/**
* Calculates the eccentric connectivity
*
* @param container Parameter is the atom container.
* @return An IntegerResult value representing the eccentric connectivity index
*/
@TestMethod("testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtomContainer container) {
IAtomContainer local = AtomContainerManipulator.removeHydrogens(container);
int natom = local.getAtomCount();
int[][] admat = AdjacencyMatrix.getMatrix(local);
int[][] distmat = PathTools.computeFloydAPSP(admat);
int eccenindex = 0;
for (int i = 0; i < natom; i++) {
int max = -1;
for (int j = 0; j < natom; j++) {
if (distmat[i][j] > max) max = distmat[i][j];
}
int degree = local.getConnectedBondsCount(i);
eccenindex += max * degree;
}
IntegerResult retval = new IntegerResult(eccenindex);
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
retval,
getDescriptorNames(),
null);
}
@TestMethod("testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtomContainer container) {
// removeHydrogens does a deep copy, so no need to clone
IAtomContainer localAtomContainer = AtomContainerManipulator.removeHydrogens(container);
CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(container.getBuilder());
Iterator<IAtom> atoms = localAtomContainer.atoms().iterator();
while (atoms.hasNext()) {
IAtom atom = atoms.next();
IAtomType type;
try {
type = matcher.findMatchingAtomType(localAtomContainer, atom);
AtomTypeManipulator.configure(atom, type);
} catch (Exception e) {
return getDummyDescriptorValue(new CDKException("Error in atom typing: " + e.getMessage()));
}
}
CDKHydrogenAdder hAdder = CDKHydrogenAdder.getInstance(container.getBuilder());
try {
hAdder.addImplicitHydrogens(localAtomContainer);
} catch (CDKException e) {
return getDummyDescriptorValue(
new CDKException("Error in hydrogen addition: " + e.getMessage()));
}
List subgraph3 = order3(localAtomContainer);
List subgraph4 = order4(localAtomContainer);
List subgraph5 = order5(localAtomContainer);
List subgraph6 = order6(localAtomContainer);
double order3s = ChiIndexUtils.evalSimpleIndex(localAtomContainer, subgraph3);
double order4s = ChiIndexUtils.evalSimpleIndex(localAtomContainer, subgraph4);
double order5s = ChiIndexUtils.evalSimpleIndex(localAtomContainer, subgraph5);
double order6s = ChiIndexUtils.evalSimpleIndex(localAtomContainer, subgraph6);
double order3v, order4v, order5v, order6v;
try {
order3v = ChiIndexUtils.evalValenceIndex(localAtomContainer, subgraph3);
order4v = ChiIndexUtils.evalValenceIndex(localAtomContainer, subgraph4);
order5v = ChiIndexUtils.evalValenceIndex(localAtomContainer, subgraph5);
order6v = ChiIndexUtils.evalValenceIndex(localAtomContainer, subgraph6);
} catch (CDKException e) {
return getDummyDescriptorValue(
new CDKException("Error in substructure search: " + e.getMessage()));
}
DoubleArrayResult retval = new DoubleArrayResult();
retval.add(order3s);
retval.add(order4s);
retval.add(order5s);
retval.add(order6s);
retval.add(order3v);
retval.add(order4v);
retval.add(order5v);
retval.add(order6v);
return new DescriptorValue(
getSpecification(), getParameterNames(), getParameters(), retval, getDescriptorNames());
}
@Test(timeout = 1000)
public void testPyrrole_Silent() throws Exception {
String smiles = "c2ccc3n([H])c1ccccc1c3(c2)";
SmilesParser smilesParser = new SmilesParser(SilentChemObjectBuilder.getInstance());
IAtomContainer molecule = smilesParser.parseSmiles(smiles);
molecule = fbot.kekuliseAromaticRings(molecule);
Assert.assertNotNull(molecule);
molecule = (IAtomContainer) AtomContainerManipulator.removeHydrogens(molecule);
int doubleBondCount = 0;
for (int i = 0; i < molecule.getBondCount(); i++) {
IBond bond = molecule.getBond(i);
Assert.assertTrue(bond.getFlag(CDKConstants.ISAROMATIC));
if (bond.getOrder() == Order.DOUBLE) doubleBondCount++;
}
Assert.assertEquals(6, doubleBondCount);
