Do not align atoms if their geometry doesn't match, for now this mean…

…s (collinear vs bent).
cdk · Oct 18, 2018 · 922672c · 922672c
1 parent c464d4f
commit 922672c
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Showing 2 changed files with 19 additions and 6 deletions.
diff --git a/tool/sdg/src/main/java/org/openscience/cdk/layout/AtomPlacer.java b/tool/sdg/src/main/java/org/openscience/cdk/layout/AtomPlacer.java
@@ -940,15 +940,14 @@ public int compare(Integer a, Integer b) {
      * -C=[N+]=N
      * -N=[N+]=N
      */
-    boolean isColinear(IAtom atom, List<IBond> bonds) {
-        if (bonds.size() != 2)
-            return false;
-
+    static boolean isColinear(IAtom atom, Iterable<IBond> bonds) {
         int numSgl = atom.getImplicitHydrogenCount() == null ? 0 : atom.getImplicitHydrogenCount();
         int numDbl = 0;
         int numTpl = 0;
+        int count  = 0;
 
         for (IBond bond : bonds) {
+            ++count;
             switch (bond.getOrder()) {
                 case SINGLE:
                     numSgl++;
@@ -966,6 +965,9 @@ boolean isColinear(IAtom atom, List<IBond> bonds) {
             }
         }
 
+        if (count != 2)
+            return false;
+
         switch (atom.getAtomicNumber()) {
             case 6:
             case 7:

diff --git a/tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java b/tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java
@@ -236,6 +236,8 @@ public final void generateCoordinates(final IReaction reaction) throws CDKExcept
                 afix.clear();
                 bfix.clear();
 
+                boolean aggresive = false;
+
                 if (largest != null && largest.getAtomCount() > 1) {
 
                     int idx = largest.getAtom(0).getProperty(CDKConstants.ATOM_ATOM_MAPPING);
@@ -246,13 +248,22 @@ public final void generateCoordinates(final IReaction reaction) throws CDKExcept
                         idx = atom.getProperty(CDKConstants.ATOM_ATOM_MAPPING);
                         final IAtom src = reference.get(idx);
                         if (src == null) continue;
+                        if (!aggresive) {
+                            // no way to get the container of 'src' without
+                            // lots of refactoring, instead we just use the
+                            // new API points - first checking these will not
+                            // fail
+                            if (src.getContainer() != null
+                                && atom.getContainer() != null
+                                && AtomPlacer.isColinear(src, src.bonds())
+                                   != AtomPlacer.isColinear(atom, atom.bonds()))
+                                continue;
+                        }
                         atom.setPoint2d(new Point2d(src.getPoint2d()));
                         afix.put(atom, src);
                     }
                 }
 
-                boolean aggresive = false;
-
                 if (!afix.isEmpty()) {
                     if (aggresive) {
                         for (IBond bond : mol.bonds()) {