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 JMatrixPanel.getMatrix()
           
 Matrix ScaleableMatrixPanel.getMatrix()
           
 

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

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 CholeskyDecomposition.getL()
          Return triangular factor.
 Matrix LUDecomposition.getL()
          Return lower 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 EigenvalueDecomposition.getV()
          Return the eigenvector matrix
 Matrix SingularValueDecomposition.getV()
          Return the right singular vectors
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 CholeskyDecomposition.solve(Matrix B)
          Solve A*X = B
 Matrix LUDecomposition.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 CholeskyDecomposition.solve(Matrix B)
          Solve A*X = B
 Matrix LUDecomposition.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.