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java.lang.Object jgromacs.analysis.Similarity
public class Similarity
Collection of methods for measuring structural similarity
Constructor Summary | |
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Similarity()
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Method Summary | |
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static FrameIndexSet |
findSimilarFramesDRMSD(Trajectory t,
jama.Matrix reference,
double cutoff)
Returns the list of frames in a trajectory that are more similar to a reference distance matrix (based on the dRMSD similarity measure) than a cutoff value |
static FrameIndexSet |
findSimilarFramesDRMSD(Trajectory t,
PointList reference,
double cutoff)
Returns the list of frames in a trajectory that are more similar to a reference frame (based on the dRMSD similarity measure) than a cutoff value |
static FrameIndexSet |
findSimilarFramesRMSD(Trajectory t,
PointList reference,
double cutoff)
Returns the set of frames in a trajectory that are more similar to a reference frame (based on the RMSD similarity measure) than a cutoff value |
static jama.Matrix |
getDifferenceDistanceMatrix(PointList points1,
PointList points2)
Calculates the difference distance matrix between two point lists |
static jama.Matrix |
getDifferenceDistanceMatrix(Structure s1,
IndexSet indices1,
Structure s2,
IndexSet indices2)
Calculates the atomic difference distance matrix between two sets of atoms defined by two index sets in two structures |
static jama.Matrix |
getDifferenceDistanceMatrix(Structure s1,
Structure s2)
Calculates the atomic difference distance matrix between two structures |
static double |
getDRMSD(jama.Matrix A,
jama.Matrix B)
Calculates dRMSD similarity between two distance matrices |
static double |
getDRMSD(PointList A,
PointList B)
Calculates dRMSD similarity between two point lists |
static double |
getDRMSD(Structure A,
IndexSet indicesA,
Structure B,
IndexSet indicesB)
Calculates dRMSD similarity between two groups of atoms |
static double |
getDRMSD(Structure A,
Structure B)
Calculates dRMSD similarity between two structures |
static java.util.ArrayList<java.lang.Double> |
getDRMSDiProfile(jama.Matrix A,
jama.Matrix B)
Calculates the dRMSDi profile between two distance matrices |
static java.util.ArrayList<java.lang.Double> |
getDRMSDiProfile(PointList A,
PointList B)
Calculates the dRMSDi profile between two point lists |
static java.util.ArrayList<java.lang.Double> |
getDRMSDiProfile(Structure A,
IndexSet indicesA,
Structure B,
IndexSet indicesB)
Calculates the dRMSDi profile between two groups of atoms |
static java.util.ArrayList<java.lang.Double> |
getDRMSDiProfile(Structure A,
Structure B)
Calculates the dRMSDi profile between two structures |
static PointList |
getMedoidDRMSD(Trajectory t)
Calculates the medoid frame of a trajectory using the dRMSD measure |
static PointList |
getMedoidRMSD(Trajectory t)
Calculates the medoid frame of a trajectory using the RMSD measure |
static double |
getRMSD(PointList A,
PointList B)
Calculates RMSD similarity between two point lists |
static double |
getRMSD(Structure A,
IndexSet indicesA,
Structure B,
IndexSet indicesB)
Calculates RMSD similarity between two groups of atoms |
static double |
getRMSD(Structure A,
Structure B)
Calculates RMSD similarity between two structures |
static java.util.ArrayList<java.lang.Double> |
getRMSDiProfile(PointList A,
PointList B)
Calculates the RMSDi profile between two point lists |
static java.util.ArrayList<java.lang.Double> |
getRMSDiProfile(Structure A,
IndexSet indicesA,
Structure B,
IndexSet indicesB)
Calculates the RMSDi profile between two groups of atoms |
static java.util.ArrayList<java.lang.Double> |
getRMSDiProfile(Structure A,
Structure B)
Calculates the RMSDi profile between two structures |
static java.util.ArrayList<java.lang.Double> |
getRMSDiProfileNoSuperposition(PointList A,
PointList B)
Calculates the RMSDi profile between two point lists without superposition |
static java.util.ArrayList<java.lang.Double> |
getRMSDiProfileNoSuperposition(Structure A,
IndexSet indicesA,
Structure B,
IndexSet indicesB)
Calculates the RMSDi profile between two groups of atoms without superposition |
static java.util.ArrayList<java.lang.Double> |
getRMSDiProfileNoSuperposition(Structure A,
Structure B)
