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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.ExtendedMolecule;
import com.actelion.research.chem.Molecule;
import com.actelion.research.gui.generic.*;
import com.actelion.research.gui.hidpi.HiDPIHelper;
import java.util.Arrays;
public class AtomQueryFeatureDialogBuilder implements GenericEventListener {
public static final String[] RING_SIZE_SHORT_TEXT = {
"",
"r0",
"r",
"r3",
"r3-4",
"r3-5",
"r3-6",
"r3-7",
"r4",
"r4-5",
"r4-6",
"r4-7",
"r>3",
"r5",
"r5-6",
"r5-7",
"r>4",
"r6",
"r6-7",
"r>5",
"r7",
"r>6",
"r>7"
};
private static final String[] RING_SIZE_OPTIONS = {
"any",
"is not in a ring",
"is in any ring",
"3 members",
"3-4 members",
"3-5 members",
"3-6 members",
"3-7 members",
"4 members",
"4-5 members",
"4-6 members",
"4-7 members",
"> 3 members",
"5 members",
"5-6 members",
"5-7 members",
"> 4 members",
"6 members",
"6-7 members",
"> 5 members",
"7 members",
"> 6 members",
"> 7 members"
};
public static final long[] RING_SIZE_VALUES = {
0, // special handling: 0 means all allowed
Molecule.cAtomQFRingSize0,
Molecule.cAtomQFNewRingSize ^ Molecule.cAtomQFRingSize0,
Molecule.cAtomQFRingSize3,
Molecule.cAtomQFRingSize3 | Molecule.cAtomQFRingSize4,
Molecule.cAtomQFRingSize3 | Molecule.cAtomQFRingSize4 | Molecule.cAtomQFRingSize5,
Molecule.cAtomQFRingSize3 | Molecule.cAtomQFRingSize4 | Molecule.cAtomQFRingSize5 | Molecule.cAtomQFRingSize6,
Molecule.cAtomQFNewRingSize ^ (Molecule.cAtomQFRingSize0 | Molecule.cAtomQFRingSizeLarge),
Molecule.cAtomQFRingSize4,
Molecule.cAtomQFRingSize4 | Molecule.cAtomQFRingSize5,
Molecule.cAtomQFRingSize4 | Molecule.cAtomQFRingSize5 | Molecule.cAtomQFRingSize6,
Molecule.cAtomQFRingSize4 | Molecule.cAtomQFRingSize5 | Molecule.cAtomQFRingSize6 | Molecule.cAtomQFRingSize7,
Molecule.cAtomQFNewRingSize ^ (Molecule.cAtomQFRingSize0 | Molecule.cAtomQFRingSize3),
Molecule.cAtomQFRingSize5,
Molecule.cAtomQFRingSize5 | Molecule.cAtomQFRingSize6,
Molecule.cAtomQFRingSize5 | Molecule.cAtomQFRingSize6 | Molecule.cAtomQFRingSize7,
Molecule.cAtomQFRingSize5 | Molecule.cAtomQFRingSize6 | Molecule.cAtomQFRingSize7 | Molecule.cAtomQFRingSizeLarge,
Molecule.cAtomQFRingSize6,
Molecule.cAtomQFRingSize6 | Molecule.cAtomQFRingSize7,
Molecule.cAtomQFRingSize6 | Molecule.cAtomQFRingSize7 | Molecule.cAtomQFRingSizeLarge,
Molecule.cAtomQFRingSize7,
Molecule.cAtomQFRingSize7 | Molecule.cAtomQFRingSizeLarge,
Molecule.cAtomQFRingSizeLarge,
};
private GenericDialog mDialog;
private GenericLabel mLabelAtomList;
private GenericTextField mTFAtomList;
private GenericCheckBox mCBAny,mCBBlocked,mCBSubstituted,mCBMatchStereo,mCBExcludeGroup;
private GenericComboBox mChoiceArom,mChoiceRingState,mChoiceSmallRingSize,mChoiceRingSize,mChoiceCharge,
mChoiceNeighbours,mChoiceHydrogen,mChoicePi, mChoiceENeighbours,mChoiceReactionParityHint,
mChoiceStereoCenter;
private ExtendedMolecule mMol;
private int mAtom;
private long mRingSizeCustomValue;
private boolean mOKSelected;
