## Uses of Class
org.biojava.bio.structure.jama.Matrix

Packages that use Matrix
org.biojava.bio.structure: Interfaces and classes for protein structure (PDB).
org.biojava.bio.structure.align: Classes for the super-imposition of structures.
org.biojava.bio.structure.align.helper: Helper classes for structural alignment.
org.biojava.bio.structure.align.pairwise: Classes for the pairwise alignment of structures.
org.biojava.bio.structure.gui: A few convenience classes to view protein structures with Jmol (if it is on the classpath), to calculate a protein structure alignment and to investigate the internals of the protein structure alignment algorithm.
org.biojava.bio.structure.jama: Matrix package for from JAMA

Uses of Matrix in org.biojava.bio.structure

Methods in org.biojava.bio.structure that return Matrix
`Matrix` `SVDSuperimposer.getRotation()` Get the Rotation matrix that is required to superimpose the two atom sets.
`static Matrix` `Calc.matrixFromEuler(double heading, double attitude, double bank)` This conversion uses NASA standard aeroplane conventions as described on page: http://www.euclideanspace.com/maths/geometry/rotations/euler/index.htm Coordinate System: right hand Positive angle: right hand Order of euler angles: heading first, then attitude, then bank.

Methods in org.biojava.bio.structure with parameters of type Matrix
`static double[]` `Calc.getXYZEuler(Matrix m)` Convert a rotation Matrix to Euler angles.
`static double[]` `Calc.getZYZEuler(Matrix m)` Gget euler angles for a matrix given in ZYZ convention.
`static void` `Calc.plus(Structure s, Matrix matrix)` calculate structure + Matrix coodinates ...
`void` `SVDSuperimposer.printMatrix(Matrix m)` Simple debug method to print a Matrix object on System.out.
`static void` `Calc.rotate(Atom atom, Matrix m)` Rotate an atom around a Matrix object.
`static void` `Calc.rotate(Group group, Matrix m)` Rotate a group object.
`static void` `Calc.rotate(Structure structure, Matrix m)` Rotate a structure object.

Uses of Matrix in org.biojava.bio.structure.align

Methods in org.biojava.bio.structure.align that return Matrix
`Matrix` `StructurePairAligner.getDistMat()` return the difference of distance matrix between the two structures

Uses of Matrix in org.biojava.bio.structure.align.helper

Methods in org.biojava.bio.structure.align.helper that return Matrix
`static Matrix` `AlignTools.getDistanceMatrix(Atom[] ca1, Atom[] ca2)` matrix of all distances between two sets of 3d coords"

Uses of Matrix in org.biojava.bio.structure.align.pairwise

Methods in org.biojava.bio.structure.align.pairwise that return Matrix
`Matrix` `AlternativeAlignment.getDistanceMatrix()` The distance matrix this alignment is based on
`static Matrix` `AlternativeAlignment.getDistanceMatrix(Atom[] ca1, Atom[] ca2)`
`Matrix` `FragmentPair.getRot()`
`Matrix` `AlternativeAlignment.getRotationMatrix()` returns the rotation matrix that needs to be applied to structure 2 to rotate on structure 1

Methods in org.biojava.bio.structure.align.pairwise with parameters of type Matrix
`static Alignable` `AligNPE.align_NPE(Matrix sim, StrucAligParameters params)` Align w/o penalizing endpags.
`static boolean` `FragmentJoiner.reduceFragments(List<FragmentPair> fragments, FragmentPair f, Matrix rmsmat)` In helices often many similar fragments can be found.
`void` `AlternativeAlignment.setDistanceMatrix(Matrix distanceMatrix)` The distance matrix this alignment is based on
`void` `FragmentPair.setRot(Matrix rot)`

Uses of Matrix in org.biojava.bio.structure.gui

Methods in org.biojava.bio.structure.gui that return Matrix
`Matrix` `ScaleableMatrixPanel.getMatrix()`
`Matrix` `JMatrixPanel.getMatrix()`

Methods in org.biojava.bio.structure.gui with parameters of type Matrix
`void` `ScaleableMatrixPanel.setMatrix(Matrix matrix)`
`void` `JMatrixPanel.setMatrix(Matrix matrix)` sets the distance matrix to be displayed

