Package ffx.potential

Class Utilities

java.lang.Object
ffx.potential.Utilities

public final class Utilities extends Object
The Utilities class provides methods to locate functional units of an organic system.
Since:
1.0
Author:
Michael J. Schnieders
  • Constructor Details

    • Utilities

      public Utilities()
  • Method Details

    • RMSCoordDev

      public static double RMSCoordDev(MolecularAssembly m1, MolecularAssembly m2)
      Finds the RMS deviation between the atoms of MolecularAssembly m1 and m2 provided they have the same number of atoms.
      Parameters:
      m1 - a MolecularAssembly object.
      m2 - a MolecularAssembly object.
      Returns:
      a double.
    • biochemistry

      public static void biochemistry(MolecularAssembly molecularAssembly, List<Atom> atoms)
      This routine sub-divides a system into groups of ions, water, hetero molecules, and polynucleotides/polypeptides.
      Parameters:
      molecularAssembly - a MolecularAssembly object.
      atoms - a List object.
    • findSeed

      public static Atom findSeed(Atom end, Atom other)
      Returns an atom bonded to the "end" atom, which is not equal to "other".
      Parameters:
      end - Atom
      other - Atom
      Returns:
      Atom
    • getChainID

      public static Character getChainID(int i)
      Determine chainID for a given polymer number.
      Parameters:
      i - int
      Returns:
      Character
    • stackTraceToString

      public static String stackTraceToString(Throwable ex)
      Gets the stack trace for an exception and converts it to a String.
      Parameters:
      ex - An exception.
      Returns:
      A String of its stack trace.