public AtomQueryFeatureDialogBuilder(GenericUIHelper dialogHelper, ExtendedMolecule mol, int atom, boolean includeReactionHints) {
mDialog = dialogHelper.createDialog(mol.isSelectedAtom(atom) ? "Atom Query Features (Multiple)" : "Atom Query Features", this);
build(mol, atom, includeReactionHints);
}
/**
* @return true if OK was pressed and potential change was applied to molecule
*/
public boolean showDialog() {
mOKSelected = false;
mDialog.showDialog();
return mOKSelected;
}
private void build(ExtendedMolecule mol, int atom, boolean includeReactionHints) {
mMol = mol;
mAtom = atom;
int gap = HiDPIHelper.scale(8);
int[] gap1 = { gap, gap/2, gap*3/2, gap/2, gap/2, gap/2, gap/2, gap/2, gap/2, gap/2, gap/2, gap*3/2, gap/4, gap/2, gap/2, gap/4 };
int[] gap2 = { gap*3/2, gap/2 };
int[] hLayout = {gap, GenericDialog.PREFERRED, gap, GenericDialog.PREFERRED, gap};
int[] vLayout = new int[1 + 2*gap1.length + (includeReactionHints ? 2*gap2.length : 0)];
int index = 0;
for (int g:gap1) {
vLayout[index++] = g;
vLayout[index++] = GenericDialog.PREFERRED;
}
if (includeReactionHints)
for (int g:gap2) {
vLayout[index++] = g;
vLayout[index++] = GenericDialog.PREFERRED;
}
vLayout[index++] = gap;
mDialog.setLayout(hLayout, vLayout);
mCBAny = mDialog.createCheckBox("Any atomic number");
mCBAny.addEventConsumer(this);
mDialog.add(mCBAny, 1,1,3,1);
mLabelAtomList = mDialog.createLabel("Excluded atoms:");
mTFAtomList = mDialog.createTextField(16, 1);
mDialog.add(mLabelAtomList, 1,3);
mDialog.add(mTFAtomList, 3,3);
mChoiceArom = mDialog.createComboBox();
mChoiceArom.addItem("any");
mChoiceArom.addItem("is aromatic");
mChoiceArom.addItem("is hetero-aromatic");
mChoiceArom.addItem("is not aromatic");
mDialog.add(mDialog.createLabel("Aromaticity:"), 1,5);
mDialog.add(mChoiceArom, 3,5);
mChoiceRingState = mDialog.createComboBox();
mChoiceRingState.addItem("any");
mChoiceRingState.addItem("0 (not in a ring)");
mChoiceRingState.addItem("0 or 2 (0 or 1 ring)");
mChoiceRingState.addItem(">=2 (any ring count)");
mChoiceRingState.addItem("2 (in 1 ring)");
mChoiceRingState.addItem("3 (bridge head; 2 rings)");
mChoiceRingState.addItem(">3 (in more than 2 rings)");
mDialog.add(mDialog.createLabel("Ring bonds:"), 1,7);
mDialog.add(mChoiceRingState, 3,7);
mChoiceSmallRingSize = mDialog.createComboBox();
mChoiceSmallRingSize.addItem("any");
mChoiceSmallRingSize.addItem("3 members");
mChoiceSmallRingSize.addItem("4 members");
mChoiceSmallRingSize.addItem("5 members");
mChoiceSmallRingSize.addItem("6 members");
mChoiceSmallRingSize.addItem("7 members");
mDialog.add(mDialog.createLabel("Smallest ring size:"), 1,9);
mDialog.add(mChoiceSmallRingSize, 3,9);
mChoiceRingSize = mDialog.createComboBox();
for (String option:RING_SIZE_OPTIONS)
mChoiceRingSize.addItem(option);
mDialog.add(mDialog.createLabel("Any ring size:"), 1,11);
mDialog.add(mChoiceRingSize, 3,11);
mChoiceCharge = mDialog.createComboBox();
mChoiceCharge.addItem("any");
mChoiceCharge.addItem("not charged");
mChoiceCharge.addItem("has negative charge");
mChoiceCharge.addItem("has positive charge");