}
@Test
public void testLargeRingSystem() throws Exception {
String smiles = "O=C1Oc6ccccc6(C(O)C1C5c2ccccc2CC(c3ccc(cc3)c4ccccc4)C5)";
SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer molecule = smilesParser.parseSmiles(smiles);
molecule = fbot.kekuliseAromaticRings(molecule);
Assert.assertNotNull(molecule);
molecule = (IAtomContainer) AtomContainerManipulator.removeHydrogens(molecule);
Assert.assertEquals(34, molecule.getAtomCount());
// we should have 14 double bonds
int doubleBondCount = 0;
for (int i = 0; i < molecule.getBondCount(); i++) {
IBond bond = molecule.getBond(i);
if (bond.getOrder() == Order.DOUBLE) doubleBondCount++;
}
Assert.assertEquals(13, doubleBondCount);
}
/** @cdk.bug 3506770 */
@Test
public void testLargeBioclipseUseCase() throws Exception {
String smiles =
"COc1ccc2[C@@H]3[C@H](COc2c1)C(C)(C)OC4=C3C(=O)C(=O)C5=C4OC(C)(C)[C@@H]6COc7cc(OC)ccc7[C@H]56";
SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer molecule = smilesParser.parseSmiles(smiles);
molecule = fbot.kekuliseAromaticRings(molecule);
Assert.assertNotNull(molecule);
molecule = (IAtomContainer) AtomContainerManipulator.removeHydrogens(molecule);
Assert.assertEquals(40, molecule.getAtomCount());
// we should have 14 double bonds
int doubleBondCount = 0;
for (int i = 0; i < molecule.getBondCount(); i++) {
IBond bond = molecule.getBond(i);
if (bond.getOrder() == Order.DOUBLE) doubleBondCount++;
}
Assert.assertEquals(10, doubleBondCount);
}
public static void main(final String[] args) {
// String mf;
// String molfile;
try {
// BufferedReader reader = new BufferedReader(new FileReader("renderTest.mol"));
// StringBuffer sbuff = new StringBuffer();
// String line;
//
// while ( (line = reader.readLine()) != null ) {
// sbuff.append(line + "\n");
// }
// reader.close();
// molfile = sbuff.toString();
// System.out.println(molfile);
// the graph
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
PubChemWebService pw = new PubChemWebService();
String PCID = "1148";
IAtomContainer container = pw.getSingleMol(PCID);
container = AtomContainerManipulator.removeHydrogens(container);
// IAtomContainer container = sp.parseSmiles("OC1C(O)=COC(CO)C1(O)");
// Render.Draw(container, "test");
IMolecule test = new Molecule(container);
StructureDiagramGenerator sdg = new StructureDiagramGenerator();
sdg.setMolecule(test);
sdg.generateCoordinates();
IMolecule mol = sdg.getMolecule();
// adds implicit H atoms to molecule
// CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(mol.getBuilder());
// for (IAtom atom : mol.atoms()) {
// IAtomType type = matcher.findMatchingAtomType(mol, atom);
// AtomTypeManipulator.configure(atom, type);
// }
//
// CDKHydrogenAdder adder = CDKHydrogenAdder.getInstance(mol.getBuilder());
// adder.addImplicitHydrogens(mol);
// AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol);
// detects aromaticity; used to display aromatic ring systems correctly
CDKHueckelAromaticityDetector.detectAromaticity(mol);
Render.Draw(mol, "test");
DisplayStructureVector test12 =
new DisplayStructureVector(200, 200, "/home/swolf/", true, true);
// test12.writeMOL2PNGFile(mol, "test_cdk12.png");
// test12.writeMOL2PDFFile(mol, new File("/home/swolf/test_cdk12.pdf"));
test12.writeMOL2SVGFile(mol, new File("/home/swolf/" + PCID + ".svg"));
// ChemRenderer crender = new ChemRenderer();
// crender.writeMOL2PNGFile(mol, new File("/home/swolf/test_new.png"));
// crender.writeMOL2EPSFile(mol, new File("/home/swolf/test_new.eps"));
// crender.writeMOL2PDFFile(mol, new File("/home/swolf/test_new.pdf"));
// crender.writeMOL2SVGFile(molfile,new File("Output.svg"));
} catch (Exception e) {
System.out.println("Error: " + e.getMessage() + ".");
e.printStackTrace();
}
}
/**
* Calculate the count of atoms of the largest chain in the supplied {@link IAtomContainer}.
