public class Dynamics
extends java.lang.Object
Constructor and Description |
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Dynamics() |
Modifier and Type | Method and Description |
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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
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static Jama.Matrix |
getAtomicCorrelationMatrix(Trajectory t,
PointList reference)
Calculates the NxN atomic correlation matrix from a trajectory and a reference frame for superposition
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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
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static Jama.Matrix |
getAtomicCovarianceMatrix(Trajectory t,
PointList reference)
Calculates the NxN atomic covariance matrix from a trajectory and a reference frame for superposition
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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)
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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
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static Jama.Matrix |
getCoordinateCorrelationMatrix(Trajectory t,
PointList reference)
Calculates the 3Nx3N coordinate correlation matrix from a trajectory and a reference frame for superposition
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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
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static Jama.Matrix |
getCoordinateCovarianceMatrix(Trajectory t,
PointList reference)
Calculates the 3Nx3N coordinate covariance matrix from a trajectory and a reference frame for superposition
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static double |
getCovarianceMatrixOverlap(Jama.Matrix covariance1,
Jama.Matrix covariance2)
Calculates the covariance overlap of two covariance matrices
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static double |
getCovarianceMatrixOverlap(Jama.Matrix covariance1,
Jama.Matrix covariance2,
int N)
Calculates the covariance overlap of two covariance matrices
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static double |
getCovarianceMatrixOverlap(Trajectory t1,
Trajectory t2)
Calculates the covariance overlap from two trajectories
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static double |
getCovarianceMatrixOverlap(Trajectory t1,
Trajectory t2,
int N)
Calculates the covariance overlap from two trajectories
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static java.util.ArrayList<java.lang.Double> |
getCumulativeVariances(Jama.Matrix covariance)
Calculates the cumulative variance profile from a covariance matrix
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static java.util.ArrayList<java.lang.Double> |
getCumulativeVariances(Trajectory t)
Calculates the cumulative variance profile from a trajectory
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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.
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static double |
getEnsembleAveragedRMSD(Trajectory t1,
Trajectory t2)
Calculates the ensemble averaged RMSD between two conformational ensembles sampled in two trajectories
as defined by Br?schweiler, 2002
(Efficient RMSD measures for the comparison of two molecular ensembles, Proteins: Structure, Function, and Bioinformatics)
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static Jama.Matrix |
getFluctuationMatrix(Trajectory t)
Calculates the F fluctuation matrix (variances of distances) from a trajectory
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static Jama.Matrix |
getFluctuationMatrix(Trajectory t,
IndexSet indices)
Calculates the F fluctuation matrix (variances of distances) for a group of atoms
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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)
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static Jama.Matrix[] |
getPCA(Jama.Matrix covariance)
Calculates the principal components and the corresponding eigenvalues from a covariance matrix
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static Jama.Matrix[] |
getPCA(Trajectory t)
Calculates the principal components and the corresponding eigenvalues from a trajectory
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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
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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
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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
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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
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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
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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
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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
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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
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static double |
getRootMeanSquareInnerProduct(Trajectory t1,
