// ******************************************************************************
   //
   // 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.bonded;
  
  import ffx.numerics.atomic.AtomicDoubleArray3D;
  import ffx.numerics.math.DoubleMath;
  import ffx.potential.bonded.RendererCache.ViewModel;
  import ffx.potential.parameters.AtomType;
  import ffx.potential.parameters.BondType;
  import ffx.potential.parameters.ForceField;
  import org.jogamp.java3d.BranchGroup;
  import org.jogamp.java3d.Geometry;
  import org.jogamp.java3d.LineArray;
  import org.jogamp.java3d.Shape3D;
  import org.jogamp.java3d.Transform3D;
  import org.jogamp.java3d.TransformGroup;
  import org.jogamp.vecmath.AxisAngle4d;
  import org.jogamp.vecmath.Vector3d;
  
  import java.io.Serial;
  import java.util.ArrayList;
  import java.util.List;
  import java.util.logging.Logger;
  
  import static ffx.numerics.math.DoubleMath.X;
  import static ffx.numerics.math.DoubleMath.angle;
  import static ffx.numerics.math.DoubleMath.length;
  import static ffx.numerics.math.DoubleMath.normalize;
  import static ffx.numerics.math.DoubleMath.scale;
  import static ffx.numerics.math.DoubleMath.sub;
  import static java.lang.String.format;
  import static org.apache.commons.math3.util.FastMath.max;
  import static org.apache.commons.math3.util.FastMath.min;
  
  /**
   * The Bond class represents a covalent bond formed between two atoms.
   *
   * @author Michael J. Schnieders
   * @since 1.0
   */
  @SuppressWarnings("CloneableImplementsClone")
  public class Bond extends BondedTerm {
  
    @Serial
    private static final long serialVersionUID = 1L;
  
    /**
     * Length in Angstroms that is added to Atomic Radii when determining if two Atoms are within
     * bonding distance
     */
    static final float BUFF = 0.7f;
  
    private static final Logger logger = Logger.getLogger(Bond.class.getName());
    // Some static variables used for computing cylinder orientations
    private static final float[] a0col = {
        0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f
    };
    private static final float[] f4a = {0.0f, 0.0f, 0.0f, 0.9f};
    private static final float[] f4b = {0.0f, 0.0f, 0.0f, 0.9f};
    private static final float[] f16 = {
        0.0f, 0.0f, 0.0f, 0.9f, 0.0f, 0.0f, 0.0f, 0.9f, 0.0f, 0.0f, 0.0f, 0.9f, 0.0f, 0.0f, 0.0f, 0.9f
    };
    private static final double[] a13d = new double[3];
    private static final double[] a23d = new double[3];
   private static final double[] mid = new double[3];
   private static final double[] diff3d = new double[3];
   private static final double[] sum3d = new double[3];
   private static final double[] coord = new double[12];
   private static final double[] y = {0.0d, 1.0d, 0.0d};
   private static final AxisAngle4d axisAngle = new AxisAngle4d();
   private static final double[] bcross = new double[4];
   private static final double[] cstart = new double[3];
   private static final Vector3d pos3d = new Vector3d();
   /**
    * List of Bonds that this Bond forms angles with
    */
   private final ArrayList<Bond> formsAngleWith = new ArrayList<>();
   /**
    * The force field BondType for this bond.
    */
   public BondType bondType = null;
   /**
    * Rigid Scale factor.
    */
   private double rigidScale = 1.0;
   // Java3D methods and variables for visualization of this Bond.
   private RendererCache.ViewModel viewModel = RendererCache.ViewModel.INVISIBLE;
   private BranchGroup branchGroup;
   private TransformGroup cy1tg, cy2tg;
   private Transform3D cy1t3d, cy2t3d;
   private Shape3D cy1, cy2;
   private Vector3d scale;
   private int detail = 3;
   private LineArray la;
   private int lineIndex;
   private boolean wireVisible = true;
 
   /**
    * Simple Bond constructor that is intended to be used with the <code>equals</code> method.
    *
    * @param n Bond id
    */
   public Bond(String n) {
     super(n);
   }
 
   /**
    * Bond constructor.
    *
    * @param a1 Atom number 1.
    * @param a2 Atom number 2.
    */
   public Bond(Atom a1, Atom a2) {
     atoms = new Atom[2];
     int i1 = a1.getIndex();
     int i2 = a2.getIndex();
     if (i1 < i2) {
       atoms[0] = a1;
       atoms[1] = a2;
     } else {
       atoms[0] = a2;
       atoms[1] = a1;
     }
     setID_Key(false);
     viewModel = RendererCache.ViewModel.WIREFRAME;
     a1.setBond(this);
     a2.setBond(this);
   }
 
