Class Superposition


  • public class Superposition
    extends java.lang.Object
    Collection of methods for superposing structures
    • Constructor Detail

      • Superposition

        public Superposition()
    • Method Detail

      • superposeTo

        public static PointList superposeTo​(PointList toBeSuperposed,
                                            PointList reference)
        Calculates the superposition of a point list to another
        Parameters:
        toBeSuperposed - the point list to be superposed
        reference - the reference point list
        Returns:
        superposed points
      • superposeTo

        public static Structure superposeTo​(Structure toBeSuperposed,
                                            Structure reference)
        Calculates the superposition of a structure to another
        Parameters:
        toBeSuperposed - the structure to be superposed
        reference - the reference structure
        Returns:
        superposed structure
      • superposeTo

        public static Structure superposeTo​(Structure toBeSuperposed,
                                            IndexSet indices1,
                                            Structure reference,
                                            IndexSet indices2)
        Calculates the superposition of a structure to another using a subset of atoms for fitting
        Parameters:
        toBeSuperposed - the structure to be superposed
        indices1 - first index set
        reference - the reference structure
        indices2 - second index set
        Returns:
        superposed structure
      • superposeTo

        public static Trajectory superposeTo​(Trajectory t,
                                             PointList reference)
        Calculates the superposition of each frame of a trajectory to a common reference frame
        Parameters:
        t - trajectory to be superposed
        reference - reference point list
        Returns:
        superposed trajectory
      • superposeTo

        public static Trajectory superposeTo​(Trajectory t,
                                             Structure reference)
        Calculates the superposition of each frame of a trajectory to a common reference frame
        Parameters:
        t - trajectory to be superposed
        reference - reference structure
        Returns:
        superposed trajectory
      • superposeTo

        public static Trajectory 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
        Parameters:
        t - trajectory to be superposed
        reference - reference structure
        indices - index set
        Returns:
        superposed trajectory
      • weightedSuperposeTo

        public static PointList weightedSuperposeTo​(PointList toBeSuperposed,
                                                    PointList reference,
                                                    java.util.ArrayList<java.lang.Double> weights)
        Calculates the weighted superposition of a point list to another
        Parameters:
        toBeSuperposed - the point list to be superposed
        reference - the reference point list
        weights - vector of weights
        Returns:
        superposed points
      • weightedSuperposeTo

        public static Structure weightedSuperposeTo​(Structure toBeSuperposed,
                                                    Structure reference,
                                                    java.util.ArrayList<java.lang.Double> weights)
        Calculates the weighted superposition of a structure to another
        Parameters:
        toBeSuperposed - the structure to be superposed
        reference - the reference structure
        weights - vector of weights
        Returns:
        superposed structure
      • weightedSuperposeTo

        public static Trajectory 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
        Parameters:
        t - trajectory to be superposed
        reference - reference point list
        weights - vector of weights
        Returns:
        superposed trajectory
      • weightedSuperposeTo

        public static Trajectory 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
        Parameters:
        t - trajectory to be superposed
        reference - reference structure
        weights - vector of weights
        Returns:
        superposed trajectory