Fix AtomTools method.

johnmay · johnmay · commit 604d348e58cf · 2020-12-15T10:19:38.000Z
diff --git a/misc/extra/src/main/java/org/openscience/cdk/geometry/AtomTools.java b/misc/extra/src/main/java/org/openscience/cdk/geometry/AtomTools.java
@@ -406,31 +406,31 @@ public static Point3d[] calculate3DCoordinates2(Point3d aPoint, Point3d bPoint,
      *    (i) 1 points  required; if A, B, C, D coplanar, no points.
      *       else vector is resultant of BA, CA, DA
      *
-     * @param aPoint to which substituents are added
-     * @param bPoint first ligand of A
-     * @param cPoint second ligand of A
-     * @param dPoint third ligand of A
+     * @param focus to which substituents are added
+     * @param aNbor first ligand of A
+     * @param bNbor second ligand of A
+     * @param cNbor third ligand of A
      * @param length A-X length
      *
      * @return Point3d nwanted points (or null if failed (coplanar))
      */
-    public static Point3d calculate3DCoordinates3(Point3d aPoint, Point3d bPoint, Point3d cPoint, Point3d dPoint,
+    public static Point3d calculate3DCoordinates3(Point3d focus, Point3d aNbor, Point3d bNbor, Point3d cNbor,
             double length) {
-        Vector3d v1 = new Vector3d(aPoint);
-        v1.sub(bPoint);
-        Vector3d v2 = new Vector3d(aPoint);
-        v2.sub(cPoint);
-        Vector3d v3 = new Vector3d(aPoint);
-        v3.sub(dPoint);
-        Vector3d v = new Vector3d(bPoint);
-        v.add(cPoint);
-        v.add(dPoint);
+        Vector3d v1 = new Vector3d(focus);
+        v1.sub(aNbor);
+        Vector3d v2 = new Vector3d(focus);
+        v2.sub(bNbor);
+        Vector3d v3 = new Vector3d(focus);
+        v3.sub(cNbor);
+        Vector3d v = new Vector3d(v1);
+        v.add(v2);
+        v.add(v3);
         if (v.length() < 0.00001) {
             return null;
         }
         v.normalize();
         v.scale(length);
-        Point3d point = new Point3d(aPoint);
+        Point3d point = new Point3d(focus);
         point.add(v);
         return point;
     }
diff --git a/misc/test-extra/src/test/java/org/openscience/cdk/geometry/AtomToolsTest.java b/misc/test-extra/src/test/java/org/openscience/cdk/geometry/AtomToolsTest.java
@@ -0,0 +1,54 @@
+/*
+ * =====================================
+ *  Copyright (c) 2020 NextMove Software
+ * =====================================
+ */
+
+package org.openscience.cdk.geometry;
+
+import org.hamcrest.number.IsCloseTo;
+import org.junit.Test;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.io.MDLV2000Reader;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
+
+import javax.vecmath.Point3d;
+import java.io.IOException;
+import java.io.StringReader;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.junit.Assert.assertNotNull;
+
+public class AtomToolsTest {
+
+    @Test
+    public void calculate3DCoordinates3() {
+        String molfile = "\n" +
+                "  Mrv1810 12152010123D          \n" +
+                "\n" +
+                "  4  3  0  0  0  0            999 V2000\n" +
+                "    2.0575    1.4744   -0.0102 O   0  0  0  0  0  0  0  0  0  0  0  0\n" +
+                "    1.5159    0.0200    0.0346 C   0  0  1  0  0  0  0  0  0  0  0  0\n" +
+                "    2.0575   -0.7460    1.2717 N   0  0  0  0  0  0  0  0  0  0  0  0\n" +
+                "   -0.0359   -0.0059   -0.0102 C   0  0  0  0  0  0  0  0  0  0  0  0\n" +
+                "  1  2  1  0  0  0  0\n" +
+                "  2  3  1  0  0  0  0\n" +
+                "  2  4  1  0  0  0  0\n" +
+                "M  END\n";
+        try (MDLV2000Reader mdlr = new MDLV2000Reader(new StringReader(molfile))) {
+            IAtomContainer mol = mdlr.read(SilentChemObjectBuilder.getInstance().newAtomContainer());
+            Point3d newP = AtomTools.calculate3DCoordinates3(
+                    mol.getAtom(1).getPoint3d(),
+                    mol.getAtom(0).getPoint3d(),
+                    mol.getAtom(2).getPoint3d(),
+                    mol.getAtom(3).getPoint3d(), 1.5);
+            assertNotNull(newP);
+            assertThat(newP.x, IsCloseTo.closeTo(2.0160, 0.001));
+            assertThat(newP.y, IsCloseTo.closeTo(-0.6871, 0.001));
+            assertThat(newP.z, IsCloseTo.closeTo(-1.1901, 0.001));
+        } catch (IOException | CDKException e) {
+            e.printStackTrace();
+        }
+    }
+}
