package org.openscience.cdk.applications;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.Writer;
import java.lang.reflect.Constructor;
import java.util.List;
import java.util.Properties;
import java.util.Vector;
import javax.vecmath.Vector2d;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.OptionBuilder;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.cli.PosixParser;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.config.AtomTypeFactory;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.rebond.RebondTool;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IChemSequence;
import org.openscience.cdk.interfaces.ICrystal;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.interfaces.IPseudoAtom;
import org.openscience.cdk.io.CDKSourceCodeWriter;
import org.openscience.cdk.io.HINWriter;
import org.openscience.cdk.io.IChemObjectIO;
import org.openscience.cdk.io.IChemObjectReader;
import org.openscience.cdk.io.IChemObjectWriter;
import org.openscience.cdk.io.MDLWriter;
import org.openscience.cdk.io.PDBWriter;
import org.openscience.cdk.io.ReaderFactory;
import org.openscience.cdk.io.SMILESWriter;
import org.openscience.cdk.io.SVGWriter;
import org.openscience.cdk.io.ShelXWriter;
import org.openscience.cdk.io.XYZWriter;
import org.openscience.cdk.io.listener.PropertiesListener;
import org.openscience.cdk.io.listener.TextGUIListener;
import org.openscience.cdk.io.program.GaussianInputWriter;
import org.openscience.cdk.io.setting.IOSetting;
import org.openscience.cdk.layout.StructureDiagramGenerator;
import org.openscience.cdk.tools.HydrogenAdder;
import org.openscience.cdk.tools.LoggingTool;
import org.openscience.cdk.tools.SaturationChecker;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
00100 public class FileConvertor {
private LoggingTool logger;
private IChemObjectBuilder builder;
private IChemObjectReader cor;
private String oformat;
private IChemObjectWriter cow;
private TextGUIListener settingListener;
private PropertiesListener propsListener;
private int level;
private Vector chemObjectNames = new Vector();
private boolean applyHAdding = false;
private boolean applyHRemoval = false;
private boolean apply2DCleanup = false;
private boolean apply3DRebonding = false;
public FileConvertor() {
logger = new LoggingTool();
LoggingTool.configureLog4j();
logger.dumpSystemProperties();
builder = DefaultChemObjectBuilder.getInstance();
settingListener = new TextGUIListener(level);
propsListener = null;
this.level = 0;
this.oformat = "cml";
chemObjectNames.add("org.openscience.cdk.Molecule");
chemObjectNames.add("org.openscience.cdk.MoleculeSet");
chemObjectNames.add("org.openscience.cdk.Crystal");
chemObjectNames.add("org.openscience.cdk.ChemModel");
chemObjectNames.add("org.openscience.cdk.ChemSequence");
chemObjectNames.add("org.openscience.cdk.ChemFile");
}
00154 public boolean convert(String ifilename) {
if (this.level > 0) System.out.println();
boolean success = false;
try {
File file = new File(ifilename);
if (file.isFile()) {
cor = getChemObjectReader(file);
if (cor == null) {
logger.warn("The format of the input file is not recognized or not supported.");
System.err.println("The format of the input file is not recognized or not supported.");
return false;
}
IChemFile content = (IChemFile)cor.read(builder.newChemFile());
if (content == null) {
return false;
}
List containersList = ChemFileManipulator.getAllAtomContainers(content);
AtomTypeFactory factory = AtomTypeFactory.getInstance(
"org/openscience/cdk/config/data/jmol_atomtypes.txt",
content.getBuilder()
);
for (int i=0; i<containersList.size(); i++) {