Calculates the RMSDi profile between two structures without superposition |
static double |
getRMSDnoSuperposition(PointList A,
PointList B)
Calculates RMSD similarity between two point lists without doing superposition |
static double |
getRMSDnoSuperposition(Structure A,
IndexSet indicesA,
Structure B,
IndexSet indicesB)
Calculates RMSD similarity between two groups of atoms without superposition |
static double |
getRMSDnoSuperposition(Structure A,
Structure B)
Calculates RMSD similarity between two structures without doing superposition |
static jama.Matrix |
getSimilarityMatrixDRMSD(Trajectory t)
Calculates the similarity matrix of all frames in a trajectory using the dRMSD measure |
static jama.Matrix |
getSimilarityMatrixDRMSD(Trajectory t,
IndexSet indices)
Calculates the similarity matrix of all frames in a trajectory using the dRMSD measure taking into account only a subset of atoms |
static jama.Matrix |
getSimilarityMatrixRMSD(Trajectory t)
Calculates the similarity matrix of all frames in a trajectory using the RMSD measure |
static jama.Matrix |
getSimilarityMatrixRMSD(Trajectory t,
IndexSet indices)
Calculates the similarity matrix of all frames in a trajectory using the RMSD measure taking into account only a subset of atoms |
static jama.Matrix |
getSimilarityMatrixWDRMSD(Trajectory t,
IndexSet indices,
jama.Matrix W)
Calculates the similarity matrix of all frames in a trajectory using the wdRMSD (weighted dRMSD) measure taking into account only a subset of atoms |
static jama.Matrix |
getSimilarityMatrixWDRMSD(Trajectory t,
jama.Matrix W)
Calculates the similarity matrix of all frames in a trajectory using the wdRMSD (weighted dRMSD) measure |
static java.util.ArrayList<java.lang.Double> |
getSimilarityTimeSeriesDRMSD(Trajectory t,
IndexSet indicesT,
Structure R,
IndexSet indicesR)
Returns the time series of dRMSD in a trajectory with regards to a reference structure taking into account only a subset of atoms |
static java.util.ArrayList<java.lang.Double> |
getSimilarityTimeSeriesDRMSD(Trajectory t,
PointList R)
Returns the time series of dRMSD in a trajectory with regards to a reference point list |
static java.util.ArrayList<java.lang.Double> |
getSimilarityTimeSeriesDRMSD(Trajectory t,
Structure R)
Returns the time series of dRMSD in a trajectory with regards to a reference structure |
static java.util.ArrayList<java.lang.Double> |
getSimilarityTimeSeriesRMSD(Trajectory t,
IndexSet indicesT,
Structure R,
IndexSet indicesR)
Returns the time series of RMSD in a trajectory with regards to a reference structure taking into account only a subset of atoms |
static java.util.ArrayList<java.lang.Double> |
getSimilarityTimeSeriesRMSD(Trajectory t,
PointList R)
Returns the time series of RMSD in a trajectory with regards to a reference point list |
static java.util.ArrayList<java.lang.Double> |
getSimilarityTimeSeriesRMSD(Trajectory t,
Structure R)
Returns the time series of RMSD in a trajectory with regards to a reference structure |
static java.util.ArrayList<java.lang.Double> |
getSimilarityTimeSeriesWDRMSD(Trajectory t,
IndexSet indicesT,
Structure R,
IndexSet indicesR,
jama.Matrix W)
Returns the time series of wdRMSD (weighted dRMSD) in a trajectory with regards to a reference structure taking into account only a subset of atoms |
static java.util.ArrayList<java.lang.Double> |
getSimilarityTimeSeriesWDRMSD(Trajectory t,
PointList R,
jama.Matrix W)
Returns the time series of wdRMSD (weighted dRMSD) in a trajectory with regards to a reference point list |
static java.util.ArrayList<java.lang.Double> |
getSimilarityTimeSeriesWDRMSD(Trajectory t,
Structure R,
jama.Matrix W)
Returns the time series of wdRMSD (weighted dRMSD) in a trajectory with regards to a reference structure |
static double |
getWDRMSD(PointList A,
PointList B,
jama.Matrix W)
Calculates the wdRMSD (weighted dRMSD) similarity of two point lists |
static double |
getWDRMSD(Structure A,
IndexSet indicesA,
Structure B,
IndexSet indicesB,
jama.Matrix W)
Calculates wdRMSD (weighted dRMSD) similarity between two groups of atoms |
static double |
getWDRMSD(Structure A,
Structure B,
jama.Matrix W)
Calculates the wdRMSD (weighted dRMSD) similarity of two structures |
static java.util.ArrayList<java.lang.Double> |
getWDRMSDiProfile(PointList A,
PointList B,
jama.Matrix W)
