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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.ExtendedMolecule;
import com.actelion.research.chem.Molecule;
import info.clearthought.layout.TableLayout;
import javax.swing.*;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.util.Arrays;
public class JAtomQueryFeatureDialog extends JDialog
implements ActionListener,ItemListener {
static final long serialVersionUID = 0x20060720;
private Component mParent;
private ExtendedMolecule mMol;
private int mAtom;
private JCheckBox mCBAny,mCBBlocked,mCBSubstituted,mCBMatchStereo,mCBExcludeGroup;
private JComboBox mChoiceArom,mChoiceRingState,mChoiceRingSize,mChoiceCharge,
mChoiceNeighbours,mChoiceHydrogen,mChoicePi;
private JTextField mTFAtomList;
private JLabel mLabelAtomList;
protected JAtomQueryFeatureDialog(Dialog parent, ExtendedMolecule mol, int atom) {
super(parent, (mol.isSelectedAtom(atom)) ? "Multiple Atom Properties" : "Atom Properties", true);
init(parent, mol, atom);
}
protected JAtomQueryFeatureDialog(Frame parent, ExtendedMolecule mol, int atom) {
super(parent, (mol.isSelectedAtom(atom)) ? "Multiple Atom Properties" : "Atom Properties", true);
init(parent, mol, atom);
}
private void init(Component parent, ExtendedMolecule mol, int atom) {
mParent = parent;
mMol = mol;
mAtom = atom;
boolean opaque = false;
JPanel p1 = new JPanel();
p1.setOpaque(opaque);
double[][] size = { {8, TableLayout.PREFERRED, 8, TableLayout.PREFERRED, 8 },
{8, TableLayout.PREFERRED,
4, TableLayout.PREFERRED,
12, TableLayout.PREFERRED,
4, TableLayout.PREFERRED,
4, TableLayout.PREFERRED,
4, TableLayout.PREFERRED,
4, TableLayout.PREFERRED,
4, TableLayout.PREFERRED,
4, TableLayout.PREFERRED,
12, TableLayout.PREFERRED,
0, TableLayout.PREFERRED,
4, TableLayout.PREFERRED,
4, TableLayout.PREFERRED} };
p1.setLayout(new TableLayout(size));
mCBAny = new JCheckBox("any atomic number");
mCBAny.setOpaque(opaque);
mCBAny.addItemListener(this);
p1.add(mCBAny, "1,1,3,1");
mLabelAtomList = new JLabel("excluded atoms:");
mLabelAtomList.setOpaque(opaque);
mTFAtomList = new JTextField(8);
p1.add(mLabelAtomList, "1,3");
p1.add(mTFAtomList, "3,3");
mChoiceArom = new JComboBox();
mChoiceArom.setOpaque(opaque);
mChoiceArom.addItem("any aromatic state");
mChoiceArom.addItem("is aromatic");
mChoiceArom.addItem("is not aromatic");
p1.add(mChoiceArom, "1,5,3,5");
mChoiceRingState = new JComboBox();
mChoiceRingState.setOpaque(opaque);
mChoiceRingState.addItem("any ring state");
mChoiceRingState.addItem("is chain atom");
mChoiceRingState.addItem("is any ring atom");
mChoiceRingState.addItem("has 2 ring bonds");
mChoiceRingState.addItem("has 3 ring bonds");
mChoiceRingState.addItem("has >3 ring bonds");
p1.add(mChoiceRingState, "1,7,3,7");
mChoiceRingSize = new JComboBox();
mChoiceRingSize.setOpaque(opaque);
mChoiceRingSize.addItem("any ring size");
mChoiceRingSize.addItem("is in 3-membered ring");
mChoiceRingSize.addItem("is in 4-membered ring");
mChoiceRingSize.addItem("is in 5-membered ring");
mChoiceRingSize.addItem("is in 6-membered ring");
mChoiceRingSize.addItem("is in 7-membered ring");
p1.add(mChoiceRingSize, "1,9,3,9");
mChoiceCharge = new JComboBox();
mChoiceCharge.setOpaque(opaque);
mChoiceCharge.addItem("any atom charge");
mChoiceCharge.addItem("has no charge");
