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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.chem.io;
import com.actelion.research.chem.Canonizer;
import com.actelion.research.chem.MolfileParser;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.reaction.Reaction;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
public abstract class CompoundFileHelper {
public static final int cFileTypeMask = 0x0003FFFF;
public static final int cFileTypeDataWarrior = 0x00000001;
public static final int cFileTypeDataWarriorTemplate = 0x00000002;
public static final int cFileTypeDataWarriorQuery = 0x00000004;
public static final int cFileTypeDataWarriorMacro = 0x00000008;
public static final int cFileTypeTextTabDelimited = 0x00000010;
public static final int cFileTypeTextCommaSeparated = 0x00000020;
public static final int cFileTypeText = cFileTypeTextTabDelimited | cFileTypeTextCommaSeparated;
public static final int cFileTypeSDV3 = 0x00000040;
public static final int cFileTypeSDV2 = 0x00000080;
public static final int cFileTypeSD = cFileTypeSDV3 | cFileTypeSDV2;
public static final int cFileTypeDataWarriorCompatibleData = cFileTypeDataWarrior | cFileTypeText | cFileTypeSD;
public static final int cFileTypeDataWarriorTemplateContaining = cFileTypeDataWarrior | cFileTypeDataWarriorQuery | cFileTypeDataWarriorTemplate;
public static final int cFileTypeRXN = 0x00000100;
public static final int cFileTypeSOM = 0x00000200;
public static final int cFileTypeJPG = 0x00000400;
public static final int cFileTypeGIF = 0x00000800;
public static final int cFileTypePNG = 0x00001000;
public static final int cFileTypeSVG = 0x00002000;
public static final int cFileTypePictureFile = cFileTypeJPG | cFileTypeGIF | cFileTypePNG | cFileTypeSVG;
public static final int cFileTypeRDV3 = 0x00004000;
public static final int cFileTypeRDV2 = 0x00008000;
public static final int cFileTypeRD = cFileTypeRDV3 | cFileTypeRDV2;
public static final int cFileTypeMOL = 0x00010000;
public static final int cFileTypePDB = 0x00020000;
public static final int cFileTypeUnknown = -1;
public static final int cFileTypeDirectory = -2;
private static File sCurrentDirectory;
private int mRecordCount,mErrorCount;
public abstract String selectOption(String message, String title, String[] option);
public abstract File selectFileToOpen(String title, int filetypes);
public abstract String selectFileToSave(String title, int filetype, String newFileName);
public abstract void showMessage(String message);
public static File getCurrentDirectory() {
return sCurrentDirectory;
}
public static void setCurrentDirectory(File d) {
sCurrentDirectory = d;
}
public ArrayList readStructuresFromFile(boolean readIdentifier) {
File file = selectFileToOpen("Please select substance file",
CompoundFileHelper.cFileTypeMOL
| CompoundFileHelper.cFileTypeSD
| CompoundFileHelper.cFileTypeDataWarrior);
return readStructuresFromFile(file, readIdentifier);
}
public ArrayList readIDCodesFromFile() {
File file = selectFileToOpen("Please select substance file",
CompoundFileHelper.cFileTypeMOL
| CompoundFileHelper.cFileTypeSD
| CompoundFileHelper.cFileTypeDataWarrior);
return readIDCodesFromFile(file);
}
public ArrayList readStructuresFromFile(File file, boolean readIdentifier) {
if (file == null)
return null;
ArrayList moleculeList = new ArrayList();
readChemObjectsFromFile(file, moleculeList, null, null, readIdentifier, false);
return moleculeList;
}
/**
* Reads all compounds as idcode list from the given file.
* @param file SD- or DataWarrior file
* @return
*/
public ArrayList readIDCodesFromFile(File file) {
if (file == null)
return null;
ArrayList idcodeList = new ArrayList();
readChemObjectsFromFile(file, null, idcodeList, null, false, false);
return idcodeList;
}
/**
* Reads all compounds as idcode list with identifiers from the given file.
* Therefore, it asks for an identifier column.
