Package ffx.potential.utils

Class Loop

java.lang.Object
ffx.potential.utils.Loop
public class Loop extends Object
Loop class.
Since:
1.0
Author:
Mallory R. Tollefson

  • Constructor Summary

    Constructors
    Constructor
    Description
    Loop(MolecularAssembly molecularAssembly)
    Constructor for Loop.
    Loop(MolecularAssembly molecularAssembly, int firstResidue, int endResidue)
    Constructor for Loop.

  • Method Summary

    Modifier and Type
    Method
    Description
    List<double[]>
    generateLoops(int firstResidue, int endResidue)
    The generateLoops method generates loop closure solutions for a specified range of residues.
    List<double[]>
    generateLoops(int firstResidue, int endResidue, double[] coordinates)
    The generateLoops method generates loop closure solutions for a specified range of residues.
    double[][]
    getRA()
    Get the rA coordinates.
    double[][]
    getRC()
    Get the rC coordinates.
    double[][]
    getRN()
    Get the rN coordinates.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

    • Loop

      public Loop(MolecularAssembly molecularAssembly, int firstResidue, int endResidue)
      Constructor for Loop.
      Parameters:
      molecularAssembly - a MolecularAssembly object.
      firstResidue - a int.
      endResidue - a int.

    • Loop

      public Loop(MolecularAssembly molecularAssembly)
      Constructor for Loop.
      Parameters:
      molecularAssembly - a MolecularAssembly object.

  • Method Details

    • generateLoops

      public List<double[]> generateLoops(int firstResidue, int endResidue, double[] coordinates)
      The generateLoops method generates loop closure solutions for a specified range of residues.
      Parameters:
      firstResidue - the first residue number.
      endResidue - the last residue number.
      coordinates - the backbone coordinates to use for the loop closure.
      Returns:
      a list of loop closure solutions.

    • generateLoops

      public List<double[]> generateLoops(int firstResidue, int endResidue)
      The generateLoops method generates loop closure solutions for a specified range of residues.
      Parameters:
      firstResidue - the first residue number.
      endResidue - the last residue number.
      Returns:
      a list of loop closure solutions.

    • getRA

      public double[][] getRA()
      Get the rA coordinates.
      Returns:
      the rA coordinates as a 2D array.

    • getRC

      public double[][] getRC()
      Get the rC coordinates.
      Returns:
      the rC coordinates as a 2D array.

    • getRN

      public double[][] getRN()
      Get the rN coordinates.
      Returns:
      the rN coordinates as a 2D array.