Reimplemented shiftContainer(IAtomContainer, Rectangle2D, Rectange2D,…

… double) originally implemented as jchempaint-primary patch 9200bdc4d68dc8f70373a62eaec51357b680d5e6 by Stefan Kuhn: fixing the detection of overlap, and added missing unit tests

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>

src/main/org/openscience/cdk/geometry/GeometryTools.java

@@ -1426,4 +1426,34 @@ public static double getBondLengthAverage3D(IAtomContainer container) {
         }
 		return bondLengthSum / bondCounter;
 	}
+
+    /**
+     * Shift the container horizontally to the right to make its bounds not
+     * overlap with the other bounds.
+     *
+     * @param container the {@link IAtomContainer} to shift to the right
+     * @param bounds    the {@link Rectangle2D} of the {@link IAtomContainer}
+     *                  to shift
+     * @param last      the bounds that is used as reference
+     * @param gap       the gap between the two {@link Rectangle2D}s
+     * @return          the {@link Rectangle2D} of the {@link IAtomContainer}
+     *                  after the shift
+     */
+    public static Rectangle2D shiftContainer(
+        IAtomContainer container, Rectangle2D bounds, Rectangle2D last,
+        double gap) {
+        // determine if the containers are overlapping
+        if (last.getMaxX() + gap >= bounds.getMinX()) {
+            double xShift = bounds.getWidth() + last.getWidth() + gap;
+            Vector2d shift = new Vector2d(xShift, 0.0);
+            GeometryTools.translate2D(container, shift);
+            return new Rectangle2D.Double(bounds.getX() + xShift,
+                                          bounds.getY(),
+                                          bounds.getWidth(),
+                                          bounds.getHeight());
+        } else {
+            // the containers are not overlapping
+            return bounds;
+        }
+    }
 }

src/test/org/openscience/cdk/geometry/GeometryToolsTest.java

@@ -377,5 +377,81 @@ public class GeometryToolsTest extends CDKTestCase {
     	Assert.assertEquals(GeometryTools.getLength2D(bond),2.23,0.01);
     }
 
+
+    @Test public void
+    testShiftContainerHorizontal_IAtomContainer_Rectangle2D_Rectangle2D_double()
+    throws Exception {
+        IAtom atom1 = new Atom("C");
+        atom1.setPoint2d(new Point2d(0,1));
+        IAtom atom2 = new Atom("C");
+        atom2.setPoint2d(new Point2d(1,0));
+        IMolecule react1 = new Molecule();
+        react1.addAtom(atom1);
+        react1.addAtom(atom2);
+        IMolecule react2 = (IMolecule)react1.clone();
+
+        // shift the second molecule right
+        GeometryTools.shiftContainer(
+            react2,
+            GeometryTools.getRectangle2D(react2),
+            GeometryTools.getRectangle2D(react1),
+            1.0
+        );
+        // assert all coordinates of the second molecule moved right
+        AtomContainerDiff.diff(react1, react2);
+        for (int i=0; i<2; i++) {
+            atom1 = react1.getAtom(0);
+            atom2 = react2.getAtom(0);
+            // so, y coordinates should be the same
+            Assert.assertEquals(
+                atom1.getPoint2d().y, atom2.getPoint2d().y, 0.0
+            );
+            // but, x coordinates should not
+            Assert.assertTrue(
+                atom1.getPoint2d().x < atom2.getPoint2d().x
+            );
+        }
+    }
+
+    /**
+     * Unit tests that tests the situation where two vertical two-atom
+     * molecules are with the same x coordinates.
+     *
+     * @throws Exception Thrown when the cloning failed.
+     */
+    @Test
+    public void testShiftContainerHorizontal_Two_vertical_molecules()
+    throws Exception {
+        IAtom atom1 = new Atom("C");
+        atom1.setPoint2d(new Point2d(0,0));
+        IAtom atom2 = new Atom("C");
+        atom2.setPoint2d(new Point2d(0,1));
+        IMolecule react1 = new Molecule();
+        react1.addAtom(atom1);
+        react1.addAtom(atom2);
+        IMolecule react2 = (IMolecule)react1.clone();
+
+        // shift the second molecule right
+        GeometryTools.shiftContainer(
+            react2,
+            GeometryTools.getRectangle2D(react2),
+            GeometryTools.getRectangle2D(react1),
+            1.0
+        );
+        // assert all coordinates of the second molecule moved right
+        AtomContainerDiff.diff(react1, react2);
+        for (int i=0; i<2; i++) {
+            atom1 = react1.getAtom(0);
+            atom2 = react2.getAtom(0);
+            // so, y coordinates should be the same
+            Assert.assertEquals(
+                atom1.getPoint2d().y, atom2.getPoint2d().y, 0.0
+            );
+            // but, x coordinates should not
+            Assert.assertTrue(
+                atom1.getPoint2d().x < atom2.getPoint2d().x
+            );
+        }
+    }
 }