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

Packages that use Matrix

Package	Description
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

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
static Alignable	AligNPE.align_NPE(Matrix sim, StrucAligParameters params)	Align w/o penalizing endpags.
static boolean	FragmentJoiner.reduceFragments(java.util.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

Modifier and Type	Method	Description
Matrix	JMatrixPanel.getMatrix()
Matrix	ScaleableMatrixPanel.getMatrix()

Methods in org.biojava.bio.structure.gui with parameters of type Matrix

Modifier and Type	Method	Description
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

Modifier and Type	Method	Description
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	LUDecomposition.getU()	Return upper triangular factor
Matrix	SingularValueDecomposition.getU()	Return the left singular vectors
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(java.io.BufferedReader input)	Read a matrix from a stream.
Matrix	CholeskyDecomposition.solve(Matrix B)	Solve A*X = B
Matrix	LUDecomposition.solve(Matrix B)	Solve A*X = B
Matrix	Matrix.solve(Matrix B)	Solve A*X = B
Matrix	QRDecomposition.solve(Matrix B)	Least squares solution of 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

Modifier and Type	Method	Description
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	CholeskyDecomposition.solve(Matrix B)	Solve A*X = B
Matrix	LUDecomposition.solve(Matrix B)	Solve A*X = B
Matrix	Matrix.solve(Matrix B)	Solve A*X = B
Matrix	QRDecomposition.solve(Matrix B)	Least squares solution of 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

Constructor	Description
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.