/**
 * nanocad.java
 * Copyright (c) 1997,1998 Will Ware, all rights reserved.
 * 
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions
 * are met:
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and other materials provided with the distribution.
 * 
 * This software is provided "as is" and any express or implied warranties,
 * including, but not limited to, the implied warranties of merchantability
 * or fitness for any particular purpose are disclaimed. In no event shall
 * Will Ware be liable for any direct, indirect, incidental, special,
 * exemplary, or consequential damages (including, but not limited to,
 * procurement of substitute goods or services; loss of use, data, or
 * profits; or business interruption) however caused and on any theory of
 * liability, whether in contract, strict liability, or tort (including
 * negligence or otherwise) arising in any way out of the use of this
 * software, even if advised of the possibility of such damage.
 */

import java.applet.*;
import java.awt.*;
import java.lang.Math;

public class nanocad extends Applet
{
  public static final String rcsid =
    "$Id: nanocad.java,v 1.30 1999/01/18 05:13:22 wware Exp $";
  private Button emin;
  private Checkbox showForces;
  private Choice knownStructure;
  private Choice getSetStructure;
  private Choice whichElement;
  private group grp;
  private Panel drawingArea;
  private int xxx, yyy;
  private atom atom1;
  private double atom1z;
  private boolean inDrawingArea, needToRepaint;
  private Label atomInfoBlab;
  private textwin structureWindow;
  private textwin debugWindow;
  private String instructions =
    "Mouse operations (S=shift, C=control) / pan: S-drag air\n" +
    "rotate: drag air / zoom: C-drag air horiz / move atom: drag atom\n" +
    "atom info: click atom / add atom: S-click air / delete atom: S-click atom\n" +
    "recenter: C-click air / perspective: C-drag air vert\n" +
    "add bond: S-drag atom to atom / delete bond: C-drag atom to atom\n" +
    "\n" +
    "Double and triple bonds: do repeated add-bonds between the same pair of\n" +
    "atoms. Valences: carbon 4, hydrogen 1, nitrogen 3, oxygen 2\n" +
    "\n" +
    "Loading and saving files must be done by cut-and-paste, due to Java's security\n" +
    "restrictions: an applet cannot read or write files on your hard disk. You can\n" +
    "load and save molecules in three text formats: NanoCAD's native format, PDB\n" +
    "format, and XYZ format. Only NanoCAD's native format will preserve info about\n" +
    "hybridization and bond order, so this is the best way to save molecules between\n" +
    "sessions.\n" +
    "\n" +
    "'Energy Minimize' takes a long time the first time, and any time you change\n" +
    "the structure (add or delete atoms or bonds), and whenever you load a new\n" +
    "structure. For any structural change, it needs to re-figure out the energy\n" +
    "terms.\n" +
    "\n" +
    "Long-range forces (electrostatic and van-der-Waals) are only partially\n" +
    "implemented so far.\n" +
    "\n" +
    "==========================================================================\n" +
    "NanoCAD in Java, January 1999\n" +
    "Copyright (c) 1997,1998,1999 Will Ware, all rights reserved.\n" +
    "\n" +
    "Redistribution and use in source and binary forms, with or without\n" +
    "modification, are permitted provided that the following conditions\n" +
    "are met:\n" +
    "1. Redistributions of source code must retain the above copyright\n" +
    "   notice, this list of conditions and the following disclaimer.\n" +
    "2. Redistributions in binary form must reproduce the above copyright\n" +
    "   notice, this list of conditions and the following disclaimer in the\n" +
    "   documentation and other materials provided with the distribution.\n" +
    "\n" +
    "This software is provided \"as is\" and any express or implied warranties,\n" +
    "including, but not limited to, the implied warranties of merchantability\n" +
    "or fitness for any particular purpose are disclaimed. In no event shall\n" +
    "Will Ware be liable for any direct, indirect, incidental, special,\n" +
    "exemplary, or consequential damages (including, but not limited to,\n" +
    "procurement of substitute goods or services; loss of use, data, or\n" +
    "profits; or business interruption) however caused and on any theory of\n" +
    "liability, whether in contract, strict liability, or tort (including\n" +
    "negligence or otherwise) arising in any way out of the use of this\n" +
    "software, even if advised of the possibility of such damage.\n";
  
