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lafitalafita
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Port methods from Calc to new Matrices class biojava#558 
1 parent 523920e commit 25c47de

3 files changed

Lines changed: 91 additions & 42 deletions

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‎biojava-structure/src/main/java/org/biojava/nbio/structure/Calc.java‎

Lines changed: 4 additions & 41 deletions
Original file line numberDiff line numberDiff line change
@@ -23,6 +23,7 @@
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package org.biojava.nbio.structure;
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import org.biojava.nbio.structure.geometry.CalcPoint;
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import org.biojava.nbio.structure.geometry.Matrices;
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import org.biojava.nbio.structure.geometry.SuperPositionSVD;
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import org.biojava.nbio.structure.jama.Matrix;
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import org.slf4j.Logger;
@@ -998,7 +999,7 @@ public static final Atom createVirtualCBAtom(AminoAcid amino)
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SuperPositionSVD svd = new SuperPositionSVD(false);
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Matrix4d transform = svd.superpose(arr1, arr2);
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Matrix rotMatrix = getRotationMatrix(transform);
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Matrix rotMatrix = Matrices.getRotationJAMA(transform);
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Atom tranMatrix = getTranslationVector(transform);
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Calc.rotate(aCB, rotMatrix);
@@ -1182,23 +1183,6 @@ public static void shift(Atom[] ca, Atom b) {
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Calc.shift(atom, b);
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}
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/**
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* Convert JAMA rotation and translation to a Vecmath transformation matrix.
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* Because the JAMA matrix is a pre-multiplication matrix and the Vecmath
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* matrix is a post-multiplication one, the rotation matrix is transposed to
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* ensure that the transformation they produce is the same.
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*
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* @param rot
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* 3x3 Rotation matrix
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* @param trans
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* 3x1 Translation matrix
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* @return 4x4 transformation matrix
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*/
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public static Matrix4d getTransformation(Matrix rot, Matrix trans) {
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return new Matrix4d(new Matrix3d(rot.getColumnPackedCopy()),
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new Vector3d(trans.getColumnPackedCopy()), 1.0);
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}
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/**
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* Convert JAMA rotation and translation to a Vecmath transformation matrix.
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* Because the JAMA matrix is a pre-multiplication matrix and the Vecmath
@@ -1215,30 +1199,9 @@ public static Matrix4d getTransformation(Matrix rot, Atom trans) {
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return new Matrix4d(new Matrix3d(rot.getColumnPackedCopy()),
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new Vector3d(trans.getCoords()), 1.0);
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}
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/**
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* Convert Vecmath transformation into a JAMA rotation matrix. Because the
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* JAMA matrix is a pre-multiplication matrix and the Vecmath matrix is a
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* post-multiplication one, the rotation matrix is transposed to ensure that
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* the transformation they produce is the same.
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*
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* @param transform
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* Matrix4d with transposed rotation matrix
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* @return
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*/
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public static Matrix getRotationMatrix(Matrix4d transform) {
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Matrix rot = new Matrix(3, 3);
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for (int i = 0; i < 3; i++) {
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for (int j = 0; j < 3; j++) {
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rot.set(j, i, transform.getElement(i, j)); // transposed
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}
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}
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return rot;
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}
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/**
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* Extract the translational vector of a Vecmath transformation.
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* Extract the translational vector as an Atom of a transformation matrix.
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*
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* @param transform
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* Matrix4d

‎biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/Matrices.java‎

Lines changed: 86 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,86 @@
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package org.biojava.nbio.structure.geometry;
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import javax.vecmath.Matrix3d;
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import javax.vecmath.Matrix4d;
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import javax.vecmath.Vector3d;
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import org.biojava.nbio.structure.jama.Matrix;
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/**
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* Matrices contains static methods to operate and transform matrices used in 3D
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* geometry (transformation matrices and rotation matrices).
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* <p>
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* This class complements and extends the functionallity of vecmath and jama.
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*
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* @author Aleix Lafita
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* @since 5.0.0
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*
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*/
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public class Matrices {
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/**
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* Convert a transformation matrix into a JAMA rotation matrix. Because the
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* JAMA matrix is a pre-multiplication matrix and the Vecmath matrix is a
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* post-multiplication one, the rotation matrix is transposed to ensure that
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* the transformation they produce is the same.
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*
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* @param transform
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* Matrix4d with transposed rotation matrix
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* @return rotation matrix as JAMA object
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*/
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public static Matrix getRotationJAMA(Matrix4d transform) {
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Matrix rot = new Matrix(3, 3);
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for (int i = 0; i < 3; i++) {
35+
for (int j = 0; j < 3; j++) {
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rot.set(j, i, transform.getElement(i, j)); // transposed
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}
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}
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return rot;
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}
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/**
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* Convert a transformation matrix into a rotation matrix.
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*
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* @param transform
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* Matrix4d
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* @return rotation matrix
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*/
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public static Matrix3d getRotationMatrix(Matrix4d transform) {
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Matrix3d rot = new Matrix3d();
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transform.setRotationScale(rot);
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return rot;
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}
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/**
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* Extract the translational vector of a transformation matrix.
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*
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* @param transform
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* Matrix4d
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* @return Vector3d translation vector
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*/
63+
public static Vector3d getTranslationVector(Matrix4d transform) {
64+
Vector3d transl = new Vector3d();
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transform.get(transl);
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return transl;
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}
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/**
70+
* Convert JAMA rotation and translation to a Vecmath transformation matrix.
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* Because the JAMA matrix is a pre-multiplication matrix and the Vecmath
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* matrix is a post-multiplication one, the rotation matrix is transposed to
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* ensure that the transformation they produce is the same.
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*
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* @param rot
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* 3x3 Rotation matrix
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* @param trans
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* 3x1 Translation matrix
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* @return 4x4 transformation matrix
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*/
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public static Matrix4d getTransformation(Matrix rot, Matrix trans) {
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return new Matrix4d(new Matrix3d(rot.getColumnPackedCopy()),
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new Vector3d(trans.getColumnPackedCopy()), 1.0);
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}
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}

‎biojava-structure/src/main/java/org/biojava/nbio/structure/geometry/SuperPositionSVD.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -135,7 +135,7 @@ public Matrix4d superpose(Point3d[] fixed, Point3d[] moved) {
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Matrix cb_tmp = centroidB.times(rot);
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Matrix tran = centroidA.minus(cb_tmp);
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138-
return Calc.getTransformation(rot, tran);
138+
return Matrices.getTransformation(rot, tran);
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}
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