// ******************************************************************************
   //
   // 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
  // the Free Software Foundation.
  //
  // Force Field X is distributed in the hope that it will be useful, but WITHOUT
  // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
  // details.
  //
  // You should have received a copy of the GNU General Public License along with
  // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
  // Place, Suite 330, Boston, MA 02111-1307 USA
  //
  // Linking this library statically or dynamically with other modules is making a
  // combined work based on this library. Thus, the terms and conditions of the
  // GNU General Public License cover the whole combination.
  //
  // As a special exception, the copyright holders of this library give you
  // permission to link this library with independent modules to produce an
  // executable, regardless of the license terms of these independent modules, and
  // to copy and distribute the resulting executable under terms of your choice,
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  // ******************************************************************************
  package ffx.potential.bonded;
  
  import ffx.potential.bonded.AminoAcidUtils.AminoAcid3;
  import ffx.potential.parameters.ForceField;
  import ffx.potential.parameters.RelativeSolvationType;
  
  import java.util.HashMap;
  import java.util.Map;
  import java.util.logging.Logger;
  
  import static java.lang.String.format;
  
  /**
   * A relative solvation term for chemical perturbations.
   *
   * @author Michael J. Schnieders
   * @author Jacob M. Litman
   * @since 1.0
   */
  public class RelativeSolvation {
  
    private static final Logger logger = Logger.getLogger(RelativeSolvation.class.getName());
    /** Look-up of non-standard energies. */
    private final Map<String, Double> nonStdEnergies;
    /** Solvation library in use. */
    private final SolvationLibrary solvationLibrary;
  
    /**
     * Constructor for RelativeSolvation.
     *
     * @param solvationLibrary a {@link ffx.potential.bonded.RelativeSolvation.SolvationLibrary}
     *     object.
     * @param forceField a {@link ffx.potential.parameters.ForceField} object.
     */
    public RelativeSolvation(SolvationLibrary solvationLibrary, ForceField forceField) {
      this.solvationLibrary = solvationLibrary;
      nonStdEnergies = new HashMap<>();
      for (RelativeSolvationType rsType : forceField.getRelativeSolvationTypes().values()) {
        String resName = rsType.getResName();
        double e = rsType.getSolvEnergy();
        if (nonStdEnergies.put(resName, e) != null) {
          logger.warning(format(" Repeat relative solvation for %s", resName));
        }
      }
    }
  
    /**
     * Gets the solvation energy (de-solvation penalty) for a given residue, allowing for sequence
     * optimization to include an estimate of energy relative to the unfolded state.
     *
     * @param residue Residue to check
     * @param checkZeroes Throws an error if not in solvation energy library
     * @return Solvation energy
     * @throws java.lang.IllegalArgumentException if any.
     * @throws java.lang.IllegalArgumentException if any.
     */
    public double getSolvationEnergy(Residue residue, boolean checkZeroes)
        throws IllegalArgumentException {
      String resName = "";
      double energy;
      Residue theRes =
          (residue instanceof MultiResidue) ? ((MultiResidue) residue).getActive() : residue;
     switch (theRes.getResidueType()) {
       case AA -> {
         if (theRes instanceof MultiResidue) {
           resName = ((MultiResidue) theRes).getActive().getName();
         } else {
           resName = theRes.getName();
         }
         energy = getAASolvationEnergy(theRes);
       }
       case NA -> {
         if (theRes instanceof MultiResidue) {
           resName = ((MultiResidue) theRes).getActive().getName();
         } else {
           resName = theRes.getName();
         }
         energy = getNASolvationEnergy(theRes);
       }
       default -> energy = 0;
     }
     if (checkZeroes && energy == 0) {
       throw new IllegalArgumentException(
           format(" Zero de-solvation energy for residue %s: likely not in solvation library.",
               resName));
     }
     return energy;
   }
 
   /** {@inheritDoc} */
   @Override
   public String toString() {
     return "Relative solvation library: " + solvationLibrary.toString();
   }
 
