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Open Source Chemistry Library
/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* 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/or other materials provided with the distribution.
* 3. Neither the name of the the copyright holder nor the
* names of its contributors may be used to endorse or promote products
* derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS 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.
*
*/
package com.actelion.research.gui;
import com.actelion.research.chem.*;
import com.actelion.research.chem.reaction.IReactionMapper;
import com.actelion.research.chem.reaction.Reaction;
import com.actelion.research.chem.reaction.ReactionArrow;
import com.actelion.research.gui.clipboard.IClipboardHandler;
import com.actelion.research.gui.dnd.MoleculeDropAdapter;
import com.actelion.research.gui.hidpi.HiDPIHelper;
import com.actelion.research.gui.hidpi.ScaledEditorKit;
import com.actelion.research.util.ColorHelper;
import com.actelion.research.util.CursorHelper;
import javax.swing.*;
import javax.swing.text.html.HTMLEditorKit;
import java.awt.*;
import java.awt.datatransfer.DataFlavor;
import java.awt.dnd.DnDConstants;
import java.awt.dnd.DropTarget;
import java.awt.event.*;
import java.awt.geom.Point2D;
import java.awt.geom.Rectangle2D;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Comparator;
public class JDrawArea extends JPanel
implements ActionListener, KeyListener, MouseListener, MouseMotionListener
{
static final long serialVersionUID = 0x20061019;
public static final int MODE_MULTIPLE_FRAGMENTS = 1;
public static final int MODE_MARKUSH_STRUCTURE = 2;
public static final int MODE_REACTION = 4;
public static final int MODE_DRAWING_OBJECTS = 8;
private static final int MAX_CONNATOMS = 8;
private static final int MIN_BOND_LENGTH_SQUARE = 100;
private static final int KEY_IS_ATOM_LABEL = 1;
private static final int KEY_IS_SUBSTITUENT = 2;
private static final int KEY_IS_VALID_START = 3;
private static final int KEY_IS_INVALID = 4;
private static final float FRAGMENT_MAX_CLICK_DISTANCE = 24.0f;
private static final float FRAGMENT_GROUPING_DISTANCE = 1.4f; // in average bond lengths
private static final float FRAGMENT_CLEANUP_DISTANCE = 1.5f; // in average bond lengths
private static final float DEFAULT_ARROW_LENGTH = 0.08f; // relative to panel width
private static final boolean USE_GRAPHICS_2D = true;
protected static final int UPDATE_NONE = 0;
protected static final int UPDATE_REDRAW = 1;
// redraw molecules and drawing objects with their current coordinates
protected static final int UPDATE_CHECK_VIEW = 2;
// redraw with on-the-fly coordinate transformation only if current coords do not fit within view area
// (new coords are generated for one draw() only; the original coords are not changed)
protected static final int UPDATE_CHECK_COORDS = 3;
// redraw with in-place coordinate transformation only if current coords do not fit within view area
// (the original atom and object coords are replaced by the new ones)
protected static final int UPDATE_SCALE_COORDS = 4;
// redraw with in-place coordinate transformation; molecules and objects are scaled to fill
// the view unless the maximum average bond length reaches the optimum.
protected static final int UPDATE_SCALE_COORDS_USE_FRAGMENTS = 5;
// as UPDATE_SCALE_COORDS but uses fragments from mFragment rather than creating a
// fresh mFragment list from mMol. Used for setting a reaction or fragment list from outside.
protected static final int UPDATE_INVENT_COORDS = 6;
// redraw with in-place coordinate transformation; first all molecules' coordinates
// are generated from scratch, then molecules and objects are scaled to fill
// the view unless the maximum average bond length reaches the optimum.
private static final int ALLOWED_DROP_ACTIONS = DnDConstants.ACTION_COPY_OR_MOVE;
private static final int cRequestNone = 0;
private static final int cRequestNewBond = 1;
private static final int cRequestNewChain = 2;
private static final int cRequestMoveSingle = 3;
private static final int cRequestMoveSelected = 4;
private static final int cRequestLassoSelect = 5;
private static final int cRequestSelectRect = 6;
private static final int cRequestZoomAndRotate = 7;
private static final int cRequestMapAtoms = 8;
private static final int cRequestCopySelected = 9;
private static final int cRequestMoveObject = 10;
private static final int cRequestCopyObject = 11;
public static final int FAKE_ATOM_NO = 100;
private Dimension mSize;
private int mMode, mChainAtoms, mCurrentTool, mOtherAtom, mOtherMass, mOtherValence, mOtherRadical,
mCurrentHiliteAtom, mCurrentHiliteBond, mPendingRequest,
mCurrentCursor, mReactantCount, mUpdateMode, mDisplayMode, mAtom1, mAtom2;
private int[] mChainAtom, mFragmentNo, mHiliteBondSet;
private double mX1, mY1, mX2, mY2;
private double[] mX, mY, mChainAtomX, mChainAtomY;
private boolean mShiftIsDown, mAltIsDown, mControlIsDown, mMouseIsDown, mIsAddingToSelection, mAtomColorSupported;
private boolean[] mIsSelectedAtom, mIsSelectedObject;
private String[] mAtomText;
private ExtendedDepictor mDepictor;
private StereoMolecule mMol; // molecule being modified directly by the drawing editor
private Molecule mUndoMol; // molecule in undo buffer
private StereoMolecule[] mFragment; // in case of MODE_MULTIPLE_FRAGMENTS contains valid stereo fragments
// for internal and external read-only-access (reconstructed at any change)
private DrawingObjectList mDrawingObjectList, mUndoDrawingObjectList;
private AbstractDrawingObject mCurrentHiliteObject;
private Polygon mLassoRegion;
private ArrayList mListeners;
private IClipboardHandler mClipboardHandler;
private JDialog mHelpDialog;
private StringBuilder mAtomKeyStrokeBuffer;
private IReactionMapper mMapper; //= new ReactionMapper();
/**
* @param mol an empty or valid stereo molecule
* @param mode 0 or a meaningful combination of the mode flags, e.g. MODE_REACTION | MODE_DRAWING_OBJECTS
*/
public JDrawArea(StereoMolecule mol, int mode)
{
mMol = mol;
mMode = mode;
setFocusable(true);
addKeyListener(this);
addMouseListener(this);
addMouseMotionListener(this);
mListeners = new ArrayList();
mCurrentTool = JDrawToolbar.cToolStdBond;
mCurrentHiliteAtom = -1;
mCurrentHiliteBond = -1;
mCurrentHiliteObject = null;
mAtom1 = -1;
mOtherAtom = 6;
mOtherMass = 0;
mOtherValence = -1;
mOtherRadical = 0;
mPendingRequest = cRequestNone;
mCurrentCursor = CursorHelper.cPointerCursor;
mAtomKeyStrokeBuffer = new StringBuilder();
if ((mMode & (MODE_REACTION | MODE_MARKUSH_STRUCTURE)) != 0) {
mMode |= (MODE_MULTIPLE_FRAGMENTS);
}
if ((mMode & (MODE_DRAWING_OBJECTS | MODE_REACTION)) != 0) {
mDrawingObjectList = new DrawingObjectList();
}
mUpdateMode = UPDATE_SCALE_COORDS;
initializeDragAndDrop(ALLOWED_DROP_ACTIONS);
/* dumpBytesOfGif("/chainCursor.gif");
dumpBytesOfGif("/deleteCursor.gif");
dumpBytesOfGif("/handCursor.gif");
dumpBytesOfGif("/handPlusCursor.gif");
dumpBytesOfGif("/fistCursor.gif");
dumpBytesOfGif("/lassoCursor.gif");
dumpBytesOfGif("/lassoPlusCursor.gif");
dumpBytesOfGif("/rectCursor.gif");
dumpBytesOfGif("/rectPlusCursor.gif"); */
}
/**
* Call this after initialization to get clipboard support
*
* @param h
*/
public void setClipboardHandler(IClipboardHandler h)
{
mClipboardHandler = h;
}
private void update(int mode)
{
mUpdateMode = Math.max(mUpdateMode, mode);
repaint();
}
public void setMapper(IReactionMapper mapper)
{
this.mMapper = mapper;
}
public void paintComponent(Graphics g)
{
super.paintComponent(g);
((Graphics2D) g).setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON);
((Graphics2D) g).setRenderingHint(RenderingHints.KEY_STROKE_CONTROL, RenderingHints.VALUE_STROKE_PURE);
Dimension theSize = getSize();
if (mSize == null || mSize.width != theSize.width || mSize.height != theSize.height) {
mSize = theSize;
if (mUpdateMode < UPDATE_CHECK_COORDS) {
mUpdateMode = UPDATE_CHECK_COORDS;
}
}
Color background = UIManager.getColor("TextArea.background");
Color foreground = UIManager.getColor("TextArea.foreground");
g.setColor(background);
g.fillRect(0, 0, theSize.width, theSize.height);
if ((mMode & MODE_REACTION) != 0 && mDrawingObjectList.size() == 0) {
float mx = 0.5f * (float) theSize.width;
float my = 0.5f * (float) theSize.height;
float dx = 0.5f * DEFAULT_ARROW_LENGTH * (float) theSize.width;
ReactionArrow arrow = new ReactionArrow();
arrow.setCoordinates(mx - dx, my, mx + dx, my);
arrow.setDeletable(false);
mDrawingObjectList.add(arrow);
}
boolean isScaledView = false;
if (mUpdateMode != UPDATE_NONE) {
if ((mMode & MODE_MULTIPLE_FRAGMENTS) != 0
&& mUpdateMode != UPDATE_SCALE_COORDS_USE_FRAGMENTS) {
analyzeFragmentMembership();
}
mDepictor = ((mMode & MODE_REACTION) != 0) ?
new ExtendedDepictor(new Reaction(mFragment, mReactantCount), mDrawingObjectList, false, USE_GRAPHICS_2D)
: ((mMode & MODE_MARKUSH_STRUCTURE) != 0) ?
new ExtendedDepictor(mFragment, mReactantCount, mDrawingObjectList, USE_GRAPHICS_2D)
: ((mMode & MODE_MULTIPLE_FRAGMENTS) != 0) ?
new ExtendedDepictor(mFragment, mDrawingObjectList, USE_GRAPHICS_2D)
: new ExtendedDepictor(mMol, mDrawingObjectList, USE_GRAPHICS_2D);
mDepictor.setForegroundColor(foreground, background);
mDepictor.setFragmentNoColor(((mMode & MODE_MULTIPLE_FRAGMENTS) == 0) ? null
: LookAndFeelHelper.isDarkLookAndFeel() ? ColorHelper.brighter(background, 0.85f)
: ColorHelper.darker(background, 0.85f));
mDepictor.setDisplayMode(mDisplayMode
| AbstractDepictor.cDModeHiliteAllQueryFeatures
| ((mCurrentTool == JDrawToolbar.cToolMapper) ?