Calculates the wdRMSDi (weighted dRMSDi) profile between two point lists |
static java.util.ArrayList<java.lang.Double> |
getWDRMSDiProfile(Structure A,
IndexSet indicesA,
Structure B,
IndexSet indicesB,
jama.Matrix W)
Calculates the wdRMSDi (weighted dRMSDi) profile between two groups of atoms |
static java.util.ArrayList<java.lang.Double> |
getWDRMSDiProfile(Structure A,
Structure B,
jama.Matrix W)
Calculates the wdRMSDi (weighted dRMSDi) profile between two structures |
Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public Similarity()
Method Detail |
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public static double getRMSD(PointList A, PointList B)
A
- first point listB
- second point list
public static double getRMSD(Structure A, Structure B)
A
- first structureB
- second structure
public static double getRMSD(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB)
A
- first structureindicesA
- index set of atoms in the first structureB
- second structureindicesB
- index set of atoms in the second structure
public static java.util.ArrayList<java.lang.Double> getRMSDiProfile(PointList A, PointList B)
A
- first point listB
- second point list
public static java.util.ArrayList<java.lang.Double> getRMSDiProfile(Structure A, Structure B)
A
- first structureB
- second structure
public static java.util.ArrayList<java.lang.Double> getRMSDiProfile(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB)
A
- first structureindicesA
- index set of atoms in the first structureB
- second structureindicesB
- index set of atoms in the second structure
public static double getRMSDnoSuperposition(PointList A, PointList B)
A
- first point listB
- second point list
public static double getRMSDnoSuperposition(Structure A, Structure B)
A
- first structureB
- second structure
public static double getRMSDnoSuperposition(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB)
A
- first structureindicesA
- index set of atoms in the first structureB
- second structureindicesB
- index set of atoms in the second structure
public static java.util.ArrayList<java.lang.Double> getRMSDiProfileNoSuperposition(PointList A, PointList B)
A
- first point listB
- second point list
public static java.util.ArrayList<java.lang.Double> getRMSDiProfileNoSuperposition(Structure A, Structure B)
A
- first structureB
- second structure
public static java.util.ArrayList<java.lang.Double> getRMSDiProfileNoSuperposition(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB)
A
- first structureindicesA
- index set of atoms in the first structureB
- second structureindicesB
- index set of atoms in the second structure
public static double getDRMSD(jama.Matrix A, jama.Matrix B)
A
- first distance matrixB
- second distance matrix
public static double getDRMSD(PointList A, PointList B)
A
- first point listB
- second point list
public static double getDRMSD(Structure A, Structure B)
A
- first structureB
- second structure
public static double getDRMSD(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB)
A
- first structureindicesA
- index set of atoms in the first structureB
- second structureindicesB
- index set of atoms in the second structure
public static java.util.ArrayList<java.lang.Double> getDRMSDiProfile(jama.Matrix A, jama.Matrix B)
A
- first distance matrixB
- second distance matrix
public static java.util.ArrayList<java.lang.Double> getDRMSDiProfile(PointList A, PointList B)
A
- first point listB
- second point list
public static java.util.ArrayList<java.lang.Double> getDRMSDiProfile(Structure A, Structure B)
A
- first structureB
- second structure
public static java.util.ArrayList<java.lang.Double> getDRMSDiProfile(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB)
A
- first structureindicesA
- index set of atoms in the first structureB
- second structureindicesB
- index set of atoms in the second structure
public static double getWDRMSD(PointList A, PointList B, jama.Matrix W)
A
- first point listB
- second point listW
- weight matrix
public static double getWDRMSD(Structure A, Structure B, jama.Matrix W)
A
- first structureB
- second structureW
- weight matrix
public static double getWDRMSD(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB, jama.Matrix W)
A
- first structureindicesA
- index set of atoms in the first structureB
- second structureindicesB
- index set of atoms in the second structureW
- weight matrix