   /**
    * Returns amino acid solvation energy based on solvation library.
    *
    * @param residue a {@link ffx.potential.bonded.Residue} object.
    * @return Solvation energy
    */
   private double getAASolvationEnergy(Residue residue) {
     return switch (solvationLibrary) {
       case WOLFENDEN -> getWolfendenSolvationEnergy(residue);
       case CABANI -> getCabaniSolvationEnergy(residue);
       case EXPLICIT -> getExplicitSolvationEnergy(residue);
       case GK -> getGKSolvationEnergy(residue);
       case MACCALLUM_SPC -> getMacCallumSPCSolvationEnergy(residue);
       case MACCALLUM_TIP4P -> getMacCallumTIP4PSolvationEnergy(residue);
       default -> 0;
     };
   }
 
   /**
    * Will return relative solvation energies for nucleic acids; currently returns 0.
    *
    * @param residue a {@link ffx.potential.bonded.Residue} object.
    * @return Relative solvation energy
    */
   private double getNASolvationEnergy(Residue residue) {
     return 0;
   }
 
   /**
    * Will return solvation energies relative to glycine for capped monomers in GK solvent; currently
    * wraps getExplicitSolvationEnergy.
    *
    * @param residue a {@link ffx.potential.bonded.Residue} object.
    * @return Relative solvation energy
    */
   private double getGKSolvationEnergy(Residue residue) {
     return getExplicitSolvationEnergy(residue);
   }
 
   /**
    * Will return solvation energies relative to glycine for capped monomers in AMOEBA solvent;
    * currently approximates this with charging energies in AMOEBA solvent.
    *
    * @param residue a {@link ffx.potential.bonded.Residue} object.
    * @return Relative solvation energy
    */
   private double getExplicitSolvationEnergy(Residue residue) {
     AminoAcid3 name = residue.getAminoAcid3();
     return switch (name) {
       case ALA -> 0.58;
       case CYS -> -0.85;
       case CYD -> -69.82;
       case ASP -> -69.45;
       case ASH -> -4.00;
       case GLU -> -71.40;
       case GLH -> -3.61;
       case PHE -> -1.59;
       case GLY -> 0.67;
       case HIS -> -45.36;
       case HID -> -8.42;
       case HIE -> -7.53;
       case ILE -> 0.14;
       case LYS -> -43.98;
       case LYD -> +0.35;
       case MET -> -3.48;
       case ASN -> -5.89;
       case PRO -> 7.82;
       case GLN -> -6.89;
       case ARG -> -42.57;
       case SER -> -2.14;
       case THR -> 0.58;
       case VAL -> 0.10;
       case TRP -> -4.64;
       case TYR -> 1.76;
       case TYD -> -41.71;
       case UNK -> nonStdEnergies.getOrDefault(residue.getName().toUpperCase(), 0.0);
       default -> 0;
     };
   }
 
   /**
    * Returns absolute solvation energies for side chain analogs as calculated by MacCallum for OPLS
    * in TIP4P solvent.
    *
    * @param residue a {@link ffx.potential.bonded.Residue} object.
    * @return Solvation energy
    */
   private double getMacCallumTIP4PSolvationEnergy(Residue residue) {
     AminoAcid3 name = residue.getAminoAcid3();
     return switch (name) {
       case ALA -> 9.8;
       case CYS -> -0.5;
       case ASP -> -30.5;
       case GLU -> -19.0;
       case PHE -> -1.2;
       case HIS -> -28.0;
       case ILE -> 12.2;
       case LYS -> -13.6;
       case LEU -> 13.7;
       case MET -> -7.1;
       case ASN -> -34.5;
       case GLN -> -31.4;
       case ARG -> -43.9;
       case SER -> -20.2;
       case THR -> -20.3;
       case VAL -> 12.0;
       case TRP -> -16.2;
       case TYR -> -18.8;
       case UNK -> nonStdEnergies.getOrDefault(residue.getName().toUpperCase(), 0.0);
       default -> 0;
     };
   }
 
   /**
    * Returns absolute solvation energies for side chain analogs as calculated by MacCallum for OPLS
    * in SPC solvent.
    *
    * @param residue a {@link ffx.potential.bonded.Residue} object.
    * @return Solvation energy
    */
   private double getMacCallumSPCSolvationEnergy(Residue residue) {
     AminoAcid3 name = residue.getAminoAcid3();
     return switch (name) {
       case ALA -> 9.3;
       case CYS -> -1.1;
       case ASP -> -30.1;
       case GLU -> -18.8;
       case PHE -> -1.4;
       case HIS -> -27.2;
       case ILE -> 11.9;
       case LYS -> -8.6;
       case LEU -> 12.6;
       case MET -> -5.1;
       case ASN -> -34.3;
       case GLN -> -30.8;
       case ARG -> -46.3;
       case SER -> -18.5;
       case THR -> -19.3;
       case VAL -> 11.3;
       case TRP -> -15.1;
       case TYR -> -18.2;
       case UNK -> nonStdEnergies.getOrDefault(residue.getName().toUpperCase(), 0.0);
       default -> 0;
     };
   }
 