AbstractDepictor.cDModeShowMapping
| AbstractDepictor.cDModeSuppressCIPParity : 0));
if ((mMode & (MODE_REACTION | MODE_MARKUSH_STRUCTURE | MODE_MULTIPLE_FRAGMENTS)) == 0) {
mDepictor.getMoleculeDepictor(0).setAtomText(mAtomText);
}
switch (mUpdateMode) {
case UPDATE_INVENT_COORDS:
case UPDATE_SCALE_COORDS:
case UPDATE_SCALE_COORDS_USE_FRAGMENTS:
cleanupCoordinates(g, mDepictor);
break;
case UPDATE_CHECK_COORDS:
DepictorTransformation t1 = mDepictor.updateCoords(g, new Rectangle2D.Double(0, 0, theSize.width, theSize.height), 0);
if (t1 != null && (mMode & MODE_MULTIPLE_FRAGMENTS) != 0) {
// in fragment mode depictor transforms mFragment[] rather than mMol
t1.applyTo(mMol);
}
break;
case UPDATE_CHECK_VIEW:
DepictorTransformation t2 = mDepictor.validateView(g, new Rectangle2D.Double(0, 0, theSize.width, theSize.height), 0);
isScaledView = (t2 != null && !t2.isVoidTransformation());
break;
}
mUpdateMode = UPDATE_NONE;
}
if (mDepictor != null) {
mDepictor.paintFragmentNumbers(g);
}
// don't hilite anything when the view is scaled and object coords don't reflect screen coords
if (!isScaledView) {
drawHiliting(g);
}
if (mDepictor != null) {
mDepictor.paintStructures(g);
mDepictor.paintDrawingObjects(g);
}
if (mCurrentHiliteAtom != -1 && mAtomKeyStrokeBuffer.length() != 0) {
int x = (int) mMol.getAtomX(mCurrentHiliteAtom);
int y = (int) mMol.getAtomY(mCurrentHiliteAtom);
String s = mAtomKeyStrokeBuffer.toString();
int validity = getAtomKeyStrokeValidity(s);
g.setColor((validity == KEY_IS_ATOM_LABEL) ? foreground
: (validity == KEY_IS_SUBSTITUENT) ? Color.BLUE
: (validity == KEY_IS_VALID_START) ? Color.GRAY : Color.RED);
if (validity == KEY_IS_INVALID)
s = s + "";
g.setFont(g.getFont().deriveFont(0, 24));
g.drawString(s, x, y);
}
g.setColor(foreground);
switch (mPendingRequest) {
case cRequestNewBond:
int x1, y1, x2, y2, xdiff, ydiff;
x1 = (int) mX1;
y1 = (int) mY1;
if (mCurrentHiliteAtom == -1 || mCurrentHiliteAtom == mAtom1) {
x2 = (int) mX2;
y2 = (int) mY2;
} else {
x2 = (int) mMol.getAtomX(mCurrentHiliteAtom);
y2 = (int) mMol.getAtomY(mCurrentHiliteAtom);
}
switch (mCurrentTool) {
case JDrawToolbar.cToolStdBond:
g.drawLine(x1, y1, x2, y2);
break;
case JDrawToolbar.cToolUpBond:
int[] x = new int[3];
int[] y = new int[3];
xdiff = (y1 - y2) / 9;
ydiff = (x2 - x1) / 9;
x[0] = x1;
y[0] = y1;
x[1] = x2 + xdiff;
y[1] = y2 + ydiff;
x[2] = x2 - xdiff;
y[2] = y2 - ydiff;
g.fillPolygon(x, y, 3);
break;
case JDrawToolbar.cToolDownBond:
int xx1, xx2, yy1, yy2;
xdiff = x2 - x1;
ydiff = y2 - y1;
for (int i = 2; i < 17; i += 2) {
xx1 = x1 + i * xdiff / 17 - i * ydiff / 128;
yy1 = y1 + i * ydiff / 17 + i * xdiff / 128;
xx2 = x1 + i * xdiff / 17 + i * ydiff / 128;
yy2 = y1 + i * ydiff / 17 - i * xdiff / 128;
g.drawLine(xx1, yy1, xx2, yy2);
}
break;
}
break;
case cRequestNewChain:
if (mChainAtoms > 0) {
g.drawLine((int) mX1, (int) mY1, (int) mChainAtomX[0], (int) mChainAtomY[0]);
}
if (mChainAtoms > 1) {
for (int i = 1; i < mChainAtoms; i++) {
g.drawLine((int) mChainAtomX[i - 1], (int) mChainAtomY[i - 1],
(int) mChainAtomX[i], (int) mChainAtomY[i]);
}
}
break;
case cRequestLassoSelect:
g.setColor(lassoColor());
g.drawPolygon(mLassoRegion);
g.setColor(foreground);
break;
case cRequestSelectRect:
int x = (mX1 < mX2) ? (int) mX1 : (int) mX2;
int y = (mY1 < mY2) ? (int) mY1 : (int) mY2;
int w = (int) Math.abs(mX2 - mX1);
int h = (int) Math.abs(mY2 - mY1);
g.setColor(lassoColor());
g.drawRect(x, y, w, h);
g.setColor(foreground);
break;
case cRequestMapAtoms:
x1 = (int) mX1;
y1 = (int) mY1;
if (mCurrentHiliteAtom == -1 || mCurrentHiliteAtom == mAtom1) {
x2 = (int) mX2;
y2 = (int) mY2;
} else {
x2 = (int) mMol.getAtomX(mCurrentHiliteAtom);
y2 = (int) mMol.getAtomY(mCurrentHiliteAtom);
}
g.setColor(mapToolColor());
g.drawLine(x1, y1, x2, y2);
g.setColor(foreground);
break;
}
}
private Color lassoColor() {
Color selectionColor = UIManager.getColor("TextArea.selectionBackground");
return ColorHelper.createColor(selectionColor, LookAndFeelHelper.isDarkLookAndFeel() ? 0.65f : 0.35f);
}
private Color selectionColor() {
return UIManager.getColor("TextArea.selectionBackground");
}
private Color mapToolColor() {
Color background = UIManager.getColor("TextArea.background");
return ColorHelper.getContrastColor(new Color(128, 0, 0), background);
}
private Color chainHiliteColor() {
Color background = UIManager.getColor("TextArea.background");
Color selectionColor = UIManager.getColor("TextArea.selectionBackground");
return ColorHelper.intermediateColor(selectionColor, background, 0.5f);
}
private void drawHiliting(Graphics g)
{
if (mHiliteBondSet != null) {
g.setColor(chainHiliteColor());
for (int i = 0; i < mHiliteBondSet.length; i++) {
hiliteBond(g, mHiliteBondSet[i]);
}
}
if (mCurrentHiliteAtom != -1) {
g.setColor(selectionColor());
hiliteAtom(g, mCurrentHiliteAtom);
if (mCurrentTool == JDrawToolbar.cToolMapper) {
int mapNo = mMol.getAtomMapNo(mCurrentHiliteAtom);
if (mapNo != 0) {
for (int atom = 0; atom < mMol.getAtoms(); atom++) {
if (atom != mCurrentHiliteAtom
&& mMol.getAtomMapNo(atom) == mapNo) {
hiliteAtom(g, atom);
}
}
}
}
}
if (mCurrentHiliteBond != -1) {
g.setColor(selectionColor());
hiliteBond(g, mCurrentHiliteBond);
}
if (mCurrentHiliteObject != null) {
mCurrentHiliteObject.hilite(g);
}
}
private void hiliteAtom(Graphics g, int atom)
{
int radius = (int) (0.32f * mMol.getAverageBondLength());
int x = (int) mMol.getAtomX(atom);
int y = (int) mMol.getAtomY(atom);
g.fillOval(x - radius, y - radius, 2 * radius, 2 * radius);
}
private void hiliteBond(Graphics g, int bond)
{
int width = (int) (0.32f * mMol.getAverageBondLength());
int x1 = (int) mMol.getAtomX(mMol.getBondAtom(0, bond));
int y1 = (int) mMol.getAtomY(mMol.getBondAtom(0, bond));
int x2 = (int) mMol.getAtomX(mMol.getBondAtom(1, bond));
int y2 = (int) mMol.getAtomY(mMol.getBondAtom(1, bond));
Stroke oldStroke = ((Graphics2D) g).getStroke();
((Graphics2D) g).setStroke(new BasicStroke((float) width, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND));
((Graphics2D) g).drawLine(x1, y1, x2, y2);
((Graphics2D) g).setStroke(oldStroke);
}
public void addDrawAreaListener(DrawAreaListener l)
{
mListeners.add(l);
}
protected void buttonPressed(int button)
{
switch (button) {
case JDrawToolbar.cButtonClear:
if (mDrawingObjectList != null) {
mDrawingObjectList.clear();
update(UPDATE_REDRAW);
}
storeState();
boolean isFragment = mMol.isFragment();
mMol.deleteMolecule();
mMol.setFragment(isFragment);
if (mUndoMol.getAllAtoms() != 0) {
fireMoleculeChanged();
}
update(UPDATE_REDRAW);
return;
case JDrawToolbar.cButtonCleanStructure:
storeState();
fireMoleculeChanged();
update(UPDATE_INVENT_COORDS);
return;
case JDrawToolbar.cButtonUndo:
restoreState();
fireMoleculeChanged();
update(UPDATE_CHECK_VIEW);
return;
}
}
public void toolChanged(int newTool)
{
if (mCurrentTool != newTool) {
setOtherAtom(-1, 0, -1, 0);
if (mCurrentTool == JDrawToolbar.cToolMapper
|| newTool == JDrawToolbar.cToolMapper) {
update(UPDATE_REDRAW);
}
mCurrentTool = newTool;
}
}
private void setOtherAtom(int atomicNo, int mass, int valence, int radical)
{
mOtherAtom = atomicNo;
mOtherMass = mass;
mOtherValence = valence;
mOtherRadical = radical;
}
public void actionPerformed(ActionEvent e)
{
String command = e.getActionCommand();
if (command.equals("Copy")) {
copy();
} else if (command.equals("Paste")) {
paste();
} else if (command.startsWith("atomColor")) {
int index = command.indexOf(':');
int atom = Integer.parseInt(command.substring(9, index));
int color = Integer.parseInt(command.substring(index + 1));
if (mMol.isSelectedAtom(atom)) {
for (int i = 0; i < mMol.getAtoms(); i++) {
if (mMol.isSelectedAtom(i)) {
mMol.setAtomColor(i, color);
}
}
} else {
mMol.setAtomColor(atom, color);
}
}
}
private void copy()
{
boolean isReaction = ((mMode & MODE_REACTION) != 0);
boolean selectionFound = false;
boolean isBothSideSelection = false;
boolean isOnProductSide = false;
ReactionArrow arrow = null;
for (int atom = 0; atom < mMol.getAllAtoms(); atom++) {
if (mMol.isSelectedAtom(atom)) {
if (!selectionFound) {
selectionFound = true;
if (!isReaction) {
break;
}
arrow = (ReactionArrow) mDrawingObjectList.get(0);
isOnProductSide = arrow.isOnProductSide(mMol.getAtomX(atom), mMol.getAtomY(atom));
} else {
if (isOnProductSide != arrow.isOnProductSide(mMol.getAtomX(atom), mMol.getAtomY(atom))) {
isBothSideSelection = true;
break;
}
}
}
}
if (isReaction) {
if (isBothSideSelection) {
copyReaction(true);
} else if (selectionFound) {
copyMolecule(true);
} else {
copyReaction(false);
}
} else {
copyMolecule(selectionFound);
}
}
private boolean copyReaction(boolean selectionOnly)
{
Reaction rx = selectionOnly ? getSelectedReaction() : getReaction();
if (rx != null && mClipboardHandler != null) {
return mClipboardHandler.copyReaction(rx);
}
return false;
}
private Reaction getSelectedReaction()
{
Reaction rxn = new Reaction();
for (int i = 0; i < mFragment.length; i++) {
StereoMolecule selectedMol = getSelectedCopy(mFragment[i]);
if (selectedMol != null) {
if (i < mReactantCount) {
rxn.addReactant(selectedMol);
} else {
rxn.addProduct(selectedMol);
}
}
}
return rxn;
}
private StereoMolecule getSelectedCopy(StereoMolecule sourceMol)
{
int atomCount = 0;
for (int atom = 0; atom < sourceMol.getAllAtoms(); atom++) {
if (sourceMol.isSelectedAtom(atom)) {
atomCount++;
}
}
if (atomCount == 0) {
return null;
}
int bondCount = 0;
for (int bond = 0; bond < sourceMol.getAllBonds(); bond++) {
if (sourceMol.isSelectedBond(bond)) {
bondCount++;
}
}
boolean[] includeAtom = new boolean[sourceMol.getAllAtoms()];
for (int atom = 0; atom < sourceMol.getAllAtoms(); atom++) {
includeAtom[atom] = sourceMol.isSelectedAtom(atom);
}
StereoMolecule destMol = new StereoMolecule(atomCount, bondCount);
sourceMol.copyMoleculeByAtoms(destMol, includeAtom, false, null);
return destMol;
}
private boolean copyMolecule(boolean selectionOnly)
{
if (mMol.getAllAtoms() != 0 && mClipboardHandler != null) {
return mClipboardHandler.copyMolecule(selectionOnly ? getSelectedCopy(mMol) : mMol);
}
return false;
}
private void paste()
{
if ((mMode & MODE_REACTION) != 0) {
if (pasteReaction()) {
return;
}
}
pasteMolecule();
}
private boolean pasteReaction()
{
boolean ret = false;
if (mClipboardHandler != null) {
Reaction rxn = mClipboardHandler.pasteReaction();
if (rxn != null) {
for (int i = 0; i < rxn.getMolecules(); i++) {
rxn.getMolecule(i).setFragment(mMol.isFragment());
}
setReaction(rxn);
ret = true;
}
}
return ret;
}
private boolean pasteMolecule()
{
boolean ret = false;
if (mClipboardHandler != null) {
StereoMolecule mol = mClipboardHandler.pasteMolecule();
if (mol != null && mol.getAllAtoms() != 0) {
if (mMol.getAllAtoms() == 0) {
boolean isFragment = mMol.isFragment();
mol.copyMolecule(mMol);
mMol.setFragment(isFragment);
moleculeChanged(true);
} else {
int avbl = (int) mMol.getAverageBondLength();
Depictor d = new Depictor(mol);
d.updateCoords(this.getGraphics(), new Rectangle2D.Double(0, 0,
this.getWidth(),
this.getHeight()),
AbstractDepictor.cModeInflateToMaxAVBL + avbl
);
int originalAtoms = mMol.getAllAtoms();
mMol.addMolecule(mol);
for (int atom = 0; atom < mMol.getAllAtoms(); atom++) {
mMol.setAtomSelection(atom, atom >= originalAtoms);
}
moleculeChanged(true);
}
}
ret = true;
}
return ret;
}
// end changes CxR
public void mousePressed(MouseEvent e)
{
if (mCurrentHiliteAtom != -1 && mAtomKeyStrokeBuffer.length() != 0)
expandAtomKeyStrokes(mAtomKeyStrokeBuffer.toString());
mAtomKeyStrokeBuffer.setLength(0);
if (handlePopupTrigger(e)) {
return;
}
if ((e.getModifiers() & InputEvent.BUTTON1_MASK) != 0) {
if (e.getClickCount() == 2) {
return;
}
mMouseIsDown = true;
updateCursor();
mousePressedButton1(e);
}
}
public void mouseReleased(MouseEvent e)
{
if (handlePopupTrigger(e)) {
return;
}
if ((e.getModifiers() & InputEvent.BUTTON1_MASK) != 0) {
if (e.getClickCount() == 2) {
handleDoubleClick(e);
