// ******************************************************************************
   //
   // 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,
  // 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.utils;
  
  import ffx.potential.ForceFieldEnergy;
  import ffx.potential.MolecularAssembly;
  import ffx.potential.Utilities;
  import ffx.potential.bonded.RotamerLibrary;
  import ffx.potential.parameters.ForceField;
  import ffx.potential.parsers.ARCFileFilter;
  import ffx.potential.parsers.FileOpener;
  import ffx.potential.parsers.ForceFieldFilter;
  import ffx.potential.parsers.INTFileFilter;
  import ffx.potential.parsers.INTFilter;
  import ffx.potential.parsers.PDBFileFilter;
  import ffx.potential.parsers.PDBFilter;
  import ffx.potential.parsers.PDBFilter.Mutation;
  import ffx.potential.parsers.SystemFilter;
  import ffx.potential.parsers.XYZFileFilter;
  import ffx.potential.parsers.XYZFilter;
  import ffx.utilities.Keyword;
  import org.apache.commons.configuration2.CompositeConfiguration;
  import org.apache.commons.io.FilenameUtils;
  
  import java.io.File;
  import java.io.IOException;
  import java.nio.file.Path;
  import java.nio.file.Paths;
  import java.util.ArrayList;
  import java.util.List;
  import java.util.logging.Level;
  import java.util.logging.Logger;
  
  import static java.lang.String.format;
  
  /**
   * The PotentialsFileOpener class specifies a Runnable object which is constructed with a File and,
   * when run, allows returning any opened MolecularAssembly objects and their associated properties.
   *
   * @author Jacob M. Litman
   * @author Michael J. Schnieders
   * @since 1.0
   */
  public class PotentialsFileOpener implements FileOpener {
  
    private static final Logger logger = Logger.getLogger(PotentialsFileOpener.class.getName());
    private final File file;
    private final Path filepath;
    private final File[] allFiles;
    private final Path[] allPaths;
    private int nThreads = -1;
    private final List<MolecularAssembly> assemblies;
    private final List<CompositeConfiguration> propertyList;
    // Presently, will just be the first element of assemblies.
    private MolecularAssembly activeAssembly;
    private CompositeConfiguration activeProperties;
    private SystemFilter filter;
    private List<Mutation> mutationsToApply;
  
    /**
     * Constructor for PotentialsFileOpener.
     *
     * @param file a {@link java.io.File} object.
     */
   public PotentialsFileOpener(File file) {
     if (!file.exists() || !file.isFile()) {
       throw new IllegalArgumentException(
           String.format(" File %s either did not exist or was not a file.", file.getName()));
     }
     this.file = file;
     Path pwdPath;
     Path absPath;
     try {
       pwdPath = Paths.get(new File("").getCanonicalPath());
     } catch (IOException ex) {
       pwdPath = Paths.get(new File("").getAbsolutePath());
     }
     try {
       absPath = Paths.get(file.getCanonicalPath());
     } catch (IOException ex) {
       absPath = Paths.get(file.getAbsolutePath());
     }
     filepath = pwdPath.relativize(absPath);
     allFiles = new File[1];
     allFiles[0] = this.file;
     allPaths = new Path[1];
     allPaths[0] = this.filepath;
     assemblies = new ArrayList<>();
     propertyList = new ArrayList<>();
   }
 
   /**
    * Constructor for PotentialsFileOpener.
    *
    * @param filename a {@link java.lang.String} object.
    */
   PotentialsFileOpener(String filename) {
     this(new File(filename));
   }
 
   /**
    * Constructor for PotentialsFileOpener.
    *
    * @param filenames an array of {@link java.lang.String} objects.
    */
   PotentialsFileOpener(String[] filenames) {
     if (filenames == null) {
       throw new IllegalArgumentException(" Array of files to be opened was null.");
     }
     int numFiles = filenames.length;
     if (numFiles == 0) {
       throw new IllegalArgumentException(" Array of files to be opened was empty.");
     }
 
     List<File> fileList = new ArrayList<>();
     List<Path> pathList = new ArrayList<>();
     Path pwdPath;
     try {
       pwdPath = Paths.get(new File("").getCanonicalPath());
     } catch (IOException ex) {
       pwdPath = Paths.get(new File("").getAbsolutePath());
     }
     for (String filename : filenames) {
       try {
         File tryFile = new File(filename);
         if (!(tryFile.exists() && tryFile.isFile())) {
           continue;
         }
         Path absPath;
         try {
           absPath = Paths.get(tryFile.getCanonicalPath());
         } catch (IOException ex) {
           absPath = Paths.get(tryFile.getAbsolutePath());
         }
         Path thisPath = pwdPath.relativize(absPath);
         fileList.add(tryFile);
         pathList.add(thisPath);
       } catch (Exception ex) {
         // Simply continue.
       }
     }
     int numAccepted = fileList.size();
     if (numAccepted < 1) {
       throw new IllegalArgumentException(" No valid files could be found to open.");
     }
     allFiles = fileList.toArray(new File[numAccepted]);
     allPaths = pathList.toArray(new Path[numAccepted]);
     this.file = allFiles[0];
     this.filepath = allPaths[0];
     assemblies = new ArrayList<>();
     propertyList = new ArrayList<>();
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Returns all MolecularAssembly objects created by this opener.
    */
   @Override
   public MolecularAssembly[] getAllAssemblies() {
     return assemblies.toArray(new MolecularAssembly[0]);
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Returns the properties of all MolecularAssembly objects created by this opener.
    */
   @Override
   public CompositeConfiguration[] getAllProperties() {
     return propertyList.toArray(new CompositeConfiguration[0]);
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Returns the first MolecularAssembly created by the run() function.
    */
   @Override
   public MolecularAssembly getAssembly() {
     return activeAssembly;
   }
 
