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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.editor;
import com.actelion.research.chem.*;
import com.actelion.research.chem.coords.CoordinateInventor;
import com.actelion.research.chem.io.RDFileParser;
import com.actelion.research.chem.io.RXNFileParser;
import com.actelion.research.chem.name.StructureNameResolver;
import com.actelion.research.chem.reaction.*;
import com.actelion.research.gui.FileHelper;
import com.actelion.research.gui.LookAndFeelHelper;
import com.actelion.research.gui.clipboard.IClipboardHandler;
import com.actelion.research.gui.generic.*;
import com.actelion.research.gui.hidpi.HiDPIHelper;
import com.actelion.research.util.ColorHelper;
import java.awt.geom.Point2D;
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.TreeMap;
public class GenericEditorArea implements GenericEventListener {
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;
public static final String TEMPLATE_TYPE_KEY = "TEMPLATE";
public static final String TEMPLATE_TYPE_REACTION_QUERIES = "REACTION_QUERIES";
public static final String TEMPLATE_SECTION_KEY = "SECTION";
public static final int DEFAULT_ALLOWED_PSEUDO_ATOMS
= Molecule.cPseudoAtomsHydrogenIsotops
| Molecule.cPseudoAtomsAminoAcids
| Molecule.cPseudoAtomR
| Molecule.cPseudoAtomsRGroups
| Molecule.cPseudoAtomAttachmentPoint;
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 int RGB_BLUE = 0xFF0000FF;
private static final int RGB_RED = 0xFFFF0000;
private static final int RGB_DARK_RED = 0xFF800000;
private static final int RGB_BLACK = 0xFF000000;
private static final int RGB_GRAY = 0xFF808080;
private static final String ITEM_COPY_STRUCTURE = "Copy Structure";
private static final String ITEM_COPY_REACTION = "Copy Reaction";
private static final String ITEM_PASTE_STRUCTURE = "Paste Structure";
private static final String ITEM_PASTE_REACTION = "Paste Reaction";
private static final String ITEM_USE_TEMPLATE = "Use Reaction Template...";
private static final String ITEM_PASTE_WITH_NAME = ITEM_PASTE_STRUCTURE + " or Name";
private static final String ITEM_LOAD_REACTION = "Open Reaction File...";
private static final String ITEM_ADD_AUTO_MAPPING = "Auto-Map Reaction";
private static final String ITEM_REMOVE_MAPPING = "Remove Manual Atom Mapping";
private static final String ITEM_FLIP_HORIZONTALLY = "Flip Horizontally";
private static final String ITEM_FLIP_VERTICALLY = "Flip Vertically";
private static final String ITEM_FLIP_ROTATE180 = "Rotate 180°";
private static final String ITEM_SHOW_HELP = "Help Me";
// development items
private static final String ITEM_SHOW_ATOM_BOND_NUMBERS = "Show Atom & Bond Numbers";
private static final String ITEM_SHOW_SYMMETRY = "Show Symmetry";
private static final String ITEM_SHOW_NORMAL = "Show Normal";
private static final long WARNING_MILLIS = 1200;
private static final float FRAGMENT_MAX_CLICK_DISTANCE = 24.0f;
private static final float FRAGMENT_GROUPING_DISTANCE = CoordinateInventor.JOIN_DISTANCE_UNCHARGED_FRAGMENTS + 0.1f; // in average bond lengths
private static final float FRAGMENT_CLEANUP_DISTANCE = CoordinateInventor.JOIN_DISTANCE_UNCHARGED_FRAGMENTS + 0.2f; // in average bond lengths
