## Uses of Classjgromacs.data.Trajectory

Packages that use Trajectory
jgromacs.analysis jgromacs.analysis is a collection of classes providing static methods for various analysis tasks
jgromacs.data jgromacs.data is a collection of classes representing multiple levels of structural data
jgromacs.io jgromacs.io provides parsers for reading and methods for writing GROMACS files

Uses of Trajectory in jgromacs.analysis

Methods in jgromacs.analysis that return Trajectory
`static Trajectory` ```Superposition.superposeTo(Trajectory t, PointList reference)```
Calculates the superposition of each frame of a trajectory to a common reference frame
`static Trajectory` ```Superposition.superposeTo(Trajectory t, Structure reference)```
Calculates the superposition of each frame of a trajectory to a common reference frame
`static Trajectory` ```Superposition.superposeTo(Trajectory t, Structure reference, IndexSet indices)```
Calculates the superposition of each frame of a trajectory to a common reference frame using a subset of atoms for fitting
`static Trajectory` ```Superposition.weightedSuperposeTo(Trajectory t, PointList reference, java.util.ArrayList<java.lang.Double> weights)```
Calculates the weighted superposition of each frame of a trajectory to a common reference frame
`static Trajectory` ```Superposition.weightedSuperposeTo(Trajectory t, Structure reference, java.util.ArrayList<java.lang.Double> weights)```
Calculates the weighted superposition of each frame of a trajectory to a common reference frame

