/**
* Creates a new instance of SmiLibRunner using a FullCombinationIterator (without reaction
* scheme) for enumerating the virtual library.
*
* @param scaffoldsPath path/name of the file that contains scaffolds as SMILES
* @param linkersPath path/name of the file that contains linkers as SMILES
* @param buildingBlocksPath path/name of the file that contains building blocks as SMILES
* @param printToCommandLine combinatorial library shall be printed to the command line true/false
* @param saveFilePath path/name of the file where the combinatorial library will be stored if it
* shall be saved in a file
* @param addHydrogens add hydrogens when save as SD file
* @param checkSmiles check SMILES for conformity with SMiLib rules true/false
*/
public SmiLibRunner(
String scaffoldsPath,
String linkersPath,
String buildingBlocksPath,
boolean printToCommandLine,
String saveFilePath,
boolean addHydrogens,
boolean checkSmiles) {
this.printToCommandLine = printToCommandLine;
try {
compAdmin =
new ComponentAdministrator(scaffoldsPath, linkersPath, buildingBlocksPath, checkSmiles);
this.iterator =
new FullCombinationIterator(
compAdmin.getNumbersOfRGroups(),
compAdmin.getNumberOfLinkers(),
compAdmin.getNumberOfBuildingBlocks());
if (printToCommandLine) smiWri = new SmilesLineWriter();
else if (saveFilePath.endsWith(".sdf"))
smiWri = new SmilesToSDFWriter(saveFilePath, addHydrogens);
else smiWri = new SmilesFileWriter(saveFilePath);
} catch (Exception ex) {
handleException(ex);
}
}
/** 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 that can be conveniently used in other Java projects
* when SmiLib is employed as a Java library.<br>
* <br>
* Example to enumerate a complete SmiLib library:
*
* <pre>
* String[] scaffolds = new String[] {"CCC[R1]"};
* String[] linkers = new String[] {"[R][A]"};
* String[] bBlocks = new String[] {"[A]Br", "[A]Cl"};
* SmilesListWriter smiWri = new SmilesListWriter();
* SmiLibRunner runner = new SmiLibRunner(scaffolds, linkers, bBlocks, null, true, smiWri);
* runner.run(); // Run SmiLib
* List<String[]> library = smiWri.getSmilesList(); // Retrieve results
* // String id = library.get(0)[0];
* // String smiles = library.get(0)[1];
* </pre>
*
* <br>
* Example to enumerate a SmiLib library according to a reaction scheme:
*
* <pre>
* String[] scaffolds = new String[] {"CCC[R1]"};
* String[] linkers = new String[] {"[R][A]"};
* String[] bBlocks = new String[] {"[A]Br", "[A]Cl"};
* String[] reactionScheme = new String[] {"1\t1\t2"}; // The reaction scheme
* SmilesListWriter smiWri = new SmilesListWriter();
* SmiLibRunner runner = new SmiLibRunner(scaffolds, linkers, bBlocks, reactionScheme, true, smiWri);
* runner.run(); // Run SmiLib
* List<String[]> library = smiWri.getSmilesList(); // Retrieve results
* // String id = library.get(0)[0];
* // String smiles = library.get(0)[1];
* </pre>
*
* <br>
*
* @param scaffolds array of source scaffolds, optionally with ID
* @param linkers array of source linkers, optionally with ID
* @param bBlocks array of source building blocks, optionally with ID
* @param reactionScheme reactionScheme as an array. If null, complete enumeration is performed
* @param checkSmiles check smiles for SmiLib conformity true/false
* @param smiWri output smiles writer
* @since 2.0 rc4
*/
public SmiLibRunner(
String[] scaffolds,
String[] linkers,
String[] bBlocks,
String[] reactionScheme,
boolean checkSmiles,
SmilesWriter smiWri) {
this.printToCommandLine = true; // Set true to avoid sending messages to stdout
try {
compAdmin = new ComponentAdministrator(scaffolds, linkers, bBlocks, checkSmiles);
if (reactionScheme == null) {
this.iterator =
new FullCombinationIterator(
compAdmin.getNumbersOfRGroups(),
compAdmin.getNumberOfLinkers(),
compAdmin.getNumberOfBuildingBlocks());
} else {
this.iterator =
new PartialCombinationIterator(
reactionScheme,
compAdmin.getNumbersOfRGroups(),
compAdmin.getNumberOfLinkers(),
compAdmin.getNumberOfBuildingBlocks());
}
this.smiWri = smiWri;
} catch (Exception exc) {
handleException(exc);
}
}
/**
* 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);
}
}
/** Enumerates the combinatorial library. */
private void enumerateLibrary() throws Exception {
boolean linkerEmpty;
int numRGroups;
int ringNumber;
int[] currentCombination;
StringBuilder intermediateProduct = new StringBuilder();
StringBuilder currentMolecule = new StringBuilder();
StringBuilder moleculeID = new StringBuilder();
// as long as new combination are available and thread shall not be stopped
while (iterator.hasNext() & !stop) {
// gets next combination
currentCombination = iterator.next();
// StringBuilder with the currentMolecule gets a reset - so you can use one Object for all
// molecules
currentMolecule
.delete(0, currentMolecule.length())
.append(compAdmin.getScaffoldString(currentCombination[0]));
// StringBuilder with molecule ID gets a reset
moleculeID
.delete(0, moleculeID.length())
.append(compAdmin.getScaffoldID(currentCombination[0]));
// gets number of variable side chains in the current scaffold
numRGroups = compAdmin.getNumberOfRGroups(currentCombination[0]);
ringNumber = 10;
// for each variable side chain
for (int i = 1; i <= numRGroups; i++) {
linkerEmpty = compAdmin.getLinker(currentCombination[i]).isEmpty();
// ringnumber is checked, so that conflicts with existing ringnumbers in scaffold-, linker-
// or buildingblock-SMILES can not occur
while (compAdmin.numberBlacklisted(
ringNumber,
currentCombination[0],
currentCombination[i],
currentCombination[i + numRGroups])) ringNumber++;
// if linker is not the empty linker
if (!linkerEmpty) {
// StringBuilder with the current intermediate gets a reset - so you can use one Object
// for all intermediates
intermediateProduct
.delete(0, intermediateProduct.length())
.append(compAdmin.getLinker(currentCombination[i]).getLinkerForConcat(ringNumber));
// current intermediate is created
smiConcat.concatenate(
intermediateProduct,
'.',
compAdmin
.getBuildingBlock(currentCombination[i + numRGroups])
.getBlockForConcat(ringNumber));
ringNumber++;
// current intermediate gets attached to the scaffold
smiConcat.concatenate(
currentMolecule,
intermediateProduct,
'.',
compAdmin.getScaffold(currentCombination[0]).getStringOfGroupWithIndex(i - 1),
ringNumber);
ringNumber++;
// if linker is the empty linker
} else {
// building block gets directly attached to the scaffold
smiConcat.concatenate(
currentMolecule,
compAdmin
.getBuildingBlock(currentCombination[i + numRGroups])
.getBlockForConcat(ringNumber),
'.',
compAdmin.getScaffold(currentCombination[0]).getStringOfGroupWithIndex(i - 1),
ringNumber);
ringNumber++;
}
// molecule ID gets an update
moleculeID
.append('.')
.append(compAdmin.getLinkerID(currentCombination[i]))
.append('_')
.append(compAdmin.getBuildingBlockID(currentCombination[i + numRGroups]));
}
// created molecule is written
smiWri.writeSMILES(currentMolecule, moleculeID);
compoundCounter++;
}
smiWri.close();
}
