// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2024.
   //
   // 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,
  // provided that you also meet, for each linked independent module, the terms
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  // module which is not derived from or based on this library. If you modify this
  // library, you may extend this exception to your version of the library, but
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  // exception statement from your version.
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  // ******************************************************************************
  package ffx.potential.parameters;
  
  import static ffx.potential.parameters.ForceField.ForceFieldType.IMPTORS;
  import static ffx.utilities.PropertyGroup.EnergyUnitConversion;
  import static ffx.utilities.PropertyGroup.PotentialFunctionParameter;
  import static java.lang.Double.parseDouble;
  import static java.lang.Integer.parseInt;
  import static org.apache.commons.math3.util.FastMath.cos;
  import static org.apache.commons.math3.util.FastMath.sin;
  import static org.apache.commons.math3.util.FastMath.toRadians;
  
  import ffx.utilities.FFXProperty;
  
  import java.util.Arrays;
  import java.util.Comparator;
  import java.util.HashMap;
  import java.util.logging.Level;
  import java.util.logging.Logger;
  
  /**
   * The ImproperTorsionType class defines an improper torsion.
   *
   * @author Michael J. Schnieders
   * @since 1.0
   */
  @FFXProperty(name = "imptors", clazz = String.class, propertyGroup = PotentialFunctionParameter, description = """
      [4 integers and up to 3 real/real/integer triples]
      Provides the values for a single AMBER-style improper torsional angle parameter.
      The first four integer modifiers give the atom class numbers for the atoms involved in the improper torsional angle to be defined.
      By convention, the third atom class of the four is the trigonal atom on which the improper torsion is centered.
      The torsional angle computed is literally that defined by the four atom classes in the order specified by the keyword.
      Each of the remaining triples of real/real/integer modifiers give the half-amplitude,
      phase offset in degrees and periodicity of a particular improper torsional term, respectively.
      Periodicities through 3-fold are allowed for improper torsional parameters.
      """)
  public final class ImproperTorsionType extends BaseType implements Comparator<String> {
  
    /**
     * A Logger for the ImproperTorsionType class.
     */
    private static final Logger logger = Logger.getLogger(ImproperTorsionType.class.getName());
  
    /**
     * Atom classes that for this Improper Torsion angle.
     */
    public final int[] atomClasses;
    /**
     * Force constant in kcal/mol.
     */
    public final double k;
    /**
     * Phases in degrees.
     */
    public final double phase;
    /**
     * Periodicity (should be 2 for an Improper Torsion).
     */
    public final int periodicity;
    /**
     * Value of cos(toRadians(phase)).
     */
    public final double cos;
   /**
    * Value of sin(toRadians(phase)).
    */
   public final double sin;
 
   /**
    * Convert angle bending energy to kcal/mole.
    */
   @FFXProperty(name = "imptorunit", propertyGroup = EnergyUnitConversion, defaultValue = "1.0", description = """
       Sets the scale factor needed to convert the energy value computed by the AMBER-style improper
       torsional angle potential into units of kcal/mole.
       The correct value is force field dependent and typically provided in the header of the master force field parameter file.
       """)
   public double impTorUnit = DEFAULT_IMPTOR_UNIT;
   public static final double DEFAULT_IMPTOR_UNIT = 1.0;
 
   /**
    * TorsionType Constructor.
    *
    * @param atomClasses Atom classes.
    * @param k           Force constant.
    * @param phase       The phase.
    * @param periodicity The periodicity.
    */
   public ImproperTorsionType(int[] atomClasses, double k, double phase, int periodicity) {
     super(IMPTORS, sortKey(atomClasses));
     this.atomClasses = atomClasses;
     double symm = 1.0;
     this.periodicity = periodicity;
     this.k = k / symm;
     this.phase = phase;
     cos = cos(toRadians(phase));
     sin = sin(toRadians(phase));
 
     assert (periodicity == 2);
   }
 
   /**
    * Average two ImproperTorsionType instances. The atom classes that define the new type must be
    * supplied.
    *
    * @param improperTorsionType1 a {@link ffx.potential.parameters.ImproperTorsionType} object.
    * @param improperTorsionType2 a {@link ffx.potential.parameters.ImproperTorsionType} object.
    * @param atomClasses          an array of {@link int} objects.
    * @return a {@link ffx.potential.parameters.ImproperTorsionType} object.
    */
   public static ImproperTorsionType average(ImproperTorsionType improperTorsionType1,
                                             ImproperTorsionType improperTorsionType2, int[] atomClasses) {
 
     if (improperTorsionType1 == null || improperTorsionType2 == null || atomClasses == null) {
       return null;
     }
 
     int periodicity = improperTorsionType1.periodicity;
     if (periodicity != improperTorsionType2.periodicity) {
       return null;
     }
 
     double forceConstant = (improperTorsionType1.k + improperTorsionType2.k) / 2.0;
     double phase = (improperTorsionType1.phase + improperTorsionType2.phase) / 2.0;
 
     return new ImproperTorsionType(atomClasses, forceConstant, phase, periodicity);
   }
 
   /**
    * Construct an ImproperTorsionType from an input string.
    *
    * @param input  The overall input String.
    * @param tokens The input String tokenized.
    * @return an ImproperTorsionType instance.
    */
   public static ImproperTorsionType parse(String input, String[] tokens) {
     if (tokens.length < 8) {
       logger.log(Level.WARNING, "Invalid IMPTORS type:\n{0}", input);
     } else {
       try {
         int[] atomClasses = new int[4];
         atomClasses[0] = parseInt(tokens[1]);
         atomClasses[1] = parseInt(tokens[2]);
         atomClasses[2] = parseInt(tokens[3]);
         atomClasses[3] = parseInt(tokens[4]);
         double k = parseDouble(tokens[5]);
         double phase = parseDouble(tokens[6]);
         int period = parseInt(tokens[7]);
         return new ImproperTorsionType(atomClasses, k, phase, period);
       } catch (NumberFormatException e) {
         String message = "Exception parsing IMPTORS type:\n" + input + "\n";
         logger.log(Level.SEVERE, message, e);
       }
     }
     return null;
   }
 
   /**
    * This method sorts the atom classes for the improper torsion.
    *
    * @param c atomClasses
    * @return lookup key
    * @since 1.0
    */
   public static String sortKey(int[] c) {
     if (c == null || c.length != 4) {
       return null;
     }
     return c[0] + " " + c[1] + " " + c[2] + " " + c[3];
   }
 
   /**
    * Returns true if the atoms can be assigned this improperTorsionType.
    *
    * @param inputClasses          The atom classes will be re-ordered if its member atoms match this
    *                              ImproperTorsionType. The trigonal atom will not change position.
    * @param allowInitialWildCards Allow wildcard match to first two classes.
    * @param allowFinalWildCard    Allow wildcard match for final class.
    * @return True if this torsionType is assignable to the atom array.
    */
   public boolean assigned(int[] inputClasses, boolean allowInitialWildCards,
                           boolean allowFinalWildCard) {
     // Assign the trigonal atom.
     if (inputClasses[2] != atomClasses[2]) {
       return false;
     }
 
     // Assign the final atom.
     if (inputClasses[3] == atomClasses[3] || (atomClasses[3] == 0 && allowFinalWildCard)) {
       // do nothing.
     } else if (inputClasses[1] == atomClasses[3]) {
       int temp = inputClasses[3];
       inputClasses[3] = inputClasses[1];
       inputClasses[1] = temp;
     } else if (inputClasses[0] == atomClasses[3]) {
       int temp = inputClasses[3];
       inputClasses[3] = inputClasses[0];
       inputClasses[0] = temp;
     } else {
       return false;
     }
 
     // Assign the second atom.
     if (inputClasses[1] == atomClasses[1] || (atomClasses[1] == 0 && allowInitialWildCards)) {
       // Do nothing.
     } else if (inputClasses[0] == atomClasses[1]) {
       int temp = inputClasses[1];
       inputClasses[1] = inputClasses[0];
       inputClasses[0] = temp;
     } else {
       return false;
     }
 
     // Assign the first atom.
     return (inputClasses[0] == atomClasses[0] || (atomClasses[0] == 0 && allowInitialWildCards));
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Implements the Comparator interface.
    *
    * @since 1.0
    */
   @Override
   public int compare(String s1, String s2) {
     String[] keys1 = s1.split(" ");
     String[] keys2 = s2.split(" ");
     int[] c1 = new int[4];
     int[] c2 = new int[4];
 
     for (int i = 0; i < 4; i++) {
       c1[i] = parseInt(keys1[i]);
       c2[i] = parseInt(keys2[i]);
     }
 
     if (c1[2] < c2[2]) {
       return -1;
     } else if (c1[2] > c2[2]) {
       return 1;
     } else if (c1[0] < c2[0]) {
       return -1;
     } else if (c1[0] > c2[0]) {
       return 1;
     } else if (c1[1] < c2[1]) {
       return -1;
     } else if (c1[1] > c2[1]) {
       return 1;
     } else if (c1[3] < c2[3]) {
       return -1;
     } else if (c1[3] > c2[3]) {
       return 1;
     }
 
     return 0;
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Override the default <code>equals</code> method.
    *
    * @since 1.0
    */
   @Override
   public boolean equals(Object o) {
     if (this == o) {
       return true;
     }
     if (o == null || getClass() != o.getClass()) {
       return false;
     }
     ImproperTorsionType improperTorsionType = (ImproperTorsionType) o;
     return Arrays.equals(atomClasses, improperTorsionType.atomClasses);
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Implementation of the <code>hashCode</code> method.
    *
    * @since 1.0
    */
   @Override
   public int hashCode() {
     return Arrays.hashCode(atomClasses);
   }
 
   /**
    * incrementClasses
    *
    * @param increment The increment to add to the atom classes.
    */
   public void incrementClasses(int increment) {
     for (int i = 0; i < atomClasses.length; i++) {
       if (atomClasses[i] != 0) {
         atomClasses[i] += increment;
       }
     }
     setKey(sortKey(atomClasses));
   }
 
   /**
    * Check if this Improper Torsion Type is defined by 1 or more atom classes equal to zero.
    *
    * @return True if there are no zero "wildcard" atom classes for this type.
    */
   public boolean noZeroClasses() {
     return atomClasses[0] != 0 && atomClasses[1] != 0 && atomClasses[3] != 0;
   }
 
   /**
    * Remap new atom classes to known internal ones.
    *
    * @param typeMap a lookup between new atom types and known atom types.
    */
   public void patchClasses(HashMap<AtomType, AtomType> typeMap) {
     int count = 0;
     for (AtomType newType : typeMap.keySet()) {
       for (int atomClass : atomClasses) {
         if (atomClass == newType.atomClass) {
           count++;
         }
       }
     }
     if (count > 0 && count < atomClasses.length) {
       for (AtomType newType : typeMap.keySet()) {
         for (int i = 0; i < atomClasses.length; i++) {
           if (atomClasses[i] == newType.atomClass) {
             AtomType knownType = typeMap.get(newType);
             atomClasses[i] = knownType.atomClass;
           }
         }
       }
       setKey(sortKey(atomClasses));
     }
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Nicely formatted Torsion angle.
    *
    * @since 1.0
    */
   @Override
   public String toString() {
     StringBuilder imptorsBuffer = new StringBuilder("imptors");
     for (int i : atomClasses) {
       imptorsBuffer.append(String.format(" %5d", i));
     }
     imptorsBuffer.append(String.format(" %7.3f %7.3f %1d", k, phase, periodicity));
 
     return imptorsBuffer.toString();
   }
 }