Package jgromacs.analysis
Class Dynamics
- java.lang.Object
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- jgromacs.analysis.Dynamics
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public class Dynamics extends java.lang.Object
Collection of methods for analysing molecular motions
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Constructor Summary
Constructors Constructor Description Dynamics()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static Jama.Matrix
getAtomicCorrelationMatrix(Trajectory t)
Calculates the NxN atomic correlation matrix from a trajectory using its first frame as the reference frame for superpositionstatic Jama.Matrix
getAtomicCorrelationMatrix(Trajectory t, PointList reference)
Calculates the NxN atomic correlation matrix from a trajectory and a reference frame for superpositionstatic Jama.Matrix
getAtomicCovarianceMatrix(Trajectory t)
Calculates the NxN atomic covariance matrix from a trajectory using its first frame as the reference frame for superpositionstatic Jama.Matrix
getAtomicCovarianceMatrix(Trajectory t, PointList reference)
Calculates the NxN atomic covariance matrix from a trajectory and a reference frame for superpositionstatic Jama.Matrix
getContactProbabilityMap(Trajectory t, double cutoff)
Calculates the (residue) contact probability map for a trajectory as defined by Wei et al, 2009 (Residual Structure in Islet Amyloid Polypeptide Mediates Its Interactions with Soluble Insulin, Biochemistry)static Jama.Matrix
getCoordinateCorrelationMatrix(Trajectory t)
Calculates the 3Nx3N coordinate correlation matrix from a trajectory using its first frame as the reference frame for superpositionstatic Jama.Matrix
getCoordinateCorrelationMatrix(Trajectory t, PointList reference)
Calculates the 3Nx3N coordinate correlation matrix from a trajectory and a reference frame for superpositionstatic Jama.Matrix
getCoordinateCovarianceMatrix(Trajectory t)
Calculates the 3Nx3N coordinate covariance matrix from a trajectory using its first frame as the reference frame for superpositionstatic Jama.Matrix
getCoordinateCovarianceMatrix(Trajectory t, PointList reference)
Calculates the 3Nx3N coordinate covariance matrix from a trajectory and a reference frame for superpositionstatic double
getCovarianceMatrixOverlap(Jama.Matrix covariance1, Jama.Matrix covariance2)
Calculates the covariance overlap of two covariance matricesstatic double
getCovarianceMatrixOverlap(Jama.Matrix covariance1, Jama.Matrix covariance2, int N)
Calculates the covariance overlap of two covariance matricesstatic double
getCovarianceMatrixOverlap(Trajectory t1, Trajectory t2)
Calculates the covariance overlap from two trajectoriesstatic double
getCovarianceMatrixOverlap(Trajectory t1, Trajectory t2, int N)
Calculates the covariance overlap from two trajectoriesstatic java.util.ArrayList<java.lang.Double>
getCumulativeVariances(Jama.Matrix covariance)
Calculates the cumulative variance profile from a covariance matrixstatic java.util.ArrayList<java.lang.Double>
getCumulativeVariances(Trajectory t)
Calculates the cumulative variance profile from a trajectorystatic Jama.Matrix
getDynamicalNetwork(Trajectory t, double cutoff, double frequency)
Calculates the dynamical network of a protein according to the definition of Sethi et al.static double
getEnsembleAveragedRMSD(Trajectory t1, Trajectory t2)
Calculates the ensemble averaged RMSD between two conformational ensembles sampled in two trajectories as defined by Brüschweiler, 2002 (Efficient RMSD measures for the comparison of two molecular ensembles, Proteins: Structure, Function, and Bioinformatics)static Jama.Matrix
getFluctuationMatrix(Trajectory t)
Calculates the F fluctuation matrix (variances of distances) from a trajectorystatic Jama.Matrix
getFluctuationMatrix(Trajectory t, IndexSet indices)
Calculates the F fluctuation matrix (variances of distances) for a group of atomsstatic double
getFluctuationOfSubsets(Trajectory t, IndexSet set1, IndexSet set2)
Calculates the fluctuation between two subsets of atoms defined as the mean of entries of the selected submatrix of matrix F (fluctuation matrix)static Jama.Matrix[]
getPCA(Jama.Matrix covariance)
Calculates the principal components and the corresponding eigenvalues from a covariance matrixstatic Jama.Matrix[]
getPCA(Trajectory t)
Calculates the principal components and the corresponding eigenvalues from a trajectorystatic java.util.ArrayList<java.lang.Double>
getRMSFaroundTheMeanProfile(Trajectory t, PointList R)
Calculates the RMSF profile from a trajectory by superposing all frames to a reference frame R and calculating the RMSDi deviations with regards to the mean structurestatic java.util.ArrayList<java.lang.Double>
getRMSFaroundTheMeanProfile(Trajectory t, Structure R)
Calculates the RMSF profile from a trajectory by superposing all frames to a reference frame R and calculating the RMSDi deviations with regards to the mean structurestatic java.util.ArrayList<java.lang.Double>