mDialog.add(mDialog.createLabel("Charge:"), 1,13);
mDialog.add(mChoiceCharge, 3,13);
mChoiceNeighbours = mDialog.createComboBox();
mChoiceNeighbours.addItem("any");
mChoiceNeighbours.addItem("exactly 1");
mChoiceNeighbours.addItem("exactly 2");
mChoiceNeighbours.addItem("exactly 3");
mChoiceNeighbours.addItem("less than 3");
mChoiceNeighbours.addItem("less than 4");
mChoiceNeighbours.addItem("at least 1");
mChoiceNeighbours.addItem("at least 2");
mChoiceNeighbours.addItem("at least 3");
mChoiceNeighbours.addItem("at least 4");
mChoiceNeighbours.addItem("1 or 2");
mChoiceNeighbours.addItem("1,2, or 3");
mChoiceNeighbours.addItem("2 or 3");
mDialog.add(mDialog.createLabel("Non-H neighbours:"), 1,15);
mDialog.add(mChoiceNeighbours, 3,15);
mChoiceENeighbours = mDialog.createComboBox();
mChoiceENeighbours.addItem("any");
mChoiceENeighbours.addItem("exactly 0");
mChoiceENeighbours.addItem("exactly 1");
mChoiceENeighbours.addItem("exactly 2");
mChoiceENeighbours.addItem("exactly 3");
mChoiceENeighbours.addItem("less than 2");
mChoiceENeighbours.addItem("less than 3");
mChoiceENeighbours.addItem("less than 4");
mChoiceENeighbours.addItem("at least 1");
mChoiceENeighbours.addItem("at least 2");
mChoiceENeighbours.addItem("at least 3");
mChoiceENeighbours.addItem("at least 4");
mChoiceENeighbours.addItem("1 or 2");
mChoiceENeighbours.addItem("1,2, or 3");
mChoiceENeighbours.addItem("2 or 3");
mDialog.add(mDialog.createLabel("Electroneg. neighbours:"), 1,17);
mDialog.add(mChoiceENeighbours, 3,17);
mChoiceHydrogen = mDialog.createComboBox();
mChoiceHydrogen.addItem("any");
mChoiceHydrogen.addItem("none");
mChoiceHydrogen.addItem("exactly 1");
mChoiceHydrogen.addItem("exactly 2");
mChoiceHydrogen.addItem("at least 1");
mChoiceHydrogen.addItem("at least 2");
mChoiceHydrogen.addItem("at least 3");
mChoiceHydrogen.addItem("less than 2");
mChoiceHydrogen.addItem("less than 3");
mChoiceHydrogen.addItem("1 or 2");
mDialog.add(mDialog.createLabel("Hydrogen count:"), 1,19);
mDialog.add(mChoiceHydrogen, 3,19);
mChoicePi = mDialog.createComboBox();
mChoicePi.addItem("any");
mChoicePi.addItem("none");
mChoicePi.addItem("exactly 1");
mChoicePi.addItem("exactly 2");
mChoicePi.addItem("at least 1");
mDialog.add(mDialog.createLabel("Pi-electron count:"), 1,21);
mDialog.add(mChoicePi,3,21);
mCBBlocked = mDialog.createCheckBox("prohibit further substitution");
mCBBlocked.addEventConsumer(this);
mDialog.add(mCBBlocked, 1,23,3,23);
mCBSubstituted = mDialog.createCheckBox("require further substitution");
mCBSubstituted.addEventConsumer(this);
mDialog.add(mCBSubstituted, 1,25,3,25);
mChoiceStereoCenter = mDialog.createComboBox();
mChoiceStereoCenter.addItem("any");
mChoiceStereoCenter.addItem("is a stereo center");
mChoiceStereoCenter.addItem("is not a stereo center");
mDialog.add(mDialog.createLabel("Stereo center:"), 1,27);
mDialog.add(mChoiceStereoCenter,3,27);
mCBMatchStereo = mDialog.createCheckBox("match stereo center");
mDialog.add(mCBMatchStereo, 1,29,3,29);
