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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.share.gui.editor.actions;
import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.NamedSubstituents;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.coords.CoordinateInventor;
import com.actelion.research.gui.generic.GenericPoint;
import com.actelion.research.share.gui.DialogResult;
import com.actelion.research.share.gui.editor.Model;
import com.actelion.research.share.gui.editor.dialogs.IAtomQueryFeaturesDialog;
import com.actelion.research.share.gui.editor.geom.GeomFactory;
import com.actelion.research.share.gui.editor.geom.IDrawContext;
import com.actelion.research.share.gui.editor.io.IKeyEvent;
import com.actelion.research.share.gui.editor.io.IMouseEvent;
/**
* Project:
* User: rufenec
* Date: 2/1/13
* Time: 4:13 PM
*/
public abstract class AtomHighlightAction extends DrawAction
{
AtomHighlightAction(Model model)
{
super(model);
}
protected GenericPoint lastHightlightPoint = null;
boolean trackHighLight(GenericPoint pt)
{
StereoMolecule mol = model.getMolecule();
int currentAtom = model.getSelectedAtom();
int atom = findAtom(mol, pt);
// Update at least when current selected atom and new selected atom differ
boolean ok = atom != -1;
lastHightlightPoint = pt;
String keyStrokes = model.getKeyStrokeBuffer().toString();
if (currentAtom != -1 && atom != currentAtom) {
if (keyStrokes.length() > 0) {
StereoMolecule currentMol = model.getMolecule();
expandAtomKeyStrokes(currentMol, currentAtom, keyStrokes);
model.getKeyStrokeBuffer().setLength(0);
}
}
if (mol != null) {
setHighlightAtom(mol, atom);
} else {
if (model.getSelectedAtom() != -1) {
model.getKeyStrokeBuffer().setLength(0);
ok = true;
}
}
atom = model.getSelectedAtom();
ok = ok | atom != -1;
return ok;
}
void setHighlightAtom(StereoMolecule mol, int atom)
{
model.setSelectedAtom(atom);
}
@Override
public boolean onMouseDown(IMouseEvent evt)
{
return false;
}
@Override
public boolean onMouseMove(IMouseEvent evt, boolean drag)
{
if (!drag) {
GenericPoint pt = new GenericPoint(evt.getX(), evt.getY());
boolean ok = trackHighLight(pt);
return ok;
} else {
return false;
}
}
@Override
public boolean paint(IDrawContext _ctx)
{
boolean ok = false;
int theAtom = model.getSelectedAtom();
StereoMolecule mol = model.getMolecule();
if (mol != null) {
if (theAtom != -1) {
drawAtomHighlight(_ctx, mol, theAtom);
ok = true;
}
}
return ok;
}
@Override
public boolean onKeyPressed(IKeyEvent evt)
{
GeomFactory factory = model.getGeomFactory();
if (evt.getCode().equals(factory.getDeleteKey())) {
int theAtom = model.getSelectedAtom();
StereoMolecule mol = model.getMolecule();
if (theAtom != -1) {
mol.deleteAtom(theAtom);
setHighlightAtom(mol, -1);
return true;
} else {
boolean update = false;
StereoMolecule m = model.getMolecule();
if (m.deleteSelectedAtoms()) {
update = true;
}
return update;
}
} else if (handleCharacter(evt)) {
return true;
}
return false;
}
private boolean handleCharacter(IKeyEvent evt)
{
int theAtom = model.getSelectedAtom();
StereoMolecule mol = model.getMolecule();
StringBuilder keyStrokeBuffer = model.getKeyStrokeBuffer();
if (mol == null) {
return false;
}
int newRadical;
String code = evt.getText();
if (theAtom != -1 /*&& !evt.isShiftDown()*/) {
char c = code != null && code.length() > 0 ? code.charAt(0) : 0;
boolean isFirst = (keyStrokeBuffer.length() == 0);
if (isFirst) {
switch (c) {
case '+':
case '-':
return mol.changeAtomCharge(theAtom, c == '+');
case '.':
newRadical = (mol.getAtomRadical(theAtom) == Molecule.cAtomRadicalStateD) ? 0 : Molecule.cAtomRadicalStateD;
mol.setAtomRadical(theAtom, newRadical);
return true;
case ':':
newRadical = (mol.getAtomRadical(theAtom) == Molecule.cAtomRadicalStateT) ? Molecule.cAtomRadicalStateS
: (mol.getAtomRadical(theAtom) == Molecule.cAtomRadicalStateS) ? 0 : Molecule.cAtomRadicalStateT;
mol.setAtomRadical(theAtom, newRadical);
return true;
case 'q':
return mol.isFragment() ? showAtomQFDialog(theAtom) : false;
case '?':
return mol.changeAtom(theAtom, 0, 0, -1, 0);
default:
break;
}
}
return handleCharacter(mol, theAtom, evt);
} else {
return handleCharsNonSelected(code);
}
}
private boolean handleCharsNonSelected(String code)
{
if ("h".equals(code)) {
model.flip(true);
return true;
} else if ("v".equals(code)) {
model.flip(false);
return true;
}
return false;
}
private void expandAtomKeyStrokes(StereoMolecule mol, int highliteAtom, String keyStrokes)
{
int atomicNo = Molecule.getAtomicNoFromLabel(keyStrokes);
if (atomicNo != 0) {
if (mol.changeAtom(highliteAtom, atomicNo, 0, -1, 0)) {
model.changed();
return;
}
}
StereoMolecule substituent = NamedSubstituents.getSubstituent(keyStrokes);
if (substituent != null) {
// 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(mol, highliteAtom, 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 = mol.getAtomX(highliteAtom) - sourceAVBL * fragment.getAtomX(0);
double dy = mol.getAtomY(highliteAtom) - sourceAVBL * fragment.getAtomY(0);
// Attach the substituent to the complete molecule and take coodinates from the
// previously created fragment-substituent species.
