactionGlyph.createSpeciesReferenceGlyph("node_" + getNextId());
     reactantGlyph.setSpeciesGlyph(speciesExporter.getSbmlGlyphByElementId(node.getElement().getElementId()).getId());
-    reactantGlyph.setCurve(createCurve(node, node instanceof Reactant));
+    Curve curve = createCurve(node.getLine(), node instanceof Reactant);
+    if (curve.getCurveSegmentCount() == 0) {
+      logger.warn(new ElementUtils().getElementTag(node) + " Problematic line");
+    }
+    reactantGlyph.setCurve(curve);
     reactantGlyph.setSpeciesReference(speciesReferenceByReactionNode.get(node));
     return reactantGlyph;
   }
 
-  private Curve createCurve(ReactionNode node, boolean reverse) {
+  private Curve createCurve(PolylineData polyline, boolean reverse) {
     Curve curve = new Curve();
-    List<Line2D> lines = node.getLine().getLines();
+    List<Line2D> lines = polyline.getLines();
     if (reverse) {
-      lines = node.getLine().reverse().getLines();
+      lines = polyline.reverse().getLines();
     }
     for (Line2D line : lines) {
       if (line.getP1().distance(line.getP2()) > Configuration.EPSILON) {
@@ -377,9 +408,6 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
         curve.addCurveSegment(segment);
       }
     }
-    if (curve.getCurveSegmentCount() == 0) {
-      logger.warn(new ElementUtils().getElementTag(node) + " Problematic line");
-    }
     return curve;
   }
 

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java

@@ -31,6 +31,7 @@ import org.sbml.jsbml.ext.render.RenderGroup;
 import org.w3c.dom.Node;
 
 import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
@@ -117,8 +118,8 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
         Reaction reactionWithLayout = source.copy();
         // getId doesn't have to be unique, therefore we concatenate with reaction
         reactionWithLayout.setIdReaction(glyph.getReaction() + "__" + glyph.getId());
-        
-        //z index
+
+        // z index
         if (glyph.getBoundingBox() != null && glyph.getBoundingBox().getPosition() != null
             && glyph.getBoundingBox().getPosition().isSetZ()) {
           reactionWithLayout.setZ((int) glyph.getBoundingBox().getPosition().getZ());
@@ -281,23 +282,6 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
   }
 
   private NodeOperator createOutputOperator(Reaction reactionWithLayout, ReactionGlyph reactionGlyph) {
-    PolylineData line = new PolylineData();
-    Curve curve = extractCurve(reactionGlyph, reactionWithLayout);
-
-    // 1 is for the process in the center
-    int min = 1;
-    if (reactionWithLayout.getReactants().size() > 1) {
-      // with operator in the output we need to leave something for the operator
-      min++;
-    }
-    for (int i = min; i < curve.getCurveSegmentCount(); i++) {
-      CurveSegment segment = curve.getCurveSegment(i);
-      if (line.getPoints().size() == 0) {
-        line.addPoint(new Point2D.Double(segment.getStart().getX(), segment.getStart().getY()));
-      }
-      line.addPoint(new Point2D.Double(segment.getEnd().getX(), segment.getEnd().getY()));
-    }
-
     NodeOperator operator;
     if (reactionWithLayout instanceof TruncationReaction) {
       operator = new TruncationOperator();
@@ -306,34 +290,14 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
     } else {
       operator = new SplitOperator();
     }
+    PolylineData line = extractCurve(reactionGlyph, reactionWithLayout, operator.getClass());
+
     operator.addOutputs(reactionWithLayout.getProducts());
     operator.setLine(line.reverse());
     return operator;
   }
 