mCBExcludeGroup = mDialog.createCheckBox("is part of exclude group");
mDialog.add(mCBExcludeGroup, 1,31,3,31);
if (includeReactionHints) {
mDialog.add(mDialog.createLabel("Stereo center hint for product:"), 1,33,3,33);
mChoiceReactionParityHint = mDialog.createComboBox();
mChoiceReactionParityHint.addItem("Copy from generic product");
mChoiceReactionParityHint.addItem("Keep reactant configuration");
mChoiceReactionParityHint.addItem("Invert reactant configuration");
mChoiceReactionParityHint.addItem("Racemise configuration");
mDialog.add(mChoiceReactionParityHint, 1,35,3,35);
}
mMol.ensureHelperArrays(Molecule.cHelperCIP);
setInitialStates();
}
@Override
public void eventHappened(GenericActionEvent e) {
if (e.getWhat() == GenericActionEvent.WHAT_OK) {
setQueryFeatures();
mOKSelected = true;
mDialog.disposeDialog();
}
else if (e.getWhat() == GenericActionEvent.WHAT_CANCEL) {
mDialog.disposeDialog();
}
else if (e.getSource() == mCBAny) {
if (e.getValue() == 1) {
mTFAtomList.setText("");
mLabelAtomList.setText("Excluded atoms:");
}
else {
mTFAtomList.setText(mMol.getAtomLabel(mAtom));
mLabelAtomList.setText("Allowed atoms:");
}
}
else if (e.getSource() == mCBBlocked) {
mCBSubstituted.setSelected(false);
mChoiceNeighbours.setSelectedIndex(0);
mChoiceENeighbours.setSelectedIndex(0);
}
else if (e.getSource() == mCBSubstituted)
mCBBlocked.setSelected(false);
}
private void setInitialStates() {
long 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));
long aromState = queryFeatures & Molecule.cAtomQFAromState;
if ((aromState & Molecule.cAtomQFHeteroAromatic) != 0)
mChoiceArom.setSelectedIndex(2);
else if (aromState == Molecule.cAtomQFAromatic)
mChoiceArom.setSelectedIndex(1);
else if (aromState == Molecule.cAtomQFNotAromatic)
mChoiceArom.setSelectedIndex(3);
else
mChoiceArom.setSelectedIndex(0);
long ringState = queryFeatures & Molecule.cAtomQFRingState;
if (ringState == (Molecule.cAtomQFNot2RingBonds | Molecule.cAtomQFNot3RingBonds | Molecule.cAtomQFNot4RingBonds))
mChoiceRingState.setSelectedIndex(1);
else if (ringState == (Molecule.cAtomQFNot3RingBonds | Molecule.cAtomQFNot4RingBonds))
mChoiceRingState.setSelectedIndex(2);
else if (ringState == Molecule.cAtomQFNotChain)
mChoiceRingState.setSelectedIndex(3);
else if (ringState == (Molecule.cAtomQFNotChain | Molecule.cAtomQFNot3RingBonds | Molecule.cAtomQFNot4RingBonds))
mChoiceRingState.setSelectedIndex(4);
else if (ringState == (Molecule.cAtomQFNotChain | Molecule.cAtomQFNot2RingBonds | Molecule.cAtomQFNot4RingBonds))
mChoiceRingState.setSelectedIndex(5);
else if (ringState == (Molecule.cAtomQFNotChain | Molecule.cAtomQFNot2RingBonds | Molecule.cAtomQFNot3RingBonds))
mChoiceRingState.setSelectedIndex(6);
else
mChoiceRingState.setSelectedIndex(0);
int smallRingSize = (int)((queryFeatures & Molecule.cAtomQFSmallRingSize) >> Molecule.cAtomQFSmallRingSizeShift);
mChoiceSmallRingSize.setSelectedIndex((smallRingSize == 0) ? 0 : smallRingSize-2);
long ringSize = queryFeatures & Molecule.cAtomQFNewRingSize;
int index = -1;
for (int i=0; i=8");