IAtomContainer container = (IAtomContainer)containersList.get(i);
java.util.Iterator atoms = container.atoms();
if (applyHAdding || applyHRemoval || apply2DCleanup || apply3DRebonding) {
while (atoms.hasNext()) {
IAtom atom = (IAtom)atoms.next();
if (!(atom instanceof IPseudoAtom)) {
try {
factory.configure(atom);
} catch (CDKException exception) {
logger.warn("Could not configure atom: ", exception.getMessage());
logger.debug(exception);
}
}
}
}
if (applyHAdding) {
logger.info("Adding Hydrogens...");
HydrogenAdder adder = new HydrogenAdder("org.openscience.cdk.tools.ValencyChecker");
adder.addExplicitHydrogensToSatisfyValency(
builder.newMolecule(container)
);
} else if (applyHRemoval) {
for (int atomi=0; atomi<container.getAtomCount(); atomi++) {
if (container.getAtom(atomi).getSymbol().equals("H")) {
container.removeAtomAndConnectedElectronContainers(container.getAtom(atomi));
}
}
}
if (apply3DRebonding) {
logger.info("Creating bonds from 3D coordinates");
RebondTool rebonder = new RebondTool(2.0, 0.5, 0.5);
rebonder.rebond(container);
SaturationChecker satChecker = new SaturationChecker();
satChecker.saturate(container);
}
if (apply2DCleanup) {
logger.info("Creating 2D coordinates");
StructureDiagramGenerator sdg = new StructureDiagramGenerator();
try {
sdg.setMolecule(builder.newMolecule(container), false);
sdg.generateCoordinates(new Vector2d(0, 1));
container = sdg.getMolecule();
logger.debug("###########", container);
} catch (Exception exc) {
System.out.println("Could not generate coordinates for this molecule.");
logger.info("Could not generate coordinates for this molecule: ", exc.getMessage());
logger.debug(exc);
System.exit(1);
}
}
}
String ofilename = getOutputFileName(ifilename, this.oformat);
FileWriter fileWriter = new FileWriter(new File(ofilename));
cow = getChemObjectWriter(this.oformat, fileWriter);
if (cow == null) {
logger.warn("Format ", oformat, " is an unsupported output format.");
System.err.println("Unsupported output format!");
return false;
}
write(content, ofilename);
cow.close();
success = true;
} else {
System.out.println("Skipping non-file.");
}
} catch (FileNotFoundException exception) {
System.out.println("File " + ifilename + " does not exist!");
} catch (Exception exception) {
logger.debug(exception);
}
return success;
}
00258 public static void main(String[] args) {
FileConvertor convertor = new FileConvertor();
String[] filesToConvert = convertor.parseCommandLineOptions(args);
for (int i=0; i < filesToConvert.length; i++) {
String inputFilename = filesToConvert[i];
System.out.print("Converting " + inputFilename + " ... ");
boolean success = convertor.convert(inputFilename);
if (success) {
System.out.println("succeeded!");
} else {
System.out.println("failed!");
}
}
}
private IChemObjectReader getChemObjectReader(File file) throws IOException {
InputStream fileReader = new FileInputStream(file);
IChemObjectReader reader = new ReaderFactory().createReader(fileReader);
if (reader != null) {
if (settingListener != null) {
reader.addChemObjectIOListener(settingListener);
}
if (propsListener != null) {
reader.addChemObjectIOListener(propsListener);
}
}
return reader;
}
private IChemObjectWriter getChemObjectWriter(String format, Writer fileWriter) {
IChemObjectWriter writer = null;
try {
if (format.equalsIgnoreCase("MOL")) {
writer = new MDLWriter(fileWriter);
} else if (format.equalsIgnoreCase("SMI")) {
writer = new SMILESWriter(fileWriter);
} else if (format.equalsIgnoreCase("SHELX")) {
writer = new ShelXWriter(fileWriter);
} else if (format.equalsIgnoreCase("SVG")) {
writer = new SVGWriter(fileWriter);
