/** 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();
}