mRingSizeCustomValue = ringSize;
mChoiceRingSize.addItem(customOption.toString());
mChoiceRingSize.setSelectedIndex(RING_SIZE_VALUES.length);
}
long neighbourFeatures = queryFeatures & Molecule.cAtomQFNeighbours;
if (neighbourFeatures == (Molecule.cAtomQFNeighbours & ~Molecule.cAtomQFNot1Neighbour))
mChoiceNeighbours.setSelectedIndex(1);
else if (neighbourFeatures == (Molecule.cAtomQFNeighbours & ~Molecule.cAtomQFNot2Neighbours))
mChoiceNeighbours.setSelectedIndex(2);
else if (neighbourFeatures == (Molecule.cAtomQFNeighbours & ~Molecule.cAtomQFNot3Neighbours))
mChoiceNeighbours.setSelectedIndex(3);
else if (neighbourFeatures == (Molecule.cAtomQFNot3Neighbours | Molecule.cAtomQFNot4Neighbours))
mChoiceNeighbours.setSelectedIndex(4);
else if (neighbourFeatures == Molecule.cAtomQFNot4Neighbours)
mChoiceNeighbours.setSelectedIndex(5);
else if (neighbourFeatures == Molecule.cAtomQFNot0Neighbours)
mChoiceNeighbours.setSelectedIndex(6);
else if (neighbourFeatures == (Molecule.cAtomQFNot0Neighbours | Molecule.cAtomQFNot1Neighbour))
mChoiceNeighbours.setSelectedIndex(7);
else if (neighbourFeatures == (Molecule.cAtomQFNot0Neighbours | Molecule.cAtomQFNot1Neighbour | Molecule.cAtomQFNot2Neighbours))
mChoiceNeighbours.setSelectedIndex(8);
else if (neighbourFeatures == (Molecule.cAtomQFNeighbours & ~Molecule.cAtomQFNot4Neighbours))
mChoiceNeighbours.setSelectedIndex(9);
else if (neighbourFeatures == (Molecule.cAtomQFNot0Neighbours | Molecule.cAtomQFNot3Neighbours | Molecule.cAtomQFNot4Neighbours))
mChoiceNeighbours.setSelectedIndex(10);
else if (neighbourFeatures == (Molecule.cAtomQFNot0Neighbours | Molecule.cAtomQFNot4Neighbours))
mChoiceNeighbours.setSelectedIndex(11);
else if (neighbourFeatures == (Molecule.cAtomQFNot0Neighbours | Molecule.cAtomQFNot1Neighbour | Molecule.cAtomQFNot4Neighbours))
mChoiceNeighbours.setSelectedIndex(12);
else
mChoiceNeighbours.setSelectedIndex(0);
long eNeighbourFeatures = queryFeatures & Molecule.cAtomQFENeighbours;
if (eNeighbourFeatures == (Molecule.cAtomQFENeighbours & ~Molecule.cAtomQFNot0ENeighbours))
mChoiceENeighbours.setSelectedIndex(1);
else if (eNeighbourFeatures == (Molecule.cAtomQFENeighbours & ~Molecule.cAtomQFNot1ENeighbour))
mChoiceENeighbours.setSelectedIndex(2);
else if (eNeighbourFeatures == (Molecule.cAtomQFENeighbours & ~Molecule.cAtomQFNot2ENeighbours))
mChoiceENeighbours.setSelectedIndex(3);
else if (eNeighbourFeatures == (Molecule.cAtomQFENeighbours & ~Molecule.cAtomQFNot3ENeighbours))
mChoiceENeighbours.setSelectedIndex(4);
else if (eNeighbourFeatures == (Molecule.cAtomQFNot2ENeighbours | Molecule.cAtomQFNot3ENeighbours | Molecule.cAtomQFNot4ENeighbours))
mChoiceENeighbours.setSelectedIndex(5);
else if (eNeighbourFeatures == (Molecule.cAtomQFNot3ENeighbours | Molecule.cAtomQFNot4ENeighbours))
mChoiceENeighbours.setSelectedIndex(6);
else if (eNeighbourFeatures == Molecule.cAtomQFNot4ENeighbours)
mChoiceENeighbours.setSelectedIndex(7);
else if (eNeighbourFeatures == Molecule.cAtomQFNot0ENeighbours)
mChoiceENeighbours.setSelectedIndex(8);
