Resolve NPE in circular fingerprint - SF bug:1357.

Change-Id: I8848d47fccc4eac2378bf55d751827281a203724 Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Feb 12, 2015 · 989fd7d · 989fd7d
1 parent f698b3d
commit 989fd7d
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diff --git a/...ptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/CircularFingerprinter.java b/...ptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/CircularFingerprinter.java
@@ -867,12 +867,14 @@ private int[] rubricTetrahedral(int aidx) {
                 xp[n] = (float) (o3d.x - x0);
                 yp[n] = (float) (o3d.y - y0);
                 zp[n] = (float) (o3d.z - z0);
-            } else {
+            } else if (o2d != null) {
                 IBond.Stereo stereo = bond.getStereo();
                 xp[n] = (float) (o2d.x - x0);
                 yp[n] = (float) (o2d.y - y0);
                 zp[n] = other == bond.getAtom(0) ? 0 : stereo == IBond.Stereo.UP ? 1 : stereo == IBond.Stereo.DOWN ? -1
                         : 0;
+            } else {
+                return null; // no 2D coordinates on some atom
             }
 
             final float dx = xp[n] - x0, dy = yp[n] - y0, dz = zp[n] - z0;

diff --git a/.../fingerprint/src/test/java/org/openscience/cdk/fingerprint/CircularFingerprinterTest.java b/.../fingerprint/src/test/java/org/openscience/cdk/fingerprint/CircularFingerprinterTest.java
@@ -61,6 +61,8 @@
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
 
+import javax.vecmath.Point2d;
+
 /**
  * @cdk.module test-standard
  */
@@ -299,11 +301,39 @@ public void iminesDetectionDoesntCauseNPE() throws Exception {
         assertNotNull(circ.getBitFingerprint(pyrazole));
     }
 
+    /**
+     * @cdk.bug 1357
+     */
+    @Test
+    public void partialCoordinatesDontCauseNPE() throws Exception {
+        IAtomContainer m = new AtomContainer();
+        m.addAtom(atom("C", 3, 0.000, 0.000));
+        m.addAtom(atom("C", 0, 1.299, -0.750));
+        m.addAtom(atom("H", 0, 0));
+        m.addAtom(atom("O", 0, 1));
+        m.addAtom(atom("C", 2, 2.598, -0.000));
+        m.addAtom(atom("C", 3, 3.897, -0.750));
+        m.addBond(0, 1, IBond.Order.SINGLE);
+        m.addBond(1, 2, IBond.Order.SINGLE);
+        m.addBond(1, 3, IBond.Order.SINGLE, IBond.Stereo.DOWN);
+        m.addBond(1, 4, IBond.Order.SINGLE);
+        m.addBond(4, 5, IBond.Order.SINGLE);
+        CircularFingerprinter circ = new CircularFingerprinter(CircularFingerprinter.CLASS_ECFP6);
+        assertNotNull(circ.getBitFingerprint(m));
+    }
+
     static IAtom atom(String symbol, int q, int h) {
         IAtom a = new Atom(symbol);
         a.setFormalCharge(q);
         a.setImplicitHydrogenCount(h);
         return a;
     }
 
+    static IAtom atom(String symbol, int h, double x, double y) {
+        IAtom a = new Atom(symbol);
+        a.setPoint2d(new Point2d(x,y));
+        a.setImplicitHydrogenCount(h);
+        return a;
+    }
+
 }