   private NodeOperator createInputOperator(Reaction reactionWithLayout, ReactionGlyph reactionGlyph) {
-    PolylineData line = new PolylineData();
-
-    Curve curve = extractCurve(reactionGlyph, reactionWithLayout);
-
-    // -1 is for the process in the center
-    int max = curve.getCurveSegmentCount() - 1;
-    if (reactionWithLayout.getProducts().size() > 1) {
-      // with operator in the output we need to leave something for the operator
-      max--;
-    }
-    for (int i = 0; i < max; i++) {
-      CurveSegment segment = curve.getCurveSegment(i);
-      if (line.getPoints().size() == 0) {
-        line.addPoint(new Point2D.Double(segment.getStart().getX(), segment.getStart().getY()));
-      }
-      line.addPoint(new Point2D.Double(segment.getEnd().getX(), segment.getEnd().getY()));
-    }
-    if (line.getPoints().size() == 0) {
-      Point2D point = reactionWithLayout.getReactants().get(0).getLine().getEndPoint();
-      line.addPoint(new Point2D.Double(point.getX(), point.getY()));
-      line.addPoint(new Point2D.Double(point.getX(), point.getY()));
-    }
 
     NodeOperator operator;
     if (reactionWithLayout instanceof HeterodimerAssociationReaction) {
@@ -341,6 +305,11 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
     } else {
       operator = new AndOperator();
     }
+    PolylineData line = extractCurve(reactionGlyph, reactionWithLayout, operator.getClass());
+    if (line.getPoints().size() == 0) {
+      line.addPoint(reactionWithLayout.getReactants().get(0).getLine().getEndPoint());
+      line.addPoint(reactionWithLayout.getReactants().get(0).getLine().getEndPoint());
+    }
     operator.addInputs(reactionWithLayout.getReactants());
     operator.setLine(line);
     return operator;
@@ -352,9 +321,14 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
    * specification).
    * 
    * @param reactionGlyph
+   * @param operator
+   *          class of {@link NodeOperator} that requires the line (this line can
+   *          be separated into 3 different segments - reactant, center, product
+   *          parts)
    * @return
    */
-  private Curve extractCurve(ReactionGlyph reactionGlyph, Reaction reaction) {
+  private PolylineData extractCurve(ReactionGlyph reactionGlyph, Reaction reaction,
+      Class<? extends NodeOperator> operator) {
     Curve curve = reactionGlyph.getCurve();
     if (curve == null) {
       curve = new Curve(getSbmlModel().getLevel(), getSbmlModel().getVersion());
@@ -370,7 +344,73 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
             + reactionGlyph.getId() + ")");
       }
     }
-    return curve;
+    if (curve.getCurveSegmentCount() == 0) {
+      return new PolylineData();
+    }
+
+    int requiredLines = 0;
+    if (reaction.getReactants().size() > 1) {
+      requiredLines++;
+    }
+    if (reaction.getProducts().size() > 1) {
+      requiredLines++;
+    }
+    int existingLines = curve.getCurveSegmentCount();
+
+    int breakPoint;
+    if (requiredLines == 2) {
+      breakPoint = existingLines / 2;
+    } else if (reaction.getReactants().size() > 1) {
+      breakPoint = existingLines;
+    } else if (reaction.getProducts().size() > 1) {
+      breakPoint = 0;
+    } else {
+      throw new InvalidArgumentException(
+          new ElementUtils().getElementTag(reaction) + "Reaction has no products and reactants");
+    }
+
+    PolylineData result = new PolylineData();
+    if (operator == TruncationOperator.class ||
+        operator == DissociationOperator.class ||
+        operator == SplitOperator.class) {
+      // Product operator
+
+      if (existingLines >= requiredLines) {
+        CurveSegment segment = curve.getCurveSegment(breakPoint);
+        result.addPoint(new Point2D.Double(segment.getStart().getX(), segment.getStart().getY()));
+        for (int i = breakPoint; i < curve.getCurveSegmentCount(); i++) {
+          segment = curve.getCurveSegment(i);
+          result.addPoint(new Point2D.Double(segment.getEnd().getX(), segment.getEnd().getY()));
+        }
+      } else {
+        CurveSegment segment = curve.getCurveSegment(0);
+        double startX = segment.getStart().getX() + (segment.getEnd().getX() - segment.getStart().getX()) / 2;
+        double startY = segment.getStart().getY() + (segment.getEnd().getY() - segment.getStart().getY()) / 2;
+        result.addPoint(new Point2D.Double(startX, startY));
+        result.addPoint(new Point2D.Double(segment.getEnd().getX(), segment.getEnd().getY()));
+      }
+
+    } else if (operator == AssociationOperator.class || operator == AndOperator.class) {
+      // Reactant operator
+
+      if (existingLines >= requiredLines) {
+        CurveSegment segment = curve.getCurveSegment(0);
+        result.addPoint(new Point2D.Double(segment.getStart().getX(), segment.getStart().getY()));
+        for (int i = 0; i < breakPoint; i++) {
+          segment = curve.getCurveSegment(i);
+          result.addPoint(new Point2D.Double(segment.getEnd().getX(), segment.getEnd().getY()));
+        }
+      } else {
+        CurveSegment segment = curve.getCurveSegment(0);
+        result.addPoint(new Point2D.Double(segment.getStart().getX(), segment.getStart().getY()));
+        double endX = segment.getStart().getX() + (segment.getEnd().getX() - segment.getStart().getX()) / 2;
+        double endY = segment.getStart().getY() + (segment.getEnd().getY() - segment.getStart().getY()) / 2;
+        result.addPoint(new Point2D.Double(endX, endY));
+      }
+    } else {
+      throw new InvalidArgumentException("Unknown operator class: " + operator);
+    }
+    return result;
   }
 