* @param file if null the user is asked for a file
* @param readIDCoords if true, then the id-coords are SPACE delimited attached to the idcode
* @return list of String[2] with idcode (index 0) and molecule name (index 1)
*/
public ArrayList readIDCodesWithNamesFromFile(File file, boolean readIDCoords) {
if (file == null)
file = selectFileToOpen("Please select substance file",
CompoundFileHelper.cFileTypeMOL
| CompoundFileHelper.cFileTypeSD
| CompoundFileHelper.cFileTypeDataWarrior);
if (file == null)
return null;
ArrayList idcodeWithIDList = new ArrayList();
readChemObjectsFromFile(file, null, null, idcodeWithIDList, false, readIDCoords);
return idcodeWithIDList;
}
private void readChemObjectsFromFile(File file,
ArrayList moleculeList,
ArrayList idcodeList,
ArrayList idcodeWithIDList,
boolean readIdentifier, boolean readIDCoords) {
mRecordCount = 0;
mErrorCount = 0;
String filename = file.getName();
int index = filename.indexOf('.');
String extention = (index == -1) ? "" : filename.substring(index).toLowerCase();
if (extention.equals(".mol")) {
MolfileParser parser = new MolfileParser();
StereoMolecule mol = parser.getCompactMolecule(file);
if (moleculeList != null)
moleculeList.add(mol);
if (idcodeList != null || idcodeWithIDList != null) {
Canonizer canonizer = new Canonizer(mol);
String idcode = canonizer.getIDCode();
String coords = canonizer.getEncodedCoordinates();
if (idcode != null && coords.length() != 0 && readIDCoords)
idcode = idcode+" "+coords;
if (idcodeList != null)
idcodeList.add(idcode);
if (idcodeWithIDList != null) {
String[] idcodeWithID = new String[2];
idcodeWithID[0] = idcode;
idcodeWithID[1] = mol.getName();
idcodeWithIDList.add(idcodeWithID);
}
}
return;
}
CompoundFileParser parser = (extention.equals(".sdf")) ?
new SDFileParser(file)
: (extention.equals(".dwar")) ?
new DWARFileParser(file)
: (extention.equals(".ode")) ?
new ODEFileParser(file) : null;
// If we create molecules,
// then we might set the name field with the proper identifier
int indexOfID = -1;
if (idcodeWithIDList != null || readIdentifier) {
String[] fieldNames = parser.getFieldNames();
if (fieldNames != null && fieldNames.length != 0) {
String id = selectOption("Select compound name or identifier", filename, fieldNames);
if (id != null)
for (int i=0; i getExtensionList(int fileTypes) {
ArrayList list = new ArrayList();
int type = 0x00000001;
while ((type & cFileTypeMask) != 0) {
if ((type & fileTypes) != 0) {
String extension = getExtension(type);
if (extension.length() != 0 && !list.contains(extension))
list.add(extension);
}
type <<= 1;
}
return list;
}
/**
* @param filetype
* @return file extension including the dot
*/
public static String getExtension(int filetype) {
String extension = "";
switch (filetype) {
case cFileTypeDataWarrior:
extension = ".dwar";
break;
case cFileTypeDataWarriorQuery:
extension = ".dwaq";
break;
case cFileTypeDataWarriorTemplate:
extension = ".dwat";
break;
case cFileTypeDataWarriorMacro:
extension = ".dwam";
break;
case cFileTypeTextTabDelimited:
extension = ".txt";
break;
case cFileTypeTextCommaSeparated:
extension = ".csv";
break;
case cFileTypeSD:
case cFileTypeSDV2:
case cFileTypeSDV3:
extension = ".sdf";
break;
case cFileTypeRD:
case cFileTypeRDV2:
case cFileTypeRDV3:
extension = ".rdf";
break;
case cFileTypeRXN:
extension = ".rxn";
break;
case cFileTypeSOM:
extension = ".dwas";
break;
case cFileTypeJPG:
extension = ".jpeg";
break;
case cFileTypeGIF:
extension = ".gif";
break;
case cFileTypePNG:
extension = ".png";
break;
case cFileTypeSVG:
extension = ".svg";
break;
case cFileTypeMOL:
extension = ".mol";
break;
case cFileTypePDB:
extension = ".pdb";
break;
}
return extension;
}
public void saveRXNFile(Reaction rxn) {
String fileName = selectFileToSave("Select reaction file", cFileTypeRXN, "Untitled Reaction");
if (fileName != null) {
String extension = ".rxn";
int dotIndex = fileName.lastIndexOf('.');
int slashIndex = fileName.lastIndexOf(File.separator);
if (dotIndex == -1
|| dotIndex < slashIndex)
fileName = fileName.concat(extension);
else if (!fileName.substring(dotIndex).equalsIgnoreCase(extension)) {
showMessage("uncompatible file name extension.");
return;
}
try {
BufferedWriter theWriter = new BufferedWriter(new FileWriter(new File(fileName)));
new RXNFileCreator(rxn).writeRXNfile(theWriter);
theWriter.close();
}
catch (IOException e) {
showMessage("IOException: "+e);
}
}
}
}
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