  public void clearScreen ()
    {
      Graphics dg = drawingArea.getGraphics();
      Rectangle r = drawingArea.bounds();
      dg.setColor (this.getBackground ());
      dg.fillRect (r.x, r.y, r.width, r.height);
    }
  public void paint (Graphics g)
    {
      clearScreen ();
      grp.paint ();
      needToRepaint = false;
    }
  private int x0, y0;  // xxx,yyy tracks the mouse, x0,y0 stands still
  private boolean dragFlag = false;
  private int mouseModifiers;
  public void atomInfo ()
    {
      atomInfoBlab.setBackground (this.getBackground ());
      atomInfoBlab.setText ("");
    }
  public void atomInfo (String s)
    {
      atomInfoBlab.setBackground (this.getBackground ());
      atomInfoBlab.setText (s);
    }
  public void atomInfo (atom a)
    {
      if (a == null)
	{
	  atomInfoBlab.setBackground (this.getBackground ());
	  atomInfoBlab.setText ("");
	  return;
	}
      a.rehybridize();
      String hinfo = "", bondinfo = "";
      switch (a.hybridization)
	{
	case atom.SP3: hinfo = "sp3"; break;
	case atom.SP2: hinfo = "sp2"; break;
	case atom.SP:  hinfo = "sp"; break;
	}
      if (a.currentNumBonds () < a.correctNumBonds ())
	{
	  bondinfo = "<too few bonds>";
	  atomInfoBlab.setBackground (Color.orange);
	}
      else if (a.currentNumBonds () > a.correctNumBonds ())
	{
	  bondinfo = "<too many bonds>";
	  atomInfoBlab.setBackground (Color.orange);
	}
      else
	atomInfoBlab.setBackground (this.getBackground ());
      atomInfoBlab.setText (a.name() + " " +
			    a.symbol() + " " +
			    hinfo + " " + bondinfo);
    }
  public boolean mouseDown (Event e, int x, int y)
    {
      Rectangle r = drawingArea.bounds();
      inDrawingArea = y < r.height;
      needToRepaint = false;
      double[] scrPos = { x, y, 0 };
      atom1 = grp.selectedAtom (scrPos, true);
      dragFlag = false;
      mouseModifiers = e.modifiers & (Event.SHIFT_MASK | Event.CTRL_MASK);
      if (atom1 != null)
	{
	  double[] atomScrPos = grp.v.xyzToScreen (atom1.x);
	  atom1z = atomScrPos[2];
	}
      else
	{
	  atom1z = 0;
	}
      atomInfo (atom1);
      xxx = x; yyy = y;
      x0 = x; y0 = y;
      return true;
    }
  public boolean mouseDrag (Event e, int x, int y)
    {
      boolean movingAtom = false;  // if moving atom, no need for extra line
      if (!dragFlag)
	if (x < x0 - 2 || x > x0 + 2 || y < y0 - 2 || y > y0 + 2)
	  dragFlag = true;
      if (dragFlag)
	{
	  needToRepaint = true;
	  if (atom1 == null)
	    {
	      switch (mouseModifiers)
		{
		default:
		  grp.v.rotate (0.01 * (x - xxx), 0.01 * (y - yyy));
		  break;
		case Event.SHIFT_MASK:
		  grp.v.pan (x - xxx, y - yyy);
		  break;
		case Event.CTRL_MASK:
		  grp.v.zoomFactor *= Math.exp (0.01 * (x - xxx));
		  grp.v.perspDist *= Math.exp (0.01 * (y - yyy));
		  break;
		}
	      clearScreen ();
	      grp.wireframePaint ();
	    }
	  else
	    {
	      switch (mouseModifiers)
		{
		default:
		  double[] scrPos = { x, y, atom1z };
		  atom1.x = grp.v.screenToXyz (scrPos);
		  movingAtom = true;
		  clearScreen ();
		  grp.wireframePaint ();
		  break;
		case Event.SHIFT_MASK:
		  clearScreen ();
		  grp.bubblePaint ();
		  break;
		case Event.CTRL_MASK:
		  clearScreen ();
		  grp.bubblePaint ();
		  break;
		}
	    }
	  xxx = x; yyy = y;
	  if (atom1 != null && !movingAtom)
	    grp.drawLineToAtom (atom1, x, y);
	}
      return true;
    }
  public boolean mouseUp (Event e, int x, int y)
    {
      double[] scrPos = { x, y, atom1z };
      Graphics g = this.getGraphics ();
      atom atom2 = grp.selectedAtom (scrPos, false);
      if (atom1 != null)
	{
	  if (dragFlag)
	    {
	      // we dragged on an atom
	      switch (mouseModifiers)
		{
		default:
		  atom1.x = grp.v.screenToXyz (scrPos);
		  atom2 = atom1;
		  break;
		case Event.SHIFT_MASK:
		  if (atom1 != atom2 && atom1 != null && atom2 != null)
		    {
		      // create a new bond if none exists, or increment the
		      // order if it does exist.
		      grp.addBond (atom1, atom2);
		    }
		  break;
		case Event.CTRL_MASK:
		  if (atom1 != atom2 && atom1 != null && atom2 != null)
		    grp.deleteBond (atom1, atom2);
		  break;
		}
	      // give information about the last atom we visited
	      atomInfo (atom2);
	    }
	  else
	    {
	      // we clicked on an atom
	      switch (mouseModifiers)
		{
		default:
		  // atom info, do nothing here
		  break;
		case Event.SHIFT_MASK:
		  if (atom1 != null)
		    {
		      atom a = null;
		      String ename = whichElement.getSelectedItem ();
		      if (ename.compareTo ("Carbon") == 0)
			a = new carbon (atom1.x[0], atom1.x[1], atom1.x[2]);
		      else if (ename.compareTo ("Nitrogen") == 0)
			a = new nitrogen (atom1.x[0], atom1.x[1], atom1.x[2]);
		      else if (ename.compareTo ("Oxygen") == 0)
			a = new oxygen (atom1.x[0], atom1.x[1], atom1.x[2]);