*
* <p>
*
* <p>The method require two parameters:
*
* <ol>
* <li>if checkAromaticity is true, the method check the aromaticity,
* <li>if false, means that the aromaticity has already been checked
* </ol>
*
* <p>
*
* <p>Same for checkRingSystem, if true the CDKConstant.ISINRING will be set
*
* @param atomContainer The {@link AtomContainer} for which this descriptor is to be calculated
* @return the number of atoms in the largest chain of this AtomContainer
* @see #setParameters
*/
@TestMethod("testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtomContainer atomContainer) {
IAtomContainer container;
try {
container = (IAtomContainer) atomContainer.clone();
} catch (CloneNotSupportedException e) {
return getDummyDescriptorValue(e);
}
// logger.debug("LargestChainDescriptor");
boolean[] originalFlag4 = new boolean[container.getAtomCount()];
for (int i = 0; i < originalFlag4.length; i++) {
originalFlag4[i] = container.getAtom(i).getFlag(4);
}
if (checkRingSystem) {
IRingSet rs;
try {
rs = new SpanningTree(container).getBasicRings();
} catch (NoSuchAtomException e) {
return getDummyDescriptorValue(e);
}
for (int i = 0; i < container.getAtomCount(); i++) {
if (rs.contains(container.getAtom(i))) {
container.getAtom(i).setFlag(CDKConstants.ISINRING, true);
}
}
}
if (checkAromaticity) {
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(container);
CDKHueckelAromaticityDetector.detectAromaticity(container);
} catch (CDKException e) {
return getDummyDescriptorValue(e);
}
}
// get rid of hydrogens in our local copy
container = AtomContainerManipulator.removeHydrogens(container);
int largestChainAtomsCount = 0;
// IAtom[] atoms = container.getAtoms();
ArrayList<IAtom> startSphere;
ArrayList<IAtom> path;
// Set all VisitedFlags to False
for (int i = 0; i < container.getAtomCount(); i++) {
container.getAtom(i).setFlag(CDKConstants.VISITED, false);
}
// logger.debug("Set all atoms to Visited False");
for (int i = 0; i < container.getAtomCount(); i++) {
IAtom atomi = container.getAtom(i);
// chain sp3
// logger.debug("atom:"+i+" maxBondOrder:"+container.getMaximumBondOrder(atoms[i])+"
// Aromatic:"+atoms[i].getFlag(CDKConstants.ISAROMATIC)+"
// Ring:"+atoms[i].getFlag(CDKConstants.ISINRING)+"
// FormalCharge:"+atoms[i].getFormalCharge()+" Charge:"+atoms[i].getCharge()+"
// Flag:"+atoms[i].getFlag(CDKConstants.VISITED));
if ((!atomi.getFlag(CDKConstants.ISAROMATIC) && !atomi.getFlag(CDKConstants.ISINRING))
& !atomi.getFlag(CDKConstants.VISITED)) {
// logger.debug("...... -> containercepted");
startSphere = new ArrayList<IAtom>();
path = new ArrayList<IAtom>();
startSphere.add(atomi);
try {
breadthFirstSearch(container, startSphere, path);
} catch (CDKException e) {
return getDummyDescriptorValue(e);
}
if (path.size() > largestChainAtomsCount) {
largestChainAtomsCount = path.size();
}
}
}
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new IntegerResult(largestChainAtomsCount),
getDescriptorNames());
}
/**
* Process spectra in the following way: Fragment each hit in KEGG starting with the lowest
* collision energy If hits were found they are used for the next measurement as input and the
* original molecule is not used.
*
* @param folder the folder
* @param file the file
*/
private void processSpectra(String folder, String file, int treeDepth) {
this.scoreMap = new HashMap<Integer, ArrayList<String>>();
if (blackList.contains(file)) {
completeLog += "Blacklisted Molecule: " + file;
histogramReal += "\n" + file + "\tBLACKLIST\t";
histogram += "\n" + file + "\tBLACKLIST\t";
histogramCompare += "\n" + file + "\tBLACKLIST\t";
return;
}
double exactMass = spectra.get(0).getExactMass();
// timing
long timeStart = System.currentTimeMillis();
HashMap<Double, Vector<String>> realScoreMap = new HashMap<Double, Vector<String>>();
int mode = spectra.get(0).getMode();
// instantiate and read in CID-KEGG.txt
String keggIdentifier = spectra.get(0).getKEGG();
completeLog +=
"\n\n============================================================================";
completeLog +=