   /**
    * Log that no BondType exists.
    *
    * @param a1         Atom 1.
    * @param a2         Atom 2.
    * @param forceField The force field in use.
    */
   public static void logNoBondType(Atom a1, Atom a2, ForceField forceField) {
     AtomType atomType1 = a1.getAtomType();
     AtomType atomType2 = a2.getAtomType();
     int[] c = {atomType1.atomClass, atomType2.atomClass};
     String key = BondType.sortKey(c);
     StringBuilder sb = new StringBuilder(
         format(" No BondType for key: %s\n %s -> %s\n %s -> %s", key,
             a1, atomType1, a2, atomType2));
     int c1 = atomType1.atomClass;
     int c2 = atomType2.atomClass;
     List<AtomType> types1 = forceField.getSimilarAtomTypes(atomType1);
     List<AtomType> types2 = forceField.getSimilarAtomTypes(atomType2);
     List<BondType> bondTypes = new ArrayList<>();
     boolean match = false;
     for (AtomType type1 : types1) {
       for (AtomType type2 : types2) {
         // Similar bond type must match at least one class.
         if ((type1.atomClass != c1) && (type1.atomClass != c2) &&
             (type2.atomClass != c1) && (type2.atomClass != c2)) {
           continue;
         }
         BondType bondType = forceField.getBondType(type1, type2);
         if (bondType != null && !bondTypes.contains(bondType)) {
           if (!match) {
             match = true;
             sb.append("\n Similar Bond Types:");
           }
           bondTypes.add(bondType);
           sb.append(format("\n  %s", bondType));
         }
       }
     }
 
     logger.severe(sb.toString());
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public int compareTo(BondedTerm b) {
     if (b == null) {
       throw new NullPointerException();
     }
     if (b == this) {
       return 0;
     }
     if (!b.getClass().isInstance(this)) {
       return super.compareTo(b);
     }
     int this0 = atoms[0].getIndex();
     int a0 = b.atoms[0].getIndex();
     if (this0 < a0) {
       return -1;
     }
     if (this0 > a0) {
       return 1;
     }
     int this1 = atoms[1].getIndex();
     int a1 = b.atoms[1].getIndex();
 
     return Integer.compare(this1, a1);
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Evaluate this Bond energy.
    */
   @Override
   public double energy(boolean gradient, int threadID, AtomicDoubleArray3D grad, AtomicDoubleArray3D lambdaGrad) {
     value = 0.0;
     energy = 0.0;
     // Only compute this term if at least one atom is being used.
     if (!getUse()) {
       return energy;
     }
     var atomA = atoms[0];
     var atomB = atoms[1];
     var va = atomA.getXYZ();
     var vb = atomB.getXYZ();
     var vab = va.sub(vb);
     value = vab.length();
     var prefactor = bondType.bondUnit * rigidScale * bondType.forceConstant;
     // dv is deviation from ideal
     var dv = value - bondType.distance;
     if (bondType.bondFunction.hasFlatBottom()) {
       if (dv > 0) {
         dv = max(0, dv - bondType.flatBottomRadius);
       } else if (dv < 0) {
         dv = min(0, dv + bondType.flatBottomRadius);
       } // Else, no adjustments needed.
     }
     var dv2 = dv * dv;
     // A Taylor expansion of the Morse potential through the fourth power of the bond length deviation.
     energy = prefactor * dv2 * (1.0 + bondType.cubic * dv + bondType.quartic * dv2);
     if (gradient) {
       // Compute the magnitude of the gradient.
       var dedr = 2.0 * prefactor * dv * (1.0 + 1.5 * bondType.cubic * dv + 2.0 * bondType.quartic * dv2);
       var de = 0.0;
       if (value > 0.0) {
         de = dedr / value;
       }
       var ga = vab.scale(de);
       var ia = atomA.getIndex() - 1;
       var ib = atomB.getIndex() - 1;
       grad.add(threadID, ia, ga);
       grad.sub(threadID, ib, ga);
     }
     value = dv;
     return energy;
   }
 