Methods in jgromacs.analysis with parameters of type Trajectory
`static PointList` ```Distances.findFrameWhereClosest(Trajectory t, int atomindex1, int atomindex2)```
Returns the frame in which two atoms are closest to each other in a simulation
`static PointList` ```Distances.findFrameWhereMostDistant(Trajectory t, int atomindex1, int atomindex2)```
Returns the frame in which two atoms are most distant from each other in a simulation
`static FrameIndexSet` ```Similarity.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
`static FrameIndexSet` ```Similarity.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
`static FrameIndexSet` ```Similarity.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
`static jama.Matrix` `Dynamics.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` ```Dynamics.getAtomicCorrelationMatrix(Trajectory t, PointList reference)```
Calculates the NxN atomic correlation matrix from a trajectory and a reference frame for superposition
`static jama.Matrix` `Dynamics.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` ```Dynamics.getAtomicCovarianceMatrix(Trajectory t, PointList reference)```
Calculates the NxN atomic covariance matrix from a trajectory and a reference frame for superposition
`static jama.Matrix` ```Distances.getContactOfMeanMatrix(Trajectory t, int distanceBetween, double cutoff)```
Calculates the contact matrix based on the mean residue distance matrix in a trajectory
`static jama.Matrix` ```Dynamics.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` `Dynamics.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` ```Dynamics.getCoordinateCorrelationMatrix(Trajectory t, PointList reference)```
Calculates the 3Nx3N coordinate correlation matrix from a trajectory and a reference frame for superposition
`static jama.Matrix` `Dynamics.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` ```Dynamics.getCoordinateCovarianceMatrix(Trajectory t, PointList reference)```
Calculates the 3Nx3N coordinate covariance matrix from a trajectory and a reference frame for superposition
`static double` ```Dynamics.getCovarianceMatrixOverlap(Trajectory t1, Trajectory t2)```
Calculates the covariance overlap from two trajectories
`static double` ```Dynamics.getCovarianceMatrixOverlap(Trajectory t1, Trajectory t2, int N)```
Calculates the covariance overlap from two trajectories
`static java.util.ArrayList<java.lang.Double>` `Dynamics.getCumulativeVariances(Trajectory t)`
Calculates the cumulative variance profile from a trajectory
`static java.util.ArrayList<Angle>` ```Angles.getDihedralChi1TimeSeries(Trajectory t, int i)```
Calculates the time series of dihedral angle Chi1 of residue #i over a trajectory The residue can be ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER,THR,TRP,TYR or VAL
`static java.util.ArrayList<Angle>` ```Angles.getDihedralChi2TimeSeries(Trajectory t, int i)```
Calculates the time series of dihedral angle Chi2 of residue #i over a trajectory The residue can only be ARG,ASN,ASP,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,TRP or TYR
`static java.util.ArrayList<Angle>` ```Angles.getDihedralChi3TimeSeries(Trajectory t, int i)```
Calculates the time series of dihedral angle Chi3 of residue #i over a trajectory The residue can only be ARG,GLN,GLU,LYS or MET
`static java.util.ArrayList<Angle>` ```Angles.getDihedralChi4TimeSeries(Trajectory t, int i)```
Calculates the time series of dihedral angle Chi4 of residue #i over a trajectory The residue can only be ARG or LYS
`static java.util.ArrayList<Angle>` ```Angles.getDihedralChi5TimeSeries(Trajectory t, int i)```
Calculates the time series of dihedral angle Chi5 of residue #i over a trajectory The residue can only be ARG
`static java.util.ArrayList<Angle>` ```Angles.getDihedralOmegaTimeSeries(Trajectory t, int i)```
Calculates the time series of dihedral angle Omega of residue #i over a trajectory
`static java.util.ArrayList<Angle>` ```Angles.getDihedralPhiTimeSeries(Trajectory t, int i)```
Calculates the time series of dihedral angle Phi of residue #i over a trajectory
`static java.util.ArrayList<Angle>` ```Angles.getDihedralPsiTimeSeries(Trajectory t, int i)```
Calculates the time series of dihedral angle Psi of residue #i over a trajectory
`static double` ```Distances.getDistanceRange(Trajectory t, int atomindex1, int atomindex2)```
Returns the range (max-min) of the distance of two atoms in a trajectory
`static java.util.ArrayList<java.lang.Double>` ```Distances.getDistanceTimeSeries(Trajectory t, IndexSet indices1, IndexSet indices2)```
Returns the time series of the distance of two sets of atoms in a trajectory
`static java.util.ArrayList<java.lang.Double>` ```Distances.getDistanceTimeSeries(Trajectory t, int atomindex, IndexSet referenceset)```
Returns the time series of the distance of a single atom and a set of atoms in a trajectory
`static java.util.ArrayList<java.lang.Double>` ```Distances.getDistanceTimeSeries(Trajectory t, int atomindex1, int atomindex2)```
Returns the time series of the distance of two atoms in a trajectory
`static jama.Matrix` ```Dynamics.getDynamicalNetwork(Trajectory t, double cutoff, double frequency)```
Calculates the dynamical network of a protein according to the definition of Sethi et al.
`static double` ```Dynamics.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` `Dynamics.getFluctuationMatrix(Trajectory t)`
Calculates the F fluctuation matrix (variances of distances) from a trajectory
`static jama.Matrix` ```Dynamics.getFluctuationMatrix(Trajectory t, IndexSet indices)```
Calculates the F fluctuation matrix (variances of distances) for a group of atoms
`static double` ```Dynamics.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 FrameIndexSet` ```Distances.getFramesWhereAtomIsCloseToPoint(Trajectory t, int atomindex, Point3D point, double cutoff)```
Returns the list of frames in the trajectory where an atoms is closer to a reference point than a given cutoff
`static FrameIndexSet` ```Distances.getFramesWhereAtomIsDistantFromPoint(Trajectory t, int atomindex, Point3D point, double cutoff)```
Returns the list of frames in the trajectory where an atoms is more distant from a reference point than a given cutoff
`static FrameIndexSet` ```Distances.getFramesWhereAtomsAreClose(Trajectory t, int atomindex1, int atomindex2, double cutoff)```
Returns the list of frames in a trajectory where two atoms are closer to each other than the given cutoff
`static FrameIndexSet` ```Distances.getFramesWhereAtomsAreDistant(Trajectory t, int atomindex1, int atomindex2, double cutoff)```
Returns the list of frames in a trajectory where two atoms are more distant from each other than the given cutoff
`static jama.Matrix` ```Distances.getFrequencyContactMatrix(Trajectory t, int distanceBetween, double cutoff, double frequency)```
Calculates the contact matrix of residues where two residues are said to be in contact if they are in contact in at least the given percentage of frames of the trajectory