"\nFile: " + spectra.get(0).getTrivialName() + " (KEGG Entry: " + keggIdentifier + ")";
// get candidates from kegg webservice...with with a given mzppm and mzabs
Vector<String> candidates =
KeggWebservice.KEGGbyMass(exactMass, (mzabs + PPMTool.getPPMDeviation(exactMass, mzppm)));
try {
GetKEGGIdentifier keggID = new GetKEGGIdentifier(folder + "CID-KEGG/CID-KEGG.txt");
// now find the corresponding KEGG entry
if (keggID.existInKEGG(spectra.get(0).getCID()))
keggIdentifier = keggID.getKEGGID(spectra.get(0).getCID());
} catch (IOException e) {
System.out.println(e.getMessage());
completeLog += "Error! Message: " + e.getMessage();
}
// comparison histogram
if (keggIdentifier.equals("none"))
histogramCompare += "\n" + file + "\t" + keggIdentifier + "\t\t" + exactMass;
else
histogramCompare +=
"\n" + file + "\t" + keggIdentifier + "\t" + candidates.size() + "\t" + exactMass;
// list of peaks which are contained in the real molecule
Vector<Peak> listOfPeaksCorresponding = new Vector<Peak>();
// list of peaks which are not contained in the real molecule
Vector<Peak> listOfPeaks = new Vector<Peak>();
// loop over all hits
for (int c = 0; c < candidates.size(); c++) {
this.foundHits = new Vector<IAtomContainer>();
// get mol file from kegg....remove "cpd:"
String candidate = KeggWebservice.KEGGgetMol(candidates.get(c).substring(4), this.keggPath);
IAtomContainer molecule = null;
try {
// write string to disk
new File(folder + file + "_Mol").mkdir();
File outFile = new File(folder + file + "_Mol/" + candidates.get(c).substring(4) + ".mol");
FileWriter out = new FileWriter(outFile);
out.write(candidate);
out.close();
// now fragment the retrieved molecule
molecule = Molfile.Read(folder + file + "_Mol/" + candidates.get(c).substring(4) + ".mol");
// now create a new folder to write the .mol files into
new File(folder + file).mkdir();
boolean status = new File(folder + file + "/" + candidates.get(c).substring(4)).mkdir();
} catch (IOException e) {
completeLog += "Error: " + candidates.get(c).substring(4) + " Message: " + e.getMessage();
} catch (CDKException e) {
completeLog += "Error: " + candidates.get(c).substring(4) + " Message: " + e.getMessage();
}
try {
// add hydrogens
CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(molecule.getBuilder());
for (IAtom atom : molecule.atoms()) {
IAtomType type = matcher.findMatchingAtomType(molecule, atom);
AtomTypeManipulator.configure(atom, type);
}
CDKHydrogenAdder hAdder = CDKHydrogenAdder.getInstance(molecule.getBuilder());
hAdder.addImplicitHydrogens(molecule);
AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule);
}
// there is a bug in cdk?? error happens when there is a S or Ti in the molecule
catch (IllegalArgumentException e) {
completeLog += "Error: " + candidates.get(c).substring(4) + " Message: " + e.getMessage();
// skip it
continue;
} catch (CDKException e) {
completeLog += "Error: " + candidates.get(c).substring(4) + " Message: " + e.getMessage();
// skip it
continue;
}
// get peak list....it is reset if this is not the first run
Vector<Peak> peakList = spectra.get(0).getPeakList();
// create a new instance
Fragmenter fragmenter =
new Fragmenter(
(Vector<Peak>) peakList.clone(),
mzabs,
mzppm,
mode,
breakAromaticRings,
quickRedundancy,
false,
false);
double combinedScore = 0;
int combinedHits = 0;
int combinedPeakCount = 0;
String peaks = "";
combinedPeakCount = peakList.size();
int count = 0;
boolean first = true;
// loop over the different collision energies
for (WrapperSpectrum spectrum : spectra) {
List<IAtomContainer> l = null;
long start = System.currentTimeMillis();
try {
if (first) {
try {
l = fragmenter.generateFragmentsInMemory(molecule, true, treeDepth);
count++;
} catch (OutOfMemoryError e) {
System.out.println("OUT OF MEMORY ERROR! " + candidates.get(c).substring(4));
completeLog +=
"Error: " + candidates.get(c).substring(4) + " Message: " + e.getMessage();
continue;
}
first = false;
} else {
peakList = spectrum.getPeakList();
combinedPeakCount += peakList.size();
// set the current peak list...