   /**
    * Find the other Atom in <b>this</b> Bond. These two atoms are said to be 1-2.
    *
    * @param a The known Atom.
    * @return The other Atom that makes up <b>this</b> Bond, or Null if Atom <code>a</code> is not
    * part of
    * <b>this</b> Bond.
    */
   public Atom get1_2(Atom a) {
     if (a == atoms[0]) {
       return atoms[1];
     }
     if (a == atoms[1]) {
       return atoms[0];
     }
     return null; // Atom not found in bond
   }
 
   /**
    * Gets the current distance between the two Atoms in this Bond.
    *
    * @return Current distance.
    */
   public double getCurrentDistance() {
     double[] x1 = new double[3];
     x1 = atoms[0].getXYZ(x1);
     double[] x2 = new double[3];
     x2 = atoms[1].getXYZ(x2);
     return DoubleMath.dist(x1, x2);
   }
 
   /**
    * Log details for this Bond energy term.
    */
   public void log() {
     logger.info(
         format(
             " %-8s %6d-%s %6d-%s %6.4f  %6.4f  %10.4f",
             "Bond",
             atoms[0].getIndex(),
             atoms[0].getAtomType().name,
             atoms[1].getIndex(),
             atoms[1].getAtomType().name,
             bondType.distance,
             value,
             energy));
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public void removeFromParent() {
     super.removeFromParent();
     cy1 = null;
     cy2 = null;
     cy1tg = null;
     cy2tg = null;
     if (cy1t3d != null) {
       RendererCache.poolTransform3D(cy1t3d);
       RendererCache.poolTransform3D(cy2t3d);
       cy1t3d = null;
       cy2t3d = null;
     }
     if (branchGroup != null) {
       branchGroup.detach();
       branchGroup.setUserData(null);
       RendererCache.poolDoubleCylinder(branchGroup);
       branchGroup = null;
     }
   }
 
   /**
    * Set a reference to the force field parameters.
    *
    * @param bondType a {@link ffx.potential.parameters.BondType} object.
    */
   public void setBondType(BondType bondType) {
     this.bondType = bondType;
   }
 
   /**
    * Return the BondType for this Bond.
    *
    * @return Returns the BondType.
    */
   public BondType getBondType() {
     return bondType;
   }
 
   /**
    * Set the color of this Bond's Java3D shapes based on the passed Atom.
    *
    * @param a Atom
    */
   public void setColor(Atom a) {
     if (viewModel != ViewModel.INVISIBLE
         && viewModel != ViewModel.WIREFRAME
         && branchGroup != null) {
       if (a == atoms[0]) {
         cy1.setAppearance(a.getAtomAppearance());
       } else if (a == atoms[1]) {
         cy2.setAppearance(a.getAtomAppearance());
       }
     }
     setWireVisible(wireVisible);
   }
 
   /**
    * Setter for the field <code>rigidScale</code>.
    *
    * @param rigidScale a double.
    */
   public void setRigidScale(double rigidScale) {
     this.rigidScale = rigidScale;
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Polymorphic setView method.
    */
   @Override
   public void setView(RendererCache.ViewModel newViewModel, List<BranchGroup> newShapes) {
     switch (newViewModel) {
       case WIREFRAME -> {
         viewModel = ViewModel.WIREFRAME;
         setWireVisible(true);
         setCylinderVisible(false, newShapes);
       }
       case SPACEFILL, INVISIBLE, RMIN -> {
         viewModel = ViewModel.INVISIBLE;
         setWireVisible(false);
         setCylinderVisible(false, newShapes);
       }
       case RESTRICT -> {
         if (!atoms[0].isSelected() || !atoms[1].isSelected()) {
           viewModel = ViewModel.INVISIBLE;
           setWireVisible(false);
           setCylinderVisible(false, newShapes);
         }
       }
       case BALLANDSTICK, TUBE -> {
         viewModel = newViewModel;
         // Get the radius to use
         double rad;
         double len = getValue() / 2.0d;
         if (viewModel == ViewModel.BALLANDSTICK) {
           rad = 0.1d * RendererCache.radius;
         } else {
           rad = 0.2d * RendererCache.radius;
         }
         if (scale == null) {
           scale = new Vector3d();
         }
         scale.set(rad, len, rad);
         setWireVisible(false);
         setCylinderVisible(true, newShapes);
       }
       case DETAIL -> {
         int res = RendererCache.detail;
         if (res != detail) {
           detail = res;
           if (branchGroup != null) {
             Geometry geom1 = RendererCache.getCylinderGeom(0, detail);
             Geometry geom2 = RendererCache.getCylinderGeom(1, detail);
             Geometry geom3 = RendererCache.getCylinderGeom(2, detail);
             cy1.removeAllGeometries();
             cy2.removeAllGeometries();
             cy1.addGeometry(geom1);
             cy1.addGeometry(geom2);
             cy1.addGeometry(geom3);
             cy2.addGeometry(geom1);
             cy2.addGeometry(geom2);
             cy2.addGeometry(geom3);
           }
         }
         if (scale == null) {
           scale = new Vector3d();
         }
         double newRadius;
         if (viewModel == ViewModel.BALLANDSTICK) {
           newRadius = 0.1d * RendererCache.radius;
         } else if (viewModel == ViewModel.TUBE) {
           newRadius = 0.2d * RendererCache.radius;
         } else {
           break;
         }
         if (newRadius != scale.x) {
           scale.x = newRadius;
           scale.y = newRadius;
           if (branchGroup != null) {
             setView(viewModel, newShapes);
           }
         }
       }
       case SHOWHYDROGEN -> {
         if (atoms[0].getAtomicNumber() == 1 || atoms[1].getAtomicNumber() == 1) {
           setView(viewModel, newShapes);
         }
       }
       case HIDEHYDROGEN -> {
         if (atoms[0].getAtomicNumber() == 1 || atoms[1].getAtomicNumber() == 1) {
           viewModel = ViewModel.INVISIBLE;
           setWireVisible(false);
           setCylinderVisible(false, newShapes);
         }
       }
       case FILL, POINTS, LINES -> {
         if (branchGroup != null && viewModel != ViewModel.INVISIBLE) {
           cy1.setAppearance(atoms[0].getAtomAppearance());
           cy2.setAppearance(atoms[1].getAtomAppearance());
         }
       }
     }
   }
 