else if (eNeighbourFeatures == (Molecule.cAtomQFNot0ENeighbours | Molecule.cAtomQFNot1ENeighbour))
mChoiceENeighbours.setSelectedIndex(9);
else if (eNeighbourFeatures == (Molecule.cAtomQFNot0ENeighbours | Molecule.cAtomQFNot1ENeighbour | Molecule.cAtomQFNot2ENeighbours))
mChoiceENeighbours.setSelectedIndex(10);
else if (eNeighbourFeatures == (Molecule.cAtomQFENeighbours & ~Molecule.cAtomQFNot4ENeighbours))
mChoiceENeighbours.setSelectedIndex(11);
else if (eNeighbourFeatures == (Molecule.cAtomQFNot0ENeighbours | Molecule.cAtomQFNot3ENeighbours | Molecule.cAtomQFNot4ENeighbours))
mChoiceENeighbours.setSelectedIndex(12);
else if (eNeighbourFeatures == (Molecule.cAtomQFNot0ENeighbours | Molecule.cAtomQFNot4ENeighbours))
mChoiceENeighbours.setSelectedIndex(13);
else if (eNeighbourFeatures == (Molecule.cAtomQFNot0ENeighbours | Molecule.cAtomQFNot1ENeighbour | Molecule.cAtomQFNot4ENeighbours))
mChoiceENeighbours.setSelectedIndex(14);
else
mChoiceENeighbours.setSelectedIndex(0);
long chargeFeatures = queryFeatures & Molecule.cAtomQFCharge;
if (chargeFeatures == (Molecule.cAtomQFNotChargeNeg | Molecule.cAtomQFNotChargePos))
mChoiceCharge.setSelectedIndex(1);
else if (chargeFeatures == (Molecule.cAtomQFNotCharge0 | Molecule.cAtomQFNotChargePos))
mChoiceCharge.setSelectedIndex(2);
else if (chargeFeatures == (Molecule.cAtomQFNotCharge0 | Molecule.cAtomQFNotChargeNeg))
mChoiceCharge.setSelectedIndex(3);
else
mChoiceCharge.setSelectedIndex(0);
long hydrogenFeatures = queryFeatures & Molecule.cAtomQFHydrogen;
if (hydrogenFeatures == (Molecule.cAtomQFNot1Hydrogen | Molecule.cAtomQFNot2Hydrogen | Molecule.cAtomQFNot3Hydrogen))
mChoiceHydrogen.setSelectedIndex(1);
else if (hydrogenFeatures == (Molecule.cAtomQFNot0Hydrogen | Molecule.cAtomQFNot2Hydrogen | Molecule.cAtomQFNot3Hydrogen))
mChoiceHydrogen.setSelectedIndex(2);
else if (hydrogenFeatures == (Molecule.cAtomQFNot0Hydrogen | Molecule.cAtomQFNot1Hydrogen | Molecule.cAtomQFNot3Hydrogen))
mChoiceHydrogen.setSelectedIndex(3);
else if (hydrogenFeatures == Molecule.cAtomQFNot0Hydrogen)
mChoiceHydrogen.setSelectedIndex(4);
else if (hydrogenFeatures == (Molecule.cAtomQFNot0Hydrogen | Molecule.cAtomQFNot1Hydrogen))
mChoiceHydrogen.setSelectedIndex(5);
else if (hydrogenFeatures == (Molecule.cAtomQFNot0Hydrogen | Molecule.cAtomQFNot1Hydrogen | Molecule.cAtomQFNot2Hydrogen))
mChoiceHydrogen.setSelectedIndex(6);
else if (hydrogenFeatures == (Molecule.cAtomQFNot2Hydrogen | Molecule.cAtomQFNot3Hydrogen))
mChoiceHydrogen.setSelectedIndex(7);
else if (hydrogenFeatures == (Molecule.cAtomQFNot3Hydrogen))
mChoiceHydrogen.setSelectedIndex(8);
else if (hydrogenFeatures == (Molecule.cAtomQFNot0Hydrogen | Molecule.cAtomQFNot3Hydrogen))
mChoiceHydrogen.setSelectedIndex(9);
else
mChoiceHydrogen.setSelectedIndex(0);
long piFeatures = queryFeatures & Molecule.cAtomQFPiElectrons;
if (piFeatures == (Molecule.cAtomQFNot1PiElectron | Molecule.cAtomQFNot2PiElectrons))
mChoicePi.setSelectedIndex(1);
else if (piFeatures == (Molecule.cAtomQFNot0PiElectrons | Molecule.cAtomQFNot2PiElectrons))
