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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.Molecule;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.gui.generic.*;
import javax.swing.*;
public class CustomAtomDialogBuilder implements GenericEventListener {
private static final String[] RADICAL_STATES = { "None", "One electron (duplet)", "Two electrons (triplet)", "Two electrons (singulet)" };
private GenericEditorArea mEditorArea;
private GenericDialog mDialog;
private StereoMolecule mMol;
private int mAtom,mOldAtomicNo,mOldAtomMass,mOldAtomValence,mOldAtomRadical;
private String mOldCustomLabel;
private GenericTextField mTextFieldLabel,mTextFieldMass,mTextFieldValence;
private GenericComboBox mComboBoxRadical;
private boolean mOKSelected;
public CustomAtomDialogBuilder(GenericUIHelper dialogHelper, GenericEditorArea editorArea,
int atomicNo, int mass, int valence, int radical, String label) {
mDialog = dialogHelper.createDialog("Atom Properties", this);
mEditorArea = editorArea;
mAtom = -1;
mOldAtomicNo = atomicNo;
mOldAtomMass = mass;
mOldAtomValence = valence;
mOldAtomRadical = radical;
mOldCustomLabel = label;
build();
}
public CustomAtomDialogBuilder(GenericUIHelper dialogHelper, GenericEditorArea editorArea, StereoMolecule mol, int atom) {
mDialog = dialogHelper.createDialog("Atom Properties", this);
mEditorArea = editorArea;
mMol = mol;
mAtom = atom;
mOldAtomicNo = mMol.getAtomicNo(atom);
mOldAtomMass = mMol.getAtomMass(atom);
mOldAtomValence = mMol.getAtomAbnormalValence(atom);
mOldAtomRadical = mMol.getAtomRadical(atom);
mOldCustomLabel = mMol.getAtomCustomLabel(atom);
build();
}
/**
* @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() {
int[] hLayout = {8, GenericDialog.PREFERRED, 8, GenericDialog.PREFERRED, 8 };
int[] vLayout = {8, GenericDialog.PREFERRED, 4, GenericDialog.PREFERRED,
12, GenericDialog.PREFERRED, 4, GenericDialog.PREFERRED,
12, GenericDialog.PREFERRED, 4, GenericDialog.PREFERRED,
12, GenericDialog.PREFERRED, 8};
mDialog.setLayout(hLayout, vLayout);
mTextFieldLabel = mDialog.createTextField(1,1);
mTextFieldLabel.addEventConsumer(this);
mDialog.add(mDialog.createLabel("Atom Label:"), 1,1);
mDialog.add(mTextFieldLabel, 3,1);
mDialog.add(mDialog.createLabel("(examples: 'D', 'Li', 'Cys', 'R12', 'R3@C')"), 1,3,3,3);
mTextFieldMass = mDialog.createTextField(1,1);
mTextFieldMass.addEventConsumer(this);
mDialog.add(mDialog.createLabel("Atom Mass:"), 1,5);
mDialog.add(mTextFieldMass, 3,5);
mDialog.add(mDialog.createLabel("(empty for natural abundance)"), 1,7,3,7);
mTextFieldValence = mDialog.createTextField(1,1);
mTextFieldValence.addEventConsumer(this);
mDialog.add(mDialog.createLabel("Abnormal Valence:"), 1,9);
mDialog.add(mTextFieldValence, 3,9);
mDialog.add(mDialog.createLabel("(empty for default valence)"), 1,11,3,11);
if (mAtom == -1) {
String label = Molecule.cAtomLabel[mOldAtomicNo];
mTextFieldLabel.setText(mOldCustomLabel == null ? label : mOldCustomLabel+"@"+label);
if (mOldAtomMass != 0)
mTextFieldMass.setText(""+mOldAtomMass);
if (mOldAtomValence != -1)
mTextFieldValence.setText(""+mOldAtomValence);