int firstAtomInMol = mol.getAllAtoms();
mol.addSubstituent(substituent, highliteAtom);
int substituentAtoms = mol.getAllAtoms() - firstAtomInMol;
for (int i = 0; i < substituentAtoms; i++) {
mol.setAtomX(firstAtomInMol + i, sourceAVBL * fragment.getAtomX(firstAtomInFragment + i) + dx);
mol.setAtomY(firstAtomInMol + i, sourceAVBL * fragment.getAtomY(firstAtomInFragment + i) + dy);
}
mol.setStereoBondsFromParity();
model.changed();
}
}
private boolean handleCharacter(StereoMolecule mol, int theAtom, IKeyEvent evt)
{
GeomFactory factory = model.getGeomFactory();
StringBuilder keyStrokeBuffer = model.getKeyStrokeBuffer();
boolean isFirst = (keyStrokeBuffer.length() == 0);
String code = evt.getText();
char c = code != null && code.length() > 0 ? code.charAt(0) : 0;
if (evt.getCode().equals(factory.getDeleteKey())) {
if (theAtom != -1) {
mol.deleteAtom(theAtom);
setHighlightAtom(mol, -1);
return true;
} else {
if (mol.deleteSelectedAtoms()) {
return true;
}
}
} else if (!isFirst && evt.getCode().equals(factory.getEscapeKey())) {
keyStrokeBuffer.setLength(0);
return true;
} else if (!isFirst && evt.getCode().equals(factory.getBackSpaceKey())) {
keyStrokeBuffer.setLength(keyStrokeBuffer.length() - 1);
return true;
} else if (evt.getCode().equals(factory.getEnterKey())) {
expandAtomKeyStrokes(mol, theAtom, keyStrokeBuffer.toString());
keyStrokeBuffer.setLength(0);
return true;
} else if (isFirst && c > 48 && c <= 57) {
addChain(mol, theAtom, c-47);
return true;
} else if ((c > 48 && c <= 57) || (c >= 65 && c <= 90) || (c >= 97 && c <= 122) || (c >= 48 && c <= 57) || (c == '-')) {
keyStrokeBuffer.append(c);
return true;
}
return false;
}
private void addChain(StereoMolecule mol, int theAtom, int chainAtoms)
{
if (mol.getFreeValence(theAtom) > 0) {
int atom1 = theAtom;
int hydrogenCount = mol.getAllAtoms() - mol.getAtoms();
for (int i = 1; i < chainAtoms; i++) {
GenericPoint pt = suggestNewX2AndY2(atom1);
int atom2 = mol.addAtom(pt.getX(), pt.getY());
if (atom2 == -1) {
break;
}
mol.addBond(atom1, atom2);
atom1 = atom2 - hydrogenCount; // new atom was added behind all hydrogens and travels now to the front
mol.ensureHelperArrays(Molecule.cHelperNeighbours);
}
}
}
private boolean showAtomQFDialog(int atom)
{
GeomFactory factory = model.getGeomFactory();
StereoMolecule mol = model.getMolecule();
if (mol != null) {
boolean showReactionHints = (model.getMode() & Model.MODE_REACTION) != 0;
IAtomQueryFeaturesDialog dlg = factory.createAtomQueryFeatureDialog(mol, atom, showReactionHints);
return dlg.doModalAt(lastHightlightPoint.getX(), lastHightlightPoint.getY()) == DialogResult.IDOK;
}
return false;
}
public int findAtom(StereoMolecule mol, GenericPoint pt)
{
int foundAtom = -1;
double pickx = pt.getX();
double picky = pt.getY();
double avbl = mol.getAverageBondLength();
double foundDistanceSquare = Float.MAX_VALUE;
double maxDistanceSquare = avbl * avbl / (avbl / 3);
int mAllAtoms = mol.getAllAtoms();
for (int atom = 0; atom < mAllAtoms; atom++) {
double x = mol.getAtomX(atom);
double y = mol.getAtomY(atom);
double distanceSquare = (pickx - x) * (pickx - x) + (picky - y) * (picky - y);
if (distanceSquare < maxDistanceSquare && distanceSquare < foundDistanceSquare) {
foundDistanceSquare = distanceSquare;
foundAtom = atom;
}
}
return foundAtom;
}
}