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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.dnd.ChemistryFlavors;
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.chem.reaction.ReactionEncoder;
import com.actelion.research.gui.clipboard.external.ChemDrawCDX;
import com.actelion.research.gui.dnd.MoleculeTransferable;
import com.actelion.research.gui.dnd.ReactionTransferable;
import com.actelion.research.gui.generic.GenericRectangle;
import com.actelion.research.gui.wmf.WMF;
import com.actelion.research.gui.wmf.WMFGraphics2D;
import com.actelion.research.util.Platform;
import com.actelion.research.util.Sketch;
import java.awt.*;
import java.awt.datatransfer.DataFlavor;
import java.awt.datatransfer.Transferable;
import java.io.*;
import java.util.ArrayList;
/**
* 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 one or more Molecule(s) from the Clipboard. On all platforms the first choice is a serialized StereoMolecule.
* Further supported formats on Windows are: MDLSK,MDLCT,MDL_MOL,CF_ENHMETAFILE with embedded sketch.
* If no supported format is found and the clipboard contains text, which can be interpreted as molfile, then the
* corresponding molecule is returned. If the clipboard contains one or multiple SMILES, IUPAC name(s) or idcode(s),
* then the corresponding molecule(s) is/are returned. These can be multiple if allowMultiple is true.
* Otherwise, if a StructureNameResolver is present, then it tries to interpret the name(s) and returns the
* corresponding molecules, which may be limited to a certain number.
* @return Molecule found or null if no molecule present on the clipboard
*/
@Override
public ArrayList pasteMolecules() {
return pasteMolecules(true, true, SmilesParser.SMARTS_MODE_GUESS);
}
/**
* Get one Molecule from the Clipboard. On all platforms the first choice is a serialized StereoMolecule.
* Further supported formats on Windows are: MDLSK,MDLCT,MDL_MOL,CF_ENHMETAFILE with embedded sketch.
* If no supported format is found and the clipboard contains text, which can be interpreted as molfile,
* SMILES (with SMARTS features), IUPAC name or idcode, then the corresponding molecule is returned.
* Otherwise, if a StructureNameResolver is present, then it tries to interpret the name.
* 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
*/
@Override
public StereoMolecule pasteMolecule() {
return pasteMolecule(true, SmilesParser.SMARTS_MODE_GUESS);
}
@Override
public StereoMolecule pasteMolecule(boolean prefer2D, int smartsMode) {
ArrayList molList = pasteMolecules(prefer2D, false, smartsMode);
return molList.size() == 0 ? null : molList.get(0);
}
/**
* Get one or more Molecule(s) from the Clipboard. On all platforms the first choice is a serialized StereoMolecule.
* Further supported formats on Windows are: MDLSK,MDLCT,MDL_MOL,CF_ENHMETAFILE with embedded sketch.
* If no supported format is found and the clipboard contains text, which can be interpreted as molfile, then the
* corresponding molecule is returned. If the clipboard contains one or multiple SMILES, IUPAC name(s) or idcode(s),
* then the corresponding molecule(s) is/are returned. These can be multiple if allowMultiple is true.
* Otherwise, if a StructureNameResolver is present, then it tries to interpret the name(s) and returns the
* corresponding molecules, which may be limited to a certain number.
* @param prefer2D if true and if the clipboard molecule has 3D coordinates, then new 2D-coords are invented
* @param allowMultiple whether multiple molecules may be generated from clipboard text, if no serialized mol or special molecule format present
* @param smartsMode SmilesParser.SMARTS_MODE for parsing strings as SMILES, i.e. how SMARTS features are considered
* @return list of molecules found or generated from SMILES, names, etc; empty list if no molecule present on the clipboard
*/
private ArrayList pasteMolecules(boolean prefer2D, boolean allowMultiple, int smartsMode) {
ArrayList molList = new ArrayList<>();
StereoMolecule mol = Platform.isWindows() ? pasteMoleculeWindowsNative(prefer2D) : pasteMoleculeLinux();
if (mol != null)
molList.add(mol);
if (molList.size() == 0) {
// get StringFlavor from clipboard and try parsing it as idcode, molfile, smiles, or (if NameResolver exists) as name
Transferable t = Toolkit.getDefaultToolkit().getSystemClipboard().getContents(null);
String text = null;
try {
text = (String)t.getTransferData(DataFlavor.stringFlavor);
}
catch (Exception ioe) {}
if (text != null) {
try {
mol = new MolfileParser().getCompactMolecule(text);
if (mol != null && mol.getAllAtoms() != 0)
molList.add(mol);
}
catch (Exception e) {}
ArrayList unresolvedNameList = null;
if (molList.size() == 0) {
boolean isFirstLine = true;
int column = -1; // in case we have a TAB-delimited table with '[idcode]' tags, use first tagged column
BufferedReader reader = new BufferedReader(new StringReader(text));
try {
String line = reader.readLine();
while (line != null) {
line = line.trim();
if (isFirstLine) {
String[] header = line.split("\\t");
for (int i=0; i();
unresolvedNameList.add(line);
}
line = reader.readLine();
}
}
catch (IOException ioe) {}
}
if (unresolvedNameList != null && unresolvedNameList.size() != 0) {
