Class Dynamics


  • public class Dynamics
    extends java.lang.Object
    Collection of methods for analysing molecular motions
    • Constructor Summary

      Constructors 
      Constructor Description
      Dynamics()  
    • 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 superposition
      static Jama.Matrix getAtomicCorrelationMatrix​(Trajectory t, PointList reference)
      Calculates the NxN atomic correlation matrix from a trajectory and a reference frame for superposition
      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
      static Jama.Matrix getAtomicCovarianceMatrix​(Trajectory t, PointList reference)
      Calculates the NxN atomic covariance matrix from a trajectory and a reference frame for superposition
      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)
      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
      static Jama.Matrix getCoordinateCorrelationMatrix​(Trajectory t, PointList reference)
      Calculates the 3Nx3N coordinate correlation matrix from a trajectory and a reference frame for superposition
      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
      static Jama.Matrix getCoordinateCovarianceMatrix​(Trajectory t, PointList reference)
      Calculates the 3Nx3N coordinate covariance matrix from a trajectory and a reference frame for superposition
      static double getCovarianceMatrixOverlap​(Jama.Matrix covariance1, Jama.Matrix covariance2)
      Calculates the covariance overlap of two covariance matrices
      static double getCovarianceMatrixOverlap​(Jama.Matrix covariance1, Jama.Matrix covariance2, int N)
      Calculates the covariance overlap of two covariance matrices
      static double getCovarianceMatrixOverlap​(Trajectory t1, Trajectory t2)
      Calculates the covariance overlap from two trajectories
      static double getCovarianceMatrixOverlap​(Trajectory t1, Trajectory t2, int N)
      Calculates the covariance overlap from two trajectories
      static java.util.ArrayList<java.lang.Double> getCumulativeVariances​(Jama.Matrix covariance)
      Calculates the cumulative variance profile from a covariance matrix
      static java.util.ArrayList<java.lang.Double> getCumulativeVariances​(Trajectory t)
      Calculates the cumulative variance profile from a trajectory
      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.
      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 trajectory
      static Jama.Matrix getFluctuationMatrix​(Trajectory t, IndexSet indices)
      Calculates the F fluctuation matrix (variances of distances) for a group of atoms
      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)
      static Jama.Matrix[] getPCA​(Jama.Matrix covariance)
      Calculates the principal components and the corresponding eigenvalues from a covariance matrix
      static Jama.Matrix[] getPCA​(Trajectory t)
      Calculates the principal components and the corresponding eigenvalues from a trajectory
      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
      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
      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
      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
      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
      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
      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
      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
      static double getRootMeanSquareInnerProduct​(Trajectory t1, Trajectory t2, int N, int M)
      Calculates the root mean square inner product (RMSIP) from two trajectories
      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)
      static java.util.ArrayList<Point3D> getTrajectoryOfAtom​(Trajectory t, int atomindex)
      Returns the trajectory of a single atom in the course of the simulation
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • Dynamics

        public Dynamics()
    • Method Detail

      • 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 - trajectory
        reference - reference frame
        Returns:
        coordinate covariance matrix
      • 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 - trajectory
        reference - reference frame
        Returns:
        atomic covariance matrix
      • 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 - trajectory
        reference - reference frame
        Returns:
        coordinate correlation matrix
      • 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 - trajectory
        reference - reference frame
        Returns:
        atomic correlation matrix
      • 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
      • 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
      • 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
      • 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
      • 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)
      • 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)
      • 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
      • 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
      • 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 matrix
        covariance2 - second covariance matrix
        N - number of principal components used from the first trajectory
        M - number of principal components used from the second trajectory
        Returns:
        root mean square inner product (RMSIP)
      • 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 trajectory
        t2 - second trajectory
        N - number of principal components used from the first trajectory
        M - number of principal components used from the second trajectory
        Returns:
        root mean square inner product (RMSIP)
      • 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 matrix
        covariance2 - second covariance matrix
        N - number of dimensions used in the calculation
        Returns:
        covariance overlap
      • getCovarianceMatrixOverlap

        public static double getCovarianceMatrixOverlap​(Jama.Matrix covariance1,
                                                        Jama.Matrix covariance2)
        Calculates the covariance overlap of two covariance matrices
        Parameters:
        covariance1 - first covariance matrix
        covariance2 - second covariance matrix
        Returns:
        covariance overlap
      • getCovarianceMatrixOverlap

        public static double getCovarianceMatrixOverlap​(Trajectory t1,
                                                        Trajectory t2,
                                                        int N)
        Calculates the covariance overlap from two trajectories
        Parameters:
        t1 - first trajectory
        t2 - second trajectory
        N - number of dimensions used in the calculation
        Returns:
        covariance overlap
      • getCovarianceMatrixOverlap

        public static double getCovarianceMatrixOverlap​(Trajectory t1,
                                                        Trajectory t2)
        Calculates the covariance overlap from two trajectories
        Parameters:
        t1 - first trajectory
        t2 - second trajectory
        Returns:
        covariance overlap
      • 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
      • 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 - trajectory
        indices - index set of atoms
        Returns:
        F fluctuation matrix
      • 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 - trajectory
        set1 - first subset
        set2 - second subset
        Returns:
        fluctuation between the two atom sets
      • 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 - trajectory
        R - reference frame
        Returns:
        RMSF profile
      • 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 - trajectory
        R - reference frame
        Returns:
        RMSF profile
      • 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 - trajectory
        indicesT - index set of atoms used from the trajectory
        R - reference frame
        indicesR - index set of atoms used from the reference frame
        Returns:
        RMSF profile
      • 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 - trajectory
        R - reference frame to which all frames are superposed
        Q - reference frame from which deviations are measured
        Returns:
        RMSF profile
      • 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 - trajectory
        R - reference frame to which all frames are superposed
        Q - reference frame from which deviations are measured
        Returns:
        RMSF profile
      • 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 - trajectory
        R - reference frame
        Returns:
        RMSF profile
      • 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 - trajectory
        R - reference frame
        Returns:
        RMSF profile
      • 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 - trajectory
        cutoff - distance cutoff for the calculation of contact matrix
        frequency - minimal frequency of frames in which two residues must be in contact
        Returns:
        weighted adjacency matrix of dynamical network
      • 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
      • 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 trajectory
        t2 - second trajectory
        Returns:
        ensemble averaged RMSD
      • 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 trajectory
        cutoff - distance cutoff
        Returns:
        contact probability matrix
      • 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 trajectory
        atomindex - index of atom
        Returns:
        atomic trajectory as an ArrayList of coordinates