Better handling of rendering labels for salts where we have a large component and an abbreviated salt.

johnmay · johnmay · commit 16505428920a · 2019-09-26T08:46:58.000+01:00
diff --git a/base/standard/src/main/java/org/openscience/cdk/geometry/GeometryUtil.java b/base/standard/src/main/java/org/openscience/cdk/geometry/GeometryUtil.java
@@ -333,26 +333,23 @@ public static double[] get2DDimension(IAtomContainer atomCon) {
     }
 
     /**
-     * Returns the minimum and maximum X and Y coordinates of the atoms in the
-     * AtomContainer. The output is returned as: <pre>
+     * Returns the minimum and maximum X and Y coordinates of the atoms.
+     * The output is returned as: <pre>
      *   minmax[0] = minX;
      *   minmax[1] = minY;
      *   minmax[2] = maxX;
      *   minmax[3] = maxY;
      * </pre>
-     * See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap
-     * renderingCoordinates) for details on coordinate sets
      *
-     * @param container Description of the Parameter
+     * @param atoms the atoms.
      * @return An four int array as defined above.
      */
-    public static double[] getMinMax(IAtomContainer container) {
+    public static double[] getMinMax(Iterable<IAtom> atoms) {
         double maxX = -Double.MAX_VALUE;
         double maxY = -Double.MAX_VALUE;
         double minX = Double.MAX_VALUE;
         double minY = Double.MAX_VALUE;
-        for (int i = 0; i < container.getAtomCount(); i++) {
-            IAtom atom = container.getAtom(i);
+        for (IAtom atom : atoms) {
             if (atom.getPoint2d() != null) {
                 if (atom.getPoint2d().x > maxX) {
                     maxX = atom.getPoint2d().x;
@@ -376,6 +373,24 @@ public static double[] getMinMax(IAtomContainer container) {
         return minmax;
     }
 
+    /**
+     * Returns the minimum and maximum X and Y coordinates of the atoms in the
+     * AtomContainer. The output is returned as: <pre>
+     *   minmax[0] = minX;
+     *   minmax[1] = minY;
+     *   minmax[2] = maxX;
+     *   minmax[3] = maxY;
+     * </pre>
+     * See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap
+     * renderingCoordinates) for details on coordinate sets
+     *
+     * @param container Description of the Parameter
+     * @return An four int array as defined above.
+     */
+    public static double[] getMinMax(IAtomContainer container) {
+        return getMinMax(container.atoms());
+    }
+
     /**
      * Translates a molecule from the origin to a new point denoted by a vector. See comment for
      * center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details
diff --git a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/AbbreviationLabel.java b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/AbbreviationLabel.java
@@ -191,7 +191,8 @@ static boolean parse(String label, List<String> tokens) {
                 continue;
             }
 
-            if (c == '/' || c == '·') {
+            // separators
+            if (c == '/' || c == '·' || c == '.' || c == '•') {
                 tokens.add(Character.toString(c));
                 i++;
                 continue;
diff --git a/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardSgroupGenerator.java b/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardSgroupGenerator.java
@@ -61,7 +61,8 @@
  */
 final class StandardSgroupGenerator {
 
-    public static final double EQUIV_THRESHOLD = 0.1;
+    public static final double          EQUIV_THRESHOLD = 0.1;
+    public static final char            BULLET          = '•';
     private final double                stroke;
     private final double                scale;
     private final double                bracketDepth;
@@ -358,11 +359,42 @@ private IRenderingElement generateAbbreviationSgroup(IAtomContainer mol, Sgroup
         final StandardGenerator.HighlightStyle style = parameters.get(StandardGenerator.Highlighting.class);
         final double glowWidth = parameters.get(StandardGenerator.OuterGlowWidth.class);
 
-        final Point2d labelCoords = GeometryUtil.get2DCenter(sgroupAtoms);
+        final Point2d labelLocation;
+        if (mol.getAtomCount() == sgroup.getAtoms().size()) {
+            labelLocation = GeometryUtil.get2DCenter(sgroupAtoms);
+        } else {
+            // contraction of part of a fragment, e.g. SALT
+            // here we work out the point we want to place the contract relative
+            // to the SGroup Atoms
+            labelLocation = new Point2d();
+            final Point2d sgrpCenter = GeometryUtil.get2DCenter(sgroupAtoms);
+            final Point2d molCenter  = GeometryUtil.get2DCenter(mol);
+            final double[] minMax    = GeometryUtil.getMinMax(sgroupAtoms);
+            double xDiff = sgrpCenter.x - molCenter.x;
+            double yDiff = sgrpCenter.y - molCenter.y;
+            if (xDiff > 0.1) {
+                labelLocation.x = minMax[0]; // min x
+                label = BULLET + label;
+            }
+            else if (xDiff < -0.1) {
+                labelLocation.x = minMax[2]; // max x
+                label = label + BULLET;
+            }
+            else {
+                labelLocation.x = sgrpCenter.x;
+                label = BULLET + label;
+            }
+            if (yDiff > 0.1)
+                labelLocation.y = minMax[1]; // min y
+            else if (yDiff < -0.1)
+                labelLocation.y = minMax[3]; // max y
+            else
+                labelLocation.y = sgrpCenter.y;
+        }
 
         ElementGroup labelgroup = new ElementGroup();
         for (Shape outline : atomGenerator.generateAbbreviatedSymbol(label, HydrogenPosition.Right)
-                                          .center(labelCoords.x, labelCoords.y)
+                                          .center(labelLocation.x, labelLocation.y)
                                           .resize(1 / scale, 1 / -scale)
                                           .getOutlines()) {
             if (highlight != null && style == StandardGenerator.HighlightStyle.Colored) {
diff --git a/display/renderbasic/src/test/java/org/openscience/cdk/renderer/generators/standard/AbbreviationLabelTest.java b/display/renderbasic/src/test/java/org/openscience/cdk/renderer/generators/standard/AbbreviationLabelTest.java
@@ -32,9 +32,7 @@
 
 import static org.hamcrest.CoreMatchers.hasItems;
 import static org.hamcrest.CoreMatchers.is;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertThat;
-import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.*;
 
 public class AbbreviationLabelTest {
 
@@ -234,6 +232,13 @@ public void formatOPO3H2() {
         assertThat(texts.get(3).style, is(-1));
     }
 
+    @Test
+    public void hydrate() {
+        List<String> tokens = new ArrayList<>();
+        AbbreviationLabel.parse("•H2O", tokens);
+        assertThat(tokens, is(Arrays.asList("•", "H2", "O")));
+    }
+
     @Test
     public void het() {
         // 'Het' not 'He'lium and 't'erts

Original file line number	Diff line number	Diff line change
`@@ -191,7 +191,8 @@ static boolean parse(String label, List<String> tokens) {`
`191`	`191`	`continue;`
`192`	`192`	`}`
`193`	`193`
`194`		`- if (c == '/' \|\| c == '·') {`
	`194`	`+ // separators`
	`195`	`+ if (c == '/' \|\| c == '·' \|\| c == '.' \|\| c == '•') {`
`195`	`196`	`tokens.add(Character.toString(c));`
`196`	`197`	`i++;`
`197`	`198`	`continue;`