return;
}
mMouseIsDown = false;
updateCursor();
mouseReleasedButton1(e);
}
}
public void mouseEntered(MouseEvent e)
{
requestFocus();
updateCursor();
}
public void mouseExited(MouseEvent e)
{
}
public void mouseClicked(MouseEvent e)
{
}
public void mouseDragged(MouseEvent e)
{
mMouseIsDown = true;
mX2 = e.getX();
mY2 = e.getY();
boolean repaintNeeded = trackHiliting(mX2, mY2, true);
switch (mPendingRequest) {
case cRequestNewChain:
double lastX, lastY;
if (mChainAtoms > 0) {
lastX = mChainAtomX[mChainAtoms - 1];
lastY = mChainAtomY[mChainAtoms - 1];
} else {
lastX = 0;
lastY = 0;
}
double avbl = mMol.getAverageBondLength();
double s0 = (int) avbl;
double s1 = (int) (0.866 * avbl);
double s2 = (int) (0.5 * avbl);
double dx = mX2 - mX1;
double dy = mY2 - mY1;
if (Math.abs(dy) > Math.abs(dx)) {
mChainAtoms = (int) (2 * Math.abs(dy) / (s0 + s2));
if (Math.abs(dy) % (s0 + s2) > s0) {
mChainAtoms++;
}
mChainAtomX = new double[mChainAtoms];
mChainAtomY = new double[mChainAtoms];
if (mX2 < mX1) {
s1 = -s1;
}
if (mY2 < mY1) {
s0 = -s0;
s2 = -s2;
}
for (int i = 0; i < mChainAtoms; i++) {
mChainAtomX[i] = mX1 + ((i + 1) / 2) * s1;
mChainAtomY[i] = mY1 + ((i + 1) / 2) * (s0 + s2);
if ((i & 1) == 0) {
mChainAtomY[i] += s0;
}
}
} else {
mChainAtoms = (int) (Math.abs(dx) / s1);
mChainAtomX = new double[mChainAtoms];
mChainAtomY = new double[mChainAtoms];
if (mX2 < mX1) {
s1 = -s1;
}
if (mY2 < mY1) {
s2 = -s2;
}
for (int i = 0; i < mChainAtoms; i++) {
mChainAtomX[i] = mX1 + (i + 1) * s1;
mChainAtomY[i] = mY1;
if ((i & 1) == 0) {
mChainAtomY[i] += s2;
}
}
}
if (mChainAtoms > 0) {
mChainAtom = new int[mChainAtoms];
for (int i = 0; i < mChainAtoms; i++) {
mChainAtom[i] = mMol.findAtom(mChainAtomX[i], mChainAtomY[i]);
if (mChainAtom[i] != -1) {
mChainAtomX[i] = mMol.getAtomX(mChainAtom[i]);
mChainAtomY[i] = mMol.getAtomY(mChainAtom[i]);
}
}
if (mChainAtomX[mChainAtoms - 1] != lastX
|| mChainAtomY[mChainAtoms - 1] != lastY) {
repaintNeeded = true;
}
} else if (lastX != 0 || lastY != 0) {
repaintNeeded = true;
}
break;
case cRequestNewBond:
if ((mX2 - mX1) * (mX2 - mX1) + (mY2 - mY1) * (mY2 - mY1) < MIN_BOND_LENGTH_SQUARE) {
suggestNewX2AndY2(mAtom1);
}
repaintNeeded = true;
break;
case cRequestMoveSingle:
mMol.setAtomX(mAtom1, mX[mAtom1] + mX2 - mX1);
mMol.setAtomY(mAtom1, mY[mAtom1] + mY2 - mY1);
if (mAtom2 != -1) {
mMol.setAtomX(mAtom2, mX[mAtom2] + mX2 - mX1);
mMol.setAtomY(mAtom2, mY[mAtom2] + mY2 - mY1);
}
update(UPDATE_CHECK_VIEW);
break;
case cRequestCopySelected:
duplicateSelected();
mPendingRequest = cRequestMoveSelected;
case cRequestMoveSelected:
if (mDrawingObjectList != null) {
for (AbstractDrawingObject drawingObject : mDrawingObjectList) {
if (drawingObject.isSelected()) {
drawingObject.translate(mX2, mY2);
}
}
}
for (int i = 0; i < mMol.getAllAtoms(); i++) {
if (mMol.isSelectedAtom(i)) {
mMol.setAtomX(i, mX[i] + mX2 - mX1);
mMol.setAtomY(i, mY[i] + mY2 - mY1);
}
}
update(UPDATE_CHECK_VIEW);
break;
case cRequestCopyObject:
mDrawingObjectList.add(mCurrentHiliteObject.clone());
mPendingRequest = cRequestMoveObject;
case cRequestMoveObject:
mCurrentHiliteObject.translate(mX2, mY2);
update(UPDATE_CHECK_VIEW);
break;
case cRequestZoomAndRotate:
boolean selectedAtomsFound = false;
for (int atom = 0; atom < mMol.getAllAtoms() && !selectedAtomsFound; atom++) {
selectedAtomsFound = mMol.isSelectedAtom(atom);
}
boolean selectedObjectsFound = false;
if (mDrawingObjectList != null) {
for (int i = 0; i < mDrawingObjectList.size() && !selectedObjectsFound; i++) {
selectedObjectsFound = mDrawingObjectList.get(i).isSelected();
}
}
double magnification = (Math.abs(mY2 - mY1) < 20) ? 1.0 : Math.exp((mY2 - mY1) / 100);
double angleChange = (Math.abs(mX2 - mX1) < 20) ? 0.0f : (mX2 - mX1) / 50;
boolean selectedOnly = (selectedAtomsFound || selectedObjectsFound);
if (mDrawingObjectList != null && (!selectedOnly || selectedObjectsFound)) {
for (int i = 0; i < mDrawingObjectList.size(); i++) {
if (!selectedOnly || mDrawingObjectList.get(i).isSelected()) {
mDrawingObjectList.get(i).zoomAndRotate(magnification, angleChange);
}
}
update(UPDATE_CHECK_VIEW);
}
if (!selectedOnly || selectedAtomsFound) {
mMol.zoomAndRotate(magnification, angleChange, selectedOnly);
update(UPDATE_CHECK_VIEW);
}
break;
case cRequestLassoSelect:
if ((Math.abs(mX2 - mLassoRegion.xpoints[mLassoRegion.npoints - 1]) < 3)
&& (Math.abs(mY2 - mLassoRegion.ypoints[mLassoRegion.npoints - 1]) < 3)) {
break;
}
mLassoRegion.npoints--;
mLassoRegion.addPoint((int) mX2, (int) mY2);
mLassoRegion.addPoint((int) mX1, (int) mY1);
case cRequestSelectRect:
Shape selectedRegion = null;
if (mPendingRequest == cRequestLassoSelect) {
selectedRegion = mLassoRegion;
} else {
selectedRegion = new Rectangle((int) Math.min(mX1, mX2), (int) Math.min(mY1, mY2),
(int) Math.abs(mX2 - mX1), (int) Math.abs(mY2 - mY1));
}
if (mDrawingObjectList != null) {
for (int i = 0; i < mDrawingObjectList.size(); i++) {
AbstractDrawingObject object = mDrawingObjectList.get(i);
boolean isSelected = object.isSurroundedBy(selectedRegion);
if ((!mIsAddingToSelection || !mIsSelectedObject[i])
&& (isSelected != object.isSelected())) {
object.setSelected(isSelected);
mUpdateMode = Math.max(mUpdateMode, UPDATE_REDRAW);
}
}
}
for (int i = 0; i < mMol.getAllAtoms(); i++) {
boolean isSelected = selectedRegion.contains((int) mMol.getAtomX(i), (int) mMol.getAtomY(i));
if ((!mIsAddingToSelection || !mIsSelectedAtom[i])
&& (isSelected != mMol.isSelectedAtom(i))) {
mMol.setAtomSelection(i, isSelected);
mUpdateMode = Math.max(mUpdateMode, UPDATE_REDRAW);
}
}
repaintNeeded = true;
break;
case cRequestMapAtoms:
repaintNeeded = true;
break;
}
if (repaintNeeded) {
repaint();
}
}
public void mouseMoved(MouseEvent e)
{
mMouseIsDown = false;
int x = e.getX();
int y = e.getY();
if (trackHiliting(x, y, false)) {
repaint();
}
updateCursor();
}
public void keyPressed(KeyEvent e)
{
if (e.getKeyCode() == KeyEvent.VK_SHIFT) {
mShiftIsDown = true;
updateCursor();
}
if (e.getKeyCode() == KeyEvent.VK_ALT) {
mAltIsDown = true;
updateCursor();
}
if (e.getKeyCode() == KeyEvent.VK_CONTROL) {
mControlIsDown = true;
updateCursor();
}
if (mControlIsDown && e.getKeyCode() == KeyEvent.VK_Z) {
restoreState();
fireMoleculeChanged();
update(UPDATE_CHECK_VIEW);
} else if (e.getKeyCode() == KeyEvent.VK_DELETE) {
storeState();
if (mCurrentTool == JDrawToolbar.cToolMapper) {
boolean found = false;
for (int atom = 0; atom < mMol.getAllAtoms(); atom++) {
if (mMol.getAtomMapNo(atom) != 0) {
mMol.setAtomMapNo(atom, 0, false);
found = true;
}
}
if (found) {
fireMoleculeChanged();
update(UPDATE_REDRAW);
}
} else if (!deleteHilited()) {
if (mMol.deleteSelectedAtoms()) {
fireMoleculeChanged();
update(UPDATE_REDRAW);
}
}
} else if (e.getKeyCode() == KeyEvent.VK_HELP || (mCurrentHiliteAtom == -1 && e.getKeyChar() == '?')) {
showHelpDialog();
return;
} else if (mCurrentHiliteBond != -1) {
char ch = e.getKeyChar();
if (ch == 'q' && mMol.isFragment()) {
showBondQFDialog(mCurrentHiliteBond);
} else if (ch >= '4' && ch <= '7') {
if (mMol.addRingToBond(mCurrentHiliteBond, ch - '0', false)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
} else if (ch == 'b') {
if (mMol.addRingToBond(mCurrentHiliteBond, 6, true)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
} else {
boolean bondChanged = (ch == '1') ? changeHighlightedBond(Molecule.cBondTypeSingle)
: (ch == '2') ? changeHighlightedBond(Molecule.cBondTypeDouble)
: (ch == '3') ? changeHighlightedBond(Molecule.cBondTypeTriple)
: (ch == 'u') ? changeHighlightedBond(Molecule.cBondTypeUp)
: (ch == 'd') ? changeHighlightedBond(Molecule.cBondTypeDown)
: (ch == 'c') ? changeHighlightedBond(Molecule.cBondTypeCross)
: (ch == 'm') ? changeHighlightedBond(Molecule.cBondTypeMetalLigand)
: false;
if (bondChanged) {
fireMoleculeChanged();
update(UPDATE_REDRAW);
}
}
} else if (mCurrentHiliteAtom != -1) {
char ch = e.getKeyChar();
boolean isFirst = (mAtomKeyStrokeBuffer.length() == 0);
if (isFirst && (ch == '+' || ch == '-')) {
storeState();
if (mMol.changeAtomCharge(mCurrentHiliteAtom, ch == '+')) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
} else if (isFirst && ch == '.') {
storeState();
int newRadical = (mMol.getAtomRadical(mCurrentHiliteAtom) == Molecule.cAtomRadicalStateD) ?
0 : Molecule.cAtomRadicalStateD;
mMol.setAtomRadical(mCurrentHiliteAtom, newRadical);
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
} else if (isFirst && ch == ':') {
storeState();
int newRadical = (mMol.getAtomRadical(mCurrentHiliteAtom) == Molecule.cAtomRadicalStateT) ? Molecule.cAtomRadicalStateS
: (mMol.getAtomRadical(mCurrentHiliteAtom) == Molecule.cAtomRadicalStateS) ? 0 : Molecule.cAtomRadicalStateT;
mMol.setAtomRadical(mCurrentHiliteAtom, newRadical);
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
} else if (isFirst && ch == 'q' && mMol.isFragment()) {
showAtomQFDialog(mCurrentHiliteAtom);
} else if (isFirst && ch == '?') {
storeState();
if (mMol.changeAtom(mCurrentHiliteAtom, 0, 0, -1, 0)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
} else if (isFirst && ch > 48 && ch <= 57) {
if (mMol.getFreeValence(mCurrentHiliteAtom) > 0) {
storeState();
int chainAtoms = ch - 47;
int atom1 = mCurrentHiliteAtom;
int hydrogenCount = mMol.getAllAtoms() - mMol.getAtoms();
for (int i = 1; i < chainAtoms; i++) {
suggestNewX2AndY2(atom1);
int atom2 = mMol.addAtom(mX2, mY2);
if (atom2 == -1) {
break;
}
mMol.addBond(atom1, atom2, Molecule.cBondTypeSingle);
atom1 = atom2 - hydrogenCount; // new atom was added behind all hydrogens and travels now to the front
mMol.ensureHelperArrays(Molecule.cHelperNeighbours);
}
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
} else if (!isFirst && e.getKeyCode() == KeyEvent.VK_ESCAPE) {
mAtomKeyStrokeBuffer.setLength(0);
update(UPDATE_REDRAW);
} else if (!isFirst && e.getKeyCode() == KeyEvent.VK_BACK_SPACE) {
mAtomKeyStrokeBuffer.setLength(mAtomKeyStrokeBuffer.length() - 1);
update(UPDATE_REDRAW);
} else if ((ch >= 65 && ch <= 90)
|| (ch >= 97 && ch <= 122)
|| (ch >= 48 && ch <= 57)
|| (ch == '-')) {
mAtomKeyStrokeBuffer.append(ch);
update(UPDATE_REDRAW);
} else if (ch == '\n' || ch == '\r') {
expandAtomKeyStrokes(mAtomKeyStrokeBuffer.toString());
}
} else if (mCurrentHiliteAtom == -1 && mCurrentHiliteBond == -1) {
if ((mMode & (MODE_REACTION | MODE_MARKUSH_STRUCTURE | MODE_MULTIPLE_FRAGMENTS)) == 0) {
char ch = e.getKeyChar();
if (ch == 'h') {
flip(true);
update(UPDATE_REDRAW);
} if (ch == 'v') {
flip(false);
update(UPDATE_REDRAW);
}
}
}
}
private boolean changeHighlightedBond(int type)
{
storeState();
return mMol.changeBond(mCurrentHiliteBond, type);
}
public void showHelpDialog()
{
if (mHelpDialog == null || !mHelpDialog.isVisible()) {
JEditorPane helpPane = new JEditorPane();
helpPane.setEditorKit(HiDPIHelper.getUIScaleFactor() == 1f ? new HTMLEditorKit() : new ScaledEditorKit());
helpPane.setEditable(false);
try {
helpPane.setPage(getClass().getResource("/html/editor/editor.html"));
} catch (Exception ex) {
helpPane.setText(ex.toString());
}
Component c = this;
while (!(c instanceof Frame || c instanceof Dialog)) {
c = c.getParent();
}
if (c instanceof Frame) {
mHelpDialog = new JDialog((Frame) c, "Actelion Structure Editor Help", false);
} else {
mHelpDialog = new JDialog((Dialog) c, "Actelion Structure Editor Help", false);
}
mHelpDialog.setSize(HiDPIHelper.scale(520), HiDPIHelper.scale(440));
mHelpDialog.getContentPane().add(new JScrollPane(helpPane,
JScrollPane.VERTICAL_SCROLLBAR_ALWAYS,
JScrollPane.HORIZONTAL_SCROLLBAR_NEVER));
int x = (c.getX() >= 8 + mHelpDialog.getWidth()) ? c.getX() - 8 - mHelpDialog.getWidth() : c.getX() + 8 + c.getWidth();
mHelpDialog.setLocation(x, c.getY());
mHelpDialog.setVisible(true);
} else {
Component c = this;
while (!(c instanceof Frame || c instanceof Dialog)) {
c = c.getParent();
}
int x = (mHelpDialog.getX() + mHelpDialog.getWidth() / 2 >= c.getX() + c.getWidth() / 2) ?