private static final float DEFAULT_ARROW_LENGTH = 0.08f; // relative to panel width
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 DEFAULT_SELECTION_BACKGROUND = 0xFF80A4C0;
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;
private static IReactionMapper sMapper;
private static String[][] sReactionQueryTemplates;
private final int mMaxAVBL;
private int mMode, mChainAtoms, mCurrentTool, mCustomAtomicNo, mCustomAtomMass, mCustomAtomValence, mCustomAtomRadical,
mCurrentHiliteAtom, mCurrentHiliteBond, mPendingRequest, mEventsScheduled, mFirstAtomKey,
mCurrentCursor, mReactantCount, mUpdateMode, mDisplayMode, mAtom1, mAtom2, mAllowedPseudoAtoms;
private int[] mChainAtom, mFragmentNo, mHiliteBondSet;
private final double mUIScaling;
private double mX1, mY1, mX2, mY2, mWidth, mHeight, mTextSizeFactor;
private double[] mX, mY, mChainAtomX, mChainAtomY;
private boolean mAltIsDown, mShiftIsDown, mMouseIsDown, mIsAddingToSelection, mAtomColorSupported, mAllowQueryFeatures,
mAllowFragmentChangeOnPasteOrDrop;
private boolean[] mIsSelectedAtom, mIsSelectedObject;
private String mCustomAtomLabel,mWarningMessage,mAtomKeyStrokeSuggestion;
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 GenericPolygon mLassoRegion;
private ArrayList mListeners;
private IClipboardHandler mClipboardHandler;
private final StringBuilder mAtomKeyStrokeBuffer;
private final GenericUIHelper mUIHelper;
private final GenericCanvas mCanvas;
/**
* @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 GenericEditorArea(StereoMolecule mol, int mode, GenericUIHelper helper, GenericCanvas canvas) {
mMol = mol;
mMode = mode;
mUIHelper = helper;
mCanvas = canvas;
mListeners = new ArrayList<>();
mCurrentTool = GenericEditorToolbar.cToolStdBond;
mCurrentHiliteAtom = -1;
mCurrentHiliteBond = -1;
mCurrentHiliteObject = null;
mAtom1 = -1;
mCustomAtomicNo = 6;
mCustomAtomMass = 0;
mCustomAtomValence = -1;
mCustomAtomRadical = 0;
mCustomAtomLabel = null;
mAllowQueryFeatures = true;
mAllowFragmentChangeOnPasteOrDrop = false;
mPendingRequest = cRequestNone;
mCurrentCursor = GenericCursorHelper.cPointerCursor;
mAtomKeyStrokeBuffer = new StringBuilder();
mAllowedPseudoAtoms = DEFAULT_ALLOWED_PSEUDO_ATOMS;
mTextSizeFactor = 1.0;
mUIScaling = HiDPIHelper.getUIScaleFactor();
mMaxAVBL = HiDPIHelper.scale(AbstractDepictor.cOptAvBondLen);
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;
/* 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"); */
}
/**
* @return null or String[n][2] with pairs of reaction name and rxn-idcode
*/
public static String[][] getReactionQueryTemplates() {
return sReactionQueryTemplates;
}
/**
* @param templates null or String[n][2] with pairs of reaction name and rxn-idcode
*/
public static void setReactionQueryTemplates(String[][] templates) {
sReactionQueryTemplates = templates;
}
public GenericUIHelper getUIHelper() {
return mUIHelper;
}
/**
* 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);
mCanvas.repaint();
}
public static void setReactionMapper(IReactionMapper mapper) {
sMapper = mapper;
}
public void paintContent(GenericDrawContext context) {
if (mWidth != mCanvas.getCanvasWidth() || mHeight != mCanvas.getCanvasHeight()) {
mWidth = mCanvas.getCanvasWidth();
mHeight = mCanvas.getCanvasHeight();
