Uses of Class
jgromacs.data.Point3D

Packages that use Point3D
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 Point3D in jgromacs.analysis
 

Methods in jgromacs.analysis that return types with arguments of type Point3D
static java.util.ArrayList<Point3D> Dynamics.getTrajectoryOfAtom(Trajectory t, int atomindex)
          Returns the trajectory of a single atom in the course of the simulation
 

Methods in jgromacs.analysis with parameters of type Point3D
static Angle Angles.getAngleBetweenPlanes(Point3D A, Point3D B, Point3D C, Point3D D)
          Calculates the angle between two planes defined by points A, B, C and points B, C, D
static Angle Angles.getAngleBetweenVectors(Point3D v1, Point3D v2)
          Calculates the angle between two vectors
static IndexSet Distances.getAtomIndicesInRadius(Structure s, Point3D point, double radius)
          Returns the index set of atoms in a structure that are closer to a reference point than a given radius
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
 

Uses of Point3D in jgromacs.data
 

Methods in jgromacs.data that return Point3D
 Point3D Point3D.crossProduct(Point3D other)
          Returns the cross product of this vector and another vector
 Point3D Residue.getAlphaCarbonCoordinates()
          Returns the position of alpha-carbon atom
 Point3D PointList.getCentroid()
          Returns the centroid of points
 Point3D Atom.getCoordinates()
          Returns the coordinates of atom
 Point3D PointList.getPoint(int i)
          Returns the point of index i
 Point3D Point3D.minus(Point3D other)
          Subtracts another vector from this vector
 Point3D Point3D.multiplyByScalar(double scalar)
          Returns this vector multiplied by a scalar
 Point3D Point3D.plus(Point3D other)
          Adds another vector to this vector
 Point3D Point3D.transformByMatrix(jama.Matrix matrix)
          Returns the resulting vector of a matrix transformation
 

Methods in jgromacs.data that return types with arguments of type Point3D
 java.util.ArrayList<Point3D> PointList.getPointsAsArrayList()
          Returns points in an ArrayList
 

Methods in jgromacs.data with parameters of type Point3D
 void PointList.addPoint(Point3D point)
          Adds a new point to the point list
 Point3D Point3D.crossProduct(Point3D other)
          Returns the cross product of this vector and another vector
 double Point3D.distance(Point3D other)
          Returns the Euclidean distance between this point and another point
 double Point3D.innerProduct(Point3D other)
          Returns the inner product of this vector and another vector
 Point3D Point3D.minus(Point3D other)
          Subtracts another vector from this vector
 Point3D Point3D.plus(Point3D other)
          Adds another vector to this vector
 void PointList.removePoint(Point3D point)
          Removes the given point from the point list
 void Structure.setAtomCoordinates(int i, Point3D coordinates)
          Sets the coordinates of atom #i
 void Residue.setAtomCoordinates(int i, Point3D coordinates)
          Sets the coordinates of atom #i
 void Structure.setAtomOfIndexCoordinates(int index, Point3D coordinates)
          Sets the coordinates of atom of given index
 void Residue.setAtomOfIndexCoordinates(int index, Point3D coordinates)
          Sets the coordinates of atom of given index
 void Atom.setCoordinates(Point3D coordinates)
          Sets the coordinates of atom
 void PointList.setPoint(int i, Point3D point)
          Replaces the point of index i with a given point
 void PointList.translate(Point3D vector)
          Translates the points by a given vector
 

Method parameters in jgromacs.data with type arguments of type Point3D
 void PointList.setPointFromArrayList(java.util.ArrayList<Point3D> points)
          Loads points from an ArrayList