c.getX() - 8 - mHelpDialog.getWidth() : c.getX() + 8 + c.getWidth();
mHelpDialog.setLocation(x, c.getY());
}
}
public void keyReleased(KeyEvent e)
{
if (e.getKeyCode() == KeyEvent.VK_SHIFT) {
mShiftIsDown = false;
updateCursor();
}
if (e.getKeyCode() == KeyEvent.VK_ALT) {
mAltIsDown = false;
updateCursor();
}
if (e.getKeyCode() == KeyEvent.VK_CONTROL) {
mControlIsDown = false;
updateCursor();
}
if ((e.getModifiers() & Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()) != 0) {
if (e.getKeyCode() == KeyEvent.VK_C) {
copy();
} else if (e.getKeyCode() == KeyEvent.VK_V) {
paste();
}
}
}
public void keyTyped(KeyEvent e)
{
}
private boolean handlePopupTrigger(MouseEvent e)
{
if (e.isPopupTrigger()) {
JPopupMenu popup = null;
if (mClipboardHandler != null) {
JMenuItem menuItem1 = new JMenuItem("Copy");
menuItem1.addActionListener(this);
if (mMol.getAllAtoms() == 0) {
menuItem1.setEnabled(false);
}
JMenuItem menuItem2 = new JMenuItem("Paste");
menuItem2.addActionListener(this);
if (popup == null) {
popup = new JPopupMenu();
}
popup.add(menuItem1);
popup.add(menuItem2);
}
if (mAtomColorSupported && mCurrentHiliteAtom != -1) {
int atomColor = mMol.getAtomColor(mCurrentHiliteAtom);
if (popup == null) {
popup = new JPopupMenu();
} else {
popup.addSeparator();
}
JMenu colorMenu = new JMenu("Set Atom Color");
addColorToMenu(colorMenu, Color.BLACK, Molecule.cAtomColorNone, atomColor == Molecule.cAtomColorNone);
addColorToMenu(colorMenu, AbstractDepictor.COLOR_BLUE, Molecule.cAtomColorBlue, atomColor == Molecule.cAtomColorBlue);
addColorToMenu(colorMenu, AbstractDepictor.COLOR_DARK_RED, Molecule.cAtomColorDarkRed, atomColor == Molecule.cAtomColorDarkRed);
addColorToMenu(colorMenu, AbstractDepictor.COLOR_RED, Molecule.cAtomColorRed, atomColor == Molecule.cAtomColorRed);
addColorToMenu(colorMenu, AbstractDepictor.COLOR_DARK_GREEN, Molecule.cAtomColorDarkGreen, atomColor == Molecule.cAtomColorDarkGreen);
addColorToMenu(colorMenu, AbstractDepictor.COLOR_GREEN, Molecule.cAtomColorGreen, atomColor == Molecule.cAtomColorGreen);
addColorToMenu(colorMenu, AbstractDepictor.COLOR_MAGENTA, Molecule.cAtomColorMagenta, atomColor == Molecule.cAtomColorMagenta);
addColorToMenu(colorMenu, AbstractDepictor.COLOR_ORANGE, Molecule.cAtomColorOrange, atomColor == Molecule.cAtomColorOrange);
popup.add(colorMenu);
}
if (popup != null) {
popup.show(this, e.getX(), e.getY());
}
return true;
}
return false;
}
private void addColorToMenu(JMenu menu, Color color, int atomColor, boolean isSelected)
{
JRadioButtonMenuItem item = new JRadioButtonMenuItem(" ", isSelected);
item.setActionCommand("atomColor" + mCurrentHiliteAtom + ":" + atomColor);
item.addActionListener(this);
item.setBackground(color);
menu.add(item);
}
private void handleDoubleClick(MouseEvent e)
{
int x = e.getX();
int y = e.getY();
int atom = mMol.findAtom(x, y);
int bond = mMol.findBond(x, y);
if (mCurrentTool == JDrawToolbar.cToolLassoPointer) {
if (mMol.isFragment()) {
if (atom != -1) {
showAtomQFDialog(atom);
} else if (bond != -1) {
showBondQFDialog(bond);
} else if (mCurrentHiliteObject != null) {
if (!mShiftIsDown) {
for (int i = 0; i < mMol.getAllAtoms(); i++) {
mMol.setAtomSelection(i, false);
}
for (int i = 0; i < mDrawingObjectList.size(); i++) {
((AbstractDrawingObject) mDrawingObjectList.get(i)).setSelected(false);
}
}
mCurrentHiliteObject.setSelected(true);
update(UPDATE_REDRAW);
}
} else {
int rootAtom = -1;
if (atom != -1) {
rootAtom = atom;
} else if (bond != -1) {
rootAtom = mMol.getBondAtom(0, bond);
}
if (rootAtom != -1 || mCurrentHiliteObject != null) {
if (!mShiftIsDown) {
for (int i = 0; i < mMol.getAllAtoms(); i++) {
mMol.setAtomSelection(i, false);
}
if (mDrawingObjectList != null) {
for (AbstractDrawingObject drawingObject : mDrawingObjectList) {
drawingObject.setSelected(false);
}
}
}
if (rootAtom != -1) {
if ((mMode & MODE_MULTIPLE_FRAGMENTS) != 0) {
int fragment = mFragmentNo[rootAtom];
for (int i = 0; i < mMol.getAllAtoms(); i++) {
if (mFragmentNo[i] == fragment) {
mMol.setAtomSelection(i, true);
}
}
} else {
int[] fragmentMember = mMol.getFragmentAtoms(rootAtom);
for (int i = 0; i < fragmentMember.length; i++) {
mMol.setAtomSelection(fragmentMember[i], true);
}
}
} else {
mCurrentHiliteObject.setSelected(true);
}
update(UPDATE_REDRAW);
}
}
} else if (mCurrentTool == JDrawToolbar.cToolAtomOther) {
if (atom != -1) {
Component c = this;
while (c.getParent() != null) {
c = c.getParent();
}
storeState();
new JAtomLabelDialog((Frame) c, mMol, atom);
mOtherAtom = mMol.getAtomicNo(atom);
mOtherMass = mMol.getAtomMass(atom);
mOtherValence = mMol.getAtomAbnormalValence(atom);
mOtherRadical = mMol.getAtomRadical(atom);
fireMoleculeChanged();
update(UPDATE_REDRAW);
}
} else if (mCurrentTool == JDrawToolbar.cToolZoom) {
int fragment = -2;
if ((mMode & MODE_MULTIPLE_FRAGMENTS) != 0) {
fragment = findFragment(x, y);
}
if (fragment != -1) {
double minX = Integer.MAX_VALUE;
double maxX = Integer.MIN_VALUE;
for (int i = 0; i < mMol.getAllAtoms(); i++) {
if (fragment == -2 || mFragmentNo[i] == fragment) {
if (minX > mMol.getAtomX(i)) {
minX = mMol.getAtomX(i);
}
if (maxX < mMol.getAtomX(i)) {
maxX = mMol.getAtomX(i);
}
}
}
if (maxX > minX) {
double centerX = (maxX + minX) / 2;
for (int i = 0; i < mMol.getAllAtoms(); i++) {
if (fragment == -2 || mFragmentNo[i] == fragment) {
mMol.setAtomX(i, 2 * centerX - mMol.getAtomX(i));
}
}
for (int i = 0; i < mMol.getAllBonds(); i++) {
if (fragment == -2 || mFragmentNo[mMol.getBondAtom(0, i)] == fragment) {
switch (mMol.getBondType(i)) {
case Molecule.cBondTypeUp:
mMol.setBondType(i, Molecule.cBondTypeDown);
break;
case Molecule.cBondTypeDown:
mMol.setBondType(i, Molecule.cBondTypeUp);
break;
}
}
}
}
fireMoleculeChanged();
update(UPDATE_REDRAW);
}
}
}
private void showAtomQFDialog(int atom)
{
Component c = this;
while (c.getParent() != null) {
c = c.getParent();
}
storeState();
new JAtomQueryFeatureDialog((Frame) c, mMol, atom);
fireMoleculeChanged();
update(UPDATE_REDRAW);
}
private void showBondQFDialog(int bond)
{
Component c = this;
while (c.getParent() != null) {
c = c.getParent();
}
storeState();
new JBondQueryFeatureDialog((Frame) c, mMol, bond);
fireMoleculeChanged();
update(UPDATE_REDRAW);
}
private void mousePressedButton1(MouseEvent e)
{
mX1 = e.getX();
mY1 = e.getY();
switch (mCurrentTool) {
case JDrawToolbar.cToolZoom:
// mX1,mY1 define anker for rotation and zooming
double x = mX1;
double y = mY1;
mAtom1 = mMol.findAtom(mX1, mY1);
if (mAtom1 != -1) {
mX1 = mMol.getAtomX(mAtom1);
mY1 = mMol.getAtomY(mAtom1);
}
mMol.zoomAndRotateInit(x, y);
if (mDrawingObjectList != null) {
for (AbstractDrawingObject drawingObject : mDrawingObjectList) {
drawingObject.zoomAndRotateInit(x, y);
}
}
storeState();
mPendingRequest = cRequestZoomAndRotate;
break;
case JDrawToolbar.cToolLassoPointer:
mPendingRequest = cRequestNone;
// if atom was hit -> move atom (and if atom is selected then all selected stuff)
mAtom1 = mMol.findAtom(mX1, mY1);
if (mAtom1 != -1) {
mAtom2 = -1;
mX1 = mMol.getAtomX(mAtom1);
mY1 = mMol.getAtomY(mAtom1);
if (mMol.isSelectedAtom(mAtom1)) {
mPendingRequest = mShiftIsDown ? cRequestCopySelected : cRequestMoveSelected;
} else {
mPendingRequest = cRequestMoveSingle;
}
}
// if bond was hit -> move bond (and if atom is selected then all selected stuff)
if (mPendingRequest == cRequestNone) {
int bondClicked = mMol.findBond(mX1, mY1);
if (bondClicked != -1) {
mAtom1 = mMol.getBondAtom(0, bondClicked);
mAtom2 = mMol.getBondAtom(1, bondClicked);
if (mMol.isSelectedBond(bondClicked)) {
mPendingRequest = mShiftIsDown ? cRequestCopySelected : cRequestMoveSelected;
} else {
mPendingRequest = cRequestMoveSingle;
}
}
}
// if object was hit -> move object (and if atom is selected then all selected stuff)
if (mPendingRequest == cRequestNone) {
if (mCurrentHiliteObject != null) {
if (mCurrentHiliteObject.isSelected()) {
mPendingRequest = mShiftIsDown ? cRequestCopySelected : cRequestMoveSelected;
} else {
mPendingRequest = (mShiftIsDown && !(mCurrentHiliteObject instanceof ReactionArrow)) ?
cRequestCopyObject : cRequestMoveObject;
}
}
}
if (mPendingRequest != cRequestNone) {
mX = new double[mMol.getAllAtoms()];
mY = new double[mMol.getAllAtoms()];
for (int i = 0; i < mMol.getAllAtoms(); i++) {
mX[i] = mMol.getAtomX(i);
mY[i] = mMol.getAtomY(i);
}
if (mDrawingObjectList != null) {
for (AbstractDrawingObject drawingObject : mDrawingObjectList) {
drawingObject.translateInit(mX1, mY1);
}
}
storeState();
break;
}
// is lasso- or rectangle-selecting
mIsSelectedAtom = new boolean[mMol.getAllAtoms()];
if (mDrawingObjectList != null) {
mIsSelectedObject = new boolean[mDrawingObjectList.size()];
}
mIsAddingToSelection = e.isShiftDown();
for (int i = 0; i < mMol.getAllAtoms(); i++) {
mIsSelectedAtom[i] = mMol.isSelectedAtom(i);
}
if (mDrawingObjectList != null) {
for (int i = 0; i < mDrawingObjectList.size(); i++) {
mIsSelectedObject[i] = mDrawingObjectList.get(i).isSelected();
}
}
if (e.isAltDown()) {
mPendingRequest = cRequestSelectRect;
} else {
mLassoRegion = new Polygon();
mLassoRegion.addPoint((int) mX1, (int) mY1);
mLassoRegion.addPoint((int) mX1, (int) mY1);
mPendingRequest = cRequestLassoSelect;
}
break;
case JDrawToolbar.cToolDelete:
storeState();
deleteAt(mX1, mY1);
break;
case JDrawToolbar.cToolUnknownParity:
int theAtom = mMol.findAtom(mX1, mY1);
if (theAtom != -1) {
storeState();
mMol.setAtomConfigurationUnknown(theAtom, !mMol.isAtomConfigurationUnknown(theAtom));
fireMoleculeChanged();
update(UPDATE_REDRAW);
}
break;
case JDrawToolbar.cToolESRAbs:
case JDrawToolbar.cToolESRAnd:
case JDrawToolbar.cToolESROr:
if (mCurrentHiliteBond != -1 && qualifiesForESR(mCurrentHiliteBond)) {
storeState();
setESRInfo(mCurrentHiliteBond, (mCurrentTool == JDrawToolbar.cToolESRAbs) ?
Molecule.cESRTypeAbs :
(mCurrentTool == JDrawToolbar.cToolESRAnd) ?