   /**
    * setWire
    *
    * @param l a {@link org.jogamp.java3d.LineArray} object.
    * @param i The index of the LineArray to use.
    */
   public void setWire(LineArray l, int i) {
     la = l;
     lineIndex = i;
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Update recomputes bonds length, Wireframe vertices, and Cylinder Transforms
    */
   @Override
   public void update() {
     // Update the Bond Length
     atoms[0].getXYZ(a13d);
     atoms[1].getXYZ(a23d);
     sub(a13d, a23d, diff3d);
     double d = length(diff3d);
     setValue(d);
     DoubleMath.add(a13d, a23d, sum3d);
     scale(sum3d, 0.5d, mid);
     // Update the Wireframe Model.
     if (la != null) {
       for (int i = 0; i < 3; i++) {
         coord[i] = a13d[i];
         coord[3 + i] = mid[i];
         coord[6 + i] = mid[i];
         coord[9 + i] = a23d[i];
       }
       la.setCoordinates(lineIndex, coord);
     }
     // Update the Bond cylinder transforms.
     if (branchGroup != null) {
       normalize(diff3d, diff3d);
       scale.y = d / 2.0d;
       setBondTransform3d(cy1t3d, mid, diff3d, d, true);
       scale(diff3d, -1.0d, diff3d);
       setBondTransform3d(cy2t3d, mid, diff3d, d, false);
       cy1tg.setTransform(cy1t3d);
       cy2tg.setTransform(cy2t3d);
     }
   }
 
   /**
    * Check to see if <b>this</b> Bond and another combine to form an angle
    *
    * @param b a {@link ffx.potential.bonded.Bond} object.
    * @return True if Bond b helps form an angle with <b>this</b> Bond
    */
   boolean formsAngleWith(Bond b) {
     for (Bond bond : formsAngleWith) {
       if (b == bond) {
         return true;
       }
     }
     return false;
   }
 
   /**
    * Finds the common Atom between <b>this</b> Bond and Bond b.
    *
    * @param b Bond to compare with.
    * @return The Atom the Bonds have in common or Null if they are the same Bond or have no atom in
    * common
    */
   Atom getCommonAtom(Bond b) {
     if (b == this || b == null) {
       return null;
     }
     if (b.atoms[0] == atoms[0]) {
       return atoms[0];
     }
     if (b.atoms[0] == atoms[1]) {
       return atoms[1];
     }
     if (b.atoms[1] == atoms[0]) {
       return atoms[0];
     }
     if (b.atoms[1] == atoms[1]) {
       return atoms[1];
     }
     return null; // Common atom not found
   }
 