if (mUpdateMode");
}
if (validity == KEY_IS_SUBSTITUENT) {
context.setRGB(RGB_GRAY);
context.drawString(x+context.getBounds(s).getWidth(), y, mAtomKeyStrokeSuggestion.substring(s.length()));
}
}
context.setRGB(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 GenericEditorToolbar.cToolStdBond:
context.drawLine(x1, y1, x2, y2);
break;
case GenericEditorToolbar.cToolUpBond:
xdiff = (y1 - y2) / 9;
ydiff = (x2 - x1) / 9;
GenericPolygon p = new GenericPolygon(3);
p.addPoint( x1, y1);
p.addPoint(x2 + xdiff, y2 + ydiff);
p.addPoint(x2 - xdiff, y2 - ydiff);
context.fillPolygon(p);
break;
case GenericEditorToolbar.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;
context.drawLine(xx1, yy1, xx2, yy2);
}
break;
}
break;
case cRequestNewChain:
if (mChainAtoms>0) {
context.drawLine((int)mX1, (int)mY1, (int)mChainAtomX[0], (int)mChainAtomY[0]);
}
if (mChainAtoms>1) {
for (int i = 1; i l) {
mListeners.add(l);
}
protected void buttonPressed(int button) {
switch (button) {
case GenericEditorToolbar.cButtonClear:
clearAll();
return;
case GenericEditorToolbar.cButtonCleanStructure:
storeState();
updateAndFireEvent(UPDATE_INVENT_COORDS);
return;
case GenericEditorToolbar.cButtonUndo:
restoreState();
updateAndFireEvent(UPDATE_CHECK_VIEW);
return;
}
}
public void clearAll() {
if (mDrawingObjectList != null) {
mDrawingObjectList.clear();
update(UPDATE_REDRAW);
}
storeState();
boolean isFragment = mMol.isFragment();
mMol.clear();
mMol.setFragment(isFragment);
if (mUndoMol.getAllAtoms() != 0)
updateAndFireEvent(UPDATE_REDRAW);
else
update(UPDATE_REDRAW);
}
public void toolChanged(int newTool) {
if (mCurrentTool != newTool) {
if (mCurrentTool == GenericEditorToolbar.cToolMapper
|| newTool == GenericEditorToolbar.cToolMapper) {
mCurrentTool = newTool;
update(UPDATE_REDRAW);
} else {
mCurrentTool = newTool;
}
}
}
public void setCustomAtom(int atomicNo, int mass, int valence, int radical, String customLabel) {
mCustomAtomicNo = atomicNo;
mCustomAtomMass = mass;
mCustomAtomValence = valence;
mCustomAtomRadical = radical;
mCustomAtomLabel = customLabel;
}
@Override
public void eventHappened(GenericEvent e) {
if (e instanceof GenericActionEvent)
eventHappened((GenericActionEvent)e);
else if (e instanceof GenericKeyEvent)
eventHappened((GenericKeyEvent)e);
else if (e instanceof GenericMouseEvent)
eventHappened((GenericMouseEvent)e);
}
private void eventHappened(GenericActionEvent e) {
String command = e.getMessage();
if (command.equals(ITEM_COPY_STRUCTURE) || command.equals(ITEM_COPY_REACTION)) {
copy();
} else if (command.equals(ITEM_PASTE_REACTION)) {
pasteReaction();
} else if (command.startsWith(ITEM_USE_TEMPLATE)) {
useTemplate(command.substring(ITEM_USE_TEMPLATE.length()));
} else if (command.startsWith(ITEM_PASTE_STRUCTURE)) {
pasteMolecule();
} else if (command.equals(ITEM_LOAD_REACTION)) {
openReaction();
} else if (command.equals(ITEM_ADD_AUTO_MAPPING)) {
autoMapReaction();
updateAndFireEvent(Math.max(mUpdateMode, UPDATE_REDRAW));
} else if (command.equals(ITEM_REMOVE_MAPPING)) {
removeManualMapping();
} else if (command.equals(ITEM_FLIP_HORIZONTALLY)) {
flip(true);
} else if (command.equals(ITEM_FLIP_VERTICALLY)) {
flip(false);
} else if (command.equals(ITEM_FLIP_ROTATE180)) {