Molecule.cESRTypeAnd : Molecule.cESRTypeOr);
fireMoleculeChanged();
update(UPDATE_REDRAW);
}
break;
case JDrawToolbar.cToolStdBond:
case JDrawToolbar.cToolUpBond:
case JDrawToolbar.cToolDownBond:
mAtom1 = mMol.findAtom(mX1, mY1);
if (mAtom1 == -1) {
int bond = mMol.findBond(mX1, mY1);
if (bond != -1) {
storeState();
int bondType = Molecule.cBondTypeIncreaseOrder;
if (mCurrentTool == JDrawToolbar.cToolUpBond) {
bondType = Molecule.cBondTypeUp;
} else if (mCurrentTool == JDrawToolbar.cToolDownBond) {
bondType = Molecule.cBondTypeDown;
}
if (mMol.changeBond(bond, bondType)) {
fireMoleculeChanged();
update(UPDATE_REDRAW);
}
break;
}
} else {
if (mMol.getAllConnAtoms(mAtom1) == MAX_CONNATOMS) {
return;
}
mX1 = mMol.getAtomX(mAtom1);
mY1 = mMol.getAtomY(mAtom1);
}
mPendingRequest = cRequestNewBond;
suggestNewX2AndY2(mAtom1);
repaint();
break;
case JDrawToolbar.cToolChain:
mAtom1 = mMol.findAtom(mX1, mY1);
if (mAtom1 != -1) {
if (mMol.getAllConnAtoms(mAtom1) == MAX_CONNATOMS) {
return;
}
mX1 = mMol.getAtomX(mAtom1);
mY1 = mMol.getAtomY(mAtom1);
}
mPendingRequest = cRequestNewChain;
mChainAtoms = 0;
break;
case JDrawToolbar.cTool3Ring:
storeState();
if (mMol.addRing(mX1, mY1, 3, false)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
break;
case JDrawToolbar.cTool4Ring:
storeState();
if (mMol.addRing(mX1, mY1, 4, false)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
break;
case JDrawToolbar.cTool5Ring:
storeState();
if (mMol.addRing(mX1, mY1, 5, false)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
break;
case JDrawToolbar.cTool6Ring:
storeState();
if (mMol.addRing(mX1, mY1, 6, false)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
break;
case JDrawToolbar.cTool7Ring:
storeState();
if (mMol.addRing(mX1, mY1, 7, false)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
break;
case JDrawToolbar.cToolAromRing:
storeState();
if (mMol.addRing(mX1, mY1, 6, true)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
break;
case JDrawToolbar.cToolPosCharge:
storeState();
if (mMol.changeAtomCharge(mX1, mY1, true)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
break;
case JDrawToolbar.cToolNegCharge:
storeState();
if (mMol.changeAtomCharge(mX1, mY1, false)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
break;
case JDrawToolbar.cToolAtomH:
storeState();
if (mMol.addOrChangeAtom(mX1, mY1, 1, 0, -1, 0)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
break;
case JDrawToolbar.cToolAtomC:
storeState();
if (mMol.addOrChangeAtom(mX1, mY1, 6, 0, -1, 0)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
break;
case JDrawToolbar.cToolAtomN:
storeState();
if (mMol.addOrChangeAtom(mX1, mY1, 7, 0, -1, 0)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
break;
case JDrawToolbar.cToolAtomO:
storeState();
if (mMol.addOrChangeAtom(mX1, mY1, 8, 0, -1, 0)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
break;
case JDrawToolbar.cToolAtomSi:
storeState();
if (mMol.addOrChangeAtom(mX1, mY1, 14, 0, -1, 0)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
break;
case JDrawToolbar.cToolAtomP:
storeState();
if (mMol.addOrChangeAtom(mX1, mY1, 15, 0, -1, 0)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
break;
case JDrawToolbar.cToolAtomS:
storeState();
if (mMol.addOrChangeAtom(mX1, mY1, 16, 0, -1, 0)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
break;
case JDrawToolbar.cToolAtomF:
storeState();
if (mMol.addOrChangeAtom(mX1, mY1, 9, 0, -1, 0)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
break;
case JDrawToolbar.cToolAtomCl:
storeState();
if (mMol.addOrChangeAtom(mX1, mY1, 17, 0, -1, 0)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
break;
case JDrawToolbar.cToolAtomBr:
storeState();
if (mMol.addOrChangeAtom(mX1, mY1, 35, 0, -1, 0)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
break;
case JDrawToolbar.cToolAtomI:
storeState();
if (mMol.addOrChangeAtom(mX1, mY1, 53, 0, -1, 0)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
break;
case JDrawToolbar.cToolAtomOther:
if (mOtherAtom != -1) {
storeState();
if (mMol.addOrChangeAtom(mX1, mY1, mOtherAtom, mOtherMass, mOtherValence, mOtherRadical)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
}
break;
case JDrawToolbar.cToolMapper:
mAtom1 = mMol.findAtom(mX1, mY1);
if (mAtom1 != -1 && mAtom1 < mMol.getAtoms()) {
mX1 = mMol.getAtomX(mAtom1);
mY1 = mMol.getAtomY(mAtom1);
mPendingRequest = cRequestMapAtoms;
}
break;
case JDrawToolbar.cToolText:
TextDrawingObject object = null;
if (mCurrentHiliteObject == null) {
object = new TextDrawingObject();
object.setCoordinates(mX1, mY1);
mDrawingObjectList.add(object);
} else if (mCurrentHiliteObject instanceof TextDrawingObject) {
object = (TextDrawingObject) mCurrentHiliteObject;
}
editTextObject(object);
storeState();
update(UPDATE_CHECK_COORDS);
break;
}
}
private void mouseReleasedButton1(MouseEvent e)
{
int pendingRequest = mPendingRequest;
mPendingRequest = cRequestNone;
switch (pendingRequest) {
case cRequestNewBond:
int stopAtom;
stopAtom = mMol.findAtom(mX2, mY2);
if (stopAtom != -1
&& mMol.getAllConnAtoms(stopAtom) == MAX_CONNATOMS) {
return;
}
storeState();
if (mAtom1 == -1) {
mAtom1 = mMol.addAtom(mX1, mY1);
}
if (stopAtom == -1) {
stopAtom = mMol.addAtom(mX2, mY2);
}
if ((mAtom1 != -1 && stopAtom != -1)) {
int bondType = Molecule.cBondTypeSingle;
if (mCurrentTool == JDrawToolbar.cToolUpBond) {
bondType = Molecule.cBondTypeUp;
}
if (mCurrentTool == JDrawToolbar.cToolDownBond) {
bondType = Molecule.cBondTypeDown;
}
mMol.addOrChangeBond(mAtom1, stopAtom, bondType);
}
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
break;
case cRequestNewChain:
storeState();
if (mChainAtoms > 0) {
if (mAtom1 == -1) {
mAtom1 = mMol.addAtom(mX1, mY1);
}
if (mChainAtom[0] == -1) {
mChainAtom[0] = mMol.addAtom(mChainAtomX[0],
mChainAtomY[0]);
}
if (mChainAtom[0] != -1) {
mMol.addBond(mAtom1, mChainAtom[0], Molecule.cBondTypeSingle);
}
}
if (mChainAtoms > 1) {
for (int i = 1; i < mChainAtoms; i++) {
if (mChainAtom[i] == -1) {
mChainAtom[i] = mMol.addAtom(mChainAtomX[i],
mChainAtomY[i]);
}
if (mChainAtom[i] != -1) {
mMol.addBond(mChainAtom[i - 1], mChainAtom[i], Molecule.cBondTypeSingle);
}
}
}
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
break;
case cRequestMoveSingle:
case cRequestMoveSelected:
case cRequestZoomAndRotate:
fireMoleculeChanged();
case cRequestMoveObject:
update(UPDATE_CHECK_COORDS);
break;
case cRequestLassoSelect:
case cRequestSelectRect:
boolean selectionChanged = false;
for (int i = 0; i < mMol.getAllAtoms(); i++) {
if (mIsSelectedAtom[i] != mMol.isSelectedAtom(i)) {
selectionChanged = true;
break;
}
}
if (selectionChanged) {
fireEvent(new DrawAreaEvent(this, DrawAreaEvent.TYPE_SELECTION_CHANGED, true));
}
repaint();
break;
case cRequestMapAtoms:
boolean mapNoChanged = false;
int atom2 = mCurrentHiliteAtom;
// System.out.printf("Map Request Atom %d => %d (%d)\n", mAtom1, mAtom2, atom2);
int mapNoAtom1 = mMol.getAtomMapNo(mAtom1);
if (atom2 == -1) {
storeState();
if (mapNoAtom1 != 0) {
mapNoChanged = true;
for (int atom = 0; atom < mMol.getAtoms(); atom++) {
if (mMol.getAtomMapNo(atom) == mapNoAtom1) {
mMol.setAtomMapNo(atom, 0, false);
}
}
if(mMapper != null)
tryAutoMapReaction();
// new MoleculeAutoMapper(mMol).autoMap();
}
} else {
storeState();
mapNoChanged = true;
// If we only clicked on a mapped atom, then reset the map number
if (mAtom1 == atom2) {
int mapNo = mMol.getAtomMapNo(mAtom1);
for (int atom = 0; atom < mMol.getAtoms(); atom++) {
if (mMol.getAtomMapNo(atom) == mapNo) {
mMol.setAtomMapNo(atom, 0, false);
}
}
} else {
// remove old mapping numbers of atom1 and atom2
int mapNoAtom2 = mMol.getAtomMapNo(atom2);
for (int atom = 0; atom < mMol.getAtoms(); atom++) {
if (mMol.getAtomMapNo(atom) == mapNoAtom1
|| mMol.getAtomMapNo(atom) == mapNoAtom2) {
mMol.setAtomMapNo(atom, 0, false);
}
}
int freeMapNo = 1;
for (int atom = 0; atom < mMol.getAtoms(); atom++) {
if (mMol.getAtomMapNo(atom) == freeMapNo) {
freeMapNo++;
atom = -1;
}
}
mMol.setAtomMapNo(mAtom1, freeMapNo, false);
mMol.setAtomMapNo(atom2, freeMapNo, false);
if(mMapper != null)
tryAutoMapReaction();
}
// new MoleculeAutoMapper(mMol).autoMap();
}
if (mapNoChanged) {
fireMoleculeChanged();
mUpdateMode = Math.max(mUpdateMode, UPDATE_REDRAW);
}
repaint();
break;
}
}
static class MySSSearcher extends SSSearcher
{
@Override
protected boolean areAtomsSimilar(int moleculeAtom, int fragmentAtom)
{
if (mMolecule.getAtomicNo(moleculeAtom) == mFragment.getAtomicNo(fragmentAtom))
if (mMolecule.isAromaticAtom(moleculeAtom) || mFragment.isAromaticAtom(fragmentAtom))
return true;
return super.areAtomsSimilar(moleculeAtom, fragmentAtom);
}
@Override
protected boolean areBondsSimilar(int moleculeBond, int fragmentBond)
{
if (mMolecule.isAromaticBond(moleculeBond) || mMolecule.isDelocalizedBond(moleculeBond) ||
mFragment.isAromaticBond(fragmentBond) || mFragment.isDelocalizedBond(fragmentBond)
)
return true;
return super.areBondsSimilar(moleculeBond, fragmentBond);
//return true;
}
}
private void tryAutoMapReaction()
{
// new MoleculeAutoMapper(mMol).autoMap();
SSSearcher sss = new MySSSearcher();
syncFragments();
Reaction rxn = getReaction();//new Reaction(reaction);
// Mark the manually mapped atoms, so we may re-assign them later
for (int i = 0; i < rxn.getMolecules(); i++) {
StereoMolecule mol = rxn.getMolecule(i);
for (int a = 0; a < mol.getAtoms(); a++) {
if (mol.getAtomMapNo(a) > 0) {
mol.setAtomicNo(a, FAKE_ATOM_NO + mol.getAtomMapNo(a));
}
}
}
rxn = mMapper.matchReaction(rxn, sss);
if (rxn != null) {
int offset = 0;
// Sync the display molecule with the reaction fragments
{
int[] fragmentAtom = new int[mFragment.length];
for (int atom = 0; atom < mMol.getAllAtoms(); atom++) {
int fragment = mFragmentNo[atom];
if (mFragment[fragment].getAtomicNo(fragmentAtom[fragment]) > FAKE_ATOM_NO) {
mMol.setAtomMapNo(atom, mFragment[fragment].getAtomicNo(fragmentAtom[fragment]) - FAKE_ATOM_NO, false);
offset = Math.max(mMol.getAtomMapNo(atom), offset);
}
fragmentAtom[fragment]++;
}
}
{
int[] fragmentAtom = new int[mFragment.length];
for (int atom = 0; atom < mMol.getAllAtoms(); atom++) {
int fragment = mFragmentNo[atom];
if (mFragment[fragment].getAtomMapNo(fragmentAtom[fragment]) > 0 && (mFragment[fragment].getAtomicNo(fragmentAtom[fragment]) <= FAKE_ATOM_NO)) {
mMol.setAtomMapNo(atom, mFragment[fragment].getAtomMapNo(fragmentAtom[fragment]) + offset, true);
}
fragmentAtom[fragment]++;
}
}
}
syncFragments();
// mMapper.resetFragments(mappedReaction);
// AStarReactionMapper m = new AStarReactionMapper();
// Reaction rxn = getReaction();
// List l = m.map(rxn);
// if (l != null && l.size() > 0) {
// AStarReactionMapper.SlimMapping sm = l.get(0);
//// int[] mps = sm.getMapping();
//// for (int i = 0; i < mps.length; i++) {
//// System.out.printf("Maps %d -> %d\n", i, mps[i]);
//// }
// m.activateMapping(sm);
//// for (int i = 0; i < mFragment.length; i++) {
//// StereoMolecule mol = mFragment[i];
//// for (int a = 0; a < mol.getAllAtoms(); a++) {
//// System.out.printf("T Map %d = %d\n", a, mol.getAtomMapNo(a));
//// }
//// }
//
// int[] fragmentAtom = new int[mFragment.length];
// for (int atom = 0; atom < mMol.getAllAtoms(); atom++) {
// int fragment = mFragmentNo[atom];
// if (mMol.getAtomMapNo(atom) == 0)
// mMol.setAtomMapNo(atom, mFragment[fragment].getAtomMapNo(fragmentAtom[fragment]), true);
// fragmentAtom[fragment]++;
// }
// }
}
/**
* Checks whether this bond is a stereo bond and whether it refers to a
* stereo center or BINAP bond, making it eligible for ESR information.
*
* @param stereoBond the up/down stereo bond
* @return
*/
private boolean qualifiesForESR(int stereoBond)
{
return mMol.isStereoBond(stereoBond) && (getESRAtom(stereoBond) != -1 || getESRBond(stereoBond) != -1);
}
/**
* Locates the stereo center with parity 1 or 2 that is defined by the stereo bond.
