Package jgromacs.analysis
Class Similarity
- java.lang.Object
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- jgromacs.analysis.Similarity
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public class Similarity extends java.lang.Object
Collection of methods for measuring structural similarity
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Constructor Summary
Constructors Constructor Description Similarity()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description 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 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
getDifferenceDistanceMatrix(Structure s1, Structure s2)
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
getDRMSD(PointList A, PointList B)
Calculates dRMSD similarity between two point listsstatic double
getDRMSD(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB)
Calculates dRMSD similarity between two groups of atomsstatic double
getDRMSD(Structure A, Structure B)
Calculates dRMSD similarity between two structuresstatic java.util.ArrayList<java.lang.Double>
getDRMSDiProfile(Jama.Matrix A, Jama.Matrix B)
Calculates the dRMSDi profile between two distance matricesstatic java.util.ArrayList<java.lang.Double>
getDRMSDiProfile(PointList A, PointList B)
Calculates the dRMSDi profile between two point listsstatic java.util.ArrayList<java.lang.Double>
getDRMSDiProfile(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB)
Calculates the dRMSDi profile between two groups of atomsstatic java.util.ArrayList<java.lang.Double>
getDRMSDiProfile(Structure A, Structure B)
Calculates the dRMSDi profile between two structuresstatic PointList
getMedoidDRMSD(Trajectory t)
Calculates the medoid frame of a trajectory using the dRMSD measurestatic PointList
getMedoidRMSD(Trajectory t)
Calculates the medoid frame of a trajectory using the RMSD measurestatic double
getRMSD(PointList A, PointList B)
Calculates RMSD similarity between two point listsstatic double
getRMSD(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB)
Calculates RMSD similarity between two groups of atomsstatic double
getRMSD(Structure A, Structure B)
Calculates RMSD similarity between two structuresstatic java.util.ArrayList<java.lang.Double>
getRMSDiProfile(PointList A, PointList B)
Calculates the RMSDi profile between two point listsstatic java.util.ArrayList<java.lang.Double>
getRMSDiProfile(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB)
Calculates the RMSDi profile between two groups of atomsstatic java.util.ArrayList<java.lang.Double>
getRMSDiProfile(Structure A, Structure B)
Calculates the RMSDi profile between two structuresstatic java.util.ArrayList<java.lang.Double>
getRMSDiProfileNoSuperposition(PointList A, PointList B)
Calculates the RMSDi profile between two point lists without superpositionstatic 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 superpositionstatic java.util.ArrayList<java.lang.Double>
getRMSDiProfileNoSuperposition(Structure A, Structure B)
Calculates the RMSDi profile between two structures without superpositionstatic double
getRMSDnoSuperposition(PointList A, PointList B)
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
getRMSDnoSuperposition(Structure A, Structure B)
Calculates RMSD similarity between two structures without doing superpositionstatic Jama.Matrix
getSimilarityMatrixDRMSD(Trajectory t)
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
getSimilarityMatrixRMSD(Trajectory t)
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 atomsstatic 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 atomsstatic 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 liststatic 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 structurestatic 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 atomsstatic 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 liststatic 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 structurestatic 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 atomsstatic 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 liststatic 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 structurestatic double
getWDRMSD(PointList A, PointList B, Jama.Matrix W)
Calculates the wdRMSD (weighted dRMSD) similarity of two point listsstatic double
getWDRMSD(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB, Jama.Matrix W)
Calculates wdRMSD (weighted dRMSD) similarity between two groups of atomsstatic double
getWDRMSD(Structure A, Structure B, Jama.Matrix W)
Calculates the wdRMSD (weighted dRMSD) similarity of two structuresstatic java.util.ArrayList<java.lang.Double>
getWDRMSDiProfile(PointList A, PointList B, Jama.Matrix W)
Calculates the wdRMSDi (weighted dRMSDi) profile between two point listsstatic 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 atomsstatic java.util.ArrayList<java.lang.Double>
getWDRMSDiProfile(Structure A, Structure B, Jama.Matrix W)
Calculates the wdRMSDi (weighted dRMSDi) profile between two structures
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Method Detail
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getRMSD
public static double getRMSD(PointList A, PointList B)
Calculates RMSD similarity between two point lists- Parameters:
A
- first point listB
- second point list- Returns:
- RMSD
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getRMSD
public static double getRMSD(Structure A, Structure B)
Calculates RMSD similarity between two structures- Parameters:
A
- first structureB
- second structure- Returns:
- RMSD
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getRMSD