		      else if (ename.compareTo ("Hydrogen") == 0)
			a = new hydrogen (atom1.x[0], atom1.x[1], atom1.x[2]);
		      grp.deleteAtom (atom1);
		      if (a != null)
			{
			  grp.addAtom (a);
			  atomInfo (a);
			}
		      else
			atomInfo();
		    }
		  else
		    atomInfo();
		  needToRepaint = true;
		  atomInfo ();
		  break;
		case Event.CTRL_MASK:
		  // do nothing for undoLastOp
		  break;
		}
	    }
	}
      else if (!dragFlag)
	{
	  // we clicked on air
	  switch (mouseModifiers)
	    {
	    default:
	      break;
	    case Event.SHIFT_MASK:
	      int sp;
	      atom a = null;
	      needToRepaint = true;
	      String ename = whichElement.getSelectedItem ();
	      if (ename.compareTo ("Carbon") == 0)
		a = new carbon ();
	      else if (ename.compareTo ("Nitrogen") == 0)
		a = new nitrogen ();
	      else if (ename.compareTo ("Oxygen") == 0)
		a = new oxygen ();
	      else if (ename.compareTo ("Hydrogen") == 0)
		a = new hydrogen ();
	      if (a != null)
		{
		  grp.addAtom (a, scrPos);
		  atomInfo (a);
		}
	      break;
	    case Event.CTRL_MASK:
	      needToRepaint = true;
	      atomInfo ();
	      grp.updateViewSize ();
	      grp.centerAtoms ();
	      break;
	    }
	}
      if (needToRepaint)
	repaint ();
      return true;
    }
  private void energyMinimize ()
    {
      double scale;
      for (scale = 0.1; scale > 0.0001; scale *= 0.9)
	grp.energyMinimizeStep (scale);
      repaint();
    }
  public boolean action (Event e, Object arg)
    {
      String s;
      if (e.target == emin)
	{
	  energyMinimize ();
	  return true;
	}
      else if (e.target == showForces)
	{
	  grp.setShowForces (showForces.getState());
	  repaint();
	  return true;
	}
      else if (e.target == knownStructure)
	{
	  switch (knownStructure.getSelectedIndex ())
	    {
	    default:
	    case 0: grp = new aspirin (drawingArea); break;
	    case 1: grp = new buckyball (drawingArea); break;
	    case 2: grp = new diamond (drawingArea); break;
	    case 3: grp = new diamrod (drawingArea); break;
	    case 4: grp = new propane (drawingArea); break;
	    case 5: grp = new tworings (drawingArea); break;
	    case 6: grp = new water (drawingArea); break;
	    case 7: grp = new group (drawingArea); break;
	    }
	  grp.setShowForces (showForces.getState());
	  debugWindow.clear();
	  grp.setTextwin(debugWindow);
	  grp.updateViewSize ();
	  repaint ();
	  return true;
	}
      else if (e.target == getSetStructure)
	{
	  int i = 0;
	  /* Notify the user, if he's about to blow away his unsaved work. */
	  String str = "Paste your file in here.";
	  if (grp.changedSinceLastSave)
	    str += " To save your work first, hit cancel.";
	  str += "\n";
	  structureWindow.setVisible(true);
	  structureWindow.setGroup(grp);
	  grp.fileMode = getSetStructure.getSelectedIndex();
	  switch (getSetStructure.getSelectedIndex())
	    {
	    default:
	    case 0: /* Load native format */
	      structureWindow.setEditable(true);
	      structureWindow.setText(str);
	      break;
	    case 1: /* Save native format */
	      structureWindow.setEditable(false);
	      structureWindow.setText(grp.getNativeFormat());
	      break;
	    case 2: /* Load PDB */
	      structureWindow.setEditable(false);
	      structureWindow.setText("Sorry, this isn't implemented yet.\n");
	      break;
	    case 3: /* Save PDB */
	      structureWindow.setEditable(false);
	      structureWindow.setText(grp.getPDB());
	      break;
	    case 4: /* Load XYZ */
	      structureWindow.setEditable(true);
	      structureWindow.setText(str);
	      break;
	    case 5: /* Save XYZ */
	      structureWindow.setEditable(false);
	      structureWindow.setText(grp.getXYZ());
	      break;
	    }
	  return true;
	}
      return false;
    }
  private void constrain (Container container, Component component,
			  int gridX, int gridY, int gridW, int gridH)
    {
      constrain (container, component, gridX, gridY, gridW, gridH,
		 GridBagConstraints.NONE, GridBagConstraints.NORTHWEST,
		 0.0, 0.0, 0, 0, 0, 0);
    }
  private void constrain (Container container, Component component,
			  int gridX, int gridY, int gridW, int gridH,
			  int fill, int anchor, double weightX,
			  double weightY, int top, int left, int bottom,
			  int right)
    {
      GridBagConstraints c = new GridBagConstraints ();
      c.gridx = gridX; c.gridy = gridY;
      c.gridwidth = gridW; c.gridheight = gridH;
      c.fill = fill; c.anchor = anchor;
      c.weightx = weightX; c.weighty = weightY;
      if (top + bottom + left + right > 0)
	c.insets = new Insets (top, left, bottom, right);
      ((GridBagLayout) container.getLayout()).setConstraints(component, c);
    }
  public void init ()
    {
      int p = 200;
      this.setBackground (new Color (p, p, p));
      Panel controls = new Panel ();
      drawingArea = new Panel ();
      
