/** Starts enumeration of the combinatorial library. */
public void run() {
// enumeration starts
if (startEnumeration) {
// start time
long start = System.nanoTime();
// if GUI mode is used, some statistics are shown
if (useGui) {
smiFrame.setStatistics(
compAdmin.getNumberOfScaffolds(),
compAdmin.getNumberOfLinkers(),
compAdmin.getNumberOfBuildingBlocks());
}
// start enumeration
try {
this.enumerateLibrary();
} catch (Throwable thr) {
handleException(thr);
}
// end time
long end = System.nanoTime();
// formats time
DecimalFormat df = new DecimalFormat("###,###,###,##0.000000000###");
// message of end of enumeration is shown in command line/GUI - NOT if library is printed to
// command line
if (useGui) {
smiFrame.setTime(start, end);
smiFrame.showEndMessage(start, end);
} else if (!printToCommandLine) {
// total time is printed out
if (compoundCounter == 1) {
System.out.println(
compoundCounter
+ " compound synthesized in "
+ df.format((double) (end - start) / 1000000000)
+ " seconds");
} else {
System.out.println(
compoundCounter
+ " compounds synthesized in "
+ df.format((double) (end - start) / 1000000000)
+ " seconds");
}
}
}
}
/**
* Creates a new instance of SmiLibRunner, used when programm is started in GUI mode.
*
* @param scaffolds array of source scaffold (with ID)
* @param linkers array of source linkers (with ID)
* @param bBlocks array of source building block (with ID)
* @param useReactionScheme use reaction scheme true/false
* @param reactionScheme reactionScheme as array
* @param targetTextArea text area where library will be written in
* @param showLibrary show library in GUI true/false
* @param saveAsFile save library as file true/false
* @param saveAsSDF save file as SD file true/false
* @param addHydrogens add implicit hydrogens when building the SD file true/false
* @param path path/name of file where library will be saved
* @param frame main frame of GUI
* @param checkSmiles check smiles for SmiLib conformity true/false
*/
public SmiLibRunner(
String[] scaffolds,
String[] linkers,
String[] bBlocks,
boolean useReactionScheme,
String[] reactionScheme,
JTextArea targetTextArea,
boolean showLibrary,
boolean saveAsFile,
boolean saveAsSDF,
boolean addHydrogens,
String path,
SmiLibFrame frame,
boolean checkSmiles) {
this.smiFrame = frame;
this.useGui = true;
// load source SMILES
try {
compAdmin = new ComponentAdministrator(scaffolds, linkers, bBlocks, checkSmiles);
if (!useReactionScheme) {
this.iterator =
new FullCombinationIterator(
compAdmin.getNumbersOfRGroups(),
compAdmin.getNumberOfLinkers(),
compAdmin.getNumberOfBuildingBlocks());
} else {
this.iterator =
new PartialCombinationIterator(
reactionScheme,
compAdmin.getNumbersOfRGroups(),
compAdmin.getNumberOfLinkers(),
compAdmin.getNumberOfBuildingBlocks());
}
smiFrame.setIterator(iterator);
smiWri =
new SmilesGuiWriter(
targetTextArea, showLibrary, saveAsFile, saveAsSDF, addHydrogens, path, smiFrame);
} catch (Exception exc) {
handleException(exc);
}
}
/**
* Centralised Exception handling. Thread ist stopped and a message for each different kind of
* message is shown/printed.
*
* @param thr cause of Error/Exception
*/
public void handleException(Throwable thr) {
startEnumeration = false;
// GUI: show JOptionpane; else: print errormessage
if (useGui) {
smiFrame.emergencyShutdown();
javax.swing.JOptionPane messageBox = new javax.swing.JOptionPane();
if (thr instanceof SmiLibConformityException) {
messageBox.showMessageDialog(
smiFrame, thr.getMessage(), "Error", javax.swing.JOptionPane.ERROR_MESSAGE);
} else if (thr instanceof ReactionSchemeException) {
messageBox.showMessageDialog(
smiFrame, thr.getMessage(), "Error", javax.swing.JOptionPane.ERROR_MESSAGE);
} else if (thr instanceof SmiLibIOException) {
messageBox.showMessageDialog(
smiFrame, thr.getMessage(), "Error", javax.swing.JOptionPane.ERROR_MESSAGE);
} else if (thr instanceof StringIndexOutOfBoundsException) {
messageBox.showMessageDialog(
smiFrame, thr.getMessage(), "Error", javax.swing.JOptionPane.ERROR_MESSAGE);
} else if (thr instanceof NumberFormatException) {
messageBox.showMessageDialog(
smiFrame,
"Invalid reaction scheme.\nPlease check reaction scheme and/or use SmiLib help!",
"Error",
javax.swing.JOptionPane.ERROR_MESSAGE);
} else if (thr instanceof java.lang.OutOfMemoryError) {
messageBox.showMessageDialog(
smiFrame,
"Java heap size overflow.\nRestart program with access to more memory!",
"Error",
javax.swing.JOptionPane.ERROR_MESSAGE);
System.exit(1);
} else if (thr instanceof SmiLibSdfException) {
messageBox.showMessageDialog(
smiFrame,
"An error occured converting SMILES to SDF.\n" + thr.getMessage(),
"Error",
javax.swing.JOptionPane.ERROR_MESSAGE);
} else {
messageBox.showMessageDialog(
smiFrame, thr.toString(), "Error", javax.swing.JOptionPane.ERROR_MESSAGE);
}
} else {
if (thr instanceof SmiLibConformityException) {
System.err.println(thr.getMessage());
System.err.println("An error occured. Program halted.");
} else if (thr instanceof ReactionSchemeException) {
System.err.println(thr.getMessage());
System.err.println("An error occured. Program halted.");
} else if (thr instanceof SmiLibIOException) {
System.err.println(thr.getMessage());
System.err.println("An error occured. Program halted.");
} else if (thr instanceof StringIndexOutOfBoundsException) {
System.err.println(thr.getMessage());
System.err.println("An error occured. Program halted.");
} else if (thr instanceof NumberFormatException) {
System.err.println(
"Invalid reaction scheme.\nPlease check reaction scheme and/or use SmiLib help!");
System.err.println("An error occured. Program halted.");
} else if (thr instanceof java.lang.OutOfMemoryError) {
System.err.println("Java heap size overflow.\nRestart program with access to more memory!");
System.err.println("An error occured. Program halted.");
System.exit(1);
} else if (thr instanceof SmiLibSdfException) {
System.err.println("An error occured converting SMILES to SDF.");
System.err.println(thr.getMessage());
System.err.println("An error occured. Program halted.");
} else {
System.err.println(thr.getMessage());
System.err.println("An error occured. Program halted.");
}
}
}