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

Packages that use Matrix

Package	Description
org.biojava.nbio.structure	Interfaces and classes for protein structure (PDB).
org.biojava.nbio.structure.align	Classes for the alignment of structures.
org.biojava.nbio.structure.align.ce	Classes related to the implementation of the CE alignment algorithm, here called jCE.
org.biojava.nbio.structure.align.gui
org.biojava.nbio.structure.align.gui.jmol	Utility methods for better interaction with Jmol.
org.biojava.nbio.structure.align.helper	Helper classes for structural alignment.
org.biojava.nbio.structure.align.model
org.biojava.nbio.structure.align.multiple
org.biojava.nbio.structure.align.multiple.util
org.biojava.nbio.structure.align.pairwise	Classes for the pairwise alignment of structures.
org.biojava.nbio.structure.align.util
org.biojava.nbio.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.nbio.structure.io.mmcif.model	Datamodel objects used for processing mmcif files.
org.biojava.nbio.structure.jama	Matrix package for from JAMA
org.biojava.nbio.structure.symmetry.utils

Uses of Matrix in org.biojava.nbio.structure

Methods in org.biojava.nbio.structure that return Matrix

Modifier and Type	Method and Description
Matrix	SVDSuperimposer.getRotation() Get the Rotation matrix that is required to superimpose the two atom sets.
static Matrix	Calc.getRotationMatrix(javax.vecmath.Matrix4d transform) Convert Vecmath transformation into a JAMA rotation matrix.
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.nbio.structure with parameters of type Matrix

Modifier and Type	Method and Description
static javax.vecmath.Matrix4d	Calc.getTransformation(Matrix rot, Atom trans) Convert JAMA rotation and translation to a Vecmath transformation matrix.
static javax.vecmath.Matrix4d	Calc.getTransformation(Matrix rot, Matrix trans) Convert JAMA rotation and translation to a Vecmath transformation matrix.
static double[]	Calc.getXYZEuler(Matrix m) Convert a rotation Matrix to Euler angles.
static double[]	Calc.getZYZEuler(Matrix m) Gets euler angles for a matrix given in ZYZ convention.
static void	Calc.plus(Structure s, Matrix matrix) calculate structure + Matrix coodinates ...
static void	Calc.rotate(Atom[] ca, Matrix matrix)
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.nbio.structure.align

Methods in org.biojava.nbio.structure.align that return Matrix

Modifier and Type	Method and Description
Matrix	StructurePairAligner.getDistMat() return the difference of distance matrix between the two structures

Uses of Matrix in org.biojava.nbio.structure.align.ce

Methods in org.biojava.nbio.structure.align.ce that return Matrix

Modifier and Type	Method and Description
Matrix	CeCalculatorEnhanced.getRotationMatrix() Gets the rotation matrix from the last call to calc_rmsd.
Matrix	CECalculator.getRotationMatrix() Gets the rotation matrix from the last call to calc_rmsd.

Methods in org.biojava.nbio.structure.align.ce with parameters of type Matrix

Modifier and Type	Method and Description
static JPanel	GuiWrapper.getScaleableMatrixPanel(Matrix m)

Uses of Matrix in org.biojava.nbio.structure.align.gui

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

Modifier and Type	Method and Description
static void	StructureAlignmentDisplay.shiftCA2(AFPChain afpChain, Atom[] ca2, Matrix m, Atom shift, Group[] twistedGroups) only shift CA positions.

Uses of Matrix in org.biojava.nbio.structure.align.gui.jmol

Methods in org.biojava.nbio.structure.align.gui.jmol that return types with arguments of type Matrix

Modifier and Type	Method and Description
List<Matrix>	MultipleAlignmentJmol.getDistanceMatrices()
abstract List<Matrix>	AbstractAlignmentJmol.getDistanceMatrices() Returns a List of internal Distance Matrices, one for each structure in the alignment.
List<Matrix>	StructureAlignmentJmol.getDistanceMatrices()

Methods in org.biojava.nbio.structure.align.gui.jmol with parameters of type Matrix

Modifier and Type	Method and Description
void	JmolPanel.rotateJmol(Matrix jmolRotation)

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

Methods in org.biojava.nbio.structure.align.helper that return Matrix

Modifier and Type	Method and Description
static Matrix	AlignTools.getDistanceMatrix(Atom[] ca1, Atom[] ca2) Matrix of all distances between two sets of Atoms.

