Redo @parit's changes for net/undirected reaction depiction on the ne…

…w reaction drawing code.
cdk · Aug 29, 2023 · 789c4dd · 789c4dd
1 parent 07a0595
commit 789c4dd
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Showing 5 changed files with 108 additions and 3 deletions.
diff --git a/app/depict/src/main/java/org/openscience/cdk/depict/ReactionBounds.java b/app/depict/src/main/java/org/openscience/cdk/depict/ReactionBounds.java
@@ -104,7 +104,7 @@ ReactionDimensions getDimensions(double padding) {
         int nCol;
         double arrowHeight      = plus.height();
         double arrowHeadLength  = plus.height();
-        double minArrowWidth    = direction != null ? 5 * arrowHeight : 0;
+        double minArrowWidth    = direction != null && direction != IReaction.Direction.UNDIRECTED ? 5 * arrowHeight : arrowHeight;
 
         double[] xOffsets, yOffsets;
         double[] xOffsetSide, yOffsetSide;

diff --git a/app/depict/src/main/java/org/openscience/cdk/depict/ReactionDepiction.java b/app/depict/src/main/java/org/openscience/cdk/depict/ReactionDepiction.java
@@ -382,12 +382,12 @@ static Bounds createArrow(IReaction.Direction direction,
                               double minHeight) {
         if (direction == null)
             return new Bounds();
-        Bounds arrow = new Bounds();
         Path2D path = new Path2D.Double();
         final double headThickness = minHeight / 3;
         final double inset = 0.8;
         final double headLength = minHeight;
         double strokeWidth = minHeight / 14;
+        Bounds arrow = new Bounds(0, -headThickness, length, +headThickness);
         switch (direction) {
             case FORWARD:
                 arrow.add(new LineElement(0, 0, length - 0.5 * headLength, 0, strokeWidth, color));
@@ -407,6 +407,13 @@ static Bounds createArrow(IReaction.Direction direction,
                 path.closePath();
                 arrow.add(GeneralPath.shapeOf(path, color));
                 break;
+            case UNDIRECTED:
+                double x1 = headThickness;
+                double x2 = length-2*headThickness;
+                double y = 0.5 * headThickness;
+                arrow.add(new LineElement(x1, -(y), x2, -(y), strokeWidth, color));
+                arrow.add(new LineElement(x1, +(y), x2, +(y), strokeWidth, color));
+                break;
             case BIDIRECTIONAL: // equilibrium?
                 arrow.add(new LineElement(0, +0.5 * headThickness, length - 0.5 * headLength, +0.5 * headThickness, strokeWidth, color));
                 path.moveTo(length, 0.5 * headThickness - 0.5 * strokeWidth);

diff --git a/app/depict/src/test/java/org/openscience/cdk/depict/DepictionTest.java b/app/depict/src/test/java/org/openscience/cdk/depict/DepictionTest.java
@@ -32,7 +32,13 @@
 import org.openscience.cdk.silent.SilentChemObjectBuilder;
 import org.openscience.cdk.smiles.SmilesParser;
 
+import java.io.BufferedReader;
+import java.io.FileOutputStream;
 import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Paths;
 import java.util.ArrayList;
@@ -124,4 +130,28 @@ void connectMolWithTitlesInSvg() throws CDKException
                 .filter(el -> stringsToFind.indexOf(el) != -1).collect(Collectors.toList());
         Assertions.assertIterableEquals(stringsToFind, foundmatches);
     }
+
+    @Test
+    void depictUndirectedReactionAsSVG()
+            throws CDKException, IOException
+    {
+        List<String> source = readResourceFile("rhea-net-reaction.svg");
+        final SmilesParser smilesParser = new SmilesParser(SilentChemObjectBuilder.getInstance());
+        IReaction rxn = smilesParser.parseReactionSmiles("O.CCCCC(N)=O>>[NH4+].CCCCC([O-])=O");
+        rxn.setDirection(IReaction.Direction.UNDIRECTED);
+        DepictionGenerator dg = new DepictionGenerator();
+        String svg = dg.depict(rxn).toSvgStr("px");
+        String[] targetLines = svg.split("\n");
+        Assertions.assertIterableEquals(source, Arrays.asList(targetLines));
+    }
+
+    private List<String> readResourceFile(String resourceName)
+            throws IOException
+    {
+        try(InputStream in = getClass().getResourceAsStream(resourceName);
+            Reader rdr = new InputStreamReader(in, StandardCharsets.UTF_8);
+            BufferedReader buff = new BufferedReader(rdr)) {
+            return buff.lines().collect(Collectors.toList());
+        }
+    }
 }
diff --git a/app/depict/src/test/resources/org/openscience/cdk/depict/rhea-net-reaction.svg b/app/depict/src/test/resources/org/openscience/cdk/depict/rhea-net-reaction.svg
diff --git a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IReaction.java b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IReaction.java
@@ -63,7 +63,15 @@ enum Direction {
         RETRO_SYNTHETIC,
         /** Reaction shows interconversion between resonance forms. Usually
          *  denoted by a double-headed arrow. */
-        RESONANCE
+        RESONANCE,
+        /**
+         * Reaction equilibrium is not known to be fully on reactant/product
+         * or in equilibrium state.
+         * Also used to represent a "net reaction" composed of several
+         * elementary steps.
+         * Often denoted by a "=" sign
+         */
+        UNDIRECTED
     }
 
     /**