rotate180();
} else if (command.equals(ITEM_SHOW_HELP)) {
showHelpDialog();
} 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=originalAtoms);
updateAndFireEvent(UPDATE_CHECK_COORDS);
}
return true;
}
private void useTemplate(String rxncode) {
storeState();
setReaction(ReactionEncoder.decode(rxncode, true));
}
private boolean atomCoordinatesCollide(StereoMolecule mol, double tolerance) {
int count = 0;
tolerance *= tolerance;
for (int i=0; i {
try {
Thread.sleep(WARNING_MILLIS);
} catch (InterruptedException ie) {
}
mWarningMessage = null;
mCanvas.repaint();
}).start();
}
private void eventHappened(GenericMouseEvent e) {
if (e.getWhat() == GenericMouseEvent.MOUSE_PRESSED) {
if (mCurrentHiliteAtom != -1 && mAtomKeyStrokeBuffer.length() != 0)
expandAtomKeyStrokes(mAtomKeyStrokeBuffer.toString());
mAtomKeyStrokeBuffer.setLength(0);
if (e.isPopupTrigger()) {
handlePopupTrigger(e.getX(), e.getY());
return;
}
if (e.getButton() == 1) {
if (e.getClickCount() == 2) {
return;
}
mMouseIsDown = true;
updateCursor();
mousePressedButton1(e);
}
}
if (e.getWhat() == GenericMouseEvent.MOUSE_RELEASED) {
if (e.isPopupTrigger()) {
handlePopupTrigger(e.getX(), e.getY());
return;
}
if (e.getButton() == 1) {
if (e.getClickCount() == 2) {
handleDoubleClick(e.getX(), e.getY());
return;
}
mMouseIsDown = false;
updateCursor();
mouseReleasedButton1();
}
}
if (e.getWhat() == GenericMouseEvent.MOUSE_ENTERED) {
mUIHelper.grabFocus();
updateCursor();
}
if (e.getWhat() == GenericMouseEvent.MOUSE_MOVED) {
mMouseIsDown = false;
int x = e.getX();
int y = e.getY();
if (trackHiliting(x, y, false)) {
mCanvas.repaint();
}
updateCursor();
}
if (e.getWhat() == GenericMouseEvent.MOUSE_DRAGGED) {
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 = getScaledAVBL();
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 (mX20) {
mChainAtom = new int[mChainAtoms];
for (int i = 0; i='4' && ch<='7') {
if (mMol.addRingToBond(mCurrentHiliteBond, ch - '0', false, getScaledAVBL()))
updateAndFireEvent(UPDATE_CHECK_COORDS);
} else if (ch == 'a' || ch == 'b') { // ChemDraw uses 'a', we use 'b' since a long time
if (mMol.addRingToBond(mCurrentHiliteBond, 6, true, getScaledAVBL()))
updateAndFireEvent(UPDATE_CHECK_COORDS);
} else {
boolean bondChanged =
(ch == '0') ? changeHighlightedBond(Molecule.cBondTypeMetalLigand)
: (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)
updateAndFireEvent(UPDATE_REDRAW);
}
} else if (mCurrentHiliteAtom != -1) {
int ch = e.getKey();
boolean isFirst = (mAtomKeyStrokeBuffer.length() == 0);
if (isFirst)
mFirstAtomKey = ch;
else {
if (mFirstAtomKey == 'l') { // if we don't want first 'l' to be a chlorine
mAtomKeyStrokeBuffer.setLength(0);
mAtomKeyStrokeBuffer.append('L');
}
mFirstAtomKey = -1;
}
if (isFirst && ch == 'l') { // if no chars are following, we interpret 'l' as chlorine analog to ChemDraw
mAtomKeyStrokeBuffer.append("Cl");
update(UPDATE_REDRAW);
} else if (isFirst && (ch == '+' || ch == '-')) {
storeState();
if (mMol.changeAtomCharge(mCurrentHiliteAtom, ch == '+'))
updateAndFireEvent(UPDATE_CHECK_COORDS);
} else if (isFirst && ch == '.') {
storeState();
int newRadical = (mMol.getAtomRadical(mCurrentHiliteAtom) == Molecule.cAtomRadicalStateD) ?