fragmenter.setPeakList((Vector<Peak>) peakList.clone());
try {
// l = fragmenter.generateFragmentsHierarchical(foundHits, true);
System.err.println("REMOVED....no improvement!");
System.exit(1);
count++;
} catch (OutOfMemoryError e) {
System.out.println("OUT OF MEMORY ERROR! " + candidates.get(c).substring(4));
completeLog +=
"Error: " + candidates.get(c).substring(4) + " Message: " + e.getMessage();
continue;
}
}
long time = System.currentTimeMillis() - start;
System.out.println("Benötigte Zeit: " + time);
System.out.println("Got " + l.size() + " fragments");
System.out.println("Needed " + fragmenter.getNround() + " calls to generateFragments()");
new File(
folder
+ file
+ "/"
+ candidates.get(c).substring(4)
+ "/"
+ spectrum.getCollisionEnergy())
.mkdir();
for (int i = 0; i < l.size(); i++) {
try {
// write fragments to disk
FileWriter w =
new FileWriter(
new File(
folder
+ file
+ "/"
+ candidates.get(c).substring(4)
+ "/"
+ spectrum.getCollisionEnergy()
+ "/frag_"
+ i
+ ".mol"));
MDLWriter mw = new MDLWriter(w);
mw.write(new Molecule(l.get(i)));
mw.close();
} catch (IOException e) {
System.out.println("IOException: " + e.toString());
completeLog +=
"Error: " + candidates.get(c).substring(4) + " Message: " + e.getMessage();
} catch (Exception e) {
System.out.println(e.toString());
completeLog +=
"Error: " + candidates.get(c).substring(4) + " Message: " + e.getMessage();
}
}
// Draw molecule and its fragments
if (showDiagrams) Render.Draw(molecule, l, "Original Molecule");
if (pdf) {
// Create PDF Output
l.add(0, molecule);
DisplayStructure ds1 = null;
// create pdf subfolder
new File(folder + file + "/" + candidates.get(c) + "pdf/").mkdir();
ds1 =
new WritePDFTable(
true,
300,
300,
0.9,
2,
false,
false,
folder + file + "/" + candidates.get(c) + "pdf/");
for (int i = 0; i < l.size(); i++) {
// ds = new displayStructure(false, 300, 300, 0.9, false, "PDF",
// "/home/basti/WorkspaceJava/TandemMSLookup/fragmenter/Test");
assert ds1 != null;
ds1.drawStructure(l.get(i), i);
}
if (ds1 != null) ds1.close();
}
// now read the saved mol files
List<IAtomContainer> fragments =
Molfile.Readfolder(
folder
+ file
+ "/"
+ candidates.get(c).substring(4)
+ "/"
+ spectrum.getCollisionEnergy());
List<IAtomContainer> fragmentsList = new ArrayList<IAtomContainer>();
for (int i = 0; i < fragments.size(); i++) {
fragmentsList.add(fragments.get(i));
}
// get the original peak list again
// spectrum = new SpectrumWrapper(folder + file + ".txt");
peakList = (Vector<Peak>) spectrum.getPeakList().clone();
// clean up peak list
CleanUpPeakList cList = new CleanUpPeakList(peakList);
Vector<Peak> cleanedPeakList = cList.getCleanedPeakList(spectrum.getExactMass());
// now find corresponding fragments to the mass
AssignFragmentPeak afp = new AssignFragmentPeak();
afp.setHydrogenTest(hydrogenTest);
afp.assignFragmentPeak(
fragments, cleanedPeakList, mzabs, mzppm, spectrum.getMode(), false);
Vector<PeakMolPair> hits = afp.getHits();
Vector<PeakMolPair> hitsAll = afp.getAllHits();
// add them to the list of already found fragments....they were found in the previous run
// with a smaller collission energy
for (PeakMolPair peakMolPair : hitsAll) {
foundHits.add(peakMolPair.getFragment());
}
combinedHits += ((combinedHits + hits.size()) - combinedHits);
// Render.Draw(molecule, foundHits, "Found Hits");
// now "real" scoring
Scoring score = new Scoring(cleanedPeakList);
double currentScore = score.computeScoring(afp.getHitsMZ());
combinedScore += currentScore;
// check for last run and create the data for the log file
if (count == spectra.size()) {
// save score in hashmap...if there are several hits with the same score --> vector of
// strings
if (realScoreMap.containsKey(combinedScore)) {
Vector<String> tempList = realScoreMap.get(combinedScore);
tempList.add(candidates.get(c).substring(4));
realScoreMap.put(combinedScore, tempList);
} else {
Vector<String> temp = new Vector<String>();