   private Class<? extends ReactionNode> getReactionNodeClass(SpeciesReferenceGlyph speciesRefernceGlyph) {

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java

@@ -563,19 +563,6 @@ public class SbmlExporterTest extends SbmlTestFunctions {
 
   }
 
-  @Test
-  public void testExportImportOfInputOperator() throws Exception {
-    Model originalModel = new CellDesignerXmlParser()
-        .createModel(new ConverterParams().filename("testFiles/cell_designer_problems/heterodimer_association.xml"));
-    Model model = getModelAfterSerializing(originalModel);
-    List<Line2D> lines1 = originalModel.getReactions().iterator().next().getLines();
-    List<Line2D> lines2 = model.getReactions().iterator().next().getLines();
-
-    ListComparator<Line2D> comparator = new ListComparator<>(new LineComparator(Configuration.EPSILON));
-    assertEquals(0, comparator.compare(lines1, lines2));
-
-  }
-
   @Test
   public void testExportImportOfAdvancedInputOperator() throws Exception {
     Model originalModel = new CellDesignerXmlParser().createModel(new ConverterParams()
@@ -585,24 +572,11 @@ public class SbmlExporterTest extends SbmlTestFunctions {
     Reaction r2 = model.getReactions().iterator().next();
     Line2D line1 = r1.getCenterLine();
     Line2D line2 = r2.getCenterLine();
-
+    
     assertEquals(0, new LineComparator().compare(line1, line2));
 
   }
 
-  @Test
-  public void testExportImportOfOutputOperator() throws Exception {
-    Model originalModel = new CellDesignerXmlParser()
-        .createModel(new ConverterParams().filename("testFiles/cell_designer_problems/dissociation.xml"));
-    Model model = getModelAfterSerializing(originalModel);
-    List<Line2D> lines1 = originalModel.getReactions().iterator().next().getLines();
-    List<Line2D> lines2 = model.getReactions().iterator().next().getLines();
-
-    ListComparator<Line2D> comparator = new ListComparator<>(new LineComparator(Configuration.EPSILON));
-    assertEquals(0, comparator.compare(lines1, lines2));
-
-  }
-
   @Test
   public void testExportImportBooleanGate() throws Exception {
     Model originalModel = new CellDesignerXmlParser()