mChoiceCharge.addItem("has negative charge");
mChoiceCharge.addItem("has positive charge");
p1.add(mChoiceCharge, "1,11,3,11");
mChoiceNeighbours = new JComboBox();
mChoiceNeighbours.setOpaque(opaque);
mChoiceNeighbours.addItem("any non-H neighbour count");
mChoiceNeighbours.addItem("has exactly 1 neighbour");
mChoiceNeighbours.addItem("has exactly 2 neighbours");
mChoiceNeighbours.addItem("has exactly 3 neighbours");
mChoiceNeighbours.addItem("has less than 3 neighbours");
mChoiceNeighbours.addItem("has less than 4 neighbours");
mChoiceNeighbours.addItem("has more than 1 neighbour");
mChoiceNeighbours.addItem("has more than 2 neighbours");
mChoiceNeighbours.addItem("has more than 3 neighbours");
p1.add(mChoiceNeighbours, "1,13,3,13");
mChoiceHydrogen = new JComboBox();
mChoiceHydrogen.setOpaque(opaque);
mChoiceHydrogen.addItem("any hydrogen count");
mChoiceHydrogen.addItem("no hydrogen");
mChoiceHydrogen.addItem("exactly 1 hydrogen");
mChoiceHydrogen.addItem("exactly 2 hydrogens");
mChoiceHydrogen.addItem("at least 1 hydrogen");
mChoiceHydrogen.addItem("at least 2 hydrogens");
mChoiceHydrogen.addItem("at least 3 hydrogens");
mChoiceHydrogen.addItem("less than 2 hydrogens");
mChoiceHydrogen.addItem("less than 3 hydrogens");
p1.add(mChoiceHydrogen, "1,15,3,15");
mChoicePi = new JComboBox();
mChoicePi.setOpaque(opaque);
mChoicePi.addItem("any pi electron count");
mChoicePi.addItem("no pi electrons");
mChoicePi.addItem("exactly 1 pi electron");
mChoicePi.addItem("exactly 2 pi electrons");
mChoicePi.addItem("at least 1 pi electron");
p1.add(mChoicePi, "1,17,3,17");
mCBBlocked = new JCheckBox("prohibit further substitution");
mCBBlocked.setOpaque(opaque);
mCBBlocked.addItemListener(this);
p1.add(mCBBlocked, "1,19,3,19");
mCBSubstituted = new JCheckBox("require further substitution");
mCBSubstituted.setOpaque(opaque);
mCBSubstituted.addItemListener(this);
p1.add(mCBSubstituted, "1,21,3,21");
mCBMatchStereo = new JCheckBox("match stereo center");
mCBMatchStereo.setOpaque(opaque);
p1.add(mCBMatchStereo, "1,23,3,23");
mCBExcludeGroup = new JCheckBox("is part of exclude group");
mCBExcludeGroup.setOpaque(opaque);
p1.add(mCBExcludeGroup, "1,25,3,25");
JPanel buttonpanel = new JPanel();
buttonpanel.setBorder(BorderFactory.createEmptyBorder(12, 8, 8, 8));
buttonpanel.setLayout(new BorderLayout());
JPanel ibp = new JPanel();
ibp.setLayout(new GridLayout(1, 2, 8, 0));
JButton bcancel = new JButton("Cancel");
bcancel.addActionListener(this);
ibp.add(bcancel);
JButton bok = new JButton("OK");
bok.addActionListener(this);
ibp.add(bok);
buttonpanel.add(ibp, BorderLayout.EAST);
getContentPane().add(p1,BorderLayout.CENTER);
getContentPane().add(buttonpanel,BorderLayout.SOUTH);
getRootPane().setDefaultButton(bok);
pack();
setLocationRelativeTo(parent);
mMol.ensureHelperArrays(Molecule.cHelperCIP);
setInitialStates();
setVisible(true);
}
public void actionPerformed(ActionEvent e) {
if (e.getActionCommand() == "Cancel")
dispose();
else if (e.getActionCommand() == "OK") {
setQueryFeatures();
dispose();
}
}
public void itemStateChanged(ItemEvent e) {
if (e.getItemSelectable() == mCBAny) {
if (mCBAny.isSelected()) {
mTFAtomList.setText("");
mLabelAtomList.setText("excluded atoms:");
}
else {
mTFAtomList.setText(mMol.getAtomLabel(mAtom));
mLabelAtomList.setText("allowed atoms:");
}
}