0 : Molecule.cAtomRadicalStateD;
mMol.setAtomRadical(mCurrentHiliteAtom, newRadical);
updateAndFireEvent(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);
updateAndFireEvent(UPDATE_CHECK_COORDS);
} else if (isFirst && ch == 'q' && mMol.isFragment()) {
showAtomQFDialog(mCurrentHiliteAtom);
} else if (isFirst && mMol.isFragment() && (ch == 'x' || ch == 'X')) {
int[] list = { 9, 17, 35, 53 };
mMol.setAtomList(mCurrentHiliteAtom, list);
updateAndFireEvent(UPDATE_CHECK_COORDS);
} else if (isFirst && ch == '?') {
storeState();
if (mMol.changeAtom(mCurrentHiliteAtom, 0, 0, -1, 0)) {
updateAndFireEvent(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=65 && ch<=90)
|| (ch>=97 && ch<=122)
|| (ch>=48 && ch<=57)
|| (ch == '-')) {
mAtomKeyStrokeBuffer.append((char)ch);
update(UPDATE_REDRAW);
} else if (ch == '\n' || ch == '\r') {
expandAtomKeyStrokes(mAtomKeyStrokeBuffer.toString());
}
} else {
if ((mMode & (MODE_REACTION | MODE_MARKUSH_STRUCTURE | MODE_MULTIPLE_FRAGMENTS)) == 0) {
int ch = e.getKey();
if (ch == 'h')
flip(true);
if (ch == 'v')
flip(false);
}
}
}
if (e.getWhat() == GenericKeyEvent.KEY_RELEASED) {
if (e.getKey() == GenericKeyEvent.KEY_SHIFT) {
mShiftIsDown = false;
updateCursor();
}
if (e.getKey() == GenericKeyEvent.KEY_ALT) {
mAltIsDown = false;
updateCursor();
}
if (e.getKey() == GenericKeyEvent.KEY_CTRL) {
updateCursor();
}
}
}
private boolean changeHighlightedBond(int type) {
storeState();
return mMol.changeBond(mCurrentHiliteBond, type);
}
private void handlePopupTrigger(int x, int y) {
GenericPopupMenu popup = null;
if (mClipboardHandler != null) {
popup = mUIHelper.createPopupMenu(this);
String item1 = analyseCopy(false) ? ITEM_COPY_REACTION : ITEM_COPY_STRUCTURE;
popup.addItem(item1, null, mMol.getAllAtoms() != 0);
String item3 = (StructureNameResolver.getInstance() == null) ? ITEM_PASTE_STRUCTURE : ITEM_PASTE_WITH_NAME;
popup.addItem(item3, null, true);
if ((mMode & MODE_REACTION) != 0) {
popup.addItem(ITEM_PASTE_REACTION, null, true);
popup.addSeparator();
if (sReactionQueryTemplates != null && mMol.isFragment()) {
boolean isSubMenu = false;
for (String[] template: sReactionQueryTemplates) {
if (TEMPLATE_SECTION_KEY.equals(template[0])) {
if (isSubMenu)
popup.endSubMenu();
popup.startSubMenu("Use " + template[1] + " Template");
isSubMenu = true;
continue;
}
if (!isSubMenu) {
popup.startSubMenu("Use Template");
isSubMenu = true;
}
popup.addItem(template[0], ITEM_USE_TEMPLATE + template[1], true);
}
popup.endSubMenu();
}
}
if ((mMode & MODE_REACTION) != 0)
popup.addItem(ITEM_LOAD_REACTION, null, true);
}
if ((mMode & MODE_REACTION) != 0 && mCurrentTool == GenericEditorToolbar.cToolMapper) {
if (popup == null)
popup = mUIHelper.createPopupMenu(this);
else
popup.addSeparator();
popup.addItem(ITEM_ADD_AUTO_MAPPING, null, true);
popup.addItem(ITEM_REMOVE_MAPPING, null, true);
}
if (mCurrentTool == GenericEditorToolbar.cToolZoom) {
if (popup == null)
popup = mUIHelper.createPopupMenu(this);
else
popup.addSeparator();