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java

@@ -7,21 +7,18 @@ import static org.junit.Assert.assertTrue;
 
 import java.io.FileNotFoundException;
 import java.util.HashSet;
-import java.util.List;
 import java.util.Set;
 
 import org.apache.log4j.Logger;
-import org.apache.log4j.spi.LoggingEvent;
-import org.junit.After;
-import org.junit.Before;
 import org.junit.Test;
 
 import lcsb.mapviewer.commands.CreateHierarchyCommand;
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
+import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reactant;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.reaction.ReactionNode;
 import lcsb.mapviewer.model.map.species.Element;
@@ -29,28 +26,10 @@ import lcsb.mapviewer.model.map.species.Gene;
 import lcsb.mapviewer.model.map.species.GenericProtein;
 import lcsb.mapviewer.model.map.species.Species;
 
-public class SbmlParserTest {
+public class SbmlParserTest extends SbmlTestFunctions {
   Logger logger = Logger.getLogger(SbmlParserTest.class);
   SbmlParser parser = new SbmlParser();
 
-  private EventStorageLoggerAppender appender;
-
-  @Before
-  public final void _setUp() throws Exception {
-    Logger.getRootLogger().removeAppender(appender);
-    appender = new EventStorageLoggerAppender();
-    Logger.getRootLogger().addAppender(appender);
-  }
-
-  @After
-  public final void _tearDown() throws Exception {
-    Logger.getRootLogger().removeAppender(appender);
-  }
-
-  protected List<LoggingEvent> getWarnings() {
-    return appender.getWarnings();
-  }
-
   @Test
   public void testParseCompartment() throws FileNotFoundException, InvalidInputDataExecption {
     Model model = parser.createModel(
@@ -188,12 +167,6 @@ public class SbmlParserTest {
     assertEquals(1, model.getCompartments().iterator().next().getMiriamData().size());
   }
 
-  @Test(expected = InvalidInputDataExecption.class)
-  public void testInvalidReactionLayout() throws Exception {
-    parser.createModel(
-        new ConverterParams().filename("testFiles/invalidReaction/reaction_with_missing_part_of_layout.xml"));
-  }
-
   @Test
   public void testEmpyModel() throws Exception {
     Model model = parser.createModel(new ConverterParams().filename("testFiles/small/empty.xml"));
@@ -259,4 +232,19 @@ public class SbmlParserTest {
     assertNotNull("Creation date is not defined", model.getCreationDate());
   }
 
+  @Test
+  public void testParseProblematicLayout() throws Exception {
+    try {
+      Model model = parser
+          .createModel(new ConverterParams().filename("testFiles/small/problematic_layout.xml"));
+      Reaction reaction = model.getReactions().iterator().next();
+      Reactant reactant = reaction.getReactants().get(0);
+      assertEquals("Reactant line should start at position 120, 40", 0,
+          reactant.getLine().getBeginPoint().distance(120, 40), Configuration.EPSILON);
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
 }

