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Packages that use Matrix | |
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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 |
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Methods in org.biojava.bio.structure that return Matrix | |
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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 | |
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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 |
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Methods in org.biojava.bio.structure.align that return Matrix | |
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Matrix |
StructurePairAligner.getDistMat()
return the difference of distance matrix between the two structures |
Uses of Matrix in org.biojava.bio.structure.align.helper |
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Methods in org.biojava.bio.structure.align.helper that return Matrix | |
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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 |
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Methods in org.biojava.bio.structure.align.pairwise that return Matrix | |
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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 | |
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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)
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Uses of Matrix in org.biojava.bio.structure.gui |
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Methods in org.biojava.bio.structure.gui that return Matrix | |
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Matrix |
JMatrixPanel.getMatrix()
|
Matrix |
ScaleableMatrixPanel.getMatrix()
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Methods in org.biojava.bio.structure.gui with parameters of type Matrix | |
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void |
JMatrixPanel.setMatrix(Matrix matrix)
sets the distance matrix to be displayed |
void |
ScaleableMatrixPanel.setMatrix(Matrix matrix)
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Uses of Matrix in org.biojava.bio.structure.jama |
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Methods in org.biojava.bio.structure.jama that return Matrix | |
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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 | |
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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 | |
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CholeskyDecomposition(Matrix Arg)
Cholesky algorithm for symmetric and positive definite matrix. |
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EigenvalueDecomposition(Matrix Arg)
Check for symmetry, then construct the eigenvalue decomposition provides a way to access D and V. |
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LUDecomposition(Matrix A)
LU Decomposition provides a data structure to access L, U and piv. |
|
QRDecomposition(Matrix A)
QR Decomposition, computed by Householder reflections. |
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SingularValueDecomposition(Matrix Arg)
Construct the singular value decomposition. |
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