/** @cdk.bug 1535055 */
@Test
public void testBug1535055() throws Exception {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer mol = sp.parseSmiles("COC(=O)c1ccc2c(c1)c1ccccc1[nH]2");
CDKHueckelAromaticityDetector.detectAromaticity(mol);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
SmilesGenerator sg = new SmilesGenerator();
sg.setUseAromaticityFlag(true);
String s1 = sg.createSMILES(mol);
String filename = "data/cml/bug1535055.cml";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
CMLReader reader = new CMLReader(ins);
IChemFile chemFile = (IChemFile) reader.read(new ChemFile());
// test the resulting ChemFile content
Assert.assertNotNull(chemFile);
IAtomContainer mol2 = ChemFileManipulator.getAllAtomContainers(chemFile).get(0);
CDKHueckelAromaticityDetector.detectAromaticity(mol2);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol2);
String s2 = sg.createSMILES(mol2);
Assert.assertTrue(s1.contains("[nH]"));
Assert.assertTrue(s2.contains("[nH]"));
}
@Test
public void testfp2() throws Exception {
SmilesParser parser = new SmilesParser(NoNotificationChemObjectBuilder.getInstance());
IFingerprinter printer = new MACCSFingerprinter();
IMolecule mol1 = parser.parseSmiles("CC(N)CCCN");
IMolecule mol2 = parser.parseSmiles("CC(N)CCC");
IMolecule mol3 = parser.parseSmiles("CCCC");
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol1);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol2);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol3);
CDKHueckelAromaticityDetector.detectAromaticity(mol1);
CDKHueckelAromaticityDetector.detectAromaticity(mol2);
CDKHueckelAromaticityDetector.detectAromaticity(mol3);
BitSet bs1 = printer.getFingerprint(mol1);
BitSet bs2 = printer.getFingerprint(mol2);
BitSet bs3 = printer.getFingerprint(mol3);
Assert.assertFalse(bs1.get(124));
Assert.assertFalse(bs2.get(124));
Assert.assertFalse(bs3.get(124));
Assert.assertFalse(FingerprinterTool.isSubset(bs1, bs2));
Assert.assertTrue(FingerprinterTool.isSubset(bs2, bs3));
}
public static void main(String[] args) throws Exception, CloneNotSupportedException, IOException {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer mol1 = sp.parseSmiles("c1cccc(COC(=O)NC(CC(C)C)C(=O)NC(CCc2ccccc2)C(=O)COC)c1");
IAtomContainer mol2 = sp.parseSmiles("c1cccc(COC(=O)NC(CC(C)C)C(=O)NCC#N)c1");
CDKHueckelAromaticityDetector.detectAromaticity(mol1);
CDKHueckelAromaticityDetector.detectAromaticity(mol2);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol2);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol1);
IAtomContainer mcs = getMcsAsNewContainer(mol1, mol2);
MoleculeImage mi = new MoleculeImage(mcs);
byte[] bytes = mi.getBytes(300, 300);
FileOutputStream fos = new FileOutputStream("test.png");
fos.write(bytes);
int[][] map = getMcsAsAtomIndexMapping(mol1, mol2);
for (int i = 0; i < map.length; i++) {
System.out.println(map[i][0] + " <-> " + map[i][1]);
}
}
public BitSet process(IAtomContainer target) throws AmbitException {
try {
IAtomContainer ac = cfg.process(target);
aromaticDetector.detectAromaticity(ac);
return getStructureKeyBits(ac);
} catch (CDKException x) {
throw new AmbitException(x.getMessage());
} catch (AmbitException x) {
throw x;
} catch (Exception x) {
throw new AmbitException(x);
}
}
@Test
public void testQuinone() throws Exception {
IAtomContainer mol = MoleculeFactory.makeQuinone();
Assert.assertNotNull("Created molecule was null", mol);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
CDKHueckelAromaticityDetector.detectAromaticity(mol);
EquivalentClassPartitioner partitioner = new EquivalentClassPartitioner(mol);
int[] eqCl = partitioner.getTopoEquivClassbyHuXu(mol);
Partition autP = ArrayToPartition.convert(eqCl, 1);
Assert.assertEquals("Wrong number of equivalent classes", 3, autP.size());
Partition expected = Partition.fromString("0,7|1,4|2,3,5,6");
Assert.assertEquals("Wrong class assignment", expected, autP);
}
private Java2DRenderer prepareRenderer(IMolecule mol) throws Exception {
Renderer2DModel r2dm;
Java2DRenderer renderer;
Dimension imgSize;
try {
CDKHueckelAromaticityDetector.detectAromaticity(mol);
} catch (CDKException cdke) {
cdke.printStackTrace();
}
try {
imgSize = new Dimension(vRenderSizeX, vRenderSizeY);
r2dm = new Renderer2DModel();
r2dm.setDrawNumbers(false);
r2dm.showAtomTypeNames();
r2dm.setBackgroundDimension(imgSize);
r2dm.setBackColor(Color.WHITE);
r2dm.setDrawNumbers(false);