converter-sbml/testFiles/small/problematic_layout.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" level="3" version="1" layout:required="false">
+  <model substanceUnits="mole" timeUnits="second" extentUnits="mole">
+    <listOfUnitDefinitions>
+      <unitDefinition id="per_second">
+        <listOfUnits>
+          <unit kind="second" exponent="-1" scale="0" multiplier="1"/>
+        </listOfUnits>
+      </unitDefinition>
+    </listOfUnitDefinitions>
+    <listOfCompartments>
+      <compartment id="default" constant="false"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species sboTerm="SBO:0000252" id="species_1" name="s2" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <species sboTerm="SBO:0000252" id="species_0" name="s1" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+      <species sboTerm="SBO:0000252" id="species_2" name="s3" compartment="default" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"/>
+    </listOfSpecies>
+    <listOfReactions>
+      <reaction sboTerm="SBO:0000176" id="re3" reversible="false" fast="false">
+        <listOfReactants>
+          <speciesReference species="species_1" constant="false"/>
+          <speciesReference species="species_0" constant="false"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="species_2" constant="false"/>
+        </listOfProducts>
+      </reaction>
+    </listOfReactions>
+    <layout:listOfLayouts xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1">
+      <layout:layout layout:id="predicted_layout">
+        <layout:dimensions layout:width="564" layout:height="217"/>
+        <layout:listOfCompartmentGlyphs>
+          <layout:compartmentGlyph layout:id="cg_default" layout:compartment="default">
+            <layout:boundingBox layout:id="bb_cg_default">
+              <layout:position layout:x="0" layout:y="0"/>
+              <layout:dimensions layout:width="484" layout:height="177"/>
+            </layout:boundingBox>
+          </layout:compartmentGlyph>
+        </layout:listOfCompartmentGlyphs>
+        <layout:listOfSpeciesGlyphs>
+          <layout:speciesGlyph layout:id="sg_re3_0_sa2" layout:species="species_1">
+            <layout:boundingBox layout:id="bb_sg_re3_0_sa2">
+              <layout:position layout:x="40" layout:y="20"/>
+              <layout:dimensions layout:width="80" layout:height="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="sg_re3_0_sa1" layout:species="species_0">
+            <layout:boundingBox layout:id="bb_sg_re3_0_sa1">
+              <layout:position layout:x="46" layout:y="117"/>
+              <layout:dimensions layout:width="80" layout:height="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+          <layout:speciesGlyph layout:id="sg_re3_0_sa3" layout:species="species_2">
+            <layout:boundingBox layout:id="bb_sg_re3_0_sa3">
+              <layout:position layout:x="364" layout:y="96"/>
+              <layout:dimensions layout:width="80" layout:height="40"/>
+            </layout:boundingBox>
+          </layout:speciesGlyph>
+        </layout:listOfSpeciesGlyphs>
+        <layout:listOfReactionGlyphs>
+          <layout:reactionGlyph layout:id="rg_re3_0" layout:reaction="re3">
+            <layout:curve>
+              <layout:listOfCurveSegments>
+                <layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
+                  <layout:start layout:x="209.6" layout:y="70.4"/>
+                  <layout:end layout:x="242" layout:y="78"/>
+                </layout:curveSegment>
+              </layout:listOfCurveSegments>
+            </layout:curve>
+            <layout:listOfSpeciesReferenceGlyphs>
+              <layout:speciesReferenceGlyph layout:id="srg_re3_0_sa2_SUBSTRATE_1" layout:speciesGlyph="sg_re3_0_sa2">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
+                      <layout:start layout:x="209.6" layout:y="70.4"/>
+                      <layout:end layout:x="120" layout:y="40"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+              <layout:speciesReferenceGlyph layout:id="srg_re3_0_sa1_SIDESUBSTRATE_1" layout:speciesGlyph="sg_re3_0_sa1">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
+                      <layout:start layout:x="209.6" layout:y="70.4"/>
+                      <layout:end layout:x="126" layout:y="137"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+              <layout:speciesReferenceGlyph layout:id="srg_re3_0_sa3_PRODUCT_1" layout:speciesGlyph="sg_re3_0_sa3">
+                <layout:curve>
+                  <layout:listOfCurveSegments>
+                    <layout:curveSegment xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:type="LineSegment">
+                      <layout:start layout:x="242" layout:y="78"/>
+                      <layout:end layout:x="364" layout:y="116"/>
+                    </layout:curveSegment>
+                  </layout:listOfCurveSegments>
+                </layout:curve>
+              </layout:speciesReferenceGlyph>
+            </layout:listOfSpeciesReferenceGlyphs>
+          </layout:reactionGlyph>
+        </layout:listOfReactionGlyphs>
+        <layout:listOfTextGlyphs>
+          <layout:textGlyph layout:id="tg_re3_0_sa2" layout:originOfText="sg_re3_0_sa2" layout:graphicalObject="sg_re3_0_sa2">
+            <layout:boundingBox layout:id="bb_tg_re3_0_sa2">
+              <layout:position layout:x="40" layout:y="20"/>
+              <layout:dimensions layout:width="80" layout:height="40"/>
+            </layout:boundingBox>