} else if (format.equalsIgnoreCase("XYZ")) {
writer = new XYZWriter(fileWriter);
} else if (format.equalsIgnoreCase("PDB")) {
writer = new PDBWriter(fileWriter);
} else if (format.equalsIgnoreCase("GIN")) {
writer = new GaussianInputWriter(fileWriter);
} else if (format.equalsIgnoreCase("CDK")) {
writer = new CDKSourceCodeWriter(fileWriter);
} else if (format.equalsIgnoreCase("HIN")) {
writer = new HINWriter(fileWriter);
}
if (writer != null) {
logger.debug(format + " -> " + writer.getClass().getName());
if (settingListener != null) {
writer.addChemObjectIOListener(settingListener);
}
if (propsListener != null) {
writer.addChemObjectIOListener(propsListener);
}
} else if (format.equalsIgnoreCase("CML")) {
Class cmlWriterClass = this.getClass().getClassLoader().loadClass("org.opscience.cdk.io.CMLWriter");
if (cmlWriterClass != null) {
writer = (IChemObjectWriter)cmlWriterClass.newInstance();
}
Constructor constructor = writer.getClass().getConstructor(new Class[]{Writer.class});
writer = (IChemObjectWriter)constructor.newInstance(new Object[]{fileWriter});
} else {
logger.debug(format + " -> null");
}
} catch (Exception exception) {
logger.error("Could not instantiate writer: ", exception.getMessage());
logger.debug(exception);
}
return writer;
}
private String getOutputFileName(String inputFilename, String outputFormat) {
String outputFilename = inputFilename.substring(0,inputFilename.lastIndexOf('.'));
outputFilename = outputFilename.substring(outputFilename.lastIndexOf(File.separatorChar) + 1);
outputFilename = outputFilename + ".";
if (outputFormat.equalsIgnoreCase("CML")) {
outputFilename = outputFilename + "cml";
} else if (outputFormat.equalsIgnoreCase("MOL")) {
outputFilename = outputFilename + "mol";
} else if (outputFormat.equalsIgnoreCase("SMI")) {
outputFilename = outputFilename + "smi";
} else if (outputFormat.equalsIgnoreCase("SHELX")) {
outputFilename = outputFilename + "res";
} else if (outputFormat.equalsIgnoreCase("SVG")) {
outputFilename = outputFilename + "svg";
} else if (outputFormat.equalsIgnoreCase("XYZ")) {
outputFilename = outputFilename + "xyz";
} else if (outputFormat.equalsIgnoreCase("PDB")) {
outputFilename = outputFilename + "pdb";
} else if (outputFormat.equalsIgnoreCase("GIN")) {
outputFilename = outputFilename + "in";
} else if (outputFormat.equalsIgnoreCase("CDK")) {
outputFilename = outputFilename + "java.fragment";
} else if (outputFormat.equalsIgnoreCase("HIN")) {
outputFilename = outputFilename + "hin";
}
return outputFilename;
}
private void printHelp(Options options) {
HelpFormatter formatter = new HelpFormatter();
formatter.printHelp("FileConvertor", options);
System.out.println();
System.out.println(" OUTPUT FORMATS:");
System.out.println(" cml Chemical Markup Language (the default)");
System.out.println(" gin Gaussian Input File");
System.out.println(" hin Hyperchem file");
System.out.println(" mol MDL molfile");
System.out.println(" pdb PDB");
System.out.println(" shelx ShelX");
System.out.println(" smi SMILES");
System.out.println(" svg Scalable Vector Graphics");
System.out.println(" xyz XYZ");
System.exit(0);
}
00392 private String[] parseCommandLineOptions(String[] args) {
Options options = new Options();
options.addOption("h", "help", false, "give this help page");
options.addOption(
OptionBuilder.withLongOpt("question").
withDescription("level of IO questions [none|fewest|some|all]").
withValueSeparator('=').
hasArg().
create("q")
);
options.addOption(
OptionBuilder.withLongOpt("outputformat").
withDescription("see below for supported formats (CML2 is default)").
withValueSeparator('=').
hasArg().
