Package jgromacs.data

Class Trajectory

  • All Implemented Interfaces:
    java.lang.Cloneable
    public class Trajectory
extends java.lang.Object
implements java.lang.Cloneable
    Objects of this class represent a single trajectory

    • Constructor Detail

      • Trajectory

        public Trajectory()
        Constructs a new Trajectory object

      • Trajectory

        public Trajectory​(java.lang.String name)
        Constructs a new Trajectory object of given name

      • Trajectory

        public Trajectory​(Structure structure)
        Constructs a new Trajectory object of given structure

      • Trajectory

        public Trajectory​(Structure[] ensemble)
        Constructs a new Trajectory object made from an ensemble of structures

    • Method Detail

      • getFrames

        public java.util.ArrayList<PointList> getFrames()
        Returns frames of the trajectory as an ArrayList object
        Returns:
        frames as an ArrayList

      • getFrameAsPointList

        public PointList getFrameAsPointList​(int i)
        Returns frame #i of the trajectory as a PointList object
        Returns:
        frame #i as a PointList

      • getFrameAsStructure

        public Structure getFrameAsStructure​(int i)
        Returns frame #i of the trajectory as a Structure object
        Returns:
        frame #i as a Structure

      • getNumberOfFrames

        public int getNumberOfFrames()
        Returns the number of frames in the trajectory
        Returns:
        number of frames

      • getName

        public java.lang.String getName()
        Returns the name of trajectory
        Returns:
        name of trajectory

      • setName

        public void setName​(java.lang.String name)
        Sets the name of trajectory
        Parameters:
        name - name of trajectory

      • getStartTime

        public double getStartTime()
        Returns the start time of trajectory
        Returns:
        start time of trajectory

      • setStartTime

        public void setStartTime​(double startTime)
        Sets the start time of trajectory
        Parameters:
        startTime - start time of trajectory

      • getTimeStep

        public double getTimeStep()
        Returns the time step of trajectory
        Returns:
        time step of trajectory

      • setTimeStep

        public void setTimeStep​(double timeStep)
        Sets the time step of trajectory
        Parameters:
        timeStep - time step of trajectory

      • setStructure

        public void setStructure​(Structure structure)
        Sets the structure described by the trajectory
        Parameters:
        structure - structure described by the trajectory

      • getMeanFrame

        public PointList getMeanFrame()
        Returns the mean frame of trajectory
        Returns:
        mean frame

      • getNumberOfAtoms

        public int getNumberOfAtoms()
        Returns the number of atoms in the trajectory
        Returns:
        number of atoms

      • getNumberOfResidues

        public int getNumberOfResidues()
        Returns the number of residues in the trajectory
        Returns:
        number of residues

      • getFirstFrameAsPointList

        public PointList getFirstFrameAsPointList()
        Returns the initial frame of trajectory as a PointList
        Returns:
        initial frame

      • getFirstFrameAsStructure

        public Structure getFirstFrameAsStructure()
        Returns the initial frame of trajectory as a Structure
        Returns:
        initial frame

      • getLastFrameAsPointList

        public PointList getLastFrameAsPointList()
        Returns the last frame of trajectory as a PointList
        Returns:
        last frame

      • getLastFrameAsStructure

        public Structure getLastFrameAsStructure()
        Returns the last frame of trajectory as a Structure
        Returns:
        last frame

      • addFrame

        public void addFrame​(PointList frame)
        Adds a new frame to the trajectory
        Parameters:
        frame - new frame

      • removeFrame

        public void removeFrame​(int i)
        Removes frame #i from the trajectory

      • setFrame

        public void setFrame​(int i,
                     PointList frame)
        Replaces frame #i with a new frame
        Parameters:
        frame - new frame

      • convertFrameIndexToTime

        public double convertFrameIndexToTime​(int frameindex)
        Converts frame index to simulation time
        Parameters:
        frameindex - frame index
        Returns:
        simulation time

      • convertTimeToFrameIndex

        public int convertTimeToFrameIndex​(double time)
        Converts simulation time to frame index
        Parameters:
        time - simulation time
        Returns:
        frame index

      • getSubTrajectory

        public Trajectory getSubTrajectory​(int startframe,
                                   int endframe)
        Returns the subtrajectory between the given start and end frames
        Parameters:
        startframe - start frame
        endframe - end frame
        Returns:
        subtrajectory

      • getSubTrajectory

        public Trajectory getSubTrajectory​(int startframe,
                                   int endframe,
                                   int frequency)
        Returns the subtrajectory between the given start and end frames using the given sampling frequency
        Parameters:
        startframe - start frame
        endframe - end frame
        frequency - sampling frequency
        Returns:
        subtrajectory

      • getSubTrajectory

        public Trajectory getSubTrajectory​(IndexSet indices)
        Returns the subtrajectory defined by the given index set
        Parameters:
        indices - index set of subtrajectory
        Returns:
        subtrajectory

      • getSubTrajectory

        public Trajectory getSubTrajectory​(FrameIndexSet framelist)
        Returns the subtrajectory defined by the given frame list
        Parameters:
        framelist - frame list
        Returns:
        subtrajectory

      • toString

        public java.lang.String toString()
        Returns the String representation of trajectory
        Overrides:
        toString in class java.lang.Object
        Returns:
        String representation

      • equals

        public boolean equals​(java.lang.Object other)
        Returns true if the two trajectories are identical
        Overrides:
        equals in class java.lang.Object
        Parameters:
        other - the other trajectory

      • hashCode

        public int hashCode()
        Returns hash code
        Overrides:
        hashCode in class java.lang.Object

      • clone

        public java.lang.Object clone()
        Returns an identical Trajectory object
        Overrides:
        clone in class java.lang.Object
        Returns:
        clone of the trajectory