popup.addItem(ITEM_FLIP_HORIZONTALLY, null, true);
popup.addItem(ITEM_FLIP_VERTICALLY, null, true);
popup.addItem(ITEM_FLIP_ROTATE180, null, true);
}
if (mAtomColorSupported && mCurrentHiliteAtom != -1) {
int atomColor = mMol.getAtomColor(mCurrentHiliteAtom);
if (popup == null)
popup = mUIHelper.createPopupMenu(this);
else
popup.addSeparator();
popup.startSubMenu("Set Atom Color");
popup.addRadioButtonItem(" ", "atomColor" + mCurrentHiliteAtom + ":" + Molecule.cAtomColorNone, RGB_BLACK, atomColor == Molecule.cAtomColorNone);
popup.addRadioButtonItem(" ", "atomColor" + mCurrentHiliteAtom + ":" + Molecule.cAtomColorBlue, AbstractDepictor.COLOR_BLUE, atomColor == Molecule.cAtomColorBlue);
popup.addRadioButtonItem(" ", "atomColor" + mCurrentHiliteAtom + ":" + Molecule.cAtomColorDarkRed, AbstractDepictor.COLOR_DARK_RED, atomColor == Molecule.cAtomColorDarkRed);
popup.addRadioButtonItem(" ", "atomColor" + mCurrentHiliteAtom + ":" + Molecule.cAtomColorRed, AbstractDepictor.COLOR_RED, atomColor == Molecule.cAtomColorRed);
popup.addRadioButtonItem(" ", "atomColor" + mCurrentHiliteAtom + ":" + Molecule.cAtomColorDarkGreen, AbstractDepictor.COLOR_DARK_GREEN, atomColor == Molecule.cAtomColorDarkGreen);
popup.addRadioButtonItem(" ", "atomColor" + mCurrentHiliteAtom + ":" + Molecule.cAtomColorGreen, AbstractDepictor.COLOR_GREEN, atomColor == Molecule.cAtomColorGreen);
popup.addRadioButtonItem(" ", "atomColor" + mCurrentHiliteAtom + ":" + Molecule.cAtomColorMagenta, AbstractDepictor.COLOR_MAGENTA, atomColor == Molecule.cAtomColorMagenta);
popup.addRadioButtonItem(" ", "atomColor" + mCurrentHiliteAtom + ":" + Molecule.cAtomColorOrange, AbstractDepictor.COLOR_ORANGE, atomColor == Molecule.cAtomColorOrange);
popup.endSubMenu();
}
if (popup == null)
popup = mUIHelper.createPopupMenu(this);
else
popup.addSeparator();
popup.addItem(ITEM_SHOW_HELP, null, true);
if (System.getProperty("development") != null) {
if (popup == null)
popup = mUIHelper.createPopupMenu(this);
else
popup.addSeparator();
popup.addItem(ITEM_SHOW_ATOM_BOND_NUMBERS, null, true);
popup.addItem(ITEM_SHOW_SYMMETRY, null, true);
popup.addItem(ITEM_SHOW_NORMAL, null, true);
}
if (popup != null)
popup.show(x, y);
}
private void handleDoubleClick(int x, int y) {
int atom = mMol.findAtom(x, y);
int bond = mMol.findBond(x, y);
if (mCurrentTool == GenericEditorToolbar.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; imMol.getAtomX(i)) {
minX = mMol.getAtomX(i);
}
if (maxXminX) {
double centerX = (maxX + minX) / 2;
for (int i = 0; i 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; i0) {
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]);
}
}
if (mChainAtoms>1) {
for (int i = 1; i %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 oldToNewMapNo = new TreeMap<>();
int nextMapNo = 1;
final int fakeAtomMassBase = 512;
// Mark the manually mapped atoms such that the mapper uses them first priority and
// to be able to re-assign them later as manually mapped.
