Package jgromacs.analysis
Class Similarity
java.lang.Object
jgromacs.analysis.Similarity
Collection of methods for measuring structural similarity
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic 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 valuestatic 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 valuestatic 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 valuestatic Jama.Matrix
getDifferenceDistanceMatrix
(PointList points1, PointList points2) Calculates the difference distance matrix between two point listsstatic 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 structuresstatic Jama.Matrix
Calculates the atomic difference distance matrix between two structuresstatic double
getDRMSD
(Jama.Matrix A, Jama.Matrix B) Calculates dRMSD similarity between two distance matricesstatic double
Calculates dRMSD similarity between two point listsstatic double
Calculates dRMSD similarity between two groups of atomsstatic double
Calculates dRMSD similarity between two structuresgetDRMSDiProfile
(Jama.Matrix A, Jama.Matrix B) Calculates the dRMSDi profile between two distance matricesCalculates the dRMSDi profile between two point listsgetDRMSDiProfile
(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB) Calculates the dRMSDi profile between two groups of atomsCalculates the dRMSDi profile between two structuresstatic PointList
Calculates the medoid frame of a trajectory using the dRMSD measurestatic PointList
Calculates the medoid frame of a trajectory using the RMSD measurestatic double
Calculates RMSD similarity between two point listsstatic double
Calculates RMSD similarity between two groups of atomsstatic double
Calculates RMSD similarity between two structuresCalculates the RMSDi profile between two point listsgetRMSDiProfile
(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB) Calculates the RMSDi profile between two groups of atomsCalculates the RMSDi profile between two structuresCalculates the RMSDi profile between two point lists without superpositiongetRMSDiProfileNoSuperposition
(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB) Calculates the RMSDi profile between two groups of atoms without superpositionCalculates the RMSDi profile between two structures without superpositionstatic double
Calculates RMSD similarity between two point lists without doing superpositionstatic double
getRMSDnoSuperposition
(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB) Calculates RMSD similarity between two groups of atoms without superpositionstatic double
Calculates RMSD similarity between two structures without doing superpositionstatic Jama.Matrix
Calculates the similarity matrix of all frames in a trajectory using the dRMSD measurestatic 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 atomsstatic Jama.Matrix
Calculates the similarity matrix of all frames in a trajectory using the RMSD measurestatic 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 atomsstatic Jama.Matrix
getSimilarityMatrixWDRMSD
(Trajectory t, Jama.Matrix W) Calculates the similarity matrix of all frames in a trajectory using the wdRMSD (weighted dRMSD) measurestatic 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 atomsgetSimilarityTimeSeriesDRMSD
(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 atomsReturns the time series of dRMSD in a trajectory with regards to a reference point listReturns the time series of dRMSD in a trajectory with regards to a reference structuregetSimilarityTimeSeriesRMSD
(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 atomsReturns the time series of RMSD in a trajectory with regards to a reference point listReturns the time series of RMSD in a trajectory with regards to a reference structuregetSimilarityTimeSeriesWDRMSD
(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 atomsgetSimilarityTimeSeriesWDRMSD
(Trajectory t, PointList R, Jama.Matrix W) Returns the time series of wdRMSD (weighted dRMSD) in a trajectory with regards to a reference point listgetSimilarityTimeSeriesWDRMSD
(Trajectory t, Structure R, Jama.Matrix W) Returns the time series of wdRMSD (weighted dRMSD) in a trajectory with regards to a reference structurestatic double
Calculates the wdRMSD (weighted dRMSD) similarity of two point listsstatic double
Calculates wdRMSD (weighted dRMSD) similarity between two groups of atomsstatic double
Calculates the wdRMSD (weighted dRMSD) similarity of two structuresgetWDRMSDiProfile
(PointList A, PointList B, Jama.Matrix W) Calculates the wdRMSDi (weighted dRMSDi) profile between two point listsgetWDRMSDiProfile
(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB, Jama.Matrix W) Calculates the wdRMSDi (weighted dRMSDi) profile between two groups of atomsgetWDRMSDiProfile
(Structure A, Structure B, Jama.Matrix W) Calculates the wdRMSDi (weighted dRMSDi) profile between two structures
-
Constructor Details
-
Similarity
public Similarity()
-
-
Method Details
-
getRMSD
Calculates RMSD similarity between two point lists- Parameters:
A
- first point listB
- second point list- Returns:
- RMSD
-
getRMSD
Calculates RMSD similarity between two structures- Parameters:
A
- first structureB
- second structure- Returns:
- RMSD
-
getRMSD
Calculates RMSD similarity between two groups of atoms- Parameters:
