Class Rotamer

java.lang.Object
ffx.potential.bonded.Rotamer

public class Rotamer extends Object
The Rotamer Class usually represents one immutable amino acid Rotamer.

It is additionally being extended to represent one nucleic acid Rotamer.

Since:
1.0
Author:
Ava M. Lynn, Jacob M. Litman
  • Field Details Link icon

    • chi1 Link icon

      public final double chi1
      Torsions chi 1-4 are used for amino acids and nucleic acids.
    • chi2 Link icon

      public final double chi2
    • chi3 Link icon

      public final double chi3
    • chi4 Link icon

      public final double chi4
    • chi5 Link icon

      public final double chi5
      Torsions chi 5-7 are only currently used for nucleic acids.
    • angles Link icon

      public final double[] angles
      An array of chi angles for this rotamer.
    • sigmas Link icon

      public final double[] sigmas
      An array of sigmas for each chi angle.
    • length Link icon

      public final int length
      Number of chi/sigma values.
    • originalState Link icon

      public ResidueState originalState
      Residue state used to initialize the rotamer.
    • isState Link icon

      public boolean isState
      Flag to indicate the rotamer was initialized from a Residue state.
    • aminoAcid3 Link icon

      public AminoAcidUtils.AminoAcid3 aminoAcid3
      The A.A. name of this residue (or null for a N.A.).
    • nucleicAcid3 Link icon

      public NucleicAcidUtils.NucleicAcid3 nucleicAcid3
      The N.A. name of this residue (or null for a A.A.).
    • isTitrating Link icon

      public boolean isTitrating
      If this flag is set, application of a rotamer requires updating force field parameters.
  • Constructor Details Link icon

  • Method Details Link icon

    • updateParameters Link icon

      public void updateParameters(Residue residue)
      Update force field parameters for force field dependent rotamers.
      Parameters:
      residue - Residue to update.
    • defaultRotamerFactory Link icon

      public static Rotamer[] defaultRotamerFactory(Residue residue)
      Factory method to construct an original-coordinates Rotamer from a residue.
      Parameters:
      residue - Residue to construct a default rotamer for.
      Returns:
      Rotamer based on the coordinates of the residue.
    • defaultRotamerFactory Link icon

      public static Rotamer[] defaultRotamerFactory(Residue residue, TitrationUtils titrationUtils)
      Factory method to construct an original-coordinates Rotamer from a residue.
      Parameters:
      residue - Residue to construct a default rotamer for.
      Returns:
      Rotamer based on the coordinates of the residue.
    • toAngleString Link icon

      public String toAngleString()
      toAngleString.
      Returns:
      a String object.
    • toString Link icon

      public String toString()
      Overrides:
      toString in class Object
    • getName Link icon

      public String getName()
    • getRotamerPhBias Link icon

      public double getRotamerPhBias()
    • getAngles Link icon

      public double[] getAngles()