   /**
    * Returns absolute solvation energies for side chain analogs as experimentally measured by Cabani
    * et al.
    *
    * @param residue a {@link ffx.potential.bonded.Residue} object.
    * @return Solvation energy
    */
   private double getCabaniSolvationEnergy(Residue residue) {
     AminoAcid3 name = residue.getAminoAcid3();
     switch (name) {
       case ALA:
         return 8.4;
       case CYS:
         return -5.2;
       case ASP:
         return -28.1;
       case GLU:
         return -27.1;
       case PHE:
         return -3.7;
       case HIS:
         return -27.4;
       case ILE:
         return 8.7;
       case LYS:
         return -15.5;
       case LEU:
         return 9.7;
       case MET:
         return 9.0;
       case ASN:
         return -40.6;
       case GLN:
         return -18.7;
       case ARG:
         return -30.1;
       case SER:
         return -21.4;
       case THR:
         return -21.0;
       case VAL:
         return 8.2;
       case TRP:
         return -12.3;
       case TYR:
         return -25.7;
       case UNK:
         return nonStdEnergies.getOrDefault(residue.getName().toUpperCase(), 0.0);
       case GLY:
       case PRO:
       default:
         return 0;
     }
   }
 
   /**
    * Returns absolute solvation energies for side chain analogs as experimentally measured by
    * Wolfenden et al.
    *
    * @param residue a {@link ffx.potential.bonded.Residue} object.
    * @return Solvation energy
    */
   private double getWolfendenSolvationEnergy(Residue residue) {
     AminoAcid3 name = residue.getAminoAcid3();
     switch (name) {
       case ALA:
         return 8.1;
       case CYS:
         return -5.1;
       case ASP:
         return -27.5;
       case GLU:
         return -26.6;
       case PHE:
         return -3.1;
       case HIS:
         return -42.1;
       case ILE:
         return 8.8;
       case LYS:
         return -18.0;
       case LEU:
         return 9.4;
       case MET:
         return -6.1;
       case ASN:
         return -39.9;
       case GLN:
         return -38.7;
       case ARG:
         return -44.8;
       case SER:
         return -20.8;
       case THR:
         return -20.1;
       case VAL:
         return 8.2;
       case TRP:
         return -24.3;
       case TYR:
         return -25.2;
       case UNK:
         return nonStdEnergies.getOrDefault(residue.getName().toUpperCase(), 0.0);
       case GLY:
       case PRO:
       default:
         return 0; // Not listed.
     }
   }
 
   /**
    * Citations: Wolfenden et al: Wolfenden, R., Andersson, L., Cullis, P. M. and Southgate, C. C. B.
    * (1981) AFFINITIES OF AMINO-ACID SIDE-CHAINS FOR SOLVENT WATER. Biochemistry. 20, 849-855
    *
    * <p>Cabani et al: Cabani, S., Gianni, P., Mollica, V. and Lepori, L. (1981) GROUP
    * CONTRIBUTIONS TO THE THERMODYNAMIC PROPERTIES OF NON-IONIC ORGANIC SOLUTES IN DILUTE
    * AQUEOUS-SOLUTION. Journal of Solution Chemistry. 10, 563-595
    *
    * <p>MacCallum OPLS libraries: Maccallum, J. L. and Tieleman, D. P. (2003) Calculation of the
    * water-cyclohexane transfer free energies of neutral amino acid side-chain analogs using the OPLS
    * all-atom force field. Journal of Computational Chemistry. 24, 1930-1935
    */
   public enum SolvationLibrary {
     WOLFENDEN, CABANI, EXPLICIT, GK, MACCALLUM_SPC, MACCALLUM_TIP4P, OPLS_EXPLICIT, OPLS_GK, AUTO, NONE
   }
 }