else if (e.getItemSelectable() == mCBBlocked && e.getStateChange() == ItemEvent.SELECTED) {
mCBSubstituted.setSelected(false);
mChoiceNeighbours.setSelectedIndex(0);
}
else if (e.getItemSelectable() == mCBSubstituted && e.getStateChange() == ItemEvent.SELECTED)
mCBBlocked.setSelected(false);
}
private void setInitialStates() {
int queryFeatures = mMol.getAtomQueryFeatures(mAtom);
if ((queryFeatures & Molecule.cAtomQFAny) != 0) {
mCBAny.setSelected(true);
mLabelAtomList.setText("excluded atoms:");
}
else
mLabelAtomList.setText("allowed atoms:");
mTFAtomList.setText(mMol.getAtomList(mAtom) == null ? "" : mMol.getAtomListString(mAtom));
if ((queryFeatures & Molecule.cAtomQFAromatic) != 0)
mChoiceArom.setSelectedIndex(1);
else if ((queryFeatures & Molecule.cAtomQFNotAromatic) != 0)
mChoiceArom.setSelectedIndex(2);
int ringState = queryFeatures & Molecule.cAtomQFRingState;
switch (ringState) {
case Molecule.cAtomQFNot2RingBonds | Molecule.cAtomQFNot3RingBonds | Molecule.cAtomQFNot4RingBonds:
mChoiceRingState.setSelectedIndex(1);
break;
case Molecule.cAtomQFNotChain:
mChoiceRingState.setSelectedIndex(2);
break;
case Molecule.cAtomQFNotChain | Molecule.cAtomQFNot3RingBonds | Molecule.cAtomQFNot4RingBonds:
mChoiceRingState.setSelectedIndex(3);
break;
case Molecule.cAtomQFNotChain | Molecule.cAtomQFNot2RingBonds | Molecule.cAtomQFNot4RingBonds:
mChoiceRingState.setSelectedIndex(4);
break;
case Molecule.cAtomQFNotChain | Molecule.cAtomQFNot2RingBonds | Molecule.cAtomQFNot3RingBonds:
mChoiceRingState.setSelectedIndex(5);
break;
}
int ringSize = (queryFeatures & Molecule.cAtomQFRingSize) >> Molecule.cAtomQFRingSizeShift;
mChoiceRingSize.setSelectedIndex((ringSize == 0) ? 0 : ringSize-2);
int neighbourFeatures = queryFeatures & Molecule.cAtomQFNeighbours;
switch (neighbourFeatures) {
case Molecule.cAtomQFNeighbours & ~Molecule.cAtomQFNot1Neighbour:
mChoiceNeighbours.setSelectedIndex(1);
break;
case Molecule.cAtomQFNeighbours & ~Molecule.cAtomQFNot2Neighbours:
mChoiceNeighbours.setSelectedIndex(2);
break;
case Molecule.cAtomQFNeighbours & ~Molecule.cAtomQFNot3Neighbours:
mChoiceNeighbours.setSelectedIndex(3);
break;
case Molecule.cAtomQFNot3Neighbours | Molecule.cAtomQFNot4Neighbours:
mChoiceNeighbours.setSelectedIndex(4);
break;
case Molecule.cAtomQFNot4Neighbours:
mChoiceNeighbours.setSelectedIndex(5);
break;
case Molecule.cAtomQFNot0Neighbours | Molecule.cAtomQFNot1Neighbour:
mChoiceNeighbours.setSelectedIndex(6);
break;
case Molecule.cAtomQFNot0Neighbours | Molecule.cAtomQFNot1Neighbour | Molecule.cAtomQFNot2Neighbours:
mChoiceNeighbours.setSelectedIndex(7);
break;
case Molecule.cAtomQFNeighbours & ~Molecule.cAtomQFNot4Neighbours:
mChoiceNeighbours.setSelectedIndex(8);
break;
}
int chargeFeatures = queryFeatures & Molecule.cAtomQFCharge;
switch (chargeFeatures) {
case Molecule.cAtomQFNotChargeNeg | Molecule.cAtomQFNotChargePos:
mChoiceCharge.setSelectedIndex(1);
break;
case Molecule.cAtomQFNotCharge0 | Molecule.cAtomQFNotChargePos:
mChoiceCharge.setSelectedIndex(2);
break;
case Molecule.cAtomQFNotCharge0 | Molecule.cAtomQFNotChargeNeg:
mChoiceCharge.setSelectedIndex(3);
break;
}
int hydrogenFeatures = queryFeatures & Molecule.cAtomQFHydrogen;
switch (hydrogenFeatures) {
case Molecule.cAtomQFNot1Hydrogen | Molecule.cAtomQFNot2Hydrogen | Molecule.cAtomQFNot3Hydrogen:
