// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2025.
   //
   // This file is part of Force Field X.
   //
   // Force Field X is free software; you can redistribute it and/or modify it
  // under the terms of the GNU General Public License version 3 as published by
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  package ffx.potential.bonded;
  
  import static org.apache.commons.math3.util.FastMath.max;
  
  import ffx.potential.bonded.AminoAcidUtils.AminoAcid3;
  import ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3;
  import ffx.potential.parameters.TitrationUtils;
  
  /**
   * The Rotamer Class usually represents one immutable amino acid Rotamer.
   * <p>
   * It is additionally being extended to represent one nucleic acid Rotamer.
   *
   * @author Ava M. Lynn
   * @author Jacob M. Litman
   * @since 1.0
   */
  public class Rotamer {
  
    /** Torsions chi 1-4 are used for amino acids and nucleic acids. */
    public final double chi1;
    public final double chi2;
    public final double chi3;
    public final double chi4;
    /** Torsions chi 5-7 are only currently used for nucleic acids. */
    public final double chi5;
    final double chi6;
    final double chi7;
  
    /**
     * An array of chi angles for this rotamer.
     */
    public final double[] angles;
    /**
     * An array of sigmas for each chi angle.
     */
    public final double[] sigmas;
    /**
     * Number of chi/sigma values.
     */
    public final int length;
    /**
     * Residue state used to initialize the rotamer.
     */
    public ResidueState originalState;
    /**
     * Flag to indicate the rotamer was initialized from a Residue state.
     */
    public boolean isState;
    /**
     * The A.A. name of this residue (or null for a N.A.).
     */
    public AminoAcid3 aminoAcid3;
    /**
     * The N.A. name of this residue (or null for a A.A.).
     */
    public NucleicAcid3 nucleicAcid3;
    /**
     * If this flag is set, application of a rotamer requires updating force field parameters.
     */
    public boolean isTitrating;
    /**
    * The TitrationUtils handles application of rotamer specific force field parameters.
    */
   private TitrationUtils titrationUtils = null;
 
   /**
    * Constructor for unknown residue types.
    *
    * @param values a double.
    */
   public Rotamer(double... values) {
     length = values.length / 2;
     angles = new double[max(length, 7)];
     sigmas = new double[max(length, 7)];
     nucleicAcid3 = null;
     aminoAcid3 = null;
     for (int i = 0; i < values.length / 2; i++) {
       int ii = 2 * i;
       angles[i] = values[ii];
       sigmas[i] = values[ii + 1];
     }
     chi1 = angles[0];
     chi2 = angles[1];
     chi3 = angles[2];
     chi4 = angles[3];
     chi5 = angles[4];
     chi6 = angles[5];
     chi7 = angles[6];
     originalState = null;
     isState = false;
     isTitrating = false;
   }
 
   /**
    * Constructor for Rotamer.
    *
    * @param aminoAcid3 a {@link AminoAcid3} object.
    * @param values a double.
    */
   public Rotamer(AminoAcid3 aminoAcid3, double... values) {
     this(values);
     this.aminoAcid3 = aminoAcid3;
   }
 
 
   /**
    * Constructor for Rotamer.
    *
    * @param nucleicAcid3 a {@link NucleicAcid3} object.
    * @param values a double.
    */
   public Rotamer(NucleicAcid3 nucleicAcid3, double... values) {
     this(values);
     this.nucleicAcid3 = nucleicAcid3;
   }
 
   /**
    * Constructor for Rotamer.
    *
    * @param aminoAcid3 a {@link AminoAcid3} object.
    * @param titrationUtils Use to apply rotamer specific force field parameters.
    * @param values a double.
    */
   public Rotamer(AminoAcid3 aminoAcid3, TitrationUtils titrationUtils, double... values) {
     this(aminoAcid3, values);
     if (titrationUtils != null) {
       this.isTitrating = true;
       this.titrationUtils = titrationUtils;
     } else {
       this.isTitrating = false;
     }
   }
 
   /**
    * Constructor for unknown residue types.
    *
    * @param residueState a {@link ffx.potential.bonded.ResidueState} object.
    * @param values a double.
    */
   public Rotamer(ResidueState residueState, double... values) {
     this(values);
     isState = true;
     originalState = residueState;
   }
 
   /**
    * Constructor for unknown residue types.
    *
    * @param residueState a {@link ffx.potential.bonded.ResidueState} object.
    * @param values a double.
    */
   public Rotamer(ResidueState residueState, TitrationUtils titrationUtils, double... values) {
     this(residueState, values);
     if (titrationUtils != null) {
       this.titrationUtils = titrationUtils;
       isTitrating = true;
     }
   }
 
   /**
    * Constructor for Rotamer.
    *
    * @param aminoAcid3 a {@link AminoAcid3} object.
    * @param residueState a {@link ffx.potential.bonded.ResidueState} object.
    * @param values a double.
    */
   public Rotamer(AminoAcid3 aminoAcid3, ResidueState residueState, double... values) {
     this(residueState, values);
     this.aminoAcid3 = aminoAcid3;
   }
 
   /**
    * Constructor for Rotamer.
    *
    * @param aminoAcid3 a {@link AminoAcid3} object.
    * @param residueState a {@link ffx.potential.bonded.ResidueState} object.
    * @param values a double.
    */
   public Rotamer(AminoAcid3 aminoAcid3, ResidueState residueState, TitrationUtils titrationUtils,
       double... values) {
     this(aminoAcid3, residueState, values);
     if (titrationUtils != null) {
       this.titrationUtils = titrationUtils;
       isTitrating = true;
     }
   }
 
