Class Dynamics

java.lang.Object
jgromacs.analysis.Dynamics

public class Dynamics extends Object
Collection of methods for analysing molecular motions
  • Constructor Details

    • Dynamics

      public Dynamics()
  • Method Details

    • 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 ArrayList<Double> getCumulativeVariances(Trajectory t)
      Calculates the cumulative variance profile from a trajectory
      Parameters:
      t - trajectory
      Returns:
      cumulative variance profile
    • getCumulativeVariances

      public static ArrayList<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 ArrayList<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 ArrayList<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 ArrayList<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 ArrayList<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 ArrayList<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 ArrayList<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 ArrayList<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 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