public BitSet getFingerprint(net.bioclipse.core.domain.IMolecule.Property urgency)
throws BioclipseException {
if (urgency == net.bioclipse.core.domain.IMolecule.Property.USE_CACHED) return fingerPrint;
if (urgency == net.bioclipse.core.domain.IMolecule.Property.USE_CALCULATED) {
Fingerprinter fp = new Fingerprinter();
try {
fingerPrint = fp.getFingerprint(getAtomContainer());
} catch (Exception e) {
throw new BioclipseException("Could not create fingerprint: " + e.getMessage());
}
}
return fingerPrint;
}
public DBMolecule(String name, AtomContainer molecule) {
super();
this.setAtomContainer(molecule);
this.name = name;
Fingerprinter fingerprinter = new Fingerprinter();
try {
fingerPrint = fingerprinter.getFingerprint(molecule);
persistedFingerPrint = makePersistedFingerPrint(fingerPrint);
} catch (Exception e) {
// If this happens often maybe something else is needed
throw new IllegalArgumentException("could not create fingerPrint for Atomcontainer:" + name);
}
smiles = "";
annotations = new ArrayList<Annotation>();
}
/**
* Returns a similarity matrix based on the tanimoto distance of the fingerprints. (Upper
* triangular matrix)
*
* @param molList the mol list
* @param similarityThreshold the similarity threshold
* @return the float[][]
* @throws CDKException the CDK exception
*/
private float[][] calculateSimilarity(boolean completeMatrix) throws CDKException {
Map<String, BitSet> candidateToFingerprint = new HashMap<String, BitSet>();
if (hasAtomContainer) {
for (String strCandidate : candidateToStructure.keySet()) {
Fingerprinter f = new Fingerprinter();
BitSet fp = f.getFingerprint(candidateToStructure.get(strCandidate));
candidateToFingerprint.put(strCandidate, fp);
}
} else {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
for (String string : candidatesToSmiles.keySet()) {
try {
IMolecule mol = sp.parseSmiles(candidatesToSmiles.get(string));
Fingerprinter f = new Fingerprinter();
BitSet fp = f.getFingerprint(mol);
candidateToFingerprint.put(string, fp);
} catch (Exception e) {
System.err.println("Error in smiles!" + e.getMessage());
}
}
}
int countJ = 0;
int countI = 0;
if (!hasAtomContainer) {
for (String candidate1 : candidatesToSmiles.keySet()) {
// System.out.print(candidate1 + " ");
for (String candidate2 : candidatesToSmiles.keySet()) {
if ((countJ < countI || candidate1.equals(candidate2)) && !completeMatrix) {
// System.out.print("x ");
countJ++;
continue;
}
float similarity =
compareFingerprints(
candidateToFingerprint.get(candidate1), candidateToFingerprint.get(candidate2));
matrix[countI][countJ] = similarity;
// allSimilarityValues.append(similarity + "\n");
countJ++;
// System.out.print(compareFingerprints(candidateToFingerprint.get(candidate1),
// candidateToFingerprint.get(candidate2)) + " ");
}
countJ = 0;
countI++;
// System.out.println("");
}
} else {
for (String candidate1 : candidateToStructure.keySet()) {
// System.out.print(candidate1 + " ");
for (String candidate2 : candidateToStructure.keySet()) {
if ((countJ < countI || candidate1.equals(candidate2)) && !completeMatrix) {
// System.out.print("x ");
countJ++;
continue;
}
float similarity =
compareFingerprints(
candidateToFingerprint.get(candidate1), candidateToFingerprint.get(candidate2));
matrix[countI][countJ] = similarity;
// allSimilarityValues.append(similarity + "\n");
countJ++;
// System.out.print(compareFingerprints(candidateToFingerprint.get(candidate1),
// candidateToFingerprint.get(candidate2)) + " ");
}
countJ = 0;
countI++;
// System.out.println("");
}
}
return matrix;
}