mChoiceHydrogen.setSelectedIndex(1);
break;
case Molecule.cAtomQFNot0Hydrogen | Molecule.cAtomQFNot2Hydrogen | Molecule.cAtomQFNot3Hydrogen:
mChoiceHydrogen.setSelectedIndex(2);
break;
case Molecule.cAtomQFNot0Hydrogen | Molecule.cAtomQFNot1Hydrogen | Molecule.cAtomQFNot3Hydrogen:
mChoiceHydrogen.setSelectedIndex(3);
break;
case Molecule.cAtomQFNot0Hydrogen:
mChoiceHydrogen.setSelectedIndex(4);
break;
case Molecule.cAtomQFNot0Hydrogen | Molecule.cAtomQFNot1Hydrogen:
mChoiceHydrogen.setSelectedIndex(5);
break;
case Molecule.cAtomQFNot0Hydrogen | Molecule.cAtomQFNot1Hydrogen | Molecule.cAtomQFNot2Hydrogen:
mChoiceHydrogen.setSelectedIndex(6);
break;
case Molecule.cAtomQFNot2Hydrogen | Molecule.cAtomQFNot3Hydrogen:
mChoiceHydrogen.setSelectedIndex(7);
break;
case Molecule.cAtomQFNot3Hydrogen:
mChoiceHydrogen.setSelectedIndex(8);
break;
}
int piFeatures = queryFeatures & Molecule.cAtomQFPiElectrons;
switch (piFeatures) {
case Molecule.cAtomQFNot1PiElectron | Molecule.cAtomQFNot2PiElectrons:
mChoicePi.setSelectedIndex(1);
break;
case Molecule.cAtomQFNot0PiElectrons | Molecule.cAtomQFNot2PiElectrons:
mChoicePi.setSelectedIndex(2);
break;
case Molecule.cAtomQFNot0PiElectrons | Molecule.cAtomQFNot1PiElectron:
mChoicePi.setSelectedIndex(3);
break;
case Molecule.cAtomQFNot0PiElectrons:
mChoicePi.setSelectedIndex(4);
break;
}
if ((queryFeatures & Molecule.cAtomQFNoMoreNeighbours) != 0)
mCBBlocked.setSelected(true);
if ((queryFeatures & Molecule.cAtomQFMoreNeighbours) != 0)
mCBSubstituted.setSelected(true);
if ((queryFeatures & Molecule.cAtomQFMatchStereo) != 0)
mCBMatchStereo.setSelected(true);
if ((queryFeatures & Molecule.cAtomQFExcludeGroup) != 0)
mCBExcludeGroup.setSelected(true);
}
private void setQueryFeatures() {
int[] atomList = createAtomList();
if (mMol.isSelectedAtom(mAtom)) {
for (int atom=0; atom 0
|| (mMol.getAtomCharge(atom)==0 && (mMol.getAtomicNo(atom)==5 || mMol.isNitrogenFamily(atom) || mMol.isChalcogene(atom)))))
queryFeatures |= Molecule.cAtomQFNoMoreNeighbours;
if (mCBSubstituted.isSelected()
&& (mMol.getFreeValence(atom) > 0
|| (mMol.getAtomCharge(atom)==0 && (mMol.getAtomicNo(atom)==5 || mMol.isNitrogenFamily(atom) || mMol.isChalcogene(atom)))))
queryFeatures |= Molecule.cAtomQFMoreNeighbours;
if (mCBMatchStereo.isSelected())
queryFeatures |= Molecule.cAtomQFMatchStereo;
if (mCBExcludeGroup.isSelected())
queryFeatures |= Molecule.cAtomQFExcludeGroup;
mMol.setAtomQueryFeature(atom, 0xFFFFFFFF, false);
mMol.setAtomQueryFeature(atom, queryFeatures, true);
}
private int[] createAtomList() {
String listString = mTFAtomList.getText();
if (listString.length() == 0)
return null;
int[] list = null;
int delimiterIndex;
do {
String label;
delimiterIndex = listString.indexOf(',');
if (delimiterIndex == -1)
label = listString;
else {
label = listString.substring(0, delimiterIndex);
if (delimiterIndex == listString.length() - 1)
listString = "";
else
listString = listString.substring(delimiterIndex+1);
}
int atomicNo = Molecule.getAtomicNoFromLabel(label);
if (atomicNo != 0) {
if (atomicNo == 1) {
JOptionPane.showMessageDialog(mParent, "'H' cannot be part of an atom list and is removed.");
}
else if (list == null) {
list = new int[1];
list[0] = atomicNo;
}
else {
boolean found = false;
for (int i=0; i © 2015 - 2025 Weber Informatics LLC | Privacy Policy