Trajectory t2,
int N,
int M)
Calculates the root mean square inner product (RMSIP) from two trajectories
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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)
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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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public static Jama.Matrix getCoordinateCovarianceMatrix(Trajectory t, PointList reference)
t
- trajectoryreference
- reference framepublic static Jama.Matrix getAtomicCovarianceMatrix(Trajectory t, PointList reference)
t
- trajectoryreference
- reference framepublic static Jama.Matrix getCoordinateCorrelationMatrix(Trajectory t, PointList reference)
t
- trajectoryreference
- reference framepublic static Jama.Matrix getAtomicCorrelationMatrix(Trajectory t, PointList reference)
t
- trajectoryreference
- reference framepublic static Jama.Matrix getCoordinateCovarianceMatrix(Trajectory t)
t
- trajectorypublic static Jama.Matrix getAtomicCovarianceMatrix(Trajectory t)
t
- trajectorypublic static Jama.Matrix getCoordinateCorrelationMatrix(Trajectory t)
t
- trajectorypublic static Jama.Matrix getAtomicCorrelationMatrix(Trajectory t)
t
- trajectorypublic static Jama.Matrix[] getPCA(Jama.Matrix covariance)
covariance
- covariance matrixpublic static Jama.Matrix[] getPCA(Trajectory t)
t
- trajectorypublic static java.util.ArrayList<java.lang.Double> getCumulativeVariances(Trajectory t)
t
- trajectorypublic static java.util.ArrayList<java.lang.Double> getCumulativeVariances(Jama.Matrix covariance)
covariance
- covariance matrixpublic static double getRootMeanSquareInnerProduct(Jama.Matrix covariance1, Jama.Matrix covariance2, int N, int M)
covariance1
- first covariance matrixcovariance2
- second covariance matrixN
- number of principal components used from the first trajectoryM
- number of principal components used from the second trajectorypublic static double getRootMeanSquareInnerProduct(Trajectory t1, Trajectory t2, int N, int M)
t1
- first trajectoryt2
- second trajectoryN
- number of principal components used from the first trajectoryM
- number of principal components used from the second trajectorypublic static double getCovarianceMatrixOverlap(Jama.Matrix covariance1, Jama.Matrix covariance2, int N)
covariance1
- first covariance matrixcovariance2
- second covariance matrixN
- number of dimensions used in the calculationpublic static double getCovarianceMatrixOverlap(Jama.Matrix covariance1, Jama.Matrix covariance2)
covariance1
- first covariance matrixcovariance2
- second covariance matrixpublic static double getCovarianceMatrixOverlap(Trajectory t1, Trajectory t2, int N)
t1
- first trajectoryt2
- second trajectoryN
- number of dimensions used in the calculationpublic static double getCovarianceMatrixOverlap(Trajectory t1, Trajectory t2)
t1
- first trajectoryt2
- second trajectorypublic static Jama.Matrix getFluctuationMatrix(Trajectory t)
t
- trajectorypublic static Jama.Matrix getFluctuationMatrix(Trajectory t, IndexSet indices)
t
- trajectoryindices
- index set of atomspublic static double getFluctuationOfSubsets(Trajectory t, IndexSet set1, IndexSet set2)
t
- trajectoryset1
- first subsetset2
- second subsetpublic static java.util.ArrayList<java.lang.Double> getRMSFprofile(Trajectory t, PointList R)
t
- trajectoryR
- reference framepublic static java.util.ArrayList<java.lang.Double> getRMSFprofile(Trajectory t, Structure R)
t
- trajectoryR
- reference framepublic static java.util.ArrayList<java.lang.Double> getRMSFprofile(Trajectory t, IndexSet indicesT, Structure R, IndexSet indicesR)
t
- trajectoryindicesT
- index set of atoms used from the trajectoryR
- reference frameindicesR
- index set of atoms used from the reference framepublic static java.util.ArrayList<java.lang.Double> getRMSFprofile(Trajectory t, PointList R, PointList Q)
t
- trajectoryR
- reference frame to which all frames are superposedQ
- reference frame from which deviations are measuredpublic static java.util.ArrayList<java.lang.Double> getRMSFprofile(Trajectory t, Structure R, Structure Q)
t
- trajectoryR
- reference frame to which all frames are superposedQ
- reference frame from which deviations are measuredpublic static java.util.ArrayList<java.lang.Double> getRMSFaroundTheMeanProfile(Trajectory t, PointList R)
t
- trajectoryR
- reference framepublic static java.util.ArrayList<java.lang.Double> getRMSFaroundTheMeanProfile(Trajectory t, Structure R)
t
- trajectoryR
- reference framepublic static Jama.Matrix getDynamicalNetwork(Trajectory t, double cutoff, double frequency)
t
- trajectorycutoff
- distance cutoff for the calculation of contact matrixfrequency
- minimal frequency of frames in which two residues must be in contactpublic static double getStructuralRadius(Trajectory t)
t
- trajectorypublic static double getEnsembleAveragedRMSD(Trajectory t1, Trajectory t2)
t1
- first trajectoryt2
- second trajectorypublic static Jama.Matrix getContactProbabilityMap(Trajectory t, double cutoff)
t
- simulation trajectorycutoff
- distance cutoffpublic static java.util.ArrayList<Point3D> getTrajectoryOfAtom(Trajectory t, int atomindex)
t
- simulation trajectoryatomindex
- index of atom