Package | Description |
---|---|
org.biojava.bio.structure |
Interfaces and classes for protein structure (PDB).
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org.biojava.bio.structure.align |
Classes for the super-imposition of structures.
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org.biojava.bio.structure.align.helper |
Helper classes for structural alignment.
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org.biojava.bio.structure.align.pairwise |
Classes for the pairwise alignment of structures.
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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.
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org.biojava.bio.structure.jama |
Matrix package for from JAMA
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Modifier and Type | Method and Description |
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Matrix |
SVDSuperimposer.getRotation()
Get the Rotation matrix that is required to superimpose the two atom sets.
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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.
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Modifier and Type | Method and Description |
---|---|
static double[] |
Calc.getXYZEuler(Matrix m)
Convert a rotation Matrix to Euler angles.
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static double[] |
Calc.getZYZEuler(Matrix m)
Gget euler angles for a matrix given in ZYZ convention.
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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.
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static void |
Calc.rotate(Atom atom,
Matrix m)
Rotate an atom around a Matrix object.
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static void |
Calc.rotate(Group group,
Matrix m)
Rotate a group object.
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static void |
Calc.rotate(Structure structure,
Matrix m)
Rotate a structure object.
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Modifier and Type | Method and Description |
---|---|
Matrix |
StructurePairAligner.getDistMat()
return the difference of distance matrix between the two structures
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Modifier and Type | Method and Description |
---|---|
static Matrix |
AlignTools.getDistanceMatrix(Atom[] ca1,
Atom[] ca2)
matrix of all distances between two sets of 3d coords"
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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
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Modifier and Type | Method and 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) |
Modifier and Type | Method and Description |
---|---|
Matrix |
ScaleableMatrixPanel.getMatrix() |
Matrix |
JMatrixPanel.getMatrix() |
Modifier and Type | Method and Description |
---|---|
void |
ScaleableMatrixPanel.setMatrix(Matrix matrix) |
void |
JMatrixPanel.setMatrix(Matrix matrix)
sets the distance matrix to be displayed
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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
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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
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Matrix |
Matrix.arrayTimesEquals(Matrix B)
Element-by-element multiplication in place, A = A.*B
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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 |
LUDecomposition.getL()
Return lower triangular factor
|
Matrix |
CholeskyDecomposition.getL()
Return 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
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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
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static Matrix |
Matrix.random(int m,
int n)
Generate matrix with random elements
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static Matrix |
Matrix.read(java.io.BufferedReader input)
Read a matrix from a stream.
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Matrix |
LUDecomposition.solve(Matrix B)
Solve A*X = B
|
Matrix |
QRDecomposition.solve(Matrix B)
Least squares solution of A*X = B
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Matrix |
CholeskyDecomposition.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'
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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
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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
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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 |
LUDecomposition.solve(Matrix B)
Solve A*X = B
|
Matrix |
QRDecomposition.solve(Matrix B)
Least squares solution of A*X = B
|
Matrix |
CholeskyDecomposition.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
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Constructor and Description |
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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.
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LUDecomposition(Matrix A)
LU Decomposition provides a data structure to access L, U and piv.
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QRDecomposition(Matrix A)
QR Decomposition, computed by Householder reflections.
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SingularValueDecomposition(Matrix Arg)
Construct the singular value decomposition.
|