For D4 terminal atoms (e.g. tButyl, CF3, SO3H etc) lay these out at 90 degree angles.

johnmay · johnmay · commit 9896c9b663f2 · 2019-07-28T13:50:25.000+01:00
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
@@ -382,7 +382,8 @@ public void placeLinearChain(IAtomContainer atomContainer, Vector2d initialBondV
             nextAtom.setFlag(CDKConstants.ISPLACED, true);
             boolean trans = false;
 
-            if (prevBond != null && isColinear(atom, molecule.getConnectedBondsList(atom))) {
+            if (prevBond != null &&
+                isColinear(atom, molecule.getConnectedBondsList(atom))) {
 
                 int atomicNumber = atom.getAtomicNumber();
                 int charge = atom.getFormalCharge();
@@ -418,6 +419,20 @@ public void placeLinearChain(IAtomContainer atomContainer, Vector2d initialBondV
         }
     }
 
+    private boolean isTerminalD4(IAtom atom) {
+        List<IBond> bonds = molecule.getConnectedBondsList(atom);
+        if (bonds.size() != 4)
+            return false;
+        int nonD1 = 0;
+        for (IBond bond : bonds) {
+            if (molecule.getConnectedBondsCount(bond.getOther(atom)) != 1) {
+                if (++nonD1 > 1)
+                    return false;
+            }
+        }
+        return true;
+    }
+
     /**
      *  Returns the next bond vector needed for drawing an extended linear chain of
      *  atoms. It assumes an angle of 120 deg for a nice chain layout and
@@ -449,7 +464,13 @@ public Vector2d getNextBondVector(IAtom atom, IAtom previousAtom, Point2d distan
 
         double angle = GeometryUtil.getAngle(previousAtom.getPoint2d().x - atom.getPoint2d().x,
                 previousAtom.getPoint2d().y - atom.getPoint2d().y);
-        double addAngle = Math.toRadians(120);
+        double addAngle;
+
+        if (isTerminalD4(atom))
+            addAngle = Math.toRadians(45);
+        else
+            addAngle = Math.toRadians(120);
+
         if (!trans) addAngle = Math.toRadians(60);
         if (isColinear(atom, molecule.getConnectedBondsList(atom))) addAngle = Math.toRadians(180);
 
