// ******************************************************************************
   //
   // 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
  // and conditions of the license of that module. An independent module is a
  // 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
  // you are not obligated to do so. If you do not wish to do so, delete this
  // exception statement from your version.
  //
  // ******************************************************************************
  package ffx.potential.bonded;
  
  import ffx.potential.parameters.ForceField;
  
  import java.io.Serial;
  import java.util.Objects;
  import java.util.logging.Logger;
  
  /**
   * The Molecule class is a general container used for simple compounds or in cases where more
   * specialized classes have not been implemented.
   *
   * @author Michael J. Schnieders
   * @since 1.0
   */
  @SuppressWarnings("CloneableImplementsClone")
  public class Molecule extends MSGroup {
  
    @Serial
    private static final long serialVersionUID = 1L;
  
    private static final Logger logger = Logger.getLogger(Molecule.class.getName());
  
    /** Residue number assigned in PDB files. */
    private int residueNum;
    /** Residue name assigned in PDB files. */
    private String residueName;
    /** Possibly redundant chainID assigned in PDB files. */
    private Character chainID;
    /** Unique segID. */
    private final String segID;
  
    /**
     * Constructor for Molecule.
     *
     * @param name a {@link java.lang.String} object.
     */
    public Molecule(String name) {
      super(name);
      residueName = name;
      residueNum = -1;
      chainID = 'A';
      segID = "A";
    }
  
    /**
     * Constructor for Molecule.
     *
     * @param name a {@link java.lang.String} object.
     * @param residueNum The residue number.
     * @param chainID a {@link java.lang.Character} object.
     * @param segID a {@link java.lang.String} object.
     */
    public Molecule(String name, int residueNum, Character chainID, String segID) {
      super(name + "-" + residueNum + " " + segID);
      this.residueName = name;
      this.residueNum = residueNum;
      this.chainID = chainID;
      this.segID = segID;
    }
  
    /**
    * Setter for the field <code>chainID</code>.
    *
    * @param c a {@link java.lang.Character} object.
    */
   public void setChainID(Character c) {
     chainID = c;
 
     for (Atom atom : getAtomList()) {
       atom.setChainID(c);
     }
   }
 
   /**
    * Setter for the field <code>residueNum</code>.
    *
    * @param residueNum The molecule number.
    */
   public void setResidueNum(int residueNum) {
     this.residueNum = residueNum;
     for (Atom atom : getAtomList()) {
       atom.setResidueNumber(residueNum);
     }
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Allows adding Atom MSNodes to the Molecule.
    */
   @Override
   public MSNode addMSNode(MSNode o) {
     Atom currentAtom = null;
     if (o instanceof Atom) {
       Atom newAtom = (Atom) o;
       Character newAlt = newAtom.getAltLoc();
       MSNode atoms = getAtomNode();
       currentAtom = (Atom) atoms.contains(newAtom);
       if (currentAtom == null) {
         currentAtom = newAtom;
         atoms.add(newAtom);
         setFinalized(false);
       } else {
         // Allow overwriting of the root alternate conformer (' ' or 'A').
         Character currentAlt = currentAtom.getAltLoc();
         if (currentAlt.equals(' ') || currentAlt.equals('A')) {
           if (!newAlt.equals(' ') && !newAlt.equals('A')) {
             newAtom.setXyzIndex(currentAtom.getXyzIndex());
             atoms.remove(currentAtom);
             currentAtom = newAtom;
             atoms.add(currentAtom);
             setFinalized(false);
           }
         }
       }
     } else {
       logger.warning(" Only an Atom can be added to a Residue.");
     }
     return currentAtom;
   }
 
   @Override
   public boolean equals(Object o) {
     if (this == o) {
       return true;
     }
     if (o == null || getClass() != o.getClass()) {
       return false;
     }
     Molecule molecule = (Molecule) o;
     return residueNum == molecule.residueNum
         && Objects.equals(residueName, molecule.residueName)
         && Objects.equals(segID, molecule.segID);
   }
 
   /** {@inheritDoc} */
   @Override
   public void finalize(boolean finalizeGeometry, ForceField forceField) {
     setFinalized(false);
     getAtomNode().setName("Atoms (" + getAtomList().size() + ")");
     if (finalizeGeometry) {
       assignBondedTerms(forceField);
       removeLeaves();
     }
     setCenter(getMultiScaleCenter(false));
     setFinalized(true);
   }
 
   /**
    * getAtom
    *
    * @param name a {@link java.lang.String} object.
    * @return a {@link ffx.potential.bonded.Atom} object.
    */
   public Atom getAtom(String name) {
     for (Atom a : getAtomList()) {
       if (a.getName().equalsIgnoreCase(name)) {
         return a;
       }
     }
     return null;
   }
 
   /**
    * Getter for the field <code>chainID</code>.
    *
    * @return a {@link java.lang.Character} object.
    */
   public Character getChainID() {
     return chainID;
   }
 
   public String getKey() {
     return residueNum + residueName + segID;
   }
 
   /**
    * Getter for the field <code>residueName</code>.
    *
    * @return a {@link java.lang.String} object.
    */
   public String getResidueName() {
     return residueName;
   }
 
   /**
    * getResidueNumber
    *
    * @return The residue number.
    */
   public int getResidueNumber() {
     return residueNum;
   }
 
   /**
    * Getter for the field <code>segID</code>.
    *
    * @return a {@link java.lang.String} object.
    */
   public String getSegID() {
     return segID;
   }
 
   @Override
   public int hashCode() {
     return Objects.hash(residueNum, residueName, segID);
   }
 
   /** {@inheritDoc} */
   @Override
   public void setName(String name) {
     if (name != null) {
       if (segID != null) {
         super.setName(name + "-" + residueNum + " " + segID);
       } else {
         super.setName(name);
       }
       this.residueName = name;
     }
   }
 }