   /**
    * Constructor for Rotamer.
    *
    * @param nucleicAcid3 a {@link NucleicAcid3} object.
    * @param residueState a {@link ffx.potential.bonded.ResidueState} object.
    * @param values a double.
    */
   public Rotamer(NucleicAcid3 nucleicAcid3, ResidueState residueState, double... values) {
     this(residueState, values);
     this.nucleicAcid3 = nucleicAcid3;
   }
 
   /**
    * Constructor for Rotamer.
    *
    * @param nucleicAcid3 a {@link NucleicAcid3} object.
    * @param residueState a {@link ffx.potential.bonded.ResidueState} object.
    * @param values a double.
    */
   public Rotamer(NucleicAcid3 nucleicAcid3, ResidueState residueState, TitrationUtils titrationUtils,
       double... values) {
     this(nucleicAcid3, residueState, values);
     if (titrationUtils != null) {
       this.titrationUtils = titrationUtils;
       isTitrating = true;
     }
   }
 
   /**
    * Update force field parameters for force field dependent rotamers.
    *
    * @param residue Residue to update.
    */
   public void updateParameters(Residue residue) {
     titrationUtils.updateResidueParameters(residue, this);
   }
 
   /**
    * Factory method to construct an original-coordinates Rotamer from a residue.
    *
    * @param residue Residue to construct a default rotamer for.
    * @return Rotamer based on the coordinates of the residue.
    */
   public static Rotamer[] defaultRotamerFactory(Residue residue) {
     return defaultRotamerFactory(residue, null);
   }
 
   /**
    * Factory method to construct an original-coordinates Rotamer from a residue.
    *
    * @param residue Residue to construct a default rotamer for.
    * @return Rotamer based on the coordinates of the residue.
    */
   public static Rotamer[] defaultRotamerFactory(Residue residue, TitrationUtils titrationUtils) {
     ResidueState resState = residue.storeState();
     double[] chi = RotamerLibrary.measureRotamer(residue, false);
 
     double[] values = new double[chi.length * 2];
     for (int i = 0; i < chi.length; i++) {
       int index = i * 2;
       values[index] = chi[i];
       values[index + 1] = 0.0;
     }
 
     switch (residue.getResidueType()) {
       case AA:
         // Only one rotamer for non-titrating cases.
         if (titrationUtils == null) {
           Rotamer[] rotamers = new Rotamer[1];
           rotamers[0] = new Rotamer(residue.getAminoAcid3(), resState, titrationUtils, values);
           return rotamers;
         }
         switch (residue.getAminoAcid3()) {
           case ASH:
             Rotamer[] rotamers = new Rotamer[2];
             rotamers[0] = new Rotamer(AminoAcid3.ASP, resState, titrationUtils, values);
             rotamers[1] = new Rotamer(AminoAcid3.ASH, resState, titrationUtils, values);
             return rotamers;
           case GLH:
             rotamers = new Rotamer[2];
             rotamers[0] = new Rotamer(AminoAcid3.GLU, resState, titrationUtils, values);
             rotamers[1] = new Rotamer(AminoAcid3.GLH, resState, titrationUtils, values);
             return rotamers;
           case HIS:
             rotamers = new Rotamer[3];
             rotamers[0] = new Rotamer(AminoAcid3.HIS, resState, titrationUtils, values);
             rotamers[1] = new Rotamer(AminoAcid3.HID, resState, titrationUtils, values);
             rotamers[2] = new Rotamer(AminoAcid3.HIE, resState, titrationUtils, values);
             return rotamers;
           case LYS:
             rotamers = new Rotamer[2];
             rotamers[0] = new Rotamer(AminoAcid3.LYS, resState, titrationUtils, values);
             rotamers[1] = new Rotamer(AminoAcid3.LYD, resState, titrationUtils, values);
             return rotamers;
           case CYS:
             rotamers = new Rotamer[2];
             rotamers[0] = new Rotamer(AminoAcid3.CYS, resState, titrationUtils, values);
             rotamers[1] = new Rotamer(AminoAcid3.CYD, resState, titrationUtils, values);
             return rotamers;
           default:
             // Null TitrationUtils reference indicates this residue does not support titration.
             rotamers = new Rotamer[1];
             rotamers[0] = new Rotamer(residue.getAminoAcid3(), resState, null, values);
             return rotamers;
         }
       case NA:
         // Null TitrationUtils reference indicates this residue does not support titration.
         Rotamer[] rotamers = new Rotamer[1];
         rotamers[0] = new Rotamer(residue.getNucleicAcid3(), resState, null, values);
         return rotamers;
       case UNK:
       default:
         // Null TitrationUtils reference to indicates this residue does not support titration.
         rotamers = new Rotamer[1];
         rotamers[0] = new Rotamer(resState, null, values);
         return rotamers;
     }
   }
 
   /**
    * toAngleString.
    *
    * @return a {@link java.lang.String} object.
    */
   public String toAngleString() {
     StringBuilder sb = new StringBuilder();
     int n = max(4, length);
     for (int i = 0; i < n; i++) {
       sb.append(String.format(" %6.1f %4.1f", angles[i], sigmas[i]));
     }
     return sb.toString();
   }
 
   /** {@inheritDoc} */
   @Override
   public String toString() {
     StringBuilder sb = new StringBuilder(getName());
     int n = max(4, length);
     for (int i = 0; i < n; i++) {
       sb.append(String.format(" %6.1f %4.1f", angles[i], sigmas[i]));
     }
     return sb.toString();
   }
 
   public String getName() {
     if (aminoAcid3 != null) {
       return aminoAcid3.toString();
     } else if (nucleicAcid3 != null) {
       return nucleicAcid3.toString();
     } else {
       return "";
     }
   }
 
   public double getRotamerPhBias() {
     return titrationUtils.getRotamerPhBias(aminoAcid3);
   }
 
   public double[] getAngles() {
     return angles;
   }
 
 }