*
* @param stereoBond
* @return stereo center atom or -1 if no stereo center found
*/
private int getESRAtom(int stereoBond)
{
int atom = mMol.getBondAtom(0, stereoBond);
if (mMol.getAtomParity(atom) != Molecule.cAtomParityNone) {
return (mMol.isAtomParityPseudo(atom)
|| (mMol.getAtomParity(atom) != Molecule.cAtomParity1
&& mMol.getAtomParity(atom) != Molecule.cAtomParity2)) ? -1 : atom;
}
if (mMol.getAtomPi(atom) == 1) {
for (int i = 0; i < mMol.getConnAtoms(atom); i++) {
if (mMol.getConnBondOrder(atom, i) == 2) {
int connAtom = mMol.getConnAtom(atom, i);
if (mMol.getAtomPi(connAtom) == 2
&& (mMol.getAtomParity(connAtom) == Molecule.cAtomParity1
|| mMol.getAtomParity(connAtom) == Molecule.cAtomParity2)) {
return connAtom;
}
}
}
}
return -1;
}
private int getESRBond(int stereoBond)
{
int bond = mMol.findBINAPChiralityBond(mMol.getBondAtom(0, stereoBond));
if (bond != -1
&& mMol.getBondParity(bond) != Molecule.cBondParityEor1
&& mMol.getBondParity(bond) != Molecule.cBondParityZor2) {
bond = -1;
}
return bond;
}
/**
* Sets the ESR information of an atom or bond.
*
*/
private void setESRInfo(int stereoBond, int type)
{
int group = -1;
int atom = getESRAtom(stereoBond);
int bond = (atom == -1) ? getESRBond(stereoBond) : -1;
// if type requires group information (type==And or type==Or)
if (type != Molecule.cESRTypeAbs) {
int maxGroup = -1;
for (int i = 0; i < mMol.getAtoms(); i++) {
if (i != atom
&& mMol.getAtomESRType(i) == type
&& (!mMol.isSelectedBond(stereoBond) || !mMol.isSelectedAtom(i))) {
int grp = mMol.getAtomESRGroup(i);
if (maxGroup < grp) {
maxGroup = grp;
}
}
}
for (int i = 0; i < mMol.getBonds(); i++) {
if (i != bond
&& mMol.getBondESRType(i) == type
&& (!mMol.isSelectedBond(stereoBond) || !mMol.isSelectedBond(i))) {
int grp = mMol.getBondESRGroup(i);
if (maxGroup < grp) {
maxGroup = grp;
}
}
}
if ((atom == -1 ? mMol.getBondESRType(bond) : mMol.getAtomESRType(atom)) != type) {
group = Math.min(maxGroup + 1, Molecule.cESRMaxGroups - 1);
} else {
group = (atom == -1) ? mMol.getBondESRGroup(bond) : mMol.getAtomESRGroup(atom);
if (mMol.isSelectedBond(stereoBond)) {
boolean selectedShareOneGroup = true;
for (int i = 0; i < mMol.getAtoms(); i++) {
if (i != atom && mMol.isSelectedAtom(i)
&& mMol.getAtomESRType(i) == type
&& mMol.getAtomESRGroup(i) != group) {
selectedShareOneGroup = false;
break;
}
}
for (int i = 0; i < mMol.getBonds(); i++) {
if (i != bond && mMol.isSelectedBond(i)
&& mMol.getBondESRType(i) == type
&& mMol.getBondESRGroup(i) != group) {
selectedShareOneGroup = false;
break;
}
}
if (selectedShareOneGroup) {
if (group <= maxGroup) {
group++;
if (group == Molecule.cESRMaxGroups) {
group = 0;
}
} else {
group = 0;
}
}
} else {
if (group <= maxGroup) {
group++;
if (group == Molecule.cESRMaxGroups) {
group = 0;
}
} else {
group = 0;
}
}
}
}
if (mMol.isSelectedBond(stereoBond)) {
for (int i = 0; i < mMol.getBonds(); i++) {
if (mMol.isSelectedBond(i) && mMol.isStereoBond(i)) {
int a = getESRAtom(i);
int b = getESRBond(i);
if (a != -1) {
mMol.setAtomESR(a, type, group);
} else if (b != -1) {
mMol.setBondESR(b, type, group);
}
}
}
} else {
if (atom != -1) {
mMol.setAtomESR(atom, type, group);
} else if (bond != -1) {
mMol.setBondESR(bond, type, group);
}
}
}
private int findFragment(double x, double y)
{
int fragment = -1;
double minDistance = Double.MAX_VALUE;
for (int atom = 0; atom < mMol.getAllAtoms(); atom++) {
double dx = mX1 - mMol.getAtomX(atom);
double dy = mY1 - mMol.getAtomY(atom);
double distance = Math.sqrt(dx * dx + dy * dy);
if (distance < FRAGMENT_MAX_CLICK_DISTANCE
&& minDistance > distance) {
minDistance = distance;
fragment = mFragmentNo[atom];
}
}
return fragment;
}
/**
* requires cHelperNeighbours
*
* @param atom
*/
private void suggestNewX2AndY2(int atom)
{
double newAngle = Math.PI * 2 / 3;
if (atom != -1) {
double angle[] = new double[MAX_CONNATOMS + 1];
for (int i = 0; i < mMol.getAllConnAtoms(atom); i++) {
angle[i] = mMol.getBondAngle(atom, mMol.getConnAtom(atom, i));
}
if (mMol.getAllConnAtoms(atom) == 1) {
if (angle[0] < -Math.PI * 5 / 6) {
newAngle = Math.PI / 3;
} else if (angle[0] < -Math.PI / 2) {
newAngle = Math.PI * 2 / 3;
} else if (angle[0] < -Math.PI / 6) {
newAngle = Math.PI / 3;
} else if (angle[0] < 0.0) {
newAngle = Math.PI * 2 / 3;
} else if (angle[0] < Math.PI / 6) {
newAngle = -Math.PI * 2 / 3;
} else if (angle[0] < Math.PI / 2) {
newAngle = -Math.PI / 3;
} else if (angle[0] < Math.PI * 5 / 6) {
newAngle = -Math.PI * 2 / 3;
} else {
newAngle = -Math.PI / 3;
}
} else {
for (int i = mMol.getAllConnAtoms(atom) - 1; i > 0; i--) { // bubble sort
for (int j = 0; j < i; j++) {
if (angle[j] > angle[j + 1]) {
double temp = angle[j];
angle[j] = angle[j + 1];
angle[j + 1] = temp;
}
}
}
angle[mMol.getAllConnAtoms(atom)] = angle[0] + Math.PI * 2;
int largestNo = 0;
double largestDiff = 0.0;
for (int i = 0; i < mMol.getAllConnAtoms(atom); i++) {
double angleDiff = angle[i + 1] - angle[i];
if (largestDiff < angleDiff) {
largestDiff = angleDiff;
largestNo = i;
}
}
newAngle = (angle[largestNo] + angle[largestNo + 1]) / 2;
}
}
double avbl = mMol.getAverageBondLength();
mX2 = ((atom == -1) ? mX1 : mMol.getAtomX(atom)) + avbl * (float) Math.sin(newAngle);
mY2 = ((atom == -1) ? mY1 : mMol.getAtomY(atom)) + avbl * (float) Math.cos(newAngle);
}
private boolean areAtomsMappingCompatible(int atom1, int atom2)
{
if (mMol.isFragment()) {
int[] atomList1 = mMol.getAtomList(atom1);
int[] atomList2 = mMol.getAtomList(atom2);
if (atomList1 == null ^ atomList2 == null) {
return false;
}
if (atomList1 != null) {
if (atomList1.length != atomList2.length) {
return false;
}
for (int i = 0; i < atomList1.length; i++) {
if (atomList1[i] != atomList2[i]) {
return false;
}
}
}
boolean isAny1 = ((mMol.getAtomQueryFeatures(atom1) & Molecule.cAtomQFAny) != 0);
boolean isAny2 = ((mMol.getAtomQueryFeatures(atom2) & Molecule.cAtomQFAny) != 0);
if (isAny1 != isAny2) {
return false;
}
}
return mMol.getAtomicNo(atom1) == mMol.getAtomicNo(atom2);
}
private boolean trackHiliting(double x, double y, boolean isDragging)
{
int theAtom = mMol.findAtom(x, y);
int theBond = -1;
if (isDragging
&& mPendingRequest == cRequestMapAtoms
&& theAtom != -1
&& (!areAtomsMappingCompatible(mAtom1, theAtom)
|| (mMol.getAtomMapNo(mAtom1) != 0 && mMol.getAtomMapNo(mAtom1) == mMol.getAtomMapNo(theAtom) && !mMol.isAutoMappedAtom(mAtom1))
|| shareSameReactionSide(mAtom1, theAtom))) {
theAtom = -1;
}
if (theAtom != -1) {
if (mCurrentTool == JDrawToolbar.cToolESRAbs
|| mCurrentTool == JDrawToolbar.cToolESRAnd
|| mCurrentTool == JDrawToolbar.cToolESROr) {
theBond = mMol.getStereoBond(theAtom);
theAtom = -1;
} else if (mCurrentTool == JDrawToolbar.cToolMapper
&& theAtom >= mMol.getAtoms()) {
theAtom = -1;
}
}
if (theBond == -1
&& theAtom == -1
&& mCurrentTool != JDrawToolbar.cToolChain
&& mCurrentTool != JDrawToolbar.cToolMapper
&& mCurrentTool != JDrawToolbar.cToolUnknownParity
&& mCurrentTool != JDrawToolbar.cToolPosCharge
&& mCurrentTool != JDrawToolbar.cToolNegCharge
&& mCurrentTool != JDrawToolbar.cToolAtomH
&& mCurrentTool != JDrawToolbar.cToolAtomC
&& mCurrentTool != JDrawToolbar.cToolAtomN
&& mCurrentTool != JDrawToolbar.cToolAtomO
&& mCurrentTool != JDrawToolbar.cToolAtomSi
&& mCurrentTool != JDrawToolbar.cToolAtomP
&& mCurrentTool != JDrawToolbar.cToolAtomS
&& mCurrentTool != JDrawToolbar.cToolAtomF
&& mCurrentTool != JDrawToolbar.cToolAtomCl
&& mCurrentTool != JDrawToolbar.cToolAtomBr
&& mCurrentTool != JDrawToolbar.cToolAtomI
&& mCurrentTool != JDrawToolbar.cToolAtomOther) {
theBond = mMol.findBond(x, y);
}
if (theBond != -1
&& (mCurrentTool == JDrawToolbar.cToolESRAbs
|| mCurrentTool == JDrawToolbar.cToolESRAnd
|| mCurrentTool == JDrawToolbar.cToolESROr)
&& !qualifiesForESR(theBond)) {
theBond = -1;
}
// don't change object hiliting while dragging
AbstractDrawingObject hiliteObject = mCurrentHiliteObject;
if (!isDragging && mDrawingObjectList != null) {
hiliteObject = null;
if (theAtom == -1 && theBond == -1
&& (mCurrentTool == JDrawToolbar.cToolLassoPointer
|| mCurrentTool == JDrawToolbar.cToolDelete
|| mCurrentTool == JDrawToolbar.cToolText)) {
for (AbstractDrawingObject theObject : mDrawingObjectList) {
if (mCurrentTool == JDrawToolbar.cToolLassoPointer
|| (mCurrentTool == JDrawToolbar.cToolDelete && !(theObject instanceof ReactionArrow))
|| (mCurrentTool == JDrawToolbar.cToolText && theObject instanceof TextDrawingObject)) {
if (theObject.checkHiliting(x, y)) {
hiliteObject = theObject;
if (mCurrentHiliteObject != null && mCurrentHiliteObject != theObject) {
mCurrentHiliteObject.clearHiliting();
}
break;
}
}
}
}
}
boolean repaintNeeded = (mCurrentHiliteAtom != theAtom
|| mCurrentHiliteBond != theBond
|| mCurrentHiliteObject != hiliteObject
|| hiliteObject != null);
if (mCurrentHiliteAtom != theAtom) {
if (mCurrentHiliteAtom != -1 && mAtomKeyStrokeBuffer.length() != 0)
expandAtomKeyStrokes(mAtomKeyStrokeBuffer.toString());
mCurrentHiliteAtom = theAtom;
mAtomKeyStrokeBuffer.setLength(0);
fireEvent(new DrawAreaEvent(this, DrawAreaEvent.TYPE_HILITE_ATOM_CHANGED, true));
}
if (mCurrentHiliteBond != theBond) {
mCurrentHiliteBond = theBond;
fireEvent(new DrawAreaEvent(this, DrawAreaEvent.TYPE_HILITE_BOND_CHANGED, true));
}
mCurrentHiliteObject = hiliteObject;
return repaintNeeded;
}
private int getAtomKeyStrokeValidity(String s)
{
if (Molecule.getAtomicNoFromLabel(s) != 0)
return KEY_IS_ATOM_LABEL;
if (NamedSubstituents.getSubstituentIDCode(s) != null)
return KEY_IS_SUBSTITUENT;
if (isValidAtomKeyStrokeStart(s))
return KEY_IS_VALID_START;
return KEY_IS_INVALID;
}
/**
* @param s
* @return true if s is either a valid atom symbol or a valid substituent name
*/
private boolean isValidAtomKeyStroke(String s)
{
return Molecule.getAtomicNoFromLabel(s) != 0
|| NamedSubstituents.getSubstituentIDCode(s) != null;
}
/**
* @param s
* @return true if adding one or more chars may still create a valid key stroke sequence
*/
private boolean isValidAtomKeyStrokeStart(String s)
{
if (s.length() < 3)
for (int i = 1; i < Molecule.cAtomLabel.length; i++)
if (Molecule.cAtomLabel[i].startsWith(s))
return true;
return NamedSubstituents.isValidSubstituentNameStart(s);
}
private void expandAtomKeyStrokes(String keyStrokes)
{
mAtomKeyStrokeBuffer.setLength(0);
int atomicNo = Molecule.getAtomicNoFromLabel(keyStrokes);
if (atomicNo != 0) {
storeState();
if (mMol.changeAtom(mCurrentHiliteAtom, atomicNo, 0, -1, 0)) {
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
return;
}
}
StereoMolecule substituent = NamedSubstituents.getSubstituent(keyStrokes);
if (substituent != null) {
storeState();
// Copy the the fragment containing the attachment point into a new molecule.
// Then attach the substituent, create new atom coordinates for the substituent,
// while retaining coordinates of the fragment.