create("o")
);
options.addOption(
OptionBuilder.withLongOpt("listoptions").
withDescription("lists the IO questions for the given format").
withValueSeparator('=').
hasArg().
create("l")
);
options.addOption(
OptionBuilder.withLongOpt("properties").
withDescription("Java properties file with the IO settings").
withValueSeparator('=').
hasArg().
create("p")
);
options.addOption(
OptionBuilder.withLongOpt("addHydrogens").
withDescription("add explicit hydrogens where missing").
create("a")
);
options.addOption(
OptionBuilder.withLongOpt("removeHydrogens").
withDescription("remove all explicit hydrogens").
create("r")
);
options.addOption(
OptionBuilder.withLongOpt("create2DCoordinates").
withDescription("create 2D coordinates using a layout algorithm").
create("2")
);
options.addOption(
OptionBuilder.withLongOpt("rebondFrom3DCoordinates").
withDescription("calculate bonds from 3D coordinates").
create("b")
);
CommandLine line = null;
try {
CommandLineParser parser = new PosixParser();
line = parser.parse(options, args);
} catch (ParseException exception) {
System.err.println("Unexpected exception: " + exception.toString());
}
if (line.hasOption("o")) {
this.oformat = line.getOptionValue("o");
}
if (line.hasOption("q")) {
String level = line.getOptionValue("q");
if ("none".equals(level)) {
settingListener = new TextGUIListener(0);
} else if ("fewest".equals(level)) {
settingListener = new TextGUIListener(1);
} else if ("some".equals(level)) {
settingListener = new TextGUIListener(2);
} else if ("all".equals(level)) {
settingListener = new TextGUIListener(3);
} else {
System.out.println("Only supported levels: none, fewest, some, all");
System.exit(1);
}
}
if (line.hasOption("l")) {
listOptionsForIOClass(line.getOptionValue("l"));
System.exit(0);
}
if (line.hasOption("p")) {
String filename = line.getOptionValue("p");
try {
File file = new File(filename);
Properties props = new Properties();
props.load(new FileInputStream(file));
propsListener = new PropertiesListener(props);
settingListener = null;
} catch (FileNotFoundException exception) {
System.out.println("Cannot find properties file: " + filename);
System.exit(1);
} catch (IOException exception) {
System.out.println("Cannot read properties file: " + filename);
System.exit(1);
}
}
if (line.hasOption("a")) {
this.applyHAdding = true;
}
if (line.hasOption("r")) {
this.applyHRemoval = true;
}
if (line.hasOption("2")) {
this.apply2DCleanup = true;
}
if (line.hasOption("b")) {
this.apply3DRebonding = true;
}
String[] filesToConvert = line.getArgs();
if (filesToConvert.length == 0 || line.hasOption("h")) {
printHelp(options);
}
return filesToConvert;
}
public void listOptionsForIOClass(String ioClassName) {
logger.debug("listing IOSetting options");
String className = "org.openscience.cdk.io." + ioClassName;
try {
Object readerOrWriter = this.getClass().getClassLoader().