}
else {
String label = mMol.getAtomLabel(mAtom);
String customLabel = mMol.getAtomCustomLabel(mAtom);
mTextFieldLabel.setText(customLabel == null ? label : customLabel+"@"+label);
if (mMol.getAtomMass(mAtom) != 0)
mTextFieldMass.setText(""+mMol.getAtomMass(mAtom));
if (mMol.getAtomAbnormalValence(mAtom) != -1)
mTextFieldValence.setText(""+mMol.getAtomAbnormalValence(mAtom));
}
mComboBoxRadical = mDialog.createComboBox();
for (String s:RADICAL_STATES)
mComboBoxRadical.addItem(s);
int state = (mAtom == -1) ? mOldAtomRadical : mMol.getAtomRadical(mAtom);
mComboBoxRadical.setSelectedIndex(state == Molecule.cAtomRadicalStateD ? 1 :
state == Molecule.cAtomRadicalStateT ? 2 :
state == Molecule.cAtomRadicalStateS ? 3 : 0);
mDialog.add(mDialog.createLabel("Radical State:"), 1,13);
mDialog.add(mComboBoxRadical, 3,13);
}
@Override
public void eventHappened(GenericActionEvent e) {
if (e.getSource() instanceof JTextField) {
processAtomLabel(false);
}
else if (e.getWhat() == GenericActionEvent.WHAT_CANCEL) {
if (mAtom != -1) {
mMol.setAtomicNo(mAtom, mOldAtomicNo);
mMol.setAtomMass(mAtom, mOldAtomMass);
mMol.setAtomAbnormalValence(mAtom, mOldAtomValence);
mMol.setAtomRadical(mAtom, mOldAtomRadical);
mMol.setAtomCustomLabel(mAtom, mOldCustomLabel);
}
mDialog.disposeDialog();
}
else if (e.getWhat() == GenericActionEvent.WHAT_OK) {
processAtomLabel(true);
mDialog.disposeDialog();
}
}
private void processAtomLabel(boolean updateDefault) {
String text = mTextFieldLabel.getText();
String customLabel = null;
if (text.length() != 0) {
int index = text.indexOf('@');
if (index != -1) {
customLabel = text.substring(0, index);
text = text.substring(index+1);
}
}
if (text.length() != 0) {
int atomicNo = Molecule.getAtomicNoFromLabel(text, mEditorArea.getAllowedPseudoAtoms());
if (atomicNo != 0 || text.equals("?")) {
int mass = 0;
if (mTextFieldMass.getText().length() != 0) {
try {
mass = Integer.parseInt(mTextFieldMass.getText());
if (mass < Molecule.cRoundedMass[atomicNo] - 18
|| mass > Molecule.cRoundedMass[atomicNo] + 12) {
mDialog.showMessage("Your mass is out of range!");
return;
}
}
catch (NumberFormatException nfe) {
mDialog.showMessage("Your mass is not a number!");
return;
}
}
int valence = -1;
if (mTextFieldValence.getText().length() != 0) {
try {
valence = Integer.parseInt(mTextFieldValence.getText());
if (valence < 0 || valence > 15) {
mDialog.showMessage("Your valence is out of range!");
return;
}
}
catch (NumberFormatException nfe) {
mDialog.showMessage("Your valence is not a number!");
return;
}
}
int radical = mComboBoxRadical.getSelectedIndex() == 1 ? Molecule.cAtomRadicalStateD :
mComboBoxRadical.getSelectedIndex() == 2 ? Molecule.cAtomRadicalStateT :
mComboBoxRadical.getSelectedIndex() == 3 ? Molecule.cAtomRadicalStateS : 0;
// set the current property set for the custom atom
if (updateDefault)
mEditorArea.setCustomAtom(atomicNo, mass, valence, radical,customLabel);
if (mAtom != -1) {
mMol.changeAtom(mAtom, atomicNo, mass, valence, radical);
mMol.setAtomCustomLabel(mAtom, customLabel);
}
mOKSelected = true;
mDialog.disposeDialog();
}
}
}
}