String[] idcodes = StructureNameResolver.resolveRemote(unresolvedNameList.toArray(new String[0]));
for (String idcode:idcodes) {
try {
mol = new IDCodeParser(prefer2D).getCompactMolecule(idcode);
if (mol != null && mol.getAllAtoms() != 0)
molList.add(mol);
} catch (Exception e) {}
}
}
}
}
if (prefer2D) {
for (StereoMolecule m:molList) {
if (m.is3D()) {
m.ensureHelperArrays(Molecule.cHelperParities); // to ensure stereo parities
new CoordinateInventor().invent(m);
}
}
}
System.out.println("returned mol(s): " + molList.size());
return molList;
}
private StereoMolecule pasteMoleculeWindowsNative(boolean prefer2D) {
byte[] buffer;
StereoMolecule mol = null;
if ((buffer = NativeClipboardAccessor.getClipboardData(NativeClipboardAccessor.NC_SERIALIZEMOLECULE)) != null) {
try {
ObjectInputStream is = new ObjectInputStream(new ByteArrayInputStream(buffer));
Object o = is.readObject();
if (o instanceof StereoMolecule) {
mol = (StereoMolecule) o;
}
is.close();
} catch (Exception e) {
e.printStackTrace();
System.out.println("Parsing NC_SERIALIZEMOLECULE during clipboard paste: Exception " + e);
}
}
System.out.println("Mol is " + mol);
if (mol == null) {
if ((buffer = NativeClipboardAccessor.getClipboardData(NativeClipboardAccessor.NC_CTAB)) != null
|| (buffer = NativeClipboardAccessor.getClipboardData(NativeClipboardAccessor.NC_MOLFILE)) != null) {
MolfileParser p = new MolfileParser();
mol = new StereoMolecule();
if (!p.parse(mol, new String(buffer))) {
mol = null;
System.out.println("Error Parsing CTAB during clipboard paste");
}
}
if (mol == null) {
if ((buffer = NativeClipboardAccessor.getClipboardData(NativeClipboardAccessor.NC_SKETCH)) != null
|| (buffer = NativeClipboardAccessor.getClipboardData(NativeClipboardAccessor.NC_EMBEDDEDSKETCH)) != null) {
try {
mol = new StereoMolecule();
if (!Sketch.createMolFromSketchBuffer(mol, buffer)) {
mol = null;
}
} catch (IOException e) {
mol = null;
e.printStackTrace();
System.out.println("Parsing NC_SKETCH during clipboard paste: Exception " + e);
}
}
}
}
String clipboardText = null;
if (mol == null) {
if ((buffer = NativeClipboardAccessor.getClipboardData(NativeClipboardAccessor.NC_IDCODE)) != null) {
clipboardText = new String(buffer);
try {
mol = new StereoMolecule();
IDCodeParser parser = new IDCodeParser(prefer2D);
parser.parse(mol,buffer);
if (mol.getAllAtoms() == 0)
mol = null;
else
System.out.printf("NC_IDCODE '%s' successfully interpreted as idcode\n",clipboardText);
} catch (Exception e) {
e.printStackTrace();
System.out.printf("NC_IDCODE '%s' could not be parsed: "+e+"\n", clipboardText);
mol = null;
}
}
}
return mol;
}
private StereoMolecule pasteMoleculeLinux() {
try {
Transferable t = Toolkit.getDefaultToolkit().getSystemClipboard().getContents(null);
return (StereoMolecule)t.getTransferData(ChemistryFlavors.DF_SERIALIZED_MOLECULE);
} catch (Exception e) {}
return null;
}
/**
* Get a Reaction from the Clipboard
*
* @return Reaction or null if no reaction present
*/
public Reaction pasteReaction() {
Reaction rxn = Platform.isWindows() ? pasteReactionWindowsNative() : pasteReactionLinux();
if (rxn == null) {
// get StringFlavor from clipboard and try parsing it as rxn-idcode, rxn-file, or reaction-smiles
Transferable t = Toolkit.getDefaultToolkit().getSystemClipboard().getContents(null);
String text = null;
try {
text = (String)t.getTransferData(DataFlavor.stringFlavor);
}
catch (Exception ioe) {}
if (text != null) {
try {
rxn = ReactionEncoder.decode(text, true);
if (rxn != null && rxn.isEmpty())
rxn = null;
}
catch (Exception e) {}
if (rxn == null) {
try {
rxn = new RXNFileParser().getReaction(text);
if (rxn != null && rxn.isEmpty())
rxn = null;
}
catch (Exception e) {}
}
if (rxn == null) {
try {
rxn = new SmilesParser().parseReaction(text);
if (rxn != null && rxn.isEmpty())
rxn = null;
}
catch (Exception e) {}
}
}
}
return rxn;
}
public Reaction pasteReactionWindowsNative() {
byte[] buffer;
Reaction rxn = null;
if ((buffer = NativeClipboardAccessor.getClipboardData(NativeClipboardAccessor.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("ClipboardHandler.pasteReaction(): Exception " + e);
}
} else if ((buffer = NativeClipboardAccessor.getClipboardData(NativeClipboardAccessor.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 = NativeClipboardAccessor.getClipboardData(NativeClipboardAccessor.NC_SKETCH)) != null) {
try {
rxn = new Reaction();
if (!Sketch.createReactionFromSketchBuffer(rxn, buffer)) {
rxn = null;
}
} catch (IOException e) {
rxn = null;
}
}
return rxn;
}
private Reaction pasteReactionLinux() {
try {
Transferable t = Toolkit.getDefaultToolkit().getSystemClipboard().getContents(null);
return (Reaction)t.getTransferData(ChemistryFlavors.DF_SERIALIZED_REACTION);
} catch (Exception e) {}
return null;
}
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) {
if (!Platform.isWindows()) {
MoleculeTransferable transferable = new MoleculeTransferable(mol);
Toolkit.getDefaultToolkit().getSystemClipboard().setContents(transferable, transferable);
return true;
}
// For now we keep the old handling for Windows...
boolean ok = false;
try {
StereoMolecule m = mol.getCompactCopy();
for (int atom=0; atom