Package jgromacs.analysis

Class Superposition

java.lang.Object
jgromacs.analysis.Superposition
public class Superposition extends Object
Collection of methods for superposing structures

  • Constructor Details

    • Superposition

      public Superposition()

  • Method Details

    • 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, ArrayList<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, ArrayList<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, ArrayList<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, ArrayList<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