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 onstatic 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 1Methods 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 onvoid
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 displayedvoid
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.\BMatrix
Matrix. arrayLeftDivideEquals(Matrix B)
Element-by-element left division in place, A = A.\BMatrix
Matrix. arrayRightDivide(Matrix B)
Element-by-element right division, C = A./BMatrix
Matrix. arrayRightDivideEquals(Matrix B)
Element-by-element right division in place, A = A./BMatrix
Matrix. arrayTimes(Matrix B)
Element-by-element multiplication, C = A.*BMatrix
Matrix. arrayTimesEquals(Matrix B)
Element-by-element multiplication in place, A = A.*Bstatic 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 matrixMatrix
EigenvalueDecomposition. getD()
Return the block diagonal eigenvalue matrixMatrix
QRDecomposition. getH()
Return the Householder vectorsMatrix
CholeskyDecomposition. getL()
Return triangular factor.Matrix
LUDecomposition. getL()
Return lower triangular factorMatrix
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 factorMatrix
QRDecomposition. getR()
Return the upper triangular factorMatrix
SingularValueDecomposition. getS()
Return the diagonal matrix of singular valuesMatrix
LUDecomposition. getU()
Return upper triangular factorMatrix
SingularValueDecomposition. getU()
Return the left singular vectorsMatrix
EigenvalueDecomposition. getV()
Return the eigenvector matrixMatrix
SingularValueDecomposition. getV()
Return the right singular vectorsstatic Matrix
Matrix. identity(int m, int n)
Generate identity matrixMatrix
Matrix. inverse()
Matrix inverse or pseudoinverseMatrix
Matrix. minus(Matrix B)
C = A - BMatrix
Matrix. minusEquals(Matrix B)
A = A - BMatrix
Matrix. plus(Matrix B)
C = A + BMatrix
Matrix. plusEquals(Matrix B)
A = A + Bstatic Matrix
Matrix. random(int m, int n)
Generate matrix with random elementsstatic Matrix
Matrix. read(java.io.BufferedReader input)
Read a matrix from a stream.Matrix
CholeskyDecomposition. solve(Matrix B)
Solve A*X = BMatrix
LUDecomposition. solve(Matrix B)
Solve A*X = BMatrix
Matrix. solve(Matrix B)
Solve A*X = BMatrix
QRDecomposition. solve(Matrix B)
Least squares solution of A*X = BMatrix
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*AMatrix
Matrix. times(Matrix B)
Linear algebraic matrix multiplication, A * BMatrix
Matrix. timesEquals(double s)
Multiply a matrix by a scalar in place, A = s*AMatrix
Matrix. transpose()
Matrix transpose.Matrix
Matrix. uminus()
Unary minusMethods 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.\BMatrix
Matrix. arrayLeftDivideEquals(Matrix B)
Element-by-element left division in place, A = A.\BMatrix
Matrix. arrayRightDivide(Matrix B)
Element-by-element right division, C = A./BMatrix
Matrix. arrayRightDivideEquals(Matrix B)
Element-by-element right division in place, A = A./BMatrix
Matrix. arrayTimes(Matrix B)
Element-by-element multiplication, C = A.*BMatrix
Matrix. arrayTimesEquals(Matrix B)
Element-by-element multiplication in place, A = A.*BMatrix
Matrix. minus(Matrix B)
C = A - BMatrix
Matrix. minusEquals(Matrix B)
A = A - BMatrix
Matrix. plus(Matrix B)
C = A + BMatrix
Matrix. plusEquals(Matrix B)
A = A + Bvoid
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 = BMatrix
LUDecomposition. solve(Matrix B)
Solve A*X = BMatrix
Matrix. solve(Matrix B)
Solve A*X = BMatrix
QRDecomposition. solve(Matrix B)
Least squares solution of A*X = BMatrix
Matrix. solveTranspose(Matrix B)
Solve X*A = B, which is also A'*X' = B'Matrix
Matrix. times(Matrix B)
Linear algebraic matrix multiplication, A * BConstructors 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.
-