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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.clipboard;
import com.actelion.research.chem.*;
import com.actelion.research.chem.coords.CoordinateInventor;
import com.actelion.research.chem.io.RXNFileCreator;
import com.actelion.research.chem.io.RXNFileParser;
import com.actelion.research.chem.name.StructureNameResolver;
import com.actelion.research.chem.reaction.Reaction;
import com.actelion.research.gui.clipboard.external.ChemDrawCDX;
import com.actelion.research.gui.wmf.WMF;
import com.actelion.research.gui.wmf.WMFGraphics2D;
import com.actelion.research.util.Sketch;
import java.awt.*;
import java.awt.datatransfer.DataFlavor;
import java.awt.datatransfer.Transferable;
import java.awt.geom.Rectangle2D;
import java.io.*;
/**
* Title: Actelion Library
* Description: Actelion Java Library
* Copyright: Copyright (c) 2002-2003
* Company: Actelion Ltd
*
* @author Thomas Sander, Christian Rufener
* @version 1.0
*/
public class ClipboardHandler implements IClipboardHandler
{
private static final byte MDLSK[] = {(byte) 'M', (byte) 'D', (byte) 'L', (byte) 'S', (byte) 'K', 0, 0};
/**
* Get a Molecule from the Clipboard. The supported formats are: MDLSK,MDLCT,MDL_MOL,CF_ENHMETAFILE with embedded sketch
* If the clipboard molecule has 3D coordinates, then new 2D-coords are invented and used instead.
*
* @return Molecule found or null if no molecule present on the clipboard
*/
public StereoMolecule pasteMolecule()
{
return pasteMolecule(true);
}
/**
* Get a Molecule from the Clipboard. The supported formats are: MDLSK,MDLCT,MDL_MOL,CF_ENHMETAFILE with embedded sketch
*
* @param prefer2D if true and if the clipboard molecule has 3D coordinates, then new 2D-coords are invented
* @return Molecule found or null if no molecule present on the clipboard
*/
public StereoMolecule pasteMolecule(boolean prefer2D)
{
byte[] buffer = null;
StereoMolecule mol = null;
if ((buffer = NativeClipboardHandler.getClipboardData(NativeClipboardHandler.NC_SERIALIZEMOLECULE)) != null) {
try {
ObjectInputStream is = new ObjectInputStream(new ByteArrayInputStream(buffer));
Object o = is.readObject();
System.out.println("Object read from Bytearray input " + o);
if (o instanceof StereoMolecule) {
mol = (StereoMolecule) o;
}
is.close();
} catch (Exception e) {
e.printStackTrace();
System.out.println("NativeClipboardAccessor.pasteMolecule(): Exception " + e);
}
}
System.out.println("Mol is " + mol);
if (mol == null) {
if ((buffer = NativeClipboardHandler.getClipboardData(NativeClipboardHandler.NC_CTAB)) != null || (buffer = NativeClipboardHandler.getClipboardData(NativeClipboardHandler.NC_MOLFILE)) != null) {
MolfileParser p = new MolfileParser();
mol = new StereoMolecule();
if (!p.parse(mol, new String(buffer))) {
mol = null;
System.err.println("Error Parsing CTAB during clipboard paste");
}
}
if (mol == null) {
if ((buffer = NativeClipboardHandler.getClipboardData(NativeClipboardHandler.NC_SKETCH)) != null || (buffer = NativeClipboardHandler.getClipboardData(NativeClipboardHandler.NC_EMBEDDEDSKETCH)) != null) {
try {
mol = new StereoMolecule();
if (!Sketch.createMolFromSketchBuffer(mol, buffer)) {
mol = null;
}
} catch (IOException e) {
mol = null;
e.printStackTrace();
System.out.println("NativeClipboardAccessor.pasteMolecule(): Exception " + e);
}
}
}
}
String clipboardText = null;
if (mol == null) {
if ((buffer = NativeClipboardHandler.getClipboardData(NativeClipboardHandler.NC_IDCODE)) != null) {
clipboardText = new String(buffer);
try {
mol = new StereoMolecule();
IDCodeParser parser = new IDCodeParser(prefer2D);
System.out.printf("Pasted string '%s'\n",clipboardText);
parser.parse(mol,buffer);
if (mol.getAllAtoms() == 0)
mol = null;
} catch (Exception e) {
mol = null;
System.out.println("NativeClipboardAccessor.pasteMolecule(): Exception " + e);
}
}
}
if (mol == null) {
// get StringFlavor from clipboard and try parsing it as molfile, smiles, or (if NameResolver exists) as name
if (clipboardText == null) {
Transferable t = Toolkit.getDefaultToolkit().getSystemClipboard().getContents(null);
try {
Object o = t.getTransferData(DataFlavor.stringFlavor);
if (o != null)
clipboardText = o.toString();
}
catch (Exception ioe) {}
}
if (clipboardText != null) {
mol = new MolfileParser().getCompactMolecule(clipboardText);
if (mol == null) {
mol = new StereoMolecule();
try {
new SmilesParser().parse(mol, clipboardText);
}
catch (Exception e) {
mol = null;
}
}
if (mol == null)
mol = StructureNameResolver.resolve(clipboardText);
}
}
if (prefer2D && mol != null && is3DMolecule(mol)) {
mol.ensureHelperArrays(Molecule.cHelperParities); // to ensure stereo parities
new CoordinateInventor().invent(mol);
// mol.setStereoBondsFromParity(); not needed anymore
}
System.out.println("returned Mol is " + mol);
return mol;
}
/**
* Get a Reaction from the Clipboard
*
* @return Reaction or null if no reaction present
*/
public Reaction pasteReaction()
{
byte[] buffer = null;
Reaction rxn = null;
if ((buffer = NativeClipboardHandler.getClipboardData(NativeClipboardHandler.NC_SERIALIZEREACTION)) != null) {
try {
ObjectInputStream is = new ObjectInputStream(new ByteArrayInputStream(buffer));
Object o = is.readObject();
if (o instanceof Reaction) {
rxn = (Reaction) o;
}
is.close();
} catch (Exception e) {
e.printStackTrace();
System.out.println("NativeClipboardAccessor.pasteReaction(): Exception " + e);
}
} else if ((buffer = NativeClipboardHandler.getClipboardData(NativeClipboardHandler.NC_CTAB)) != null) {
RXNFileParser p = new RXNFileParser();
rxn = new Reaction();
try {
if (!p.parse(rxn, new String(buffer)))
rxn = null;
} catch (Exception e) {
System.err.println("Error parsing Reaction Buffer " + e);
rxn = null;
}
} else if ((buffer = NativeClipboardHandler.getClipboardData(NativeClipboardHandler.NC_SKETCH)) != null) {
try {
rxn = new Reaction();
if (!Sketch.createReactionFromSketchBuffer(rxn, buffer)) {
rxn = null;
}
} catch (IOException e) {
rxn = null;
}
}
return rxn;
}
public boolean copyMolecule(String molfile)
{
StereoMolecule m = new StereoMolecule();
MolfileParser p = new MolfileParser();
p.parse(m, molfile);
return copyMolecule(m);
}
/**
* Copies a molecule to the clipboard in various formats:
* ENHMETAFILE with an embedded sketch
* MDLSK Sketch
* MDLCT MDL molfile
*/
public boolean copyMolecule(StereoMolecule mol)
{
boolean ok = false;
try {
StereoMolecule m = mol.getCompactCopy();
for (int atom=0; atom© 2015 - 2025 Weber Informatics LLC | Privacy Policy