temp.add(candidates.get(c).substring(4));
realScoreMap.put(combinedScore, temp);
}
// save score in hashmap...if there are several hits with the same
// amount of identified peaks --> ArrayList
if (scoreMap.containsKey(combinedHits)) {
ArrayList<String> tempList = scoreMap.get(combinedHits);
tempList.add(candidates.get(c).substring(4));
scoreMap.put(combinedHits, tempList);
} else {
ArrayList<String> temp = new ArrayList<String>();
temp.add(candidates.get(c).substring(4));
scoreMap.put(combinedHits, temp);
}
}
// get all the identified peaks
for (int i = 0; i < hits.size(); i++) {
peaks += hits.get(i).getPeak().getMass() + " ";
listOfPeaks.add(hits.get(i).getPeak());
if (keggIdentifier.equals(candidates.get(c).substring(4)))
listOfPeaksCorresponding.add(hits.get(i).getPeak());
}
List<IAtomContainer> hitsListTest = new ArrayList<IAtomContainer>();
for (int i = 0; i < hits.size(); i++) {
List<IAtomContainer> hitsList = new ArrayList<IAtomContainer>();
hitsList.add(AtomContainerManipulator.removeHydrogens(hits.get(i).getFragment()));
hitsListTest.add(hits.get(i).getFragment());
// Render.Highlight(AtomContainerManipulator.removeHydrogens(molecule), hitsList ,
// Double.toString(hits.get(i).getPeak()));
}
if (showDiagrams)
Render.Draw(molecule, hitsListTest, "Fragmente von: " + candidates.get(c));
} catch (CDKException e) {
System.out.println("CDK error!" + e.getMessage());
completeLog += "CDK Error! " + e.getMessage() + "File: " + candidates.get(c).substring(4);
} catch (FileNotFoundException e) {
System.out.println("File not found" + e.getMessage());
completeLog +=
"File not found error! " + e.getMessage() + "File: " + candidates.get(c).substring(4);
} catch (IOException e) {
System.out.println("IO error: " + e.getMessage());
completeLog += "IO Error! " + e.getMessage() + "File: " + candidates.get(c).substring(4);
} catch (Exception e) {
System.out.println("Error" + e.getMessage());
completeLog += "Error! " + e.getMessage() + "File: " + candidates.get(c).substring(4);
} catch (OutOfMemoryError e) {
System.out.println("Out of memory: " + e.getMessage() + "\n" + e.getStackTrace());
System.gc();
completeLog +=
"Out of memory! " + e.getMessage() + "File: " + candidates.get(c).substring(4);
}
}
// write things to log file
foundPeaks += combinedHits;
allPeaks += combinedPeakCount;
completeLog +=
"\nFile: "
+ candidates.get(c).substring(4)
+ "\t #Peaks: "
+ combinedPeakCount
+ "\t #Found: "
+ combinedHits;
completeLog += "\tPeaks: " + peaks;
}
// easy scoring
Integer[] keylist = new Integer[scoreMap.keySet().size()];
Object[] keys = scoreMap.keySet().toArray();
for (int i = 0; i < keys.length; i++) {
keylist[i] = Integer.parseInt(keys[i].toString());
}
Arrays.sort(keylist);
String scoreList = "";
int rank = 0;
for (int i = keylist.length - 1; i >= 0; i--) {
boolean check = false;
for (int j = 0; j < scoreMap.get(keylist[i]).size(); j++) {
scoreList += "\n" + keylist[i] + " - " + scoreMap.get(keylist[i]).get(j);
if (keggIdentifier.equals(scoreMap.get(keylist[i]).get(j))) {
check = true;
}
// worst case: count all which are better or have a equal position
rank++;
}
if (check) {
histogram += "\n" + file + "\t" + keggIdentifier + "\t" + rank + "\t" + exactMass;
}
}
if (keggIdentifier.equals("none")) {
histogram += "\n" + file + "\t" + keggIdentifier + "\t\t" + exactMass;
}
completeLog += "\n\n*****************Scoring*****************************";
completeLog += "Supposed to be: " + keggIdentifier;
completeLog += scoreList;
completeLog += "\n*****************************************************\n\n";
// easy scoring end
// real scoring
Double[] keysScore = new Double[realScoreMap.keySet().size()];
keysScore = realScoreMap.keySet().toArray(keysScore);
Arrays.sort(keysScore);
String scoreListReal = "";
rank = 0;
for (int i = keysScore.length - 1; i >= 0; i--) {
boolean check = false;
for (int j = 0; j < realScoreMap.get(keysScore[i]).size(); j++) {