   /**
    * Find the Atom that <b>this</b> Bond and Bond b do not have in common.
    *
    * @param b Bond to compare with
    * @return The Atom that Bond b and <b>this</b> Bond do not have in common, or Null if they have no
    * Atom in common
    */
   Atom getOtherAtom(Bond b) {
     if (b == this || b == null) {
       return null;
     }
     if (b.atoms[0] == atoms[0]) {
       return atoms[1];
     }
     if (b.atoms[0] == atoms[1]) {
       return atoms[0];
     }
     if (b.atoms[1] == atoms[0]) {
       return atoms[1];
     }
     if (b.atoms[1] == atoms[1]) {
       return atoms[0];
     }
     return null;
   }
 
   /**
    * sameGroup
    *
    * @return a boolean.
    */
   boolean sameGroup() {
     return atoms[0].getParent() == atoms[1].getParent();
   }
 
   /**
    * Specifies <b>this</b> Bond helps form an angle with the given Bond
    *
    * @param b Bond that forms an angle with <b>this</b> Bond
    */
   void setAngleWith(Bond b) {
     formsAngleWith.add(b);
   }
 
   /**
    * Create the Bond Scenegraph Objects.
    *
    * @param newShapes List
    */
   private void initJ3D(List<BranchGroup> newShapes) {
     detail = RendererCache.detail;
     branchGroup = RendererCache.doubleCylinderFactory(atoms[0], atoms[1], detail);
     cy1tg = (TransformGroup) branchGroup.getChild(0);
     cy2tg = (TransformGroup) branchGroup.getChild(1);
     cy1 = (Shape3D) cy1tg.getChild(0);
     cy2 = (Shape3D) cy2tg.getChild(0);
     newShapes.add(branchGroup);
     cy1t3d = RendererCache.transform3DFactory();
     cy2t3d = RendererCache.transform3DFactory();
     update();
   }
 
   /**
    * setBondTransform3d
    *
    * @param t3d    a {@link org.jogamp.java3d.Transform3D} object.
    * @param pos    an array of double.
    * @param orient an array of double.
    * @param len    a double.
    * @param newRot a boolean.
    */
   private void setBondTransform3d(
       Transform3D t3d, double[] pos, double[] orient, double len, boolean newRot) {
     // Bond Orientation
     if (newRot) {
       double angle = angle(orient, y);
       X(y, orient, bcross);
       bcross[3] = angle - Math.PI;
       axisAngle.set(bcross);
     }
     // Scale the orientation vector to be a fourth the bond length
     // and add it to the position vector of the first atom
     scale(orient, len / 4.0d, cstart);
     DoubleMath.add(cstart, pos, cstart);
     pos3d.set(cstart);
     t3d.setTranslation(pos3d);
     t3d.setRotation(axisAngle);
     t3d.setScale(scale);
   }
 
   /**
    * Manage cylinder visibility.
    *
    * @param visible   boolean
    * @param newShapes List
    */
   private void setCylinderVisible(boolean visible, List<BranchGroup> newShapes) {
     if (!visible) {
       // Make this Bond invisible.
       if (branchGroup != null) {
         cy1.setPickable(false);
         cy1.setAppearance(RendererCache.nullAp);
         cy2.setPickable(false);
         cy2.setAppearance(RendererCache.nullAp);
         // branchGroup = null;
       }
     } else if (branchGroup == null) {
       // Get Java3D primitives from the RendererCache
       initJ3D(newShapes);
     } else {
       // Scale the cylinders to match the current ViewModel
       cy1t3d.setScale(scale);
       cy1tg.setTransform(cy1t3d);
       cy2t3d.setScale(scale);
       cy2tg.setTransform(cy2t3d);
       cy1.setAppearance(atoms[0].getAtomAppearance());
       cy2.setAppearance(atoms[1].getAtomAppearance());
     }
   }
 
   /**
    * Manage wireframe visibility.
    *
    * @param visible a boolean.
    */
   private void setWireVisible(boolean visible) {
     if (!visible) {
       wireVisible = false;
       la.setColors(lineIndex, a0col);
     } else {
       wireVisible = true;
       float[] cols = f16;
       float[] col1 = f4a;
       float[] col2 = f4b;
       atoms[0].getAtomColor().get(col1);
       atoms[1].getAtomColor().get(col2);
       for (int i = 0; i < 3; i++) {
         cols[i] = col1[i];
         cols[4 + i] = col1[i];
         cols[8 + i] = col2[i];
         cols[12 + i] = col2[i];
       }
       la.setColors(lineIndex, cols);
     }
   }
 }