// ******************************************************************************
   //
   // 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.parsers;
  
  import ffx.potential.parameters.AngleTorsionType;
  import ffx.potential.parameters.AngleType;
  import ffx.potential.parameters.AtomType;
  import ffx.potential.parameters.BioType;
  import ffx.potential.parameters.BondType;
  import ffx.potential.parameters.ForceField;
  import ffx.potential.parameters.MultipoleType;
  import ffx.potential.parameters.OutOfPlaneBendType;
  import ffx.potential.parameters.PiOrbitalTorsionType;
  import ffx.potential.parameters.StretchBendType;
  import ffx.potential.parameters.StretchTorsionType;
  import ffx.potential.parameters.TorsionTorsionType;
  import ffx.potential.parameters.TorsionType;
  import ffx.potential.parameters.UreyBradleyType;
  import ffx.potential.parameters.VDWType;
  import org.w3c.dom.Document;
  import org.w3c.dom.Element;
  
  import javax.xml.parsers.DocumentBuilder;
  import javax.xml.parsers.DocumentBuilderFactory;
  import javax.xml.transform.OutputKeys;
  import javax.xml.transform.Transformer;
  import javax.xml.transform.TransformerException;
  import javax.xml.transform.TransformerFactory;
  import javax.xml.transform.dom.DOMSource;
  import javax.xml.transform.stream.StreamResult;
  import java.text.SimpleDateFormat;
  import java.util.ArrayList;
  import java.util.Date;
  import java.util.HashMap;
  import java.util.List;
  import java.util.Map;
  import java.util.logging.Logger;
  
  /**
   * The OpenMMXmlFilter class creates an OpenMM-style XML file from a ForceField object. Work is underway to parse
   * OpenMM XML files into ForceField objects (AMBER & CHARMM).
   *
   * @author Jacob M. Miller
   */
  public class OpenMMXmlFilter {
  
    /**
     * A Logger for the XmlFilter class.
     */
    private static final Logger logger = Logger.getLogger(OpenMMXmlFilter.class.getName());
  
    /**
     * The ForceField object that will be written to an XML.
     */
    private final ForceField forceField;
  
    /**
     * The path to write the XML file to. Should not include '.xml' on end.
     */
    private String outputName;
  
    /**
     * Constructor for outputting XML.
     *
    * @param forceField a {@link ffx.potential.parameters.ForceField} object.
    */
   public OpenMMXmlFilter(ForceField forceField) {
     this.forceField = forceField;
   }
 
   /**
    * Constructor for outputting XML with output path specified.
    *
    * @param forceField a {@link ffx.potential.parameters.ForceField} object.
    * @param saveName   a String with the output path.
    */
   public OpenMMXmlFilter(ForceField forceField, String saveName) {
     this.forceField = forceField;
     this.outputName = saveName;
   }
 
   /**
    * Create an OpenMM XML file for the given force field.
    *
    * @throws Exception
    */
   public void toXML() throws Exception {
     // CREATE XML ROOT NODES AND FILL IN BASIC INFO
     // Instantiate Document building objects
     DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
     DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
     Document doc = dBuilder.newDocument();
 
     // Create Root Node "ForceField"
     Element rootElement = doc.createElement("ForceField");
     doc.appendChild(rootElement);
 
     // Create Info Section
     Element infoNode = doc.createElement("Info");
     rootElement.appendChild(infoNode);
 
     // Set Source node to the force field name
     Element srcNode = doc.createElement("Source");
     srcNode.setTextContent(forceField.getString("forcefield", "UNKNOWN"));
     infoNode.appendChild(srcNode);
 
     // Set the date
     Element dateNode = doc.createElement("DateGenerated");
     SimpleDateFormat ft = new SimpleDateFormat("yyyy-MM-dd");
     String date = ft.format(new Date());
     dateNode.setTextContent(date);
     infoNode.appendChild(dateNode);
 
     // Add Atom Types
     Element atomTypes = AtomType.getXMLAtomTypes(doc, forceField);
     if (atomTypes != null) {
       rootElement.appendChild(atomTypes);
     } else {
       throw new Exception(" The force field defines no atom types.");
     }
 
     // Add Residues
     Map<String, BioType> bioTypes = forceField.getBioTypeMap();
     if (!bioTypes.values().isEmpty()) {
       Map<String, ArrayList<BioType>> moleculeDict = new HashMap<>();
       for (BioType bioType : bioTypes.values()) {
         if (!moleculeDict.containsKey(bioType.moleculeName)) {
           moleculeDict.put(bioType.moleculeName, new ArrayList<>());
         }
         ArrayList<BioType> moleculeBioTypes = moleculeDict.get(bioType.moleculeName);
         moleculeBioTypes.add(bioType);
       }
       Element residuesNode = doc.createElement("Residues");
       buildExtraResidues(moleculeDict, doc, residuesNode);
       rootElement.appendChild(residuesNode);
     } else {
       logger.info("WARNING: No BioTypes defined for force field, therefore no OpenMM residues are created.");
     }
 
     // Add Bond Types
     Element bondForce = BondType.getXMLForce(doc, forceField);
     if (bondForce != null) {
       rootElement.appendChild(bondForce);
     }
 
     // Add Angle Types
     Element angleForce = AngleType.getXMLForce(doc, forceField);
     if (angleForce != null) {
       rootElement.appendChild(angleForce);
     }
 
     // Add OutOfPlaneBend Types
     Element outOfPlaneBendForce = OutOfPlaneBendType.getXMLForce(doc, forceField);
     if (outOfPlaneBendForce != null) {
       rootElement.appendChild(outOfPlaneBendForce);
     }
 