int[] fragmentAtom = new int[mFragment.length];
for (int atom = 0; atomfakeAtomMassBase);
if (hasFakeAtomMass) {
// rescue new mapNo
int newMapNo = mFragment[fragment].getAtomMass(fragmentAtom[fragment]) - fakeAtomMassBase;
// repair fake atom mass
mFragment[fragment].setAtomMass(fragmentAtom[fragment], mMol.getAtomMass(atom));
mMol.setAtomMapNo(atom, newMapNo, false);
mFragment[fragment].setAtomMapNo(fragmentAtom[fragment], newMapNo, false);
} else {
// take generated mapNo from reaction
int generatedMapNo = mFragment[fragment].getAtomMapNo(fragmentAtom[fragment]);
Integer newMapNo = 0;
if (generatedMapNo != 0) {
newMapNo = oldToNewMapNo.get(generatedMapNo);
if (newMapNo == null)
oldToNewMapNo.put(generatedMapNo, newMapNo = nextMapNo++);
}
mMol.setAtomMapNo(atom, newMapNo, true);
mFragment[fragment].setAtomMapNo(fragmentAtom[fragment], newMapNo, true);
}
fragmentAtom[fragment]++;
}
} else {
// restore original atom masses in fragments and copy molecule's mapping number into fragments
fragmentAtom = new int[mFragment.length];
for (int atom = 0; atom 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; idistance) {
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; i0; i--) { // bubble sort
for (int j = 0; jangle[j + 1]) {
double temp = angle[j];
angle[j] = angle[j + 1];
angle[j + 1] = temp;
}
}
}
angle[mMol.getAllConnAtomsPlusMetalBonds(atom)] = angle[0] + Math.PI * 2;
int largestNo = 0;
double largestDiff = 0.0;
for (int i = 0; i=mMol.getAtoms()) {
theAtom = -1;
}
}
if (theBond == -1
&& theAtom == -1
&& mCurrentTool != GenericEditorToolbar.cToolChain
&& mCurrentTool != GenericEditorToolbar.cToolMapper
&& mCurrentTool != GenericEditorToolbar.cToolUnknownParity
&& mCurrentTool != GenericEditorToolbar.cToolPosCharge
&& mCurrentTool != GenericEditorToolbar.cToolNegCharge
&& mCurrentTool != GenericEditorToolbar.cToolAtomH
&& mCurrentTool != GenericEditorToolbar.cToolAtomC
&& mCurrentTool != GenericEditorToolbar.cToolAtomN
&& mCurrentTool != GenericEditorToolbar.cToolAtomO
&& mCurrentTool != GenericEditorToolbar.cToolAtomSi
&& mCurrentTool != GenericEditorToolbar.cToolAtomP
&& mCurrentTool != GenericEditorToolbar.cToolAtomS
&& mCurrentTool != GenericEditorToolbar.cToolAtomF
&& mCurrentTool != GenericEditorToolbar.cToolAtomCl
&& mCurrentTool != GenericEditorToolbar.cToolAtomBr
&& mCurrentTool != GenericEditorToolbar.cToolAtomI
&& mCurrentTool != GenericEditorToolbar.cToolCustomAtom) {
theBond = mMol.findBond(x, y);
}
if (theBond != -1
&& (mCurrentTool == GenericEditorToolbar.cToolESRAbs
|| mCurrentTool == GenericEditorToolbar.cToolESRAnd
|| mCurrentTool == GenericEditorToolbar.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 == GenericEditorToolbar.cToolLassoPointer
|| mCurrentTool == GenericEditorToolbar.cToolDelete
|| mCurrentTool == GenericEditorToolbar.cToolText)) {
for (AbstractDrawingObject theObject : mDrawingObjectList) {
if (mCurrentTool == GenericEditorToolbar.cToolLassoPointer
|| (mCurrentTool == GenericEditorToolbar.cToolDelete && !(theObject instanceof ReactionArrow))
|| (mCurrentTool == GenericEditorToolbar.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);
fireEventLater(new EditorEvent(this, EditorEvent.WHAT_HILITE_ATOM_CHANGED, true));