mChoicePi.setSelectedIndex(2);
else if (piFeatures == (Molecule.cAtomQFNot0PiElectrons | Molecule.cAtomQFNot1PiElectron))
mChoicePi.setSelectedIndex(3);
else if (piFeatures == Molecule.cAtomQFNot0PiElectrons)
mChoicePi.setSelectedIndex(4);
else
mChoicePi.setSelectedIndex(0);
if ((queryFeatures & Molecule.cAtomQFNoMoreNeighbours) != 0)
mCBBlocked.setSelected(true);
if ((queryFeatures & Molecule.cAtomQFMoreNeighbours) != 0)
mCBSubstituted.setSelected(true);
long stereoFeatures = queryFeatures & Molecule.cAtomQFStereoState;
if (stereoFeatures == Molecule.cAtomQFIsStereo)
mChoiceStereoCenter.setSelectedIndex(1);
else if (stereoFeatures == Molecule.cAtomQFIsNotStereo)
mChoiceStereoCenter.setSelectedIndex(2);
else
mChoiceStereoCenter.setSelectedIndex(0);
if ((queryFeatures & Molecule.cAtomQFMatchStereo) != 0)
mCBMatchStereo.setSelected(true);
if ((queryFeatures & Molecule.cAtomQFExcludeGroup) != 0)
mCBExcludeGroup.setSelected(true);
if (mChoiceReactionParityHint != null) {
long rxnStereo = queryFeatures & Molecule.cAtomQFRxnParityHint;
if (rxnStereo == Molecule.cAtomQFRxnParityRetain)
mChoiceReactionParityHint.setSelectedIndex(1);
else if (rxnStereo == Molecule.cAtomQFRxnParityInvert)
mChoiceReactionParityHint.setSelectedIndex(2);
else if (rxnStereo == Molecule.cAtomQFRxnParityRacemize)
mChoiceReactionParityHint.setSelectedIndex(3);
else
mChoiceReactionParityHint.setSelectedIndex(0);
}
}
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;
switch (mChoiceStereoCenter.getSelectedIndex()) {
case 1: // is stereo center
queryFeatures |= Molecule.cAtomQFIsStereo;
break;
case 2: // is no stereo center
queryFeatures |= Molecule.cAtomQFIsNotStereo;
break;
}
if (mCBMatchStereo.isSelected())
queryFeatures |= Molecule.cAtomQFMatchStereo;
if (mCBExcludeGroup.isSelected())
queryFeatures |= Molecule.cAtomQFExcludeGroup;
if (mChoiceReactionParityHint != null) {
switch (mChoiceReactionParityHint.getSelectedIndex()) {
case 1:
queryFeatures |= Molecule.cAtomQFRxnParityRetain;
break;
case 2:
queryFeatures |= Molecule.cAtomQFRxnParityInvert;
break;
case 3:
queryFeatures |= Molecule.cAtomQFRxnParityRacemize;
break;
}
}
mMol.setAtomQueryFeature(atom, 0xFFFFFFFF, false);
mMol.setAtomQueryFeature(atom, queryFeatures, true);
}
private int[] createAtomList() {
int[] list = null;
String listString = mTFAtomList.getText().trim();
while (listString.length() != 0) {
String label;
int delimiterIndex = listString.indexOf(',');
if (delimiterIndex == -1) {
label = listString.trim();
listString = "";
}
else {
label = listString.substring(0, delimiterIndex).trim();
listString = listString.substring(delimiterIndex+1).trim();
}
// support and expand MDL halogen shortcut
if (label.equals("X")) {
if (listString.length() != 0)
listString = ",";
listString = listString.concat("F,Cl,Br,I");
continue;
}
int atomicNo = Molecule.getAtomicNoFromLabel(label);
if (atomicNo != 0) {
if (atomicNo == 1) {
mDialog.showMessage("'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