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sblivensbliven
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Adding TestSymmetryAxes prior to refactoring
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‎biojava-structure/src/test/java/org/biojava/nbio/structure/symmetry/internal/TestSymmetryAxes.java‎

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package org.biojava.nbio.structure.symmetry.internal;
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import static org.junit.Assert.*;
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import java.util.Arrays;
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import java.util.List;
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import javax.vecmath.AxisAngle4d;
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import javax.vecmath.Matrix4d;
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import javax.vecmath.Vector3d;
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import org.junit.Test;
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public class TestSymmetryAxes {
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@Test
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public void testClosedCase() {
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// D4 case
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SymmetryAxes axes = new SymmetryAxes();
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// Level 1 is C4 along Z
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Matrix4d r90 = new Matrix4d();
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r90.set(new AxisAngle4d(0, 0, 1, Math.PI/2));
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// number of times to apply this op for each repeat
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List<Integer> repeats = Arrays.asList(0,0,1,1,2,2,3,3);
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// aligned repeats
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List<List<Integer>> superposition = Arrays.asList(
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Arrays.asList(0,1,2,3,4,5,6,7),
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Arrays.asList(2,3,4,5,6,7,0,1));
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axes.addAxis(r90, superposition, repeats, 4);
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// Level 2 is C2 along X
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Matrix4d r180 = new Matrix4d();
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r180.set(new AxisAngle4d(1, 0, 0, Math.PI));
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repeats = Arrays.asList(0,1,0,1,0,1,0,1);
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superposition = Arrays.asList(
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Arrays.asList(0,1),
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Arrays.asList(1,0));
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axes.addAxis(r180, superposition, repeats, 2);
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assertEquals(2,axes.getElementaryAxes().size());
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Matrix4d expectedEven = new Matrix4d();
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expectedEven.set(1);
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Matrix4d expectedOdd = new Matrix4d(r180);
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assertEquals(expectedEven, axes.getRepeatTransform(0));
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assertEquals(expectedOdd, axes.getRepeatTransform(1));
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expectedEven.mul(r90);
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expectedOdd.mul(r180,expectedEven);
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assertEquals(expectedEven, axes.getRepeatTransform(2));
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assertEquals(expectedOdd, axes.getRepeatTransform(3));
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expectedEven.mul(r90);
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expectedOdd.mul(r180,expectedEven);
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assertEquals(expectedEven, axes.getRepeatTransform(4));
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assertEquals(expectedOdd, axes.getRepeatTransform(5));
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expectedEven.mul(r90);
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expectedOdd.mul(r180,expectedEven);
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assertEquals(expectedEven, axes.getRepeatTransform(6));
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assertEquals(expectedOdd, axes.getRepeatTransform(7));
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List<List<Integer>> relation = Arrays.asList(
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Arrays.asList(0,1,2,3,4,5,6,7),
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Arrays.asList(2,3,4,5,6,7,0,1)
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);
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assertEquals(relation,axes.getRepeatRelation(0));
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relation = Arrays.asList(
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Arrays.asList(0,1),
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Arrays.asList(1,0)
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);
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assertEquals(relation,axes.getRepeatRelation(1));
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assertNull(axes.getRepeatRelation(2));
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}
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@Test
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public void testOpenCase() {
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// D4 case
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SymmetryAxes axes = new SymmetryAxes();
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// Level 1 is R4 along X
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Matrix4d t10 = new Matrix4d();
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t10.set(1,new Vector3d(1,0,0));
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List<Integer> repeats = Arrays.asList(0,0,1,1,2,2,3,3);
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List<List<Integer>> superposition = Arrays.asList(
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Arrays.asList(0,1,2,3,4,5),
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Arrays.asList(2,3,4,5,6,7));
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axes.addAxis(t10, superposition, repeats, 4);
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// Level 2 is C2 along X
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Matrix4d r180 = new Matrix4d();
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r180.set(new AxisAngle4d(1, 0, 0, Math.PI));
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repeats = Arrays.asList(0,1,0,1,0,1,0,1);
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superposition = Arrays.asList(
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Arrays.asList(0,1),
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Arrays.asList(1,0));
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axes.addAxis(r180, superposition, repeats, 2);
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assertEquals(2,axes.getElementaryAxes().size());
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Matrix4d expectedEven = new Matrix4d();
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expectedEven.set(1);
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Matrix4d expectedOdd = new Matrix4d(r180);
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assertEquals(expectedEven, axes.getRepeatTransform(0));
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assertEquals(expectedOdd, axes.getRepeatTransform(1));
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expectedEven.mul(t10);
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expectedOdd.mul(r180,expectedEven);
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assertEquals(expectedEven, axes.getRepeatTransform(2));
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assertEquals(expectedOdd, axes.getRepeatTransform(3));
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expectedEven.mul(t10);
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expectedOdd.mul(r180,expectedEven);
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assertEquals(expectedEven, axes.getRepeatTransform(4));
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assertEquals(expectedOdd, axes.getRepeatTransform(5));
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expectedEven.mul(t10);
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expectedOdd.mul(r180,expectedEven);
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assertEquals(expectedEven, axes.getRepeatTransform(6));
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assertEquals(expectedOdd, axes.getRepeatTransform(7));
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List<List<Integer>> relation = Arrays.asList(
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Arrays.asList(0,1,2,3,4,5),
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Arrays.asList(2,3,4,5,6,7)
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);
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assertEquals(relation,axes.getRepeatRelation(0));
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relation = Arrays.asList(
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Arrays.asList(0,1),
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Arrays.asList(1,0)
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);
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assertEquals(relation,axes.getRepeatRelation(1));
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assertNull(axes.getRepeatRelation(2));
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}
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}

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