Package ffx.potential.bonded

Class SturmMethod

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

  • Constructor Summary

    Constructors
    Constructor
    Description
    SturmMethod()
    SturmMethod constructor with termination criteria for polynomial solver.

  • Method Summary

    Modifier and Type
    Method
    Description
    double[][]
    getr_o()
    Used only in JUnit testing.
    int
    solveSturm(int order, double[] poly_coeffs, double[] roots)
    Solve using the Sturm method.
    File
    writePDBBackbone(double[][] r_n, double[][] r_a, double[][] r_c, int stt_res, int end_res, MolecularAssembly molAss, int counter, boolean writeFile)
    Write out loop coordinates and determine oxygen placement.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • SturmMethod

      public SturmMethod()
      SturmMethod constructor with termination criteria for polynomial solver.

  • Method Details

    • getr_o

      public double[][] getr_o()
      Used only in JUnit testing.
      Returns:
      oxygen coordinates.

    • solveSturm

      public int solveSturm(int order, double[] poly_coeffs, double[] roots)
      Solve using the Sturm method.
      Parameters:
      order - the order of the polynomial.
      poly_coeffs - the coefficients of the polynomial.
      roots - the array to hold the roots.

    • writePDBBackbone

      public File writePDBBackbone(double[][] r_n, double[][] r_a, double[][] r_c, int stt_res, int end_res, MolecularAssembly molAss, int counter, boolean writeFile)
      Write out loop coordinates and determine oxygen placement.
      Parameters:
      r_n - the coordinates of the nitrogen atoms.
      r_a - the coordinates of the alpha carbon atoms.
      r_c - the coordinates of the carbonyl carbon atoms.
      stt_res - a int.
      end_res - a int.
      molAss - a MolecularAssembly object.
      counter - a int.
      writeFile - a boolean.
      Returns:
      the File.