   /**
    * Getter for the field <code>filter</code>.
    *
    * @return a {@link ffx.potential.parsers.SystemFilter} object.
    */
   public SystemFilter getFilter() {
     return filter;
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Returns the properties associated with the first MolecularAssembly.
    */
   @Override
   public CompositeConfiguration getProperties() {
     return activeProperties;
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>At present, parses the PDB, XYZ, INT, or ARC file from the constructor and creates
    * MolecularAssembly and properties objects.
    */
   @Override
   public void run() {
     int numFiles = allFiles.length;
     for (int i = 0; i < numFiles; i++) {
       File fileI = allFiles[i];
       Path pathI = allPaths[i];
       MolecularAssembly assembly = new MolecularAssembly(pathI.toString());
       assembly.setFile(fileI);
       CompositeConfiguration properties = Keyword.loadProperties(fileI);
       ForceFieldFilter forceFieldFilter = new ForceFieldFilter(properties);
       ForceField forceField = forceFieldFilter.parse();
       String[] patches = properties.getStringArray("patch");
       for (String patch : patches) {
         logger.info(" Attempting to read force field patch from " + patch + ".");
         CompositeConfiguration patchConfiguration = new CompositeConfiguration();
         try {
           patchConfiguration.addProperty("propertyFile", fileI.getCanonicalPath());
         } catch (IOException e) {
           logger.log(Level.INFO, " Error loading {0}.", patch);
         }
         patchConfiguration.addProperty("parameters", patch);
         forceFieldFilter = new ForceFieldFilter(patchConfiguration);
         ForceField patchForceField = forceFieldFilter.parse();
         forceField.append(patchForceField);
         if (RotamerLibrary.addRotPatch(patch)) {
           logger.info(format(" Loaded rotamer definitions from patch %s.", patch));
         }
       }
       assembly.setForceField(forceField);
       if (new PDBFileFilter().acceptDeep(fileI)) {
         filter = new PDBFilter(fileI, assembly, forceField, properties);
       } else if (new XYZFileFilter().acceptDeep(fileI)) {
         filter = new XYZFilter(fileI, assembly, forceField, properties);
       } else if (new INTFileFilter().acceptDeep(fileI) || new ARCFileFilter().accept(fileI)) {
         filter = new INTFilter(fileI, assembly, forceField, properties);
       } else {
         throw new IllegalArgumentException(
             format(" File %s could not be recognized as a valid PDB, XYZ, INT, or ARC file.",
                 pathI));
       }
 
       /* If on-open mutations requested, add them to filter. */
       if (mutationsToApply != null && !mutationsToApply.isEmpty()) {
         if (!(filter instanceof PDBFilter)) {
           throw new UnsupportedOperationException(
               "Applying mutations during open only supported by PDB filter atm.");
         }
         ((PDBFilter) filter).mutate(mutationsToApply);
       }
 
       if (filter.readFile()) {
         if (!(filter instanceof PDBFilter)) {
           Utilities.biochemistry(assembly, filter.getAtomList());
         }
         filter.applyAtomProperties();
         assembly.finalize(true, forceField);
         ForceFieldEnergy energy;
         if (nThreads > 0) {
           energy = ForceFieldEnergy.energyFactory(assembly, nThreads);
         } else {
           energy = ForceFieldEnergy.energyFactory(assembly);
         }
         assembly.setPotential(energy);
         assemblies.add(assembly);
         propertyList.add(properties);
 
         if (filter instanceof PDBFilter pdbFilter) {
           List<Character> altLocs = pdbFilter.getAltLocs();
           if (altLocs.size() > 1 || altLocs.get(0) != ' ') {
             StringBuilder altLocString = new StringBuilder("\n Alternate locations found [ ");
             for (Character c : altLocs) {
               // Do not report the root conformer.
               if (c == ' ') {
                 continue;
               }
               altLocString.append(format("(%s) ", c));
             }
             altLocString.append("]\n");
             logger.info(altLocString.toString());
           }
 
           /*
            Alternate conformers may have different chemistry, so
            they each need to be their own MolecularAssembly.
           */
           for (Character c : altLocs) {
             if (c.equals(' ') || c.equals('A')) {
               continue;
             }
             MolecularAssembly newAssembly = new MolecularAssembly(pathI.toString());
             newAssembly.setFile(fileI);
             newAssembly.setForceField(assembly.getForceField());
             pdbFilter.setAltID(newAssembly, c);
             pdbFilter.clearSegIDs();
             if (pdbFilter.readFile()) {
               String fileName = assembly.getFile().getAbsolutePath();
               newAssembly.setName(FilenameUtils.getBaseName(fileName) + " " + c);
               filter.applyAtomProperties();
               newAssembly.finalize(true, assembly.getForceField());
               if (nThreads > 0) {
                 energy = ForceFieldEnergy.energyFactory(assembly, nThreads);
               } else {
                 energy = ForceFieldEnergy.energyFactory(assembly);
               }
               newAssembly.setPotential(energy);
               assemblies.add(newAssembly);
             }
           }
         }
       } else {
         logger.warning(String.format(" Failed to read file %s", fileI));
       }
     }
     activeAssembly = assemblies.get(0);
     activeProperties = propertyList.get(0);
   }
 
   /**
    * setMutations.
    *
    * @param mutations a {@link java.util.List} object.
    */
   void setMutations(List<Mutation> mutations) {
     mutationsToApply = mutations;
   }
 
   /**
    * Setter for the field <code>nThreads</code>.
    *
    * @param nThreads Set the number of threads to use for energy calculations.
    */
   void setNThreads(int nThreads) {
     this.nThreads = nThreads;
   }
 }