Package ffx.potential.bonded

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

    • chi1

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

    • chi2

      public final double chi2

    • chi3

      public final double chi3

    • chi4

      public final double chi4

    • chi5

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

    • angles

      public final double[] angles
      An array of chi angles for this rotamer.

    • sigmas

      public final double[] sigmas
      An array of sigmas for each chi angle.

    • length

      public final int length
      Number of chi/sigma values.

    • originalState

      public ResidueState originalState
      Residue state used to initialize the rotamer.

    • isState

      public boolean isState
      Flag to indicate the rotamer was initialized from a Residue state.

    • aminoAcid3

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

    • nucleicAcid3

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

    • isTitrating

      public boolean isTitrating
      If this flag is set, application of a rotamer requires updating force field parameters.

  • Constructor Details

  • Method Details

    • updateParameters

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

    • defaultRotamerFactory

      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

      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

      public String toAngleString()
      toAngleString.
      Returns:
      a String object.

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • getName

      public String getName()

    • getRotIndex

      public int getRotIndex()

    • getRotamerPhBias

      public double getRotamerPhBias()

    • getAngles

      public double[] getAngles()