     // Add Torsion Types
     Element torsionForce = TorsionType.getXMLForce(doc, forceField);
     if (torsionForce != null) {
       rootElement.appendChild(torsionForce);
     }
 
     // Add PiOrbitalTorsion Types
     Element piOrbitalTorsionForce = PiOrbitalTorsionType.getXMLElement(doc, forceField);
     if (piOrbitalTorsionForce != null) {
       rootElement.appendChild(piOrbitalTorsionForce);
     }
 
     // Add StretchTorsion Types
     Element stretchTorsionForce = StretchTorsionType.getXMLForce(doc, forceField);
     if (stretchTorsionForce != null) {
       rootElement.appendChild(stretchTorsionForce);
     }
 
     // Add AngleTorsion Types
     Element angleTorsionForce = AngleTorsionType.getXMLForce(doc, forceField);
     if (angleTorsionForce != null) {
       rootElement.appendChild(angleTorsionForce);
     }
 
     // Add StretchBend Types
     Element stretchBendForce = StretchBendType.getXMLForce(doc, forceField);
     if (stretchBendForce != null) {
       rootElement.appendChild(stretchBendForce);
     }
 
     // Add TorsionTorsion Type
     Element torsionTorsionForce = TorsionTorsionType.getXMLForce(doc, forceField);
     if (torsionTorsionForce != null) {
       rootElement.appendChild(torsionTorsionForce);
     }
 
     // Add VDW and VDWPair Types
     Element vdwForce = VDWType.getXMLForce(doc, forceField);
     if (vdwForce != null) {
       rootElement.appendChild(vdwForce);
     }
 
     // Add Multipole and Polarize Types
     Element multipoleForce = MultipoleType.getXMLForce(doc, forceField);
     if (multipoleForce != null) {
       rootElement.appendChild(multipoleForce);
     }
 
     // Add UreyBradley Types
     Element ureyBradleyForce = UreyBradleyType.getXMLForce(doc, forceField);
     if (ureyBradleyForce != null) {
       rootElement.appendChild(ureyBradleyForce);
     }
 
     // Write XML to 'force field name'.xml
     writeXML(doc);
   }
 
   /**
    * Build residues not found in OpenMM finalResidues.xml
    *
    * @param moleculeDict Map containing molecules and their BioTypes.
    * @param doc          Document with XML Nodes.
    * @param residuesNode Residues Node that will contain individual Residue nodes with Atoms and Bonds.
    */
   private static void buildExtraResidues(Map<String, ArrayList<BioType>> moleculeDict, Document doc, Element residuesNode) {
     // Loop over molecules
     for (String mol : moleculeDict.keySet()) {
       // Create Residue node for each molecule
       Element resNode = doc.createElement("Residue");
       resNode.setAttribute("name", mol);
       residuesNode.appendChild(resNode);
       List<String> order = new ArrayList<>();
       List<String> froms = new ArrayList<>();
       List<String> tos = new ArrayList<>();
 
       // Go through all atoms inside the molecule (keys)
       int atomCount = 0;
       int bondCount = 0;
       for (BioType bioType : moleculeDict.get(mol)) {
         String atom = bioType.atomName;
         Element atomNode = doc.createElement("Atom");
         atomNode.setAttribute("name", atom);
         atomNode.setAttribute("type", String.valueOf(bioType.atomType));
         resNode.appendChild(atomNode);
         atomCount++;
         String[] bonds = bioType.bonds;
         // Go through all atoms (bonds) that the defined atom is bonded to
         for (String bond : bonds) {
           BioType bondBioType = null;
           for (BioType bioType2 : moleculeDict.get(mol)) {
             if (bioType2.atomName.equals(bond)) {
               bondBioType = bioType2;
               break;
             }
           }
 
           // Record each bond and avoid duplicates by only adding the bond if the atomType is less than the bondAtomType.
           if (bioType.index < bondBioType.index) {
             froms.add(atom);
             tos.add(bond);
             bondCount++;
           }
         }
         // Add each atom in the order they have been added to the Residue node.
         order.add(atom);
       }
 
       // add Bond nodes using the order the Atom nodes were placed
       for (int i = 0; i < froms.size(); i++) {
         Element bondNode = doc.createElement("Bond");
         bondNode.setAttribute("from", String.valueOf(order.indexOf(froms.get(i))));
         bondNode.setAttribute("to", String.valueOf(order.indexOf(tos.get(i))));
         resNode.appendChild(bondNode);
       }
       logger.info(" Added " + atomCount + " atoms and "
           + bondCount + " bonds to residue " + mol + ".");
     }
   }
 
   /**
    * Create an OpenMM-style XML file from the Document object that was created in toXML().
    *
    * @param doc Document object containing XML nodes.
    * @throws TransformerException
    */
   private void writeXML(Document doc) throws TransformerException {
     String saveName;
     if (outputName != null) {
       saveName = outputName;
     } else {
       saveName = forceField.getString("forcefield", "UNKNOWN");
     }
 
     TransformerFactory tfFactory = TransformerFactory.newInstance();
     Transformer transformer = tfFactory.newTransformer();
 
     transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes"); // if want to hide first line XML version/encoding
     transformer.setOutputProperty(OutputKeys.INDENT, "yes"); // print with indentation
 
     DOMSource src = new DOMSource(doc);
     StreamResult result = new StreamResult(saveName + ".xml");
     transformer.transform(src, result);
   }
 }