Uses of Matrix in org.biojava.nbio.structure.align.model

Methods in org.biojava.nbio.structure.align.model that return Matrix

Modifier and Type	Method and Description
Matrix[]	AFPChain.getBlockRotationMatrix()
Matrix	AFPChain.getDisTable1()
Matrix	AFPChain.getDisTable2()
Matrix	AFPChain.getDistanceMatrix() A matrix with ca1length rows and ca2length columns.
Matrix	AFP.getM()

Methods in org.biojava.nbio.structure.align.model with parameters of type Matrix

Modifier and Type	Method and Description
void	AFPChain.setBlockRotationMatrix(Matrix[] blockRotationMatrix)
void	AFPChain.setDisTable1(Matrix disTable1)
void	AFPChain.setDisTable2(Matrix disTable2)
void	AFPChain.setDistanceMatrix(Matrix distanceMatrix) A matrix with ca1length rows and ca2length columns.
void	AFP.setM(Matrix m)

Uses of Matrix in org.biojava.nbio.structure.align.multiple

Methods in org.biojava.nbio.structure.align.multiple that return types with arguments of type Matrix

Modifier and Type	Method and Description
List<Matrix>	MultipleAlignmentEnsembleImpl.getDistanceMatrix()
List<Matrix>	MultipleAlignmentEnsemble.getDistanceMatrix() Returns the List containing the interatomic distance Matrix of each structure.

Uses of Matrix in org.biojava.nbio.structure.align.multiple.util

Methods in org.biojava.nbio.structure.align.multiple.util that return Matrix

Modifier and Type	Method and Description
static Matrix	MultipleAlignmentTools.getAverageResidueDistances(List<Atom[]> transformed) The average residue distance Matrix contains the average distance from each residue to all other residues aligned with it.
static Matrix	MultipleAlignmentTools.getAverageResidueDistances(MultipleAlignment msa) The average residue distance Matrix contains the average distance from each residue to all other residues aligned with it.
static Matrix	MultipleAlignmentTools.getRMSDMatrix(MultipleAlignment msa) Calculate the RMSD matrix of a MultipleAlignment, that is, entry (i,j) of the matrix contains the RMSD between structures i and j.

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

Methods in org.biojava.nbio.structure.align.pairwise that return Matrix

Modifier and Type	Method and 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.nbio.structure.align.pairwise with parameters of type Matrix

Modifier and Type	Method and Description
static Alignable	AligNPE.align_NPE(Matrix sim, StrucAligParameters params) Align without penalizing end-gaps.
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.nbio.structure.align.util

Methods in org.biojava.nbio.structure.align.util that return Matrix

Modifier and Type	Method and Description
Matrix	RotationAxis.getFullMatrix() Returns a matrix that describes both rotation and translation.
Matrix	RotationAxis.getRotationMatrix() Get the rotation matrix corresponding to this axis
Matrix	RotationAxis.getRotationMatrix(double theta) Get the rotation matrix corresponding to a rotation about this axis
static Matrix	AFPAlignmentDisplay.getRotMax(AFPChain afpChain, Atom[] ca1, Atom[] ca2)

Methods in org.biojava.nbio.structure.align.util with parameters of type Matrix

Modifier and Type	Method and Description
static double	RotationAxis.getAngle(Matrix rotation) Calculate the rotation angle for a given matrix

Constructors in org.biojava.nbio.structure.align.util with parameters of type Matrix

Constructor and Description
RotationAxis(Matrix rotation, Atom translation) Determine the location of the rotation axis based on a rotation matrix and a translation vector