Uses of Matrix in org.biojava.bio.structure.jama

Methods in org.biojava.bio.structure.jama that return Matrix
`Matrix` `Matrix.arrayLeftDivide(Matrix B)` Element-by-element left division, C = A.\B
`Matrix` `Matrix.arrayLeftDivideEquals(Matrix B)` Element-by-element left division in place, A = A.\B
`Matrix` `Matrix.arrayRightDivide(Matrix B)` Element-by-element right division, C = A./B
`Matrix` `Matrix.arrayRightDivideEquals(Matrix B)` Element-by-element right division in place, A = A./B
`Matrix` `Matrix.arrayTimes(Matrix B)` Element-by-element multiplication, C = A.*B
`Matrix` `Matrix.arrayTimesEquals(Matrix B)` Element-by-element multiplication in place, A = A.*B
`static Matrix` `Matrix.constructWithCopy(double[][] A)` Construct a matrix from a copy of a 2-D array.
`Matrix` `Matrix.copy()` Make a deep copy of a matrix
`Matrix` `EigenvalueDecomposition.getD()` Return the block diagonal eigenvalue matrix
`Matrix` `QRDecomposition.getH()` Return the Householder vectors
`Matrix` `LUDecomposition.getL()` Return lower triangular factor
`Matrix` `CholeskyDecomposition.getL()` Return triangular factor.
`Matrix` `Matrix.getMatrix(int[] r, int[] c)` Get a submatrix.
`Matrix` `Matrix.getMatrix(int[] r, int j0, int j1)` Get a submatrix.
`Matrix` `Matrix.getMatrix(int i0, int i1, int[] c)` Get a submatrix.
`Matrix` `Matrix.getMatrix(int i0, int i1, int j0, int j1)` Get a submatrix.
`Matrix` `QRDecomposition.getQ()` Generate and return the (economy-sized) orthogonal factor
`Matrix` `QRDecomposition.getR()` Return the upper triangular factor
`Matrix` `SingularValueDecomposition.getS()` Return the diagonal matrix of singular values
`Matrix` `SingularValueDecomposition.getU()` Return the left singular vectors
`Matrix` `LUDecomposition.getU()` Return upper triangular factor
`Matrix` `SingularValueDecomposition.getV()` Return the right singular vectors
`Matrix` `EigenvalueDecomposition.getV()` Return the eigenvector matrix
`static Matrix` `Matrix.identity(int m, int n)` Generate identity matrix
`Matrix` `Matrix.inverse()` Matrix inverse or pseudoinverse
`Matrix` `Matrix.minus(Matrix B)` C = A - B
`Matrix` `Matrix.minusEquals(Matrix B)` A = A - B
`Matrix` `Matrix.plus(Matrix B)` C = A + B
`Matrix` `Matrix.plusEquals(Matrix B)` A = A + B
`static Matrix` `Matrix.random(int m, int n)` Generate matrix with random elements
`static Matrix` `Matrix.read(BufferedReader input)` Read a matrix from a stream.
`Matrix` `QRDecomposition.solve(Matrix B)` Least squares solution of A*X = B
`Matrix` `Matrix.solve(Matrix B)` Solve A*X = B
`Matrix` `LUDecomposition.solve(Matrix B)` Solve A*X = B
`Matrix` `CholeskyDecomposition.solve(Matrix B)` Solve A*X = B
`Matrix` `Matrix.solveTranspose(Matrix B)` Solve X*A = B, which is also A'*X' = B'
`Matrix` `Matrix.times(double s)` Multiply a matrix by a scalar, C = s*A
`Matrix` `Matrix.times(Matrix B)` Linear algebraic matrix multiplication, A * B
`Matrix` `Matrix.timesEquals(double s)` Multiply a matrix by a scalar in place, A = s*A
`Matrix` `Matrix.transpose()` Matrix transpose.
`Matrix` `Matrix.uminus()` Unary minus

Methods in org.biojava.bio.structure.jama with parameters of type Matrix
`Matrix` `Matrix.arrayLeftDivide(Matrix B)` Element-by-element left division, C = A.\B
`Matrix` `Matrix.arrayLeftDivideEquals(Matrix B)` Element-by-element left division in place, A = A.\B
`Matrix` `Matrix.arrayRightDivide(Matrix B)` Element-by-element right division, C = A./B
`Matrix` `Matrix.arrayRightDivideEquals(Matrix B)` Element-by-element right division in place, A = A./B
`Matrix` `Matrix.arrayTimes(Matrix B)` Element-by-element multiplication, C = A.*B
`Matrix` `Matrix.arrayTimesEquals(Matrix B)` Element-by-element multiplication in place, A = A.*B
`Matrix` `Matrix.minus(Matrix B)` C = A - B
`Matrix` `Matrix.minusEquals(Matrix B)` A = A - B
`Matrix` `Matrix.plus(Matrix B)` C = A + B
`Matrix` `Matrix.plusEquals(Matrix B)` A = A + B
`void` `Matrix.setMatrix(int[] r, int[] c, Matrix X)` Set a submatrix.
`void` `Matrix.setMatrix(int[] r, int j0, int j1, Matrix X)` Set a submatrix.
`void` `Matrix.setMatrix(int i0, int i1, int[] c, Matrix X)` Set a submatrix.
`void` `Matrix.setMatrix(int i0, int i1, int j0, int j1, Matrix X)` Set a submatrix.
`Matrix` `QRDecomposition.solve(Matrix B)` Least squares solution of A*X = B
`Matrix` `Matrix.solve(Matrix B)` Solve A*X = B
`Matrix` `LUDecomposition.solve(Matrix B)` Solve A*X = B
`Matrix` `CholeskyDecomposition.solve(Matrix B)` Solve A*X = B
`Matrix` `Matrix.solveTranspose(Matrix B)` Solve X*A = B, which is also A'*X' = B'
`Matrix` `Matrix.times(Matrix B)` Linear algebraic matrix multiplication, A * B

Constructors in org.biojava.bio.structure.jama with parameters of type Matrix
`CholeskyDecomposition(Matrix Arg)` Cholesky algorithm for symmetric and positive definite matrix.
`EigenvalueDecomposition(Matrix Arg)` Check for symmetry, then construct the eigenvalue decomposition provides a way to access D and V.
`LUDecomposition(Matrix A)` LU Decomposition provides a data structure to access L, U and piv.
`QRDecomposition(Matrix A)` QR Decomposition, computed by Householder reflections.
`SingularValueDecomposition(Matrix Arg)` Construct the singular value decomposition.