      structureWindow = new textwin("Structure load/save window", "", false);
      structureWindow.setVisible(false);
      structureWindow.setFont (new Font("Courier", Font.PLAIN, 12));
      debugWindow = new textwin("Debug window", "", false);
      debugWindow.setVisible(false);
      GridBagLayout gridbag = new GridBagLayout ();
      this.setLayout (gridbag);
      
      // this is kind of kludgey, but if I don't put drawingArea first
      // in the gridbag, I don't know how to correctly translate the
      // coordinates between this applet and the drawingArea panel.
      constrain (this, drawingArea, 0, 0, 1, 1,
		 GridBagConstraints.BOTH,
		 GridBagConstraints.NORTH,
		 1.0, 1.0, 0, 0, 0, 0);
      
      showForces = new Checkbox ("Forces");
      showForces.setState (false);
      
      emin = new Button ("Energy Minimize");
      
      knownStructure = new Choice ();
      knownStructure.addItem ("aspirin");
      knownStructure.addItem ("buckyball");
      knownStructure.addItem ("diamond");
      knownStructure.addItem ("diamond rod");
      knownStructure.addItem ("propane");
      knownStructure.addItem ("two rings");
      knownStructure.addItem ("water");
      knownStructure.addItem ("-Clear-");
      knownStructure.select ("aspirin");
      
      whichElement = new Choice ();
      whichElement.addItem ("Carbon");
      whichElement.addItem ("Hydrogen");
      whichElement.addItem ("Oxygen");
      whichElement.addItem ("Nitrogen");
      whichElement.addItem ("-Delete-");
      whichElement.select ("Carbon");
      
      getSetStructure = new Choice ();
      getSetStructure.addItem ("Load Native");
      getSetStructure.addItem ("Save Native");
      getSetStructure.addItem ("Load PDB");
      getSetStructure.addItem ("Save PDB");
      getSetStructure.addItem ("Load XYZ");
      getSetStructure.addItem ("Save XYZ");
      getSetStructure.select ("Load Native");
      
      grp = new aspirin (drawingArea);
      if (debugWindow.isVisible())
	debugWindow.clear();
      grp.setTextwin(debugWindow);
      grp.v.zoomFactor = 25;
      
      controls.add (showForces);
      controls.add (emin);
      controls.add (knownStructure);
      controls.add (whichElement);
      controls.add (getSetStructure);
      constrain (this, controls, 0, 1, 1, 1);
      
      TextArea instrucs = new TextArea (5, 100);
      instrucs.setText(instructions);
      instrucs.setEditable (false);
      constrain (this, instrucs, 0, 2, 1, 1);
      
      String spaces = "                              "; /* 30 spaces */
      atomInfoBlab = new Label (spaces + spaces + spaces + spaces + spaces);
      constrain (this, atomInfoBlab, 0, 3, 1, 1);
      
      this.add (drawingArea);
      this.add (controls);
      this.add (instrucs);
      this.add (atomInfoBlab);

      grp.v.updateSize(600, 300);
      this.repaint ();
      this.show ();
    }
  public void start()
    {
      grp.updateViewSize ();
    }
}