loadClass(className).newInstance();
IOSetting[] settings = new IOSetting[0];
if (readerOrWriter instanceof IChemObjectIO) {
IChemObjectIO ioClass = (IChemObjectIO)readerOrWriter;
settings = ioClass.getIOSettings();
} else {
String message = "This class is not a CDK ChemObjectIO class";
System.out.println(message);
logger.error(message);
return;
}
TextGUIListener listener = new TextGUIListener(4);
listener.setInputReader(null);
for (int i=0; i<settings.length; i++) {
IOSetting setting = settings[i];
if (setting != null) {
listener.processIOSettingQuestion(setting);
} else {
String message = "This IOSetting is null";
System.out.println(message);
logger.warn(message);
}
}
} catch (ClassNotFoundException exception) {
String message = "This Reader/Writer does not exist: " + className;
System.out.println(message);
logger.error(message);
logger.debug(exception);
} catch (InstantiationException exception) {
String message = "Could not instantiate the class: " + className;
System.out.println(message);
logger.error(message);
logger.debug(exception);
} catch (Exception exception) {
System.out.println("An unknown exception occured: " + exception.toString());
logger.debug(exception);
}
}
00563 private void write(IChemFile chemFile, String outputFilename) throws IOException {
if (cow.accepts(chemFile.getClass())) {
try {
cow.write(chemFile);
} catch (CDKException e) {
logger.error("Could not write ChemFile. FIXME: I should recurse!");
}
} else {
logger.info("Cannot write ChemFile, recursing into ChemSequence's.");
int count = chemFile.getChemSequenceCount();
boolean needMoreFiles = (cow.accepts(IChemSequence.class)) && (count > 1);
for (int i=0; i < count; i++) {
if (needMoreFiles) {
cow.close();
String fname = outputFilename + "." + (i+1);
FileWriter fileWriter = new FileWriter(new File(fname));
cow = getChemObjectWriter(this.oformat, fileWriter);
}
write(chemFile.getChemSequence(i), outputFilename);
}
}
}
private void write(IChemSequence sequence, String outputFilename) throws IOException {
try {
cow.write(sequence);
} catch (CDKException exception) {
int count = sequence.getChemModelCount();
boolean needMoreFiles = (cow.accepts(IChemModel.class)) && (count > 1);
logger.info("Cannot write ChemSequence, recursing into ChemModel's.");
for (int i=0; i < count; i++) {
if (needMoreFiles) {
cow.close();
String fname = outputFilename + "." + (i+1);
FileWriter fileWriter = new FileWriter(new File(fname));
cow = getChemObjectWriter(this.oformat, fileWriter);
}
write(sequence.getChemModel(i), outputFilename);
}
}
}
private void write(IChemModel cm, String outputFilename) throws IOException {
try {
cow.write(cm);
} catch (CDKException exception) {
logger.info("Cannot write ChemModel, trying Crystal.");
ICrystal crystal = cm.getCrystal();
if (crystal != null) {
write(crystal, outputFilename);
}
IMoleculeSet som = cm.getMoleculeSet();
if (som != null) {
write(som, outputFilename);
}
}
}
private void write(ICrystal c, String outputFilename) throws IOException {
try {
cow.write(c);
} catch (CDKException exception) {
logger.error("Cannot write Crystal: ", exception.getMessage());
}
}
private void write(IMoleculeSet som, String outputFilename) throws IOException {
try {
if (apply2DCleanup) {
logger.info("Creating 2D coordinates");
java.util.Iterator mols = som.molecules();
StructureDiagramGenerator sdg = new StructureDiagramGenerator();
while (mols.hasNext()) {
IMolecule molecule = (IMolecule)mols.next();
try {
sdg.setMolecule(molecule, false);
sdg.generateCoordinates(new Vector2d(0, 1));
molecule = sdg.getMolecule();
} catch (Exception exception) {
System.out.println("Could not generate coordinates for this molecule.");
System.exit(1);
}
}
}
cow.write(som);
} catch (CDKException exception) {
int count = som.getMoleculeCount();
boolean needMoreFiles = (cow.accepts(IMoleculeSet.class)) && (count > 1);
logger.info("Cannot write MoleculeSet, recursing into Molecules's.");
for (int i=0; i < count; i++) {
if (needMoreFiles) {
cow.close();
String fname = outputFilename + "." + (i+1);
FileWriter fileWriter = new FileWriter(new File(fname));
cow = getChemObjectWriter(this.oformat, fileWriter);
}
write(som.getMolecule(i), outputFilename);
}
}
}
private void write(IMolecule molecule, String outputFilename) throws IOException {
try {
cow.write(molecule);
} catch (CDKException exception) {
logger.error("Cannot write molecule: ", exception.getMessage());
logger.debug(exception);
}
}
}