StereoMolecule fragment = new StereoMolecule();
fragment.addFragment(mMol, mCurrentHiliteAtom, null);
double sourceAVBL = fragment.getAverageBondLength();
int firstAtomInFragment = fragment.getAllAtoms();
for (int atom = 0; atom < fragment.getAllAtoms(); atom++)
fragment.setAtomMarker(atom, true);
fragment.addSubstituent(substituent, 0);
new CoordinateInventor(CoordinateInventor.MODE_KEEP_MARKED_ATOM_COORDS).invent(fragment);
double dx = mMol.getAtomX(mCurrentHiliteAtom) - sourceAVBL * fragment.getAtomX(0);
double dy = mMol.getAtomY(mCurrentHiliteAtom) - sourceAVBL * fragment.getAtomY(0);
// Attach the substituent to the complete molecule and take coodinates from the
// previously created fragment-substituent species.
int firstAtomInMol = mMol.getAllAtoms();
mMol.addSubstituent(substituent, mCurrentHiliteAtom);
int substituentAtoms = mMol.getAllAtoms() - firstAtomInMol;
for (int i = 0; i < substituentAtoms; i++) {
mMol.setAtomX(firstAtomInMol + i, sourceAVBL * fragment.getAtomX(firstAtomInFragment + i) + dx);
mMol.setAtomY(firstAtomInMol + i, sourceAVBL * fragment.getAtomY(firstAtomInFragment + i) + dy);
}
mMol.setStereoBondsFromParity();
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
}
private AbstractDrawingObject findDrawingObject(double x, double y, String type, boolean forDeletion)
{
if (mDrawingObjectList != null) {
for (AbstractDrawingObject drawingObject : mDrawingObjectList) {
if ((type == null || type.equals(drawingObject.getTypeString())
&& !forDeletion || drawingObject.isDeletable())
&& drawingObject.contains(x, y)) {
return drawingObject;
}
}
}
return null;
}
private void editTextObject(TextDrawingObject object)
{
Component c = this;
while (c.getParent() != null) {
c = c.getParent();
}
new JTextDrawingObjectDialog((Frame) c, object);
boolean nonWhiteSpaceFound = false;
for (int i = 0; i < object.getText().length(); i++) {
if (!Character.isWhitespace(object.getText().charAt(i))) {
nonWhiteSpaceFound = true;
break;
}
}
if (!nonWhiteSpaceFound) {
mDrawingObjectList.remove(object);
}
repaint();
}
private boolean shareSameReactionSide(int atom1, int atom2)
{
ReactionArrow arrow = (ReactionArrow) mDrawingObjectList.get(0);
return !(arrow.isOnProductSide(mMol.getAtomX(atom1), mMol.getAtomY(atom1))
^ arrow.isOnProductSide(mMol.getAtomX(atom2), mMol.getAtomY(atom2)));
}
protected void restoreState()
{
if (mUndoMol == null) {
return;
}
mUndoMol.copyMolecule(mMol);
mDrawingObjectList = (mUndoDrawingObjectList == null) ?
null : new DrawingObjectList(mUndoDrawingObjectList);
}
protected void storeState()
{
if (mUndoMol == null) {
mUndoMol = new Molecule();
}
mMol.copyMolecule(mUndoMol);
mUndoDrawingObjectList = (mDrawingObjectList == null) ?
null : new DrawingObjectList(mDrawingObjectList);
}
private boolean deleteHilited()
{
if (mCurrentHiliteAtom != -1) {
mMol.deleteAtom(mCurrentHiliteAtom);
mCurrentHiliteAtom = -1;
fireMoleculeChanged();
update(UPDATE_REDRAW);
return true;
}
if (mCurrentHiliteBond != -1) {
mMol.deleteBondAndSurrounding(mCurrentHiliteBond);
mCurrentHiliteBond = -1;
fireMoleculeChanged();
update(UPDATE_REDRAW);
return true;
}
if (mCurrentHiliteObject != null && mCurrentHiliteObject.isDeletable()) {
mDrawingObjectList.remove(mCurrentHiliteObject);
mCurrentHiliteObject = null;
update(UPDATE_REDRAW);
return true;
}
return false;
}
private boolean deleteAt(double x, double y)
{
if (mMol.deleteAtomOrBond(x, y)) {
fireMoleculeChanged();
update(UPDATE_REDRAW);
return true;
}
AbstractDrawingObject drawingObject = findDrawingObject(x, y, null, true);
if (drawingObject != null) {
mDrawingObjectList.remove(drawingObject);
mCurrentHiliteObject = null;
update(UPDATE_REDRAW);
return true;
}
return false;
}
private void duplicateSelected()
{
int atomCount = 0;
for (int atom = 0; atom < mMol.getAllAtoms(); atom++) {
if (mMol.isSelectedAtom(atom)) {
atomCount++;
}
}
// int bondCount = 0;
// for (int bond=0; bond= 0; i--) {
AbstractDrawingObject object = (AbstractDrawingObject) mDrawingObjectList.get(i);
if (object.isSelected() && !(object instanceof ReactionArrow)) {
mDrawingObjectList.add(object.clone());
}
}
}
}
private void fireMoleculeChanged()
{
fireEvent(new DrawAreaEvent(this, DrawAreaEvent.TYPE_MOLECULE_CHANGED, true));
}
private void fireEvent(DrawAreaEvent e)
{
for (DrawAreaListener l : mListeners) {
l.contentChanged(e);
}
}
/**
* Use this to inform the JDrawArea after changing its molecule from outside.
*/
public void moleculeChanged()
{
moleculeChanged(false);
}
/**
* Ideally don't use this from outside JDrawArea. Use moleculeChanged() instead.
*
* @param userChange is true if the change was done within the editor
*/
public void moleculeChanged(boolean userChange)
{
fireEvent(new DrawAreaEvent(this, DrawAreaEvent.TYPE_MOLECULE_CHANGED, userChange));
update(UPDATE_SCALE_COORDS);
}
public StereoMolecule getMolecule()
{
return mMol;
}
public void setMolecule(StereoMolecule theMolecule)
{
if (mMol == theMolecule) {
return;
}
mMol = theMolecule;
storeState();
moleculeChanged(false);
}
public StereoMolecule[] getFragments()
{
return mFragment;
}
public void setFragments(StereoMolecule[] fragment)
{
mMol.deleteMolecule();
mFragment = fragment;
for (int i = 0; i < fragment.length; i++) {
mMol.addMolecule(mFragment[i]);
}
storeState();
mFragmentNo = new int[mMol.getAllAtoms()];
for (int atom = 0, f = 0; f < mFragment.length; f++) {
for (int j = 0; j < mFragment[f].getAllAtoms(); j++) {
mFragmentNo[atom++] = f;
}
}
fireEvent(new DrawAreaEvent(this, DrawAreaEvent.TYPE_MOLECULE_CHANGED, false));
mMode = MODE_MULTIPLE_FRAGMENTS;
update(UPDATE_SCALE_COORDS_USE_FRAGMENTS);
}
/**
* @return mapped reaction with absolute coordinates, but without drawing objects
*/
public Reaction getReaction()
{
if ((mMode & MODE_REACTION) == 0 || mFragment == null) {
return null;
}
Reaction rxn = new Reaction();
for (int i = 0; i < mFragment.length; i++) {
if (i < mReactantCount) {
rxn.addReactant(mFragment[i]);
} else {
rxn.addProduct(mFragment[i]);
}
}
return rxn;
}
/**
* @return mapped reaction with absolute coordinates and drawing objects
*/
public Reaction getReactionAndDrawings()
{
Reaction rxn = getReaction();
if (rxn != null) {
rxn.setDrawingObjects(getDrawingObjects());
}
return rxn;
}
public void setReaction(Reaction rxn)
{
mMol.deleteMolecule();
mFragment = new StereoMolecule[rxn.getMolecules()];
mReactantCount = rxn.getReactants();
boolean isFragment = false;
for (int i = 0; i < rxn.getMolecules(); i++) {
isFragment |= rxn.getMolecule(i).isFragment();
mFragment[i] = rxn.getMolecule(i);
mMol.addMolecule(mFragment[i]);
}
mMol.setFragment(isFragment);
storeState();
mFragmentNo = new int[mMol.getAllAtoms()];
for (int atom = 0, f = 0; f < mFragment.length; f++) {
for (int j = 0; j < mFragment[f].getAllAtoms(); j++) {
mFragmentNo[atom++] = f;
}
}
fireEvent(new DrawAreaEvent(this, DrawAreaEvent.TYPE_MOLECULE_CHANGED, false));
mMode = MODE_MULTIPLE_FRAGMENTS | MODE_REACTION;
update(UPDATE_SCALE_COORDS_USE_FRAGMENTS);
}
public MarkushStructure getMarkushStructure()
{
if ((mMode & MODE_MARKUSH_STRUCTURE) == 0) {
return null;
}
MarkushStructure markush = new MarkushStructure();
for (int i = 0; i < mFragment.length; i++) {
if (i < mReactantCount) {
markush.addCore(mFragment[i]);
} else {
markush.addRGroup(mFragment[i]);
}
}
return markush;
}
public void setMarkushStructure(MarkushStructure markush)
{
mMol.deleteMolecule();
mFragment = new StereoMolecule[markush.getCoreCount() + markush.getRGroupCount()];
mReactantCount = markush.getCoreCount();
boolean isFragment = false;
for (int i = 0; i < markush.getCoreCount() + markush.getRGroupCount(); i++) {
mFragment[i] = (i < markush.getCoreCount()) ? markush.getCoreStructure(i)
: markush.getRGroup(i - markush.getCoreCount());
isFragment |= mFragment[i].isFragment();
mMol.addMolecule(mFragment[i]);
}
mMol.setFragment(isFragment);
storeState();
mFragmentNo = new int[mMol.getAllAtoms()];
for (int atom = 0, f = 0; f < mFragment.length; f++) {
for (int j = 0; j < mFragment[f].getAllAtoms(); j++) {
mFragmentNo[atom++] = f;
}
}
fireEvent(new DrawAreaEvent(this, DrawAreaEvent.TYPE_MOLECULE_CHANGED, false));
mMode = MODE_MULTIPLE_FRAGMENTS | MODE_MARKUSH_STRUCTURE;
update(UPDATE_SCALE_COORDS_USE_FRAGMENTS);
}
public void setDisplayMode(int dMode)
{
mDisplayMode = dMode;
update(UPDATE_REDRAW);
}
/**
* Defines additional atom text to be displayed in top right
* position of some/all atom label. If the atom is charged, then
* the atom text follows the charge information.
* If using atom text make sure to update it accordingly, if atom
* indexes change due to molecule changes.
* Atom text is not supported for MODE_REACTION, MODE_MULTIPLE_FRAGMENTS or MODE_MARKUSH_STRUCTURE.
*
* @param atomText String[] matching atom indexes (may contain null entries)
*/
public void setAtomText(String[] atomText)
{
mAtomText = atomText;
}
public DrawingObjectList getDrawingObjects()
{
return mDrawingObjectList;
}
public void setDrawingObjects(DrawingObjectList drawingObjectList)
{
mDrawingObjectList = drawingObjectList;
storeState();
update(UPDATE_SCALE_COORDS);
}
// Added by CXR
public int getMode()
{
return mMode;
}
public int getHiliteAtom()
{
return mCurrentHiliteAtom;
}
public int getHiliteBond()
{
return mCurrentHiliteBond;
}
public void setHiliteBondSet(int[] bondSet)
{
mHiliteBondSet = bondSet;
update(UPDATE_REDRAW);
}
public void setReactionMode(boolean rxn)
{
if (rxn) {
Molecule m[] = this.getFragments();
if (m == null) {
setReaction(new Reaction(new StereoMolecule[]{new StereoMolecule(this.getMolecule())}, 1));
} else {
mMode = MODE_MULTIPLE_FRAGMENTS | MODE_REACTION;
Reaction r = getReaction();
setReaction(r);
}
} else {
mMode &= ~MODE_REACTION;
}
}
// CXR Need this method for derived components
protected void setUpdateMode(int mode)
{
mUpdateMode = mode;
}
public boolean isAtomColorSupported()
{
return mAtomColorSupported;
}
public void setAtomColorSupported(boolean acs)
{
mAtomColorSupported = acs;
}
private void cleanupCoordinates(Graphics g, ExtendedDepictor depictor)
{
int selectedAtomCount = 0;
for (int atom = 0; atom < mMol.getAllAtoms(); atom++) {
if (mMol.isSelectedAtom(atom)) {
selectedAtomCount++;
}
}
boolean selectedOnly = (selectedAtomCount != 0 && selectedAtomCount != mMol.getAllAtoms());
if ((mMode & MODE_MULTIPLE_FRAGMENTS) == 0) {
cleanupMoleculeCoordinates(g, depictor, selectedOnly);
} else {
cleanupMultiFragmentCoordinates(g, depictor, selectedOnly);
}
if (selectedOnly)
mMol.removeAtomMarkers();
}
private void cleanupMoleculeCoordinates(Graphics g, ExtendedDepictor depictor, boolean selectedOnly)
{
if (mUpdateMode == UPDATE_INVENT_COORDS) {
if (selectedOnly) {
for (int atom = 0; atom < mMol.getAllAtoms(); atom++) {
mMol.setAtomMarker(atom, !mMol.isSelectedAtom(atom));
}
}
new CoordinateInventor(selectedOnly ? CoordinateInventor.MODE_KEEP_MARKED_ATOM_COORDS : 0).invent(mMol);
mMol.setStereoBondsFromParity();
}
depictor.updateCoords(g, new Rectangle2D.Double(0, 0, getWidth(), getHeight()), maxUpdateMode());
}
private void cleanupMultiFragmentCoordinates(Graphics g, ExtendedDepictor depictor, boolean selectedOnly)
{
if (selectedOnly && mUpdateMode == UPDATE_INVENT_COORDS) {
int[] fragmentAtom = new int[mFragment.length];
for (int atom = 0; atom < mMol.getAllAtoms(); atom++) {
int fragment = mFragmentNo[atom];
mFragment[fragment].setAtomMarker(fragmentAtom[fragment], !mMol.isSelectedAtom(atom));
fragmentAtom[fragment]++;
}
}
Rectangle2D.Double[] boundingRect = new Rectangle2D.Double[mFragment.length];
// float fragmentWidth = 0.0f;
for (int fragment = 0; fragment < mFragment.length; fragment++) {
if (mUpdateMode == UPDATE_INVENT_COORDS) {
new CoordinateInventor(selectedOnly ? CoordinateInventor.MODE_KEEP_MARKED_ATOM_COORDS : 0).invent(mFragment[fragment]);
mFragment[fragment].setStereoBondsFromParity();
}
Depictor d = new Depictor(mFragment[fragment]);
d.updateCoords(g, null, AbstractDepictor.cModeInflateToMaxAVBL);
boundingRect[fragment] = d.getBoundingRect();
// fragmentWidth += boundingRect[fragment].width;
}
double spacing = FRAGMENT_CLEANUP_DISTANCE * AbstractDepictor.cOptAvBondLen;
double avbl = mMol.getAverageBondLength();
double arrowWidth = ((mMode & MODE_REACTION) == 0) ?