}
if (mCurrentHiliteBond != theBond) {
mCurrentHiliteBond = theBond;
fireEventLater(new EditorEvent(this, EditorEvent.WHAT_HILITE_BOND_CHANGED, true));
}
mCurrentHiliteObject = hiliteObject;
return repaintNeeded;
}
private int getAtomKeyStrokeValidity(String s){
if (Molecule.getAtomicNoFromLabel(s, mAllowedPseudoAtoms) != 0)
return KEY_IS_ATOM_LABEL;
mAtomKeyStrokeSuggestion = NamedSubstituents.identify(s);
if (mAtomKeyStrokeSuggestion == null)
return isValidAtomKeyStrokeStart(s) ? KEY_IS_VALID_START : KEY_IS_INVALID;
if (mAtomKeyStrokeSuggestion.isEmpty())
return KEY_IS_VALID_START;
else
return KEY_IS_SUBSTITUENT;
}
/**
* @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=0; i--) {
AbstractDrawingObject object = mDrawingObjectList.get(i);
if (object.isSelected() && !(object instanceof ReactionArrow)) {
mDrawingObjectList.add(object.clone());
}
}
}
}
private void fireEventLater(EditorEvent e) {
final int what = e.getWhat();
if ((what & mEventsScheduled) == 0) {
mUIHelper.runLater(() -> {
mEventsScheduled &= ~what;
for (GenericEventListener l : mListeners)
l.eventHappened(e);
} );
mEventsScheduled |= what;
}
}
/**
* Redraws the molecule(s) or the reaction after scaling coordinates.
* Then analyses fragment membership and recreate individual molecules, reaction, or markush structure
* Then, fires molecule change events with userChange=false, i.e. external change.
*/
public void moleculeChanged() {
update(UPDATE_SCALE_COORDS);
fireEventLater(new EditorEvent(this, EditorEvent.WHAT_MOLECULE_CHANGED, false));
}
/**
* Redraws the molecule(s) or the reaction after scaling coordinates.
* Then analyses fragment membership and recreate individual molecules, reaction, or markush structure
* Then, fires molecule change events with userChange=false, i.e. external change.
* @param updateMode
*/
private void updateAndFireEvent(int updateMode) {
update(updateMode);
fireEventLater(new EditorEvent(this, EditorEvent.WHAT_MOLECULE_CHANGED, true));
}
public StereoMolecule getMolecule()
{
return mMol;
}
public void setMolecule (StereoMolecule theMolecule){
if (mMol == theMolecule) {
return;
}
storeState();
mMol = theMolecule;
mMode = 0;
mDrawingObjectList = null;
moleculeChanged();
}
public StereoMolecule[] getFragments() {
return mFragment;
}
public void setFragments(StereoMolecule[]fragment) {
mMol.clear();
mFragment = fragment;
for (int i = 0; ifragment2) {
mergeFragments[fragment1][fragment2] = true;
} else {
mergeFragments[fragment2][fragment1] = true;
}
}
}
}
}
int[] newFragmentIndex = new int[fragments];
for (int fragment = 0; fragmentmaxIndex) {
newFragmentIndex[k]--;
}
}
}
}
}
}
for (int atom = 0; atom {
if ((mMode & (MODE_REACTION | MODE_MARKUSH_STRUCTURE)) != 0) {
if (fragmentDescriptor1[1] != fragmentDescriptor2[1]) {
return (fragmentDescriptor1[1] == 0) ? -1 : 1;
}
}
return Double.compare(cog[fragmentDescriptor1[0]].x + cog[fragmentDescriptor1[0]].y,
cog[fragmentDescriptor2[0]].x + cog[fragmentDescriptor2[0]].y);
});
int[] newFragmentIndex = new int[fragments];
for (int fragment = 0; fragment1 ? new Point2D.Double(sumx / atoms, sumy / atoms) : null;
}
private void rotate180() {
boolean selectedOnly = false;
for (int atom = 0; atom