Uses of Class
jgromacs.data.PointList

Packages that use PointList

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

Uses of PointList in jgromacs.analysis

Methods in jgromacs.analysis that return PointList

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 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 PointList	Superposition.superposeTo(PointList toBeSuperposed, PointList reference) Calculates the superposition of a point list to another
static PointList	Superposition.weightedSuperposeTo(PointList toBeSuperposed, PointList reference, java.util.ArrayList<java.lang.Double> weights) Calculates the weighted superposition of a point list to another

Methods in jgromacs.analysis with parameters of type PointList

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, PointList reference) Calculates the NxN atomic correlation matrix from a trajectory and a 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.getContactMatrix(PointList points, double cutoff) Calculates the contact matrix from a point list
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, PointList reference) Calculates the 3Nx3N coordinate covariance matrix from a trajectory and a reference frame for superposition
static jama.Matrix	Similarity.getDifferenceDistanceMatrix(PointList points1, PointList points2) Calculates the difference distance matrix between two point lists
static jama.Matrix	Distances.getDistanceMatrix(PointList points) Calculates the distance matrix from a point list
static double	Similarity.getDRMSD(PointList A, PointList B) Calculates dRMSD similarity between two point lists
static java.util.ArrayList<java.lang.Double>	Similarity.getDRMSDiProfile(PointList A, PointList B) Calculates the dRMSDi profile between two point lists
static double	Similarity.getRMSD(PointList A, PointList B) Calculates RMSD similarity between two point lists
static java.util.ArrayList<java.lang.Double>	Similarity.getRMSDiProfile(PointList A, PointList B) Calculates the RMSDi profile between two point lists
static java.util.ArrayList<java.lang.Double>	Similarity.getRMSDiProfileNoSuperposition(PointList A, PointList B) Calculates the RMSDi profile between two point lists without superposition
static double	Similarity.getRMSDnoSuperposition(PointList A, PointList B) Calculates RMSD similarity between two point lists without doing superposition
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.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>	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.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.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 double	Similarity.getWDRMSD(PointList A, PointList B, jama.Matrix W) Calculates the wdRMSD (weighted dRMSD) similarity of two point lists
static java.util.ArrayList<java.lang.Double>	Similarity.getWDRMSDiProfile(PointList A, PointList B, jama.Matrix W) Calculates the wdRMSDi (weighted dRMSDi) profile between two point lists
static PointList	Superposition.superposeTo(PointList toBeSuperposed, PointList reference) Calculates the superposition of a point list to another
static Trajectory	Superposition.superposeTo(Trajectory t, PointList reference) Calculates the superposition of each frame of a trajectory to a common reference frame
static PointList	Superposition.weightedSuperposeTo(PointList toBeSuperposed, PointList reference, java.util.ArrayList<java.lang.Double> weights) Calculates the weighted superposition of a point list to another
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

Uses of PointList in jgromacs.data

Methods in jgromacs.data that return PointList

PointList	Structure.getAllAtomCoordinates() Returns the coordinates of all atoms
PointList	Residue.getAllAtomCoordinates() Returns the coordinates of all atoms
PointList	Trajectory.getFirstFrameAsPointList() Returns the initial frame of trajectory as a PointList
PointList	Trajectory.getFrameAsPointList(int i) Returns frame #i of the trajectory as a PointList object
PointList	Trajectory.getLastFrameAsPointList() Returns the last frame of trajectory as a PointList
PointList	Trajectory.getMeanFrame() Returns the mean frame of trajectory
PointList	PointList.getSubList(java.util.ArrayList<java.lang.Integer> indices) Returns a subset of points defined by an ArrayList of indices

Methods in jgromacs.data that return types with arguments of type PointList

java.util.ArrayList<PointList>

Trajectory.getFrames() Returns frames of the trajectory as an ArrayList object

Methods in jgromacs.data with parameters of type PointList

void	Trajectory.addFrame(PointList frame) Adds a new frame to the trajectory
void	Structure.setAllAtomCoordinates(PointList pointlist) Sets the coordinates of all atoms
void	Residue.setAllAtomCoordinates(PointList pointlist) Sets the coordinates of all atoms
void	Trajectory.setFrame(int i, PointList frame) Replaces frame #i with a new frame