public static java.util.ArrayList<java.lang.Double> getWDRMSDiProfile(PointList A, PointList B, jama.Matrix W)
A
- first point listB
- second point listW
- weight matrix
public static java.util.ArrayList<java.lang.Double> getWDRMSDiProfile(Structure A, Structure B, jama.Matrix W)
A
- first structureB
- second structureW
- weight matrix
public static java.util.ArrayList<java.lang.Double> getWDRMSDiProfile(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB, jama.Matrix W)
A
- first structureindicesA
- index set of atoms in the first structureB
- second structureindicesB
- index set of atoms in the second structureW
- weight matrix
public static jama.Matrix getSimilarityMatrixRMSD(Trajectory t)
t
- trajectory
public static jama.Matrix getSimilarityMatrixRMSD(Trajectory t, IndexSet indices)
t
- trajectoryindices
- index set of atoms
public static jama.Matrix getSimilarityMatrixDRMSD(Trajectory t)
t
- trajectory
public static jama.Matrix getSimilarityMatrixDRMSD(Trajectory t, IndexSet indices)
t
- trajectoryindices
- index set of atoms
public static jama.Matrix getSimilarityMatrixWDRMSD(Trajectory t, jama.Matrix W)
t
- trajectoryW
- weight matrix
public static jama.Matrix getSimilarityMatrixWDRMSD(Trajectory t, IndexSet indices, jama.Matrix W)
t
- trajectoryindices
- index set of atomsW
- weight matrix
public static java.util.ArrayList<java.lang.Double> getSimilarityTimeSeriesRMSD(Trajectory t, PointList R)
t
- trajectoryR
- reference point list
public static java.util.ArrayList<java.lang.Double> getSimilarityTimeSeriesRMSD(Trajectory t, Structure R)
t
- trajectoryR
- reference structure
public static java.util.ArrayList<java.lang.Double> getSimilarityTimeSeriesRMSD(Trajectory t, IndexSet indicesT, Structure R, IndexSet indicesR)
t
- trajectoryindicesT
- index set of atoms in the trajectoryR
- reference structureindicesR
- index set of atoms in the reference structure
public static java.util.ArrayList<java.lang.Double> getSimilarityTimeSeriesDRMSD(Trajectory t, PointList R)
t
- trajectoryR
- reference point list
public static java.util.ArrayList<java.lang.Double> getSimilarityTimeSeriesDRMSD(Trajectory t, Structure R)
t
- trajectoryR
- reference structure
public static java.util.ArrayList<java.lang.Double> getSimilarityTimeSeriesDRMSD(Trajectory t, IndexSet indicesT, Structure R, IndexSet indicesR)
t
- trajectoryindicesT
- index set of atoms in the trajectoryR
- reference structureindicesR
- index set of atoms in the reference structure
public static java.util.ArrayList<java.lang.Double> getSimilarityTimeSeriesWDRMSD(Trajectory t, PointList R, jama.Matrix W)
t
- trajectoryR
- reference point listW
- weight matrix
public static java.util.ArrayList<java.lang.Double> getSimilarityTimeSeriesWDRMSD(Trajectory t, Structure R, jama.Matrix W)
t
- trajectoryR
- reference structureW
- weight matrix
public static java.util.ArrayList<java.lang.Double> getSimilarityTimeSeriesWDRMSD(Trajectory t, IndexSet indicesT, Structure R, IndexSet indicesR, jama.Matrix W)
t
- trajectoryindicesT
- index set of atoms in the trajectoryR
- reference structureindicesR
- index set of atoms in the reference structureW
- weight matrix
public static jama.Matrix getDifferenceDistanceMatrix(PointList points1, PointList points2)
points1
- first point listpoints2
- second point list
public static jama.Matrix getDifferenceDistanceMatrix(Structure s1, Structure s2)
s1
- first structures2
- second structure
public static jama.Matrix getDifferenceDistanceMatrix(Structure s1, IndexSet indices1, Structure s2, IndexSet indices2)
s1
- first structureindices1
- first index sets2
- second structureindices2
- second index set
public static FrameIndexSet findSimilarFramesRMSD(Trajectory t, PointList reference, double cutoff)
t
- trajectoryreference
- reference framecutoff
- similarity cutoff
public static FrameIndexSet findSimilarFramesDRMSD(Trajectory t, PointList reference, double cutoff)
t
- trajectoryreference
- reference framecutoff
- similarity cutoff
public static FrameIndexSet findSimilarFramesDRMSD(Trajectory t, jama.Matrix reference, double cutoff)
t
- trajectoryreference
- reference distance matrixcutoff
- similarity cutoff
public static PointList getMedoidRMSD(Trajectory t)
t
- trajectory
public static PointList getMedoidDRMSD(Trajectory t)
t
- trajectory
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