scoreListReal += "\n" + keysScore[i] + " - " + realScoreMap.get(keysScore[i]).get(j);
if (keggIdentifier.compareTo(realScoreMap.get(keysScore[i]).get(j)) == 0) {
check = true;
}
// worst case: count all which are better or have a equal position
rank++;
}
if (check) {
histogramReal += "\n" + file + "\t" + keggIdentifier + "\t" + rank + "\t" + exactMass;
}
}
if (keggIdentifier.equals("none")) {
histogramReal += "\n" + file + "\t" + keggIdentifier + "\t\t" + exactMass;
}
// timing
long timeEnd = System.currentTimeMillis() - timeStart;
sumTime += timeEnd;
completeLog += "\n\n*****************Scoring(Real)*****************************";
completeLog += "Supposed to be: " + keggIdentifier;
completeLog += "\nTime: " + timeEnd;
completeLog += scoreListReal;
completeLog += "\n*****************************************************\n\n";
// write the data for peak histogram to log file
for (int i = 0; i < listOfPeaks.size(); i++) {
histogramPeaksAll += listOfPeaks.get(i) + "\n";
}
// filter the peaks which are contained in the all peaks list. (exclusive)
for (int i = 0; i < listOfPeaksCorresponding.size(); i++) {
for (int j = 0; j < listOfPeaks.size(); j++) {
Double valueA = listOfPeaks.get(j).getMass();
Double valueB = listOfPeaksCorresponding.get(i).getMass();
if (valueA.compareTo(valueB) == 0) {
listOfPeaks.remove(j);
}
}
}
for (int i = 0; i < listOfPeaks.size(); i++) {
histogramPeaks += listOfPeaks.get(i) + " ";
}
for (int i = 0; i < listOfPeaksCorresponding.size(); i++) {
histogramPeaksReal += listOfPeaksCorresponding.get(i) + " ";
}
}
/**
* calculates the kier shape indices for an atom container
*
* @param container AtomContainer
* @return kier1, kier2 and kier3 are returned as arrayList of doubles
* @throws CDKException Possible Exceptions
*/
@Override
public DescriptorValue calculate(IAtomContainer container) {
IAtomContainer atomContainer;
try {
atomContainer = (IAtomContainer) container.clone();
} catch (CloneNotSupportedException e) {
DoubleArrayResult kierValues = new DoubleArrayResult(3);
kierValues.add(Double.NaN);
kierValues.add(Double.NaN);
kierValues.add(Double.NaN);
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
kierValues,
getDescriptorNames());
}
atomContainer = AtomContainerManipulator.removeHydrogens(atomContainer);
// org.openscience.cdk.interfaces.IAtom[] atoms = atomContainer.getAtoms();
java.util.List firstAtomNeighboors;
java.util.List secondAtomNeighboors;
java.util.List thirdAtomNeighboors;
DoubleArrayResult kierValues = new DoubleArrayResult(3);
double bond1;
double bond2;
double bond3;
double kier1;
double kier2;
double kier3;
double atomsCount = atomContainer.getAtomCount();
ArrayList<Double> singlePaths = new ArrayList<Double>();
ArrayList<String> doublePaths = new ArrayList<String>();
ArrayList<String> triplePaths = new ArrayList<String>();
double[] sorterFirst = new double[2];
double[] sorterSecond = new double[3];
String tmpbond2;
String tmpbond3;
for (int a1 = 0; a1 < atomsCount; a1++) {
bond1 = 0;
firstAtomNeighboors = atomContainer.getConnectedAtomsList(atomContainer.getAtom(a1));
for (int a2 = 0; a2 < firstAtomNeighboors.size(); a2++) {
bond1 =
atomContainer.getBondNumber(
atomContainer.getAtom(a1), (IAtom) firstAtomNeighboors.get(a2));
if (!singlePaths.contains(new Double(bond1))) {
singlePaths.add(bond1);
java.util.Collections.sort(singlePaths);
}
secondAtomNeighboors =
atomContainer.getConnectedAtomsList((IAtom) firstAtomNeighboors.get(a2));
for (int a3 = 0; a3 < secondAtomNeighboors.size(); a3++) {
bond2 =
atomContainer.getBondNumber(
(IAtom) firstAtomNeighboors.get(a2), (IAtom) secondAtomNeighboors.get(a3));
if (!singlePaths.contains(new Double(bond2))) {
singlePaths.add(bond2);
}
sorterFirst[0] = bond1;
sorterFirst[1] = bond2;
java.util.Arrays.sort(sorterFirst);
tmpbond2 = sorterFirst[0] + "+" + sorterFirst[1];
if (!doublePaths.contains(tmpbond2) && (bond1 != bond2)) {
doublePaths.add(tmpbond2);
}
thirdAtomNeighboors =