r2dm.setUseAntiAliasing(true);
r2dm.setColorAtomsByType(true);
r2dm.setShowImplicitHydrogens(true);
r2dm.setShowExplicitHydrogens(this.showHydrogen);
r2dm.setIsCompact(this.isCompact);
r2dm.setShowReactionBoxes(false);
r2dm.setKekuleStructure(false);
r2dm.setBondWidth(3);
// r2dm.setFont(new java.awt.Font("SansSerif", java.awt.Font.PLAIN, 14));
renderer = new Java2DRenderer(r2dm);
// 1200,900
// create renderer to render MOLString into an java.awt.Image
// renders 2D structures
} catch (Exception e) {
e.printStackTrace();
throw new Exception("Creation of renderer failed");
}
return renderer;
}
/**
* Fixes Aromaticity of the molecule i.e. need to find rings and aromaticity again since added H's
*
* @param mol
*/
@TestMethod("testFixAromaticity")
public static void configure(IAtomContainer mol) {
// need to find rings and aromaticity again since added H's
IRingSet ringSet = null;
try {
AllRingsFinder arf = new AllRingsFinder();
ringSet = arf.findAllRings(mol);
} catch (Exception e) {
e.printStackTrace();
}
try {
// figure out which atoms are in aromatic rings:
CDKHydrogenAdder cdk = CDKHydrogenAdder.getInstance(DefaultChemObjectBuilder.getInstance());
cdk.addImplicitHydrogens(mol);
ExtAtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
CDKHueckelAromaticityDetector.detectAromaticity(mol);
// figure out which rings are aromatic:
RingSetManipulator.markAromaticRings(ringSet);
// figure out which simple (non cycles) rings are aromatic:
// only atoms in 6 membered rings are aromatic
// determine largest ring that each atom is a part of
for (int i = 0; i < mol.getAtomCount(); i++) {
mol.getAtom(i).setFlag(CDKConstants.ISAROMATIC, false);
jloop:
for (int j = 0; j < ringSet.getAtomContainerCount(); j++) {
// logger.debug(i+"\t"+j);
IRing ring = (IRing) ringSet.getAtomContainer(j);
if (!ring.getFlag(CDKConstants.ISAROMATIC)) {
continue jloop;
}
boolean haveatom = ring.contains(mol.getAtom(i));
// logger.debug("haveatom="+haveatom);
if (haveatom && ring.getAtomCount() == 6) {
mol.getAtom(i).setFlag(CDKConstants.ISAROMATIC, true);
}
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
@Test
public void testWriteAromatic() throws Exception {
StringWriter stringWriter = new StringWriter();
IAtomContainer benzene = TestMoleculeFactory.makeBenzene();
addImplicitHydrogens(benzene);
CDKHueckelAromaticityDetector.detectAromaticity(benzene);
SMILESWriter smilesWriter = new SMILESWriter(stringWriter);
Properties prop = new Properties();
prop.setProperty("UseAromaticity", "true");
PropertiesListener listener = new PropertiesListener(prop);
smilesWriter.addChemObjectIOListener(listener);
smilesWriter.customizeJob();
smilesWriter.write(benzene);
smilesWriter.close();
Assert.assertFalse(stringWriter.toString().contains("C=C"));
Assert.assertTrue(stringWriter.toString().contains("ccc"));
}
/**
* Prepare the target molecule for analysis.
*
* <p>We perform ring perception and aromaticity detection and set up the appropriate properties.
* Right now, this function is called each time we need to do a query and this is inefficient.
*
* @throws CDKException if there is a problem in ring perception or aromaticity detection, which
* is usually related to a timeout in the ring finding code.
*/
private void initializeMolecule() throws CDKException {
// Code copied from
// org.openscience.cdk.qsar.descriptors.atomic.AtomValenceDescriptor;
Map<String, Integer> valencesTable = new HashMap<String, Integer>();
valencesTable.put("H", 1);
valencesTable.put("Li", 1);
valencesTable.put("Be", 2);
valencesTable.put("B", 3);
valencesTable.put("C", 4);
valencesTable.put("N", 5);
valencesTable.put("O", 6);
valencesTable.put("F", 7);
valencesTable.put("Na", 1);
valencesTable.put("Mg", 2);
valencesTable.put("Al", 3);
valencesTable.put("Si", 4);
valencesTable.put("P", 5);
valencesTable.put("S", 6);
valencesTable.put("Cl", 7);
valencesTable.put("K", 1);
valencesTable.put("Ca", 2);
valencesTable.put("Ga", 3);
valencesTable.put("Ge", 4);
valencesTable.put("As", 5);
valencesTable.put("Se", 6);
valencesTable.put("Br", 7);
valencesTable.put("Rb", 1);
valencesTable.put("Sr", 2);
valencesTable.put("In", 3);
valencesTable.put("Sn", 4);
valencesTable.put("Sb", 5);
valencesTable.put("Te", 6);
valencesTable.put("I", 7);
valencesTable.put("Cs", 1);
valencesTable.put("Ba", 2);
valencesTable.put("Tl", 3);
valencesTable.put("Pb", 4);
valencesTable.put("Bi", 5);
valencesTable.put("Po", 6);
valencesTable.put("At