getRMSFprofile(Trajectory t, IndexSet indicesT, Structure R, IndexSet indicesR)
Calculates the RMSF profile of a group of atoms from a trajectory and a reference frame for superpositionstatic java.util.ArrayList<java.lang.Double>
getRMSFprofile(Trajectory t, PointList R)
Calculates the RMSF profile from a trajectory and a reference frame for superpositionstatic java.util.ArrayList<java.lang.Double>
getRMSFprofile(Trajectory t, PointList R, PointList Q)
Calculates the RMSF profile from a trajectory by superposing all frames to a reference frame R and calculating the RMSDi deviations with regards to a reference frame Qstatic java.util.ArrayList<java.lang.Double>
getRMSFprofile(Trajectory t, Structure R)
Calculates the RMSF profile from a trajectory and a reference frame for superpositionstatic java.util.ArrayList<java.lang.Double>
getRMSFprofile(Trajectory t, Structure R, Structure Q)
Calculates the RMSF profile from a trajectory by superposing all frames to a reference frame R and calculating the RMSDi deviations with regards to a reference frame Qstatic double
getRootMeanSquareInnerProduct(Jama.Matrix covariance1, Jama.Matrix covariance2, int N, int M)
Calculates the root mean square inner product (RMSIP) from two covariance matricesstatic double
getRootMeanSquareInnerProduct(Trajectory t1, Trajectory t2, int N, int M)
Calculates the root mean square inner product (RMSIP) from two trajectoriesstatic double
getStructuralRadius(Trajectory t)
Calculates the structural radius of the conformational ensemble sampled in the trajectory as defined by Kuzmanic and Zagrovic, 2010 (Determination of Ensemble-Average Pairwise Root Mean-Square Deviation from Experimental B-Factors, Biophysical Journal)static java.util.ArrayList<Point3D>
getTrajectoryOfAtom(Trajectory t, int atomindex)
Returns the trajectory of a single atom in the course of the simulation
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Method Detail
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getCoordinateCovarianceMatrix
public static Jama.Matrix getCoordinateCovarianceMatrix(Trajectory t, PointList reference)
Calculates the 3Nx3N coordinate covariance matrix from a trajectory and a reference frame for superposition- Parameters:
t
- trajectoryreference
- reference frame- Returns:
- coordinate covariance matrix
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getAtomicCovarianceMatrix
public static Jama.Matrix getAtomicCovarianceMatrix(Trajectory t, PointList reference)
Calculates the NxN atomic covariance matrix from a trajectory and a reference frame for superposition- Parameters:
t
- trajectoryreference
- reference frame- Returns:
- atomic covariance matrix
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getCoordinateCorrelationMatrix
public static Jama.Matrix getCoordinateCorrelationMatrix(Trajectory t, PointList reference)
Calculates the 3Nx3N coordinate correlation matrix from a trajectory and a reference frame for superposition- Parameters:
t
- trajectoryreference
- reference frame- Returns:
- coordinate correlation matrix
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getAtomicCorrelationMatrix
public static Jama.Matrix getAtomicCorrelationMatrix(Trajectory t, PointList reference)
Calculates the NxN atomic correlation matrix from a trajectory and a reference frame for superposition- Parameters:
t
- trajectoryreference
- reference frame- Returns:
- atomic correlation matrix
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getCoordinateCovarianceMatrix
public static Jama.Matrix getCoordinateCovarianceMatrix(Trajectory t)
Calculates the 3Nx3N coordinate covariance matrix from a trajectory using its first frame as the reference frame for superposition- Parameters:
t
- trajectory- Returns:
- coordinate covariance matrix
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getAtomicCovarianceMatrix
public static Jama.Matrix getAtomicCovarianceMatrix(Trajectory t)
Calculates the NxN atomic covariance matrix from a trajectory using its first frame as the reference frame for superposition- Parameters:
t
- trajectory- Returns:
- atomic covariance matrix
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getCoordinateCorrelationMatrix
public static Jama.Matrix getCoordinateCorrelationMatrix(Trajectory t)
Calculates the 3Nx3N coordinate correlation matrix from a trajectory using its first frame as the reference frame for superposition- Parameters:
t
- trajectory- Returns:
- coordinate correlation matrix
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getAtomicCorrelationMatrix
public static Jama.Matrix getAtomicCorrelationMatrix(Trajectory t)
Calculates the NxN atomic correlation matrix from a trajectory using its first frame as the reference frame for superposition- Parameters:
t
- trajectory- Returns:
- atomic correlation matrix
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getPCA
public static Jama.Matrix[] getPCA(Jama.Matrix covariance)
Calculates the principal components and the corresponding eigenvalues from a covariance matrix- Parameters:
covariance
- covariance matrix- Returns:
- a Matrix array containing D (block diagonal eigenvalue matrix) and V (principal component matrix)
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getPCA
public static Jama.Matrix[] getPCA(Trajectory t)
Calculates the principal components and the corresponding eigenvalues from a trajectory- Parameters:
t
- trajectory- Returns:
- a Matrix array containing D (block diagonal eigenvalue matrix) and V (principal component matrix)
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getCumulativeVariances
public static java.util.ArrayList<java.lang.Double> getCumulativeVariances(Trajectory t)
Calculates the cumulative variance profile from a trajectory- Parameters:
t
- trajectory- Returns:
- cumulative variance profile
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getCumulativeVariances
public static java.util.ArrayList<java.lang.Double> getCumulativeVariances(Jama.Matrix covariance)
Calculates the cumulative variance profile from a covariance matrix- Parameters:
covariance
- covariance matrix- Returns:
- cumulative variance profile
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getRootMeanSquareInnerProduct
public static double getRootMeanSquareInnerProduct(Jama.Matrix covariance1, Jama.Matrix covariance2, int N, int M)
Calculates the root mean square inner product (RMSIP) from two covariance matrices- Parameters:
covariance1
- first covariance matrixcovariance2
- second covariance matrixN
- number of principal components used from the first trajectoryM
- number of principal components used from the second trajectory- Returns:
- root mean square inner product (RMSIP)
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getRootMeanSquareInnerProduct
public static double getRootMeanSquareInnerProduct(Trajectory t1, Trajectory t2, int N, int M)
Calculates the root mean square inner product (RMSIP) from two trajectories- Parameters:
t1
- first trajectoryt2
- second trajectoryN
- number of principal components used from the first trajectoryM
- number of principal components used from the second trajectory- Returns:
- root mean square inner product (RMSIP)
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getCovarianceMatrixOverlap
public static double getCovarianceMatrixOverlap(Jama.Matrix covariance1, Jama.Matrix covariance2, int N)
Calculates the covariance overlap of two covariance matrices- Parameters:
covariance1
- first covariance matrixcovariance2
- second covariance matrixN
- number of dimensions used in the calculation- Returns:
- covariance overlap
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getCovarianceMatrixOverlap
public static double getCovarianceMatrixOverlap(Jama.Matrix covariance1, Jama.Matrix covariance2)
Calculates the covariance overlap of two covariance matrices- Parameters:
covariance1
- first covariance matrixcovariance2
- second covariance matrix- Returns:
- covariance overlap
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getCovarianceMatrixOverlap
public static double getCovarianceMatrixOverlap(Trajectory t1, Trajectory t2, int N)
Calculates the covariance overlap from two trajectories- Parameters:
t1
- first trajectoryt2
- second trajectoryN
- number of dimensions used in the calculation- Returns:
- covariance overlap
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getCovarianceMatrixOverlap
public static double getCovarianceMatrixOverlap(Trajectory t1, Trajectory t2)
Calculates the covariance overlap from two trajectories- Parameters:
t1
- first trajectoryt2
- second trajectory- Returns:
- covariance overlap
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getFluctuationMatrix
public static Jama.Matrix getFluctuationMatrix(Trajectory t)
Calculates the F fluctuation matrix (variances of distances) from a trajectory- Parameters:
t
- trajectory- Returns:
- F fluctuation matrix
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getFluctuationMatrix
public static Jama.Matrix getFluctuationMatrix(Trajectory t, IndexSet indices)
Calculates the F fluctuation matrix (variances of distances) for a group of atoms- Parameters:
t
- trajectoryindices
- index set of atoms- Returns:
- F fluctuation matrix
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getFluctuationOfSubsets
public static double getFluctuationOfSubsets(Trajectory t, IndexSet set1, IndexSet set2)
Calculates the fluctuation between two subsets of atoms defined as the mean of entries of the selected submatrix of matrix F (fluctuation matrix)- Parameters:
t
- trajectoryset1
- first subsetset2
- second subset- Returns:
- fluctuation between the two atom sets
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getRMSFprofile
public static java.util.ArrayList<java.lang.Double> getRMSFprofile(Trajectory t, PointList R)
Calculates the RMSF profile from a trajectory and a reference frame for superposition- Parameters:
t
- trajectoryR
- reference frame- Returns:
- RMSF profile
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getRMSFprofile
public static java.util.ArrayList<java.lang.Double> getRMSFprofile(Trajectory t, Structure R)
Calculates the RMSF profile from a trajectory and a reference frame for superposition- Parameters:
t
- trajectoryR
- reference frame- Returns:
- RMSF profile
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getRMSFprofile
public static java.util.ArrayList<java.lang.Double> getRMSFprofile(Trajectory t, IndexSet indicesT, Structure R, IndexSet indicesR)
Calculates the RMSF profile of a group of atoms from a trajectory and a reference frame for superposition- Parameters:
t
- trajectoryindicesT
- index set of atoms used from the trajectoryR
- reference frameindicesR
- index set of atoms used from the reference frame- Returns:
- RMSF profile
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getRMSFprofile
public static java.util.ArrayList<java.lang.Double> getRMSFprofile(Trajectory t, PointList R, PointList Q)
Calculates the RMSF profile from a trajectory by superposing all frames to a reference frame R and calculating the RMSDi deviations with regards to a reference frame Q- Parameters:
t
- trajectoryR
- reference frame to which all frames are superposedQ
- reference frame from which deviations are measured- Returns:
- RMSF profile
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getRMSFprofile
public static java.util.ArrayList<java.lang.Double> getRMSFprofile(Trajectory t, Structure R, Structure Q)
Calculates the RMSF profile from a trajectory by superposing all frames to a reference frame R and calculating the RMSDi deviations with regards to a reference frame Q- Parameters:
t
- trajectoryR
- reference frame to which all frames are superposedQ
- reference frame from which deviations are measured- Returns:
- RMSF profile
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getRMSFaroundTheMeanProfile
public static java.util.ArrayList<java.lang.Double> getRMSFaroundTheMeanProfile(Trajectory t, PointList R)
Calculates the RMSF profile from a trajectory by superposing all frames to a reference frame R and calculating the RMSDi deviations with regards to the mean structure- Parameters:
t
- trajectoryR
- reference frame- Returns:
- RMSF profile
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getRMSFaroundTheMeanProfile
public static java.util.ArrayList<java.lang.Double> getRMSFaroundTheMeanProfile(Trajectory t, Structure R)
Calculates the RMSF profile from a trajectory by superposing all frames to a reference frame R and calculating the RMSDi deviations with regards to the mean structure- Parameters:
t
- trajectoryR
- reference frame- Returns:
- RMSF profile
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getDynamicalNetwork
public static Jama.Matrix getDynamicalNetwork(Trajectory t, double cutoff, double frequency)
Calculates the dynamical network of a protein according to the definition of Sethi et al. 2009 (Dynamical networks in tRNA:protein complexes, PNAS)- Parameters:
t
- trajectorycutoff
- distance cutoff for the calculation of contact matrixfrequency
- minimal frequency of frames in which two residues must be in contact- Returns:
- weighted adjacency matrix of dynamical network
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getStructuralRadius
public static double getStructuralRadius(Trajectory t)
Calculates the structural radius of the conformational ensemble sampled in the trajectory as defined by Kuzmanic and Zagrovic, 2010 (Determination of Ensemble-Average Pairwise Root Mean-Square Deviation from Experimental B-Factors, Biophysical Journal)- Parameters:
t
- trajectory- Returns:
- structural radius
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getEnsembleAveragedRMSD
public static double getEnsembleAveragedRMSD(Trajectory t1, Trajectory t2)
Calculates the ensemble averaged RMSD between two conformational ensembles sampled in two trajectories as defined by Brüschweiler, 2002 (Efficient RMSD measures for the comparison of two molecular ensembles, Proteins: Structure, Function, and Bioinformatics)- Parameters:
t1
- first trajectoryt2
- second trajectory- Returns:
- ensemble averaged RMSD
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getContactProbabilityMap
public static Jama.Matrix getContactProbabilityMap(Trajectory t, double cutoff)
Calculates the (residue) contact probability map for a trajectory as defined by Wei et al, 2009 (Residual Structure in Islet Amyloid Polypeptide Mediates Its Interactions with Soluble Insulin, Biochemistry)- Parameters:
t
- simulation trajectorycutoff
- distance cutoff- Returns:
- contact probability matrix
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getTrajectoryOfAtom
public static java.util.ArrayList<Point3D> getTrajectoryOfAtom(Trajectory t, int atomindex)
Returns the trajectory of a single atom in the course of the simulation- Parameters:
t
- simulation trajectoryatomindex
- index of atom- Returns:
- atomic trajectory as an ArrayList of coordinates
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