`static double` ```Distances.getMaximalDistance(Trajectory t, int atomindex1, int atomindex2)```
Returns the maximal distance of two atoms in a trajectory
`static jama.Matrix` `Distances.getMeanAtomicDistanceMatrix(Trajectory t)`
Calculates the mean distance matrix of all atoms in a trajectory
`static jama.Matrix` ```Distances.getMeanAtomicDistanceMatrix(Trajectory t, IndexSet indices)```
Calculates the mean distance matrix of atoms of given indices in a trajectory
`static double` ```Distances.getMeanDistance(Trajectory t, int atomindex1, int atomindex2)```
Returns the mean of the distance of two atoms in a trajectory
`static jama.Matrix` ```Distances.getMeanResidueDistanceMatrix(Trajectory t, int distanceBetween)```
Calculates the mean distance matrix of residues in a trajectory by the given method
`static PointList` `Similarity.getMedoidDRMSD(Trajectory t)`
Calculates the medoid frame of a trajectory using the dRMSD measure
`static PointList` `Similarity.getMedoidRMSD(Trajectory t)`
Calculates the medoid frame of a trajectory using the RMSD measure
`static double` ```Distances.getMinimalDistance(Trajectory t, int atomindex1, int atomindex2)```
Returns the minimal distance of two atoms in a trajectory
`static jama.Matrix[]` `Dynamics.getPCA(Trajectory t)`
Calculates the principal components and the corresponding eigenvalues from a trajectory
`static java.util.ArrayList<java.lang.Double>` ```Dynamics.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>` ```Dynamics.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>` ```Dynamics.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>` ```Dynamics.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>` ```Dynamics.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>` ```Dynamics.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>` ```Dynamics.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` ```Dynamics.getRootMeanSquareInnerProduct(Trajectory t1, Trajectory t2, int N, int M)```
Calculates the root mean square inner product (RMSIP) from two trajectories
`static jama.Matrix` `Similarity.getSimilarityMatrixDRMSD(Trajectory t)`
Calculates the similarity matrix of all frames in a trajectory using the dRMSD measure
`static jama.Matrix` ```Similarity.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
`static jama.Matrix` `Similarity.getSimilarityMatrixRMSD(Trajectory t)`
Calculates the similarity matrix of all frames in a trajectory using the RMSD measure
`static jama.Matrix` ```Similarity.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
`static jama.Matrix` ```Similarity.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
`static jama.Matrix` ```Similarity.getSimilarityMatrixWDRMSD(Trajectory t, jama.Matrix W)```
Calculates the similarity matrix of all frames in a trajectory using the wdRMSD (weighted dRMSD) measure
`static java.util.ArrayList<java.lang.Double>` ```Similarity.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
`static java.util.ArrayList<java.lang.Double>` ```Similarity.getSimilarityTimeSeriesDRMSD(Trajectory t, PointList R)```
Returns the time series of dRMSD in a trajectory with regards to a reference point list
`static java.util.ArrayList<java.lang.Double>` ```Similarity.getSimilarityTimeSeriesDRMSD(Trajectory t, Structure R)```
Returns the time series of dRMSD in a trajectory with regards to a reference structure
`static java.util.ArrayList<java.lang.Double>` ```Similarity.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
`static java.util.ArrayList<java.lang.Double>` ```Similarity.getSimilarityTimeSeriesRMSD(Trajectory t, PointList R)```
Returns the time series of RMSD in a trajectory with regards to a reference point list
`static java.util.ArrayList<java.lang.Double>` ```Similarity.getSimilarityTimeSeriesRMSD(Trajectory t, Structure R)```
Returns the time series of RMSD in a trajectory with regards to a reference structure
`static java.util.ArrayList<java.lang.Double>` ```Similarity.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
`static java.util.ArrayList<java.lang.Double>` ```Similarity.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
`static java.util.ArrayList<java.lang.Double>` ```Similarity.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
`static double` `Dynamics.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<Angle>` ```Angles.getTorsionAngleTimeSeries(Trajectory t, int atom1, int atom2, int atom3, int atom4)```
Calculates the time series of torsion angle over a trajectory defined by four atoms
`static java.util.ArrayList<Point3D>` ```Dynamics.getTrajectoryOfAtom(Trajectory t, int atomindex)```
Returns the trajectory of a single atom in the course of the simulation
`static double` ```Distances.getVarianceOfDistance(Trajectory t, int atomindex1, int atomindex2)```
Returns the variance of the distance of two atoms in a trajectory
`static Trajectory` ```Superposition.superposeTo(Trajectory t, PointList reference)```
Calculates the superposition of each frame of a trajectory to a common reference frame
`static Trajectory` ```Superposition.superposeTo(Trajectory t, Structure reference)```
Calculates the superposition of each frame of a trajectory to a common reference frame
`static Trajectory` ```Superposition.superposeTo(Trajectory t, Structure reference, IndexSet indices)```
Calculates the superposition of each frame of a trajectory to a common reference frame using a subset of atoms for fitting
`static Trajectory` ```Superposition.weightedSuperposeTo(Trajectory t, PointList reference, java.util.ArrayList<java.lang.Double> weights)```
Calculates the weighted superposition of each frame of a trajectory to a common reference frame
`static Trajectory` ```Superposition.weightedSuperposeTo(Trajectory t, Structure reference, java.util.ArrayList<java.lang.Double> weights)```
Calculates the weighted superposition of each frame of a trajectory to a common reference frame

Uses of Trajectory in jgromacs.data

Methods in jgromacs.data that return Trajectory
` Trajectory` `Trajectory.getSubTrajectory(FrameIndexSet framelist)`
Returns the subtrajectory defined by the given frame list
` Trajectory` `Trajectory.getSubTrajectory(IndexSet indices)`
Returns the subtrajectory defined by the given index set
` Trajectory` ```Trajectory.getSubTrajectory(int startframe, int endframe)```
Returns the subtrajectory between the given start and end frames
` Trajectory` ```Trajectory.getSubTrajectory(int startframe, int endframe, int frequency)```
Returns the subtrajectory between the given start and end frames using the given sampling frequency

Uses of Trajectory in jgromacs.io

Methods in jgromacs.io that return Trajectory
`static Trajectory` ```IOData.readDumpedTrajectory(Structure structure, java.lang.String filename)```
Reads a trajectory from the given dumped XTC or TRR file
`static Trajectory` ```IOData.readTrajectory(Structure structure, java.lang.String filename)```
Reads a trajectory from the given XTC or TRR file