A
- first structureindicesA
- index set of atoms in the first structureB
- second structureindicesB
- index set of atoms in the second structure- Returns:
- RMSD
-
getRMSDiProfile
Calculates the RMSDi profile between two point lists- Parameters:
A
- first point listB
- second point list- Returns:
- RMSDi profile
-
getRMSDiProfile
Calculates the RMSDi profile between two structures- Parameters:
A
- first structureB
- second structure- Returns:
- RMSDi profile
-
getRMSDiProfile
public static ArrayList<Double> getRMSDiProfile(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB) Calculates the RMSDi profile between two groups of atoms- Parameters:
A
- first structureindicesA
- index set of atoms in the first structureB
- second structureindicesB
- index set of atoms in the second structure- Returns:
- RMSDi profile
-
getRMSDnoSuperposition
Calculates RMSD similarity between two point lists without doing superposition- Parameters:
A
- first point listB
- second point list- Returns:
- RMSD without superposition
-
getRMSDnoSuperposition
Calculates RMSD similarity between two structures without doing superposition- Parameters:
A
- first structureB
- second structure- Returns:
- RMSD without superposition
-
getRMSDnoSuperposition
public static double getRMSDnoSuperposition(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB) Calculates RMSD similarity between two groups of atoms without superposition- Parameters:
A
- first structureindicesA
- index set of atoms in the first structureB
- second structureindicesB
- index set of atoms in the second structure- Returns:
- RMSD without superposition
-
getRMSDiProfileNoSuperposition
Calculates the RMSDi profile between two point lists without superposition- Parameters:
A
- first point listB
- second point list- Returns:
- RMSDi profile without superposition
-
getRMSDiProfileNoSuperposition
Calculates the RMSDi profile between two structures without superposition- Parameters:
A
- first structureB
- second structure- Returns:
- RMSDi profile without superposition
-
getRMSDiProfileNoSuperposition
public static ArrayList<Double> getRMSDiProfileNoSuperposition(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB) Calculates the RMSDi profile between two groups of atoms without superposition- Parameters:
A
- first structureindicesA
- index set of atoms in the first structureB
- second structureindicesB
- index set of atoms in the second structure- Returns:
- RMSDi profile without superposition
-
getDRMSD
public static double getDRMSD(Jama.Matrix A, Jama.Matrix B) Calculates dRMSD similarity between two distance matrices- Parameters:
A
- first distance matrixB
- second distance matrix- Returns:
- dRMSD
-
getDRMSD
Calculates dRMSD similarity between two point lists- Parameters:
A
- first point listB
- second point list- Returns:
- dRMSD
-
getDRMSD
Calculates dRMSD similarity between two structures- Parameters:
A
- first structureB
- second structure- Returns:
- dRMSD
-
getDRMSD
Calculates dRMSD similarity between two groups of atoms- Parameters:
A
- first structureindicesA
- index set of atoms in the first structureB
- second structureindicesB
- index set of atoms in the second structure- Returns:
- dRMSD
-
getDRMSDiProfile
Calculates the dRMSDi profile between two distance matrices- Parameters:
A
- first distance matrixB
- second distance matrix- Returns:
- dRMSDi profile
-
getDRMSDiProfile
Calculates the dRMSDi profile between two point lists- Parameters:
A
- first point listB
- second point list- Returns:
- dRMSDi profile
-
getDRMSDiProfile
Calculates the dRMSDi profile between two structures- Parameters:
A
- first structureB
- second structure- Returns:
- dRMSDi profile
-
getDRMSDiProfile
public static ArrayList<Double> getDRMSDiProfile(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB) Calculates the dRMSDi profile between two groups of atoms- Parameters:
A
- first structureindicesA
- index set of atoms in the first structureB
- second structureindicesB
- index set of atoms in the second structure- Returns:
- dRMSDi profile
-
getWDRMSD
Calculates the wdRMSD (weighted dRMSD) similarity of two point lists- Parameters:
A
- first point listB
- second point listW
- weight matrix- Returns:
- wdRMSD
-
getWDRMSD
Calculates the wdRMSD (weighted dRMSD) similarity of two structures- Parameters:
A
- first structureB
- second structureW
- weight matrix- Returns:
- wdRMSD
-
getWDRMSD
public static double getWDRMSD(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB, Jama.Matrix W) Calculates wdRMSD (weighted dRMSD) similarity between two groups of atoms- Parameters:
A
- first structureindicesA
- index set of atoms in the first structureB
- second structureindicesB
- index set of atoms in the second structureW
- weight matrix- Returns:
- wdRMSD
-
getWDRMSDiProfile
Calculates the wdRMSDi (weighted dRMSDi) profile between two point lists- Parameters:
A
- first point listB
- second point listW
- weight matrix- Returns:
- wdRMSDi profile
-
getWDRMSDiProfile
Calculates the wdRMSDi (weighted dRMSDi) profile between two structures- Parameters:
A
- first structureB
- second structureW
- weight matrix- Returns:
- wdRMSDi profile
-
getWDRMSDiProfile
public static ArrayList<Double> getWDRMSDiProfile(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB, Jama.Matrix W) Calculates the wdRMSDi (weighted dRMSDi) profile between two groups of atoms- Parameters:
A
- first structureindicesA
- index set of atoms in the first structureB
- second structureindicesB
- index set of atoms in the second structureW
- weight matrix- Returns:
- wdRMSDi profile
-
getSimilarityMatrixRMSD
Calculates the similarity matrix of all frames in a trajectory using the RMSD measure- Parameters:
t
- trajectory- Returns:
- similarity matrix
-
getSimilarityMatrixRMSD
Calculates the similarity matrix of all frames in a trajectory using the RMSD measure taking into account only a subset of atoms- Parameters:
t
- trajectoryindices
- index set of atoms- Returns:
- similarity matrix
-
getSimilarityMatrixDRMSD
Calculates the similarity matrix of all frames in a trajectory using the dRMSD measure- Parameters:
t
- trajectory- Returns:
- similarity matrix
-
getSimilarityMatrixDRMSD
Calculates the similarity matrix of all frames in a trajectory using the dRMSD measure taking into account only a subset of atoms- Parameters:
t
- trajectoryindices
- index set of atoms- Returns:
- similarity matrix
-
getSimilarityMatrixWDRMSD
Calculates the similarity matrix of all frames in a trajectory using the wdRMSD (weighted dRMSD) measure- Parameters:
t
- trajectoryW
- weight matrix- Returns:
- similarity matrix
-
getSimilarityMatrixWDRMSD
Calculates the similarity matrix of all frames in a trajectory using the wdRMSD (weighted dRMSD) measure taking into account only a subset of atoms- Parameters:
t
- trajectoryindices
- index set of atomsW
- weight matrix- Returns:
- similarity matrix
-
getSimilarityTimeSeriesRMSD
Returns the time series of RMSD in a trajectory with regards to a reference point list- Parameters:
t
- trajectoryR
- reference point list- Returns:
- time series of RMSD
-
getSimilarityTimeSeriesRMSD
Returns the time series of RMSD in a trajectory with regards to a reference structure- Parameters:
t
- trajectoryR
- reference structure- Returns:
- time series of RMSD
-
getSimilarityTimeSeriesRMSD
public static ArrayList<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- Parameters:
t
- trajectoryindicesT
- index set of atoms in the trajectoryR
- reference structureindicesR
- index set of atoms in the reference structure- Returns:
- time series of RMSD
-
getSimilarityTimeSeriesDRMSD
Returns the time series of dRMSD in a trajectory with regards to a reference point list- Parameters:
t
- trajectoryR
- reference point list- Returns:
- time series of dRMSD
-
getSimilarityTimeSeriesDRMSD
Returns the time series of dRMSD in a trajectory with regards to a reference structure- Parameters:
t
- trajectoryR
- reference structure- Returns:
- time series of dRMSD
-
getSimilarityTimeSeriesDRMSD
public static ArrayList<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- Parameters:
t
- trajectoryindicesT
- index set of atoms in the trajectoryR
- reference structureindicesR
- index set of atoms in the reference structure- Returns:
- time series of dRMSD
-
getSimilarityTimeSeriesWDRMSD
public static ArrayList<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- Parameters:
t
- trajectoryR
- reference point listW
- weight matrix- Returns:
- time series of wdRMSD
-
getSimilarityTimeSeriesWDRMSD
public static ArrayList<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- Parameters:
t
- trajectoryR
- reference structureW
- weight matrix- Returns:
- time series of wdRMSD
-
getSimilarityTimeSeriesWDRMSD
public static ArrayList<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- Parameters:
t
- trajectoryindicesT
- index set of atoms in the trajectoryR
- reference structureindicesR
- index set of atoms in the reference structureW
- weight matrix- Returns:
- time series of wdRMSD
-
getDifferenceDistanceMatrix
Calculates the difference distance matrix between two point lists- Parameters:
points1
- first point listpoints2
- second point list- Returns:
- difference distance matrix
-
getDifferenceDistanceMatrix
Calculates the atomic difference distance matrix between two structures- Parameters:
s1
- first structures2
- second structure- Returns:
- difference distance matrix
-
getDifferenceDistanceMatrix
public 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- Parameters:
s1
- first structureindices1
- first index sets2
- second structureindices2
- second index set- Returns:
- difference distance matrix
-
findSimilarFramesRMSD
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- Parameters:
t
- trajectoryreference
- reference framecutoff
- similarity cutoff- Returns:
- frame index set
-
findSimilarFramesDRMSD
public 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- Parameters:
t
- trajectoryreference
- reference framecutoff
- similarity cutoff- Returns:
- frame list
-
findSimilarFramesDRMSD
public 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- Parameters:
t
- trajectoryreference
- reference distance matrixcutoff
- similarity cutoff- Returns:
- frame list
-
getMedoidRMSD
Calculates the medoid frame of a trajectory using the RMSD measure- Parameters:
t
- trajectory- Returns:
- medoid frame
-
getMedoidDRMSD
Calculates the medoid frame of a trajectory using the dRMSD measure- Parameters:
t
- trajectory- Returns:
- medoid frame
-