public static double getRMSD(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB)
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
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getRMSDiProfile
public static java.util.ArrayList<java.lang.Double> getRMSDiProfile(PointList A, PointList B)
Calculates the RMSDi profile between two point lists- Parameters:
A
- first point listB
- second point list- Returns:
- RMSDi profile
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getRMSDiProfile
public static java.util.ArrayList<java.lang.Double> getRMSDiProfile(Structure A, Structure B)
Calculates the RMSDi profile between two structures- Parameters:
A
- first structureB
- second structure- Returns:
- RMSDi profile
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getRMSDiProfile
public 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- 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
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getRMSDnoSuperposition
public static double getRMSDnoSuperposition(PointList A, PointList B)
Calculates RMSD similarity between two point lists without doing superposition- Parameters:
A
- first point listB
- second point list- Returns:
- RMSD without superposition
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getRMSDnoSuperposition
public static double getRMSDnoSuperposition(Structure A, Structure B)
Calculates RMSD similarity between two structures without doing superposition- Parameters:
A
- first structureB
- second structure- Returns:
- RMSD without superposition
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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
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getRMSDiProfileNoSuperposition
public static java.util.ArrayList<java.lang.Double> getRMSDiProfileNoSuperposition(PointList A, PointList B)
Calculates the RMSDi profile between two point lists without superposition- Parameters:
A
- first point listB
- second point list- Returns:
- RMSDi profile without superposition
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getRMSDiProfileNoSuperposition
public static java.util.ArrayList<java.lang.Double> getRMSDiProfileNoSuperposition(Structure A, Structure B)
Calculates the RMSDi profile between two structures without superposition- Parameters:
A
- first structureB
- second structure- Returns:
- RMSDi profile without superposition
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getRMSDiProfileNoSuperposition
public 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- 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
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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
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getDRMSD
public static double getDRMSD(PointList A, PointList B)
Calculates dRMSD similarity between two point lists- Parameters:
A
- first point listB
- second point list- Returns:
- dRMSD
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getDRMSD
public static double getDRMSD(Structure A, Structure B)
Calculates dRMSD similarity between two structures- Parameters:
A
- first structureB
- second structure- Returns:
- dRMSD
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getDRMSD
public static double getDRMSD(Structure A, IndexSet indicesA, Structure B, IndexSet indicesB)
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
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getDRMSDiProfile
public static java.util.ArrayList<java.lang.Double> getDRMSDiProfile(Jama.Matrix A, Jama.Matrix B)
Calculates the dRMSDi profile between two distance matrices- Parameters:
A
- first distance matrixB
- second distance matrix- Returns:
- dRMSDi profile
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getDRMSDiProfile
public static java.util.ArrayList<java.lang.Double> getDRMSDiProfile(PointList A, PointList B)
Calculates the dRMSDi profile between two point lists- Parameters:
A
- first point listB
- second point list- Returns:
- dRMSDi profile
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getDRMSDiProfile
public static java.util.ArrayList<java.lang.Double> getDRMSDiProfile(Structure A, Structure B)
Calculates the dRMSDi profile between two structures- Parameters:
A
- first structureB
- second structure- Returns:
- dRMSDi profile
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getDRMSDiProfile
public 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- 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
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getWDRMSD
public static double getWDRMSD(PointList A, PointList B, Jama.Matrix W)
Calculates the wdRMSD (weighted dRMSD) similarity of two point lists- Parameters:
A
- first point listB
- second point listW
- weight matrix- Returns:
- wdRMSD
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getWDRMSD
public static double getWDRMSD(Structure A, Structure B, Jama.Matrix W)
Calculates the wdRMSD (weighted dRMSD) similarity of two structures- Parameters:
A
- first structureB
- second structureW
- weight matrix- Returns:
- wdRMSD
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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
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getWDRMSDiProfile
public 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- Parameters:
A
- first point listB
- second point listW
- weight matrix- Returns:
- wdRMSDi profile
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getWDRMSDiProfile
public static java.util.ArrayList<java.lang.Double> getWDRMSDiProfile(Structure A, Structure B, Jama.Matrix W)
Calculates the wdRMSDi (weighted dRMSDi) profile between two structures- Parameters:
A
- first structureB
- second structureW
- weight matrix- Returns:
- wdRMSDi profile
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getWDRMSDiProfile
public 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- 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
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getSimilarityMatrixRMSD
public static Jama.Matrix getSimilarityMatrixRMSD(Trajectory t)
Calculates the similarity matrix of all frames in a trajectory using the RMSD measure- Parameters:
t
- trajectory- Returns:
- similarity matrix
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getSimilarityMatrixRMSD
public 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- Parameters:
t
- trajectoryindices
- index set of atoms- Returns:
- similarity matrix
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getSimilarityMatrixDRMSD
public static Jama.Matrix getSimilarityMatrixDRMSD(Trajectory t)
Calculates the similarity matrix of all frames in a trajectory using the dRMSD measure- Parameters:
t
- trajectory- Returns:
- similarity matrix
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getSimilarityMatrixDRMSD
public 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- Parameters:
t
- trajectoryindices
- index set of atoms- Returns:
- similarity matrix
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getSimilarityMatrixWDRMSD
public 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- Parameters:
t
- trajectoryW
- weight matrix- Returns:
- similarity matrix
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getSimilarityMatrixWDRMSD
public 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- Parameters:
t
- trajectoryindices
- index set of atomsW
- weight matrix- Returns:
- similarity matrix
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getSimilarityTimeSeriesRMSD
public 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- Parameters:
t
- trajectoryR
- reference point list- Returns:
- time series of RMSD
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getSimilarityTimeSeriesRMSD
public 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- Parameters:
t
- trajectoryR
- reference structure- Returns:
- time series of RMSD
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getSimilarityTimeSeriesRMSD
public 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- 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
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getSimilarityTimeSeriesDRMSD
public 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- Parameters:
t
- trajectoryR
- reference point list- Returns:
- time series of dRMSD
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getSimilarityTimeSeriesDRMSD
public 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- Parameters:
t
- trajectoryR
- reference structure- Returns:
- time series of dRMSD
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getSimilarityTimeSeriesDRMSD
public 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- 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
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getSimilarityTimeSeriesWDRMSD
public 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- Parameters:
t
- trajectoryR
- reference point listW
- weight matrix- Returns:
- time series of wdRMSD
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getSimilarityTimeSeriesWDRMSD
public 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- Parameters:
t
- trajectoryR
- reference structureW
- weight matrix- Returns:
- time series of wdRMSD
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getSimilarityTimeSeriesWDRMSD
public 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- 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
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getDifferenceDistanceMatrix
public static Jama.Matrix getDifferenceDistanceMatrix(PointList points1, PointList points2)
Calculates the difference distance matrix between two point lists- Parameters:
points1
- first point listpoints2
- second point list- Returns:
- difference distance matrix
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getDifferenceDistanceMatrix
public static Jama.Matrix getDifferenceDistanceMatrix(Structure s1, Structure s2)
Calculates the atomic difference distance matrix between two structures- Parameters:
s1
- first structures2
- second structure- Returns:
- difference distance matrix
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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
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findSimilarFramesRMSD
public 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- Parameters:
t
- trajectoryreference
- reference framecutoff
- similarity cutoff- Returns:
- frame index set
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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
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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
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getMedoidRMSD
public static PointList getMedoidRMSD(Trajectory t)
Calculates the medoid frame of a trajectory using the RMSD measure- Parameters:
t
- trajectory- Returns:
- medoid frame
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getMedoidDRMSD
public static PointList getMedoidDRMSD(Trajectory t)
Calculates the medoid frame of a trajectory using the dRMSD measure- Parameters:
t
- trajectory- Returns:
- medoid frame
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