//******************************************************************************
   //
   // 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.
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  // 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
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  // permission to link this library with independent modules to produce an
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  //******************************************************************************
  package ffx.algorithms.commands;
  
  import ffx.algorithms.cli.AlgorithmsCommand;
  import ffx.numerics.Potential;
  import ffx.potential.ForceFieldEnergy;
  import ffx.potential.MolecularAssembly;
  import ffx.potential.bonded.Polymer;
  import ffx.potential.bonded.Residue;
  import ffx.potential.bonded.Rotamer;
  import ffx.potential.bonded.RotamerLibrary;
  import ffx.potential.parameters.ForceField;
  import ffx.potential.parsers.ForceFieldFilter;
  import ffx.potential.parsers.PDBFilter;
  import ffx.utilities.FFXBinding;
  import ffx.utilities.Keyword;
  import org.apache.commons.configuration2.CompositeConfiguration;
  import picocli.CommandLine.Command;
  import picocli.CommandLine.Option;
  import picocli.CommandLine.Parameters;
  
  import java.io.File;
  import java.util.ArrayList;
  import java.util.Arrays;
  import java.util.Collections;
  import java.util.List;
  
  import static ffx.utilities.StringUtils.parseAtomRanges;
  
  /**
   * The MutatePDB script mutates residue(s) of a PDB file.
   * <br>
   * Usage:
   * <br>
   * ffxc MutatePDB [options] &lt;pdb&gt;
   */
  @Command(description = " Mutate PDB residue(s).", name = "MutatePDB")
  public class MutatePDB extends AlgorithmsCommand {
  
    /**
     * -r or --resid Residue numbers.
     */
    @Option(names = {"--resid", "-r"}, paramLabel = "1", defaultValue = "1",
        description = "Residue number(s).")
    private String resIDs;
  
    /**
     * -n or --resname New residue names.
     */
    @Option(names = {"--resname", "-n"}, paramLabel = "ALA", defaultValue = "ALA",
        description = "New residue name(s).")
    private String resNameString;
  
    /**
     * -ch or --chain Single character chain name (default is ' '). If only one chain exists, that chain will be mutated.
     */
    @Option(names = {"--chain", "--ch"}, paramLabel = " ", defaultValue = " ",
        description = "Single character chain name (default is ' ').")
    private String chainString;
  
    /**
     * -R or --rotamer Rotamer number to apply.
     */
   @Option(names = {"--rotamer", "-R"}, paramLabel = "-1", defaultValue = "-1",
       description = "Rotamer number to apply.")
   private int rotamer;
 
   /**
    * --allChains  Mutate all copies of a chain in a multimeric protein.
    */
   @Option(names = {"--allChains"}, paramLabel = "false", defaultValue = "false",
       description = "Mutate all copies of a chains in a multimeric protein.")
   private boolean allChains;
 
   /**
    * A PDB filename.
    */
   @Parameters(arity = "1", paramLabel = "file",
       description = "A PDB input file.")
   private String filename;
 
   private ForceFieldEnergy forceFieldEnergy;
 
   /**
    * MutatePDB Constructor.
    */
   public MutatePDB() {
     super();
   }
 
   /**
    * MutatePDB Constructor.
    *
    * @param binding The Binding to use.
    */
   public MutatePDB(FFXBinding binding) {
     super(binding);
   }
 
   /**
    * MutatePDB constructor that sets the command line arguments.
    *
    * @param args Command line arguments.
    */
   public MutatePDB(String[] args) {
     super(args);
   }
 
   /**
    * Execute the script.
    */
   @Override
   public MutatePDB run() {
 
     if (!init()) {
       return this;
     }
 
     // The "false" assembly provides access to the chainIDs without compromising the mutated molecular assembly.
     // Used if --allChains is true.
 
     // Load the MolecularAssembly.
     MolecularAssembly falseAssembly = getActiveAssembly(filename);
     if (falseAssembly == null) {
       logger.info(helpString());
       return this;
     }
 
     List<Integer> resIDint = parseAtomRanges("residueID", resIDs, falseAssembly.getAtomList().size());
 
     String[] resNameArr = Arrays.stream(resNameString.split("\\.|,|;")).map(String::trim).toArray(String[]::new);
 
     String[] chainStringArr = Arrays.stream(chainString.split("\\.|,|;")).map(String::trim).toArray(String[]::new);
     String s = "";
     for (String sub : chainStringArr) {
       if (sub.length() >= 2) {
         logger.warning("Chain ID's have to be single characters separated by commas!");
         return this;
       } else {
         s += sub;
       }
     }
     char[] chainArr = s.toCharArray();
 
     // For every chain, mutate the residue.
     Polymer[] chains = falseAssembly.getChains();
 
     if (chains.length == 1 && chainArr.length == 0) {
       chainArr = new char[]{chains[0].getChainID()};
     }
 
     if (resIDint.size() != resNameArr.length) { // || resIDint.size() != chainArr.length) {
       logger.warning("The number of chains, residue names, and residue ids must be the same!");
       return this;
     }
 
     int destRotamer = 0;
     if (rotamer > -1) {
       destRotamer = rotamer;
     }
 
     // Read in command line.
     File structureFile = new File(filename);
     int index = filename.lastIndexOf(".");
     String name = filename.substring(0, index);
     MolecularAssembly molecularAssembly = new MolecularAssembly(name);
     molecularAssembly.setFile(structureFile);
 
     CompositeConfiguration properties = Keyword.loadProperties(structureFile);
     ForceFieldFilter forceFieldFilter = new ForceFieldFilter(properties);
     ForceField forceField = forceFieldFilter.parse();
     molecularAssembly.setForceField(forceField);
 
     PDBFilter pdbFilter = new PDBFilter(structureFile, molecularAssembly, forceField, properties);
 
     List<PDBFilter.Mutation> mutations = new ArrayList<>();
     for (int i = 0; i <= resIDint.size() - 1; i++) {
       // need to add one to get the correct resID because parseAtomRanges removes one
       if (allChains) {
         for (Polymer currentChain : chains) {
           logger.info("\n Mutating residue number " + (resIDint.get(i) + 1) + " of chain " + currentChain.getChainID() + " to " + resNameArr[i]);
           mutations.add(new PDBFilter.Mutation(resIDint.get(i) + 1, currentChain.getChainID(), resNameArr[i]));
         }
       } else {
         logger.info("\n Mutating residue number " + (resIDint.get(i) + 1) + " of chain " + chainArr[i] + " to " + resNameArr[i]);
         mutations.add(new PDBFilter.Mutation(resIDint.get(i) + 1, chainArr[i], resNameArr[i]));
       }
     }
     pdbFilter.mutate(mutations);
 
     pdbFilter.readFile();
     pdbFilter.applyAtomProperties();
     molecularAssembly.finalize(true, forceField);
 
     if (destRotamer > -1) {
       if (allChains) {
         chains = molecularAssembly.getChains();
         for (Polymer currentChain : chains) {
           for (int i = 0; i <= resIDint.size() - 1; i++) {
             Residue residue = currentChain.getResidue(resIDint.get(i) + 1);
             Rotamer[] rotamers = residue.getRotamers();
             if (rotamers != null && rotamers.length > 0) {
               RotamerLibrary.applyRotamer(residue, rotamers[destRotamer]);
             } else {
               logger.info(" No rotamer to apply.");
             }
           }
         }
       } else {
         for (int i = 0; i <= resIDint.size() - 1; i++) {
           Polymer polymer = molecularAssembly.getChain(String.valueOf(chainArr[i]));
           Residue residue = polymer.getResidue(resIDint.get(i) + 1);
           Rotamer[] rotamers = residue.getRotamers();
           if (rotamers != null && rotamers.length > destRotamer) {
             RotamerLibrary.applyRotamer(residue, rotamers[destRotamer]);
           } else {
             logger.info(" No rotamer to apply.");
           }
         }
       }
     }
     pdbFilter.writeFile(structureFile, false);
 
     for (PDBFilter.Mutation mut : mutations) {
       mut.calculateTorsion();
     }
 
     forceFieldEnergy = molecularAssembly.getPotentialEnergy();
 
     return this;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public List<Potential> getPotentials() {
     List<Potential> potentials;
     if (forceFieldEnergy == null) {
       potentials = Collections.emptyList();
     } else {
       potentials = Collections.singletonList(forceFieldEnergy);
     }
     return potentials;
   }
 
 }