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

Methods in org.biojava.nbio.structure.gui that return Matrix

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

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

Modifier and Type	Method and Description
void	JMatrixPanel.setMatrix(Matrix matrix) sets the distance matrix to be displayed
void	ScaleableMatrixPanel.setMatrix(Matrix matrix)

Uses of Matrix in org.biojava.nbio.structure.io.mmcif.model

Methods in org.biojava.nbio.structure.io.mmcif.model that return Matrix

Modifier and Type	Method and Description
Matrix	PdbxStructOperList.getMatrix()

Methods in org.biojava.nbio.structure.io.mmcif.model with parameters of type Matrix

Modifier and Type	Method and Description
void	PdbxStructOperList.setMatrix(Matrix matrix)

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

Methods in org.biojava.nbio.structure.jama that return Matrix

Modifier and Type	Method and 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	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	CholeskyDecomposition.solve(Matrix B) Solve A*X = B
Matrix	QRDecomposition.solve(Matrix B) Least squares solution of A*X = B
Matrix	LUDecomposition.solve(Matrix B) Solve A*X = B
Matrix	Matrix.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.nbio.structure.jama with parameters of type Matrix

Modifier and Type	Method and 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	QRDecomposition.solve(Matrix B) Least squares solution of A*X = B
Matrix	LUDecomposition.solve(Matrix B) Solve A*X = B
Matrix	Matrix.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.nbio.structure.jama with parameters of type Matrix

Constructor and Description
CholeskyDecomposition(Matrix Arg) Cholesky algorithm for symmetric and positive definite matrix.
EigenvalueDecomposition(Matrix Arg) Check for symmetry, then construct the eigenvalue decomposition Structure 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.

Uses of Matrix in org.biojava.nbio.structure.symmetry.utils

Methods in org.biojava.nbio.structure.symmetry.utils that return Matrix

Modifier and Type	Method and Description
static Matrix	SymmetryTools.blankOutCEOrig(Atom[] ca2, int rows, int cols, CECalculator calculator, Matrix origM, int blankWindowSize)
static Matrix	SymmetryTools.blankOutPreviousAlignment(AFPChain afpChain, Atom[] ca2, int rows, int cols, CECalculator calculator, Matrix max, int blankWindowSize)
Matrix	SymmetryTools.getDkMatrix(Atom[] ca1, Atom[] ca2, int fragmentLength, double[] dist1, double[] dist2, int rows, int cols)
static Matrix	SymmetryTools.getDkMatrix(Atom[] ca1, Atom[] ca2, int k, int fragmentLength)
static Matrix	SymmetryTools.grayOutCEOrig(Atom[] ca2, int rows, int cols, CECalculator calculator, Matrix origM, int blankWindowSize, double[] gradientPolyCoeff, double gradientExpCoeff) Grays out the main diagonal of a duplicated distance matrix.
static Matrix	SymmetryTools.grayOutPreviousAlignment(AFPChain afpChain, Atom[] ca2, int rows, int cols, CECalculator calculator, Matrix max, int blankWindowSize, double[] gradientPolyCoeff, double gradientExpCoeff)

Methods in org.biojava.nbio.structure.symmetry.utils with parameters of type Matrix

Modifier and Type	Method and Description
static Matrix	SymmetryTools.blankOutCEOrig(Atom[] ca2, int rows, int cols, CECalculator calculator, Matrix origM, int blankWindowSize)
static Matrix	SymmetryTools.blankOutPreviousAlignment(AFPChain afpChain, Atom[] ca2, int rows, int cols, CECalculator calculator, Matrix max, int blankWindowSize)
static Matrix	SymmetryTools.grayOutCEOrig(Atom[] ca2, int rows, int cols, CECalculator calculator, Matrix origM, int blankWindowSize, double[] gradientPolyCoeff, double gradientExpCoeff) Grays out the main diagonal of a duplicated distance matrix.
static Matrix	SymmetryTools.grayOutPreviousAlignment(AFPChain afpChain, Atom[] ca2, int rows, int cols, CECalculator calculator, Matrix max, int blankWindowSize, double[] gradientPolyCoeff, double gradientExpCoeff)