0f
: (mUpdateMode == UPDATE_SCALE_COORDS_USE_FRAGMENTS) ?
DEFAULT_ARROW_LENGTH * getWidth()
: ((ReactionArrow) mDrawingObjectList.get(0)).getLength() * AbstractDepictor.cOptAvBondLen / avbl;
double rawX = 0.5 * spacing;
for (int fragment = 0; fragment <= mFragment.length; fragment++) {
if ((mMode & MODE_REACTION) != 0 && fragment == mReactantCount) {
((ReactionArrow) mDrawingObjectList.get(0)).setCoordinates(
rawX - spacing / 2, getHeight() / 2, rawX - spacing / 2 + arrowWidth, getHeight() / 2);
rawX += arrowWidth;
}
if (fragment == mFragment.length) {
break;
}
double dx = rawX - boundingRect[fragment].x;
double dy = 0.5 * (getHeight() - boundingRect[fragment].height)
- boundingRect[fragment].y;
mFragment[fragment].translateCoords(dx, dy);
rawX += spacing + boundingRect[fragment].width;
}
depictor.updateCoords(g, new Rectangle2D.Double(0, 0, getWidth(), getHeight()), maxUpdateMode());
int[] fragmentAtom = new int[mFragment.length];
for (int atom = 0; atom < mMol.getAllAtoms(); atom++) {
int fragment = mFragmentNo[atom];
mMol.setAtomX(atom, mFragment[fragment].getAtomX(fragmentAtom[fragment]));
mMol.setAtomY(atom, mFragment[fragment].getAtomY(fragmentAtom[fragment]));
fragmentAtom[fragment]++;
}
mMol.setStereoBondsFromParity();
}
private void analyzeFragmentMembership()
{
mMol.ensureHelperArrays(Molecule.cHelperParities);
int[] fragmentNo = new int[mMol.getAllAtoms()];
int fragments = mMol.getFragmentNumbers(fragmentNo, false);
fragments = joinCloseFragments(fragmentNo, fragments);
sortFragmentsByPosition(fragmentNo, fragments);
mFragmentNo = fragmentNo;
mFragment = mMol.getFragments(fragmentNo, fragments);
}
private void syncFragments()
{
mMol.ensureHelperArrays(Molecule.cHelperParities);
int[] fragmentNo = new int[mMol.getAllAtoms()];
int fragments = mMol.getFragmentNumbers(fragmentNo, false);
// fragments = joinCloseFragments(fragmentNo, fragments);
sortFragmentsByPosition(fragmentNo, fragments);
mFragmentNo = fragmentNo;
mFragment = mMol.getFragments(fragmentNo, fragments);
for (StereoMolecule m : mFragment) {
m.ensureHelperArrays(Molecule.cHelperParities);
}
}
private int joinCloseFragments(int[] fragmentNo, int fragments)
{
if (fragments < 2) {
return fragments;
}
boolean[][] mergeFragments = new boolean[fragments][];
for (int i = 1; i < fragments; i++) {
mergeFragments[i] = new boolean[i];
}
double avbl = mMol.getAverageBondLength();
for (int atom1 = 1; atom1 < mMol.getAllAtoms(); atom1++) {
for (int atom2 = 0; atom2 < atom1; atom2++) {
double dx = mMol.getAtomX(atom2) - mMol.getAtomX(atom1);
double dy = mMol.getAtomY(atom2) - mMol.getAtomY(atom1);
double distance = Math.sqrt(dx * dx + dy * dy);
if (distance < FRAGMENT_GROUPING_DISTANCE * avbl) {
int fragment1 = fragmentNo[atom1];
int fragment2 = fragmentNo[atom2];
if (fragment1 != fragment2) {
if (fragment1 > fragment2) {
mergeFragments[fragment1][fragment2] = true;
} else {
mergeFragments[fragment2][fragment1] = true;
}
}
}
}
}
int[] newFragmentIndex = new int[fragments];
for (int fragment = 0; fragment < fragments; fragment++) {
newFragmentIndex[fragment] = fragment;
}
int mergeCount = 0;
for (int i = 1; i < fragments; i++) {
for (int j = 0; j < i; j++) {
if (mergeFragments[i][j]) {
int index1 = newFragmentIndex[i];
int index2 = newFragmentIndex[j];
if (index1 != index2) {
mergeCount++;
int minIndex = Math.min(index1, index2);
int maxIndex = Math.max(index1, index2);
for (int k = 0; k < fragments; k++) {
if (newFragmentIndex[k] == maxIndex) {
newFragmentIndex[k] = minIndex;
} else if (newFragmentIndex[k] > maxIndex) {
newFragmentIndex[k]--;
}
}
}
}
}
}
for (int atom = 0; atom < mMol.getAllAtoms(); atom++) {
fragmentNo[atom] = newFragmentIndex[fragmentNo[atom]];
}
return fragments - mergeCount;
}
private void sortFragmentsByPosition(int[] fragmentNo, int fragments)
{
int[][] fragmentDescriptor = new int[fragments][((mMode & (MODE_REACTION | MODE_MARKUSH_STRUCTURE)) != 0) ? 2 : 1];
for (int fragment = 0; fragment < fragments; fragment++) {
fragmentDescriptor[fragment][0] = fragment;
}
Point[] fragmentCOG = calculateFragmentCenterOfGravity(fragmentNo, fragments);
if ((mMode & MODE_REACTION) != 0) {
mReactantCount = 0;
ReactionArrow arrow = ((mMode & MODE_REACTION) != 0) ? (ReactionArrow) mDrawingObjectList.get(0) : null;
for (int fragment = 0; fragment < fragments; fragment++) {
fragmentDescriptor[fragment][1] = (arrow.isOnProductSide(fragmentCOG[fragment].x,
fragmentCOG[fragment].y)) ? 1 : 0;
if (fragmentDescriptor[fragment][1] == 0) {
mReactantCount++;
}
}
} else if ((mMode & MODE_MARKUSH_STRUCTURE) != 0) {
mReactantCount = fragments;
for (int atom = 0; atom < mMol.getAllAtoms(); atom++) {
if (mMol.getAtomicNo(atom) == 0 && fragmentDescriptor[fragmentNo[atom]][1] == 0) {
fragmentDescriptor[fragmentNo[atom]][1] = 1;
mReactantCount--;
}
}
}
final Point[] cog = fragmentCOG;
Arrays.sort(fragmentDescriptor, new Comparator()
{
public int compare(int[] fragmentDescriptor1, int[] fragmentDescriptor2)
{
if ((mMode & (MODE_REACTION | MODE_MARKUSH_STRUCTURE)) != 0) {
if (fragmentDescriptor1[1] != fragmentDescriptor2[1]) {
return (fragmentDescriptor1[1] == 0) ? -1 : 1;
}
}
return (cog[fragmentDescriptor1[0]].x
+ cog[fragmentDescriptor1[0]].y
< cog[fragmentDescriptor2[0]].x
+ cog[fragmentDescriptor2[0]].y) ? -1 : 1;
}
});
int[] newFragmentIndex = new int[fragments];
Point[] centerOfGravity = new Point[fragments];
for (int fragment = 0; fragment < fragments; fragment++) {
int oldIndex = ((int[]) fragmentDescriptor[fragment])[0];
newFragmentIndex[oldIndex] = fragment;
centerOfGravity[fragment] = fragmentCOG[oldIndex];
}
fragmentCOG = centerOfGravity;
for (int atom1 = 0; atom1 < mMol.getAllAtoms(); atom1++) {
fragmentNo[atom1] = newFragmentIndex[fragmentNo[atom1]];
}
}
private Point[] calculateFragmentCenterOfGravity(int[] fragmentNo, int fragments)
{
Point[] fragmentCOG = new Point[fragments];
int[] fragmentAtoms = new int[fragments];
for (int fragment = 0; fragment < fragments; fragment++) {
fragmentCOG[fragment] = new Point(0, 0);
}
for (int atom = 0; atom < mMol.getAllAtoms(); atom++) {
fragmentCOG[fragmentNo[atom]].x += mMol.getAtomX(atom);
fragmentCOG[fragmentNo[atom]].y += mMol.getAtomY(atom);
fragmentAtoms[fragmentNo[atom]]++;
}
for (int fragment = 0; fragment < fragments; fragment++) {
fragmentCOG[fragment].x /= fragmentAtoms[fragment];
fragmentCOG[fragment].y /= fragmentAtoms[fragment];
}
return fragmentCOG;
}
private void updateCursor()
{
int cursor = -1;
switch (mCurrentTool) {
case JDrawToolbar.cToolZoom:
cursor = CursorHelper.cZoomCursor;
break;
case JDrawToolbar.cToolLassoPointer:
if ((mCurrentHiliteAtom != -1 && mMol.isSelectedAtom(mCurrentHiliteAtom))
|| (mCurrentHiliteBond != -1 && mMol.isSelectedBond(mCurrentHiliteBond))) {
cursor = mMouseIsDown ? CursorHelper.cFistCursor
: mShiftIsDown ? CursorHelper.cHandPlusCursor
: CursorHelper.cHandCursor;
} else if (mCurrentHiliteAtom != -1
|| mCurrentHiliteBond != -1) {
cursor = CursorHelper.cPointerCursor;
} else if (mCurrentHiliteObject != null) {
cursor = mMouseIsDown ? CursorHelper.cFistCursor
: (mShiftIsDown
&& !(mCurrentHiliteObject instanceof ReactionArrow)) ?
CursorHelper.cHandPlusCursor : CursorHelper.cHandCursor;
} else {
cursor = mShiftIsDown ?
(mAltIsDown ? CursorHelper.cSelectRectPlusCursor : CursorHelper.cLassoPlusCursor)
: (mAltIsDown ? CursorHelper.cSelectRectCursor : CursorHelper.cLassoCursor);
}
break;
case JDrawToolbar.cToolDelete:
cursor = CursorHelper.cDeleteCursor;
break;
case JDrawToolbar.cToolChain:
cursor = CursorHelper.cChainCursor;
break;
case JDrawToolbar.cToolText:
cursor = CursorHelper.cTextCursor;
break;
default:
cursor = CursorHelper.cPointerCursor;
break;
}
if (mCurrentCursor != cursor) {
mCurrentCursor = cursor;
setCursor(CursorHelper.getCursor(cursor));
}
}
private void initializeDragAndDrop(int dropAction)
{
if (dropAction != DnDConstants.ACTION_NONE) {
MoleculeDropAdapter d = new MoleculeDropAdapter()
{
public void onDropMolecule(StereoMolecule m, Point pt)
{
if (m != null && m.getAllAtoms() != 0) {
for (int atom = 0; atom < mMol.getAllAtoms(); atom++) {
mMol.setAtomSelection(atom, false); // deselect all current atoms
}
double avbl = mMol.getAverageBondLength();
double dropAVBL = m.getAverageBondLength();
m.scaleCoords(avbl / dropAVBL);
Point cog = new Point();
for (int atom = 0; atom < m.getAllAtoms(); atom++) {
m.setAtomSelection(atom, true); // select all new atoms
cog.x += m.getAtomX(atom);
cog.y += m.getAtomY(atom);
}
cog.x /= m.getAllAtoms();
cog.y /= m.getAllAtoms();
m.translateCoords(pt.x - cog.x, pt.y - cog.y);
m.removeAtomColors();
m.removeBondHiliting();
mMol.addMolecule(m);
fireMoleculeChanged();
update(UPDATE_CHECK_COORDS);
}
}
};
new DropTarget(this, dropAction, d, true, new OurFlavorMap());
}
}
// This class is needed for inter-jvm drag&drop. Although not neccessary for standard environments, it prevents
// nasty "no native data was transfered" errors. It still might create ClassNotFoundException in the first place by
// the SystemFlavorMap, but as I found it does not hurt, since the context classloader will be installed after
// the first call. I know, that this depends heavely on a specific behaviour of the systemflavormap, but for now
// there's nothing I can do about it.
static class OurFlavorMap implements java.awt.datatransfer.FlavorMap
{
@Override
public java.util.Map getNativesForFlavors(DataFlavor[] dfs)
{
java.awt.datatransfer.FlavorMap m = java.awt.datatransfer.SystemFlavorMap.getDefaultFlavorMap();
return m.getNativesForFlavors(dfs);
}
@Override
public java.util.Map getFlavorsForNatives(String[] natives)
{
java.awt.datatransfer.FlavorMap m = java.awt.datatransfer.SystemFlavorMap.getDefaultFlavorMap();
return m.getFlavorsForNatives(natives);
}
}
/* private void dumpBytesOfGif(String imageFileName) {
byte[] data = new byte[10000];
try {
BufferedInputStream in=new BufferedInputStream(getClass().getResourceAsStream(imageFileName));
int count = in.read(data);
Image image = Toolkit.getDefaultToolkit().createImage(data);
PixelGrabber pg = new PixelGrabber(image, 0, 0, 16, 16, false);
try {
pg.grabPixels();
byte[] pixels = (byte[])pg.getPixels();
int pixelRow = 0;
for (int i=0; i 0 ? new Point2D.Double(sumx / atoms, sumy / atoms) : null;
}
private void flip(boolean horiz)
{
Point2D pt = calculateCenterOfGravity();
if (pt != null) {
// center
moveCoords((float)-pt.getX(), (float)-pt.getY());
if (horiz) {
scaleCoords(-1,1);
} else {
scaleCoords(1,-1);
}
moveCoords((float)pt.getX(), (float)pt.getY());
// invert stereo bonds
for (int bond=0; bond © 2015 - 2025 Weber Informatics LLC | Privacy Policy