atomContainer.getConnectedAtomsList((IAtom) secondAtomNeighboors.get(a3));
for (int a4 = 0; a4 < thirdAtomNeighboors.size(); a4++) {
bond3 =
atomContainer.getBondNumber(
(IAtom) secondAtomNeighboors.get(a3), (IAtom) thirdAtomNeighboors.get(a4));
if (!singlePaths.contains(new Double(bond3))) {
singlePaths.add(bond3);
}
sorterSecond[0] = bond1;
sorterSecond[1] = bond2;
sorterSecond[2] = bond3;
java.util.Arrays.sort(sorterSecond);
tmpbond3 = sorterSecond[0] + "+" + sorterSecond[1] + "+" + sorterSecond[2];
if (!triplePaths.contains(tmpbond3)) {
if ((bond1 != bond2) && (bond1 != bond3) && (bond2 != bond3)) {
triplePaths.add(tmpbond3);
}
}
}
}
}
}
if (atomsCount == 1) {
kier1 = 0;
kier2 = 0;
kier3 = 0;
} else {
kier1 =
(((atomsCount) * ((atomsCount - 1) * (atomsCount - 1)))
/ (singlePaths.size() * singlePaths.size()));
if (atomsCount == 2) {
kier2 = 0;
kier3 = 0;
} else {
if (doublePaths.size() == 0) kier2 = Double.NaN;
else
kier2 =
(((atomsCount - 1) * ((atomsCount - 2) * (atomsCount - 2)))
/ (doublePaths.size() * doublePaths.size()));
if (atomsCount == 3) {
kier3 = 0;
} else {
if (atomsCount % 2 != 0) {
if (triplePaths.size() == 0) kier3 = Double.NaN;
else
kier3 =
(((atomsCount - 1) * ((atomsCount - 3) * (atomsCount - 3)))
/ (triplePaths.size() * triplePaths.size()));
} else {
if (triplePaths.size() == 0) kier3 = Double.NaN;
else
kier3 =
(((atomsCount - 3) * ((atomsCount - 2) * (atomsCount - 2)))
/ (triplePaths.size() * triplePaths.size()));
}
}
}
}
kierValues.add(kier1);
kierValues.add(kier2);
kierValues.add(kier3);
return new DescriptorValue(
getSpecification(), getParameterNames(), getParameters(), kierValues, getDescriptorNames());
}
/** A unit test for JUnit */
@Test
public void testCisResorcinol() throws Exception {
HydrogenPlacer hydrogenPlacer = new HydrogenPlacer();
IAtomContainer mol1 = new AtomContainer();
SmilesGenerator sg = new SmilesGenerator();
mol1.addAtom(new Atom("O", new Point2d(3, 1)));
// 1
mol1.addAtom(new Atom("H", new Point2d(2, 0)));
// 2
mol1.addAtom(new Atom("C", new Point2d(2, 1)));
// 3
mol1.addAtom(new Atom("C", new Point2d(1, 1)));
// 4
mol1.addAtom(new Atom("C", new Point2d(1, 4)));
// 5
mol1.addAtom(new Atom("C", new Point2d(1, 5)));
// 6
mol1.addAtom(new Atom("C", new Point2d(1, 2)));
// 7
mol1.addAtom(new Atom("C", new Point2d(2, 2)));
// 1
mol1.addAtom(new Atom("O", new Point2d(3, 2)));
// 2
mol1.addAtom(new Atom("H", new Point2d(2, 3)));
// 3
mol1.addBond(0, 2, IBond.Order.SINGLE, IBond.Stereo.DOWN);
// 1
mol1.addBond(1, 2, IBond.Order.SINGLE, IBond.Stereo.UP);
// 2
mol1.addBond(2, 3, IBond.Order.SINGLE);
// 3
mol1.addBond(3, 4, IBond.Order.SINGLE);
// 4
mol1.addBond(4, 5, IBond.Order.SINGLE);
// 5
mol1.addBond(5, 6, IBond.Order.SINGLE);
// 6
mol1.addBond(6, 7, IBond.Order.SINGLE);
// 3
mol1.addBond(7, 8, IBond.Order.SINGLE, IBond.Stereo.UP);
// 4
mol1.addBond(7, 9, IBond.Order.SINGLE, IBond.Stereo.DOWN);
// 5
mol1.addBond(7, 2, IBond.Order.SINGLE);
// 6
try {
addExplicitHydrogens(mol1);
hydrogenPlacer.placeHydrogens2D(mol1, 1.0);
IsotopeFactory ifac = IsotopeFactory.getInstance(mol1.getBuilder());
ifac.configureAtoms(mol1);
} catch (IOException ex) {
} catch (ClassNotFoundException ex) {
}
String smiles1 = null;
if (standAlone) {
display(mol1);
}
try {
smiles1 = sg.createSMILES(mol1, true, new boolean[mol1.getBondCount()]);
} catch (Exception exc) {
System.out.println(exc);
if (!standAlone) {
Assert.fail();
}
}
if (standAlone) {
System.err.println("SMILES 1: " + smiles1);
}
Assert.assertNotNull(smiles1);
Assert.assertEquals(
"[H]O[C@]1(C([H])([H])C([H])([H])C([H])([H])C([H])([H])[C@]1(O[H])([H]))([H])", smiles1);
mol1 = AtomContainerManipulator.removeHydrogens(mol1);
try {
smiles1 = sg.createSMILES(mol1);
} catch (Exception exc) {
System.out.println(exc);
if (!standAlone) {
Assert.fail();
}
}
if (standAlone) {
System.err.println("SMILES 1: " + smiles1);
}
Assert.assertNotNull(smiles1);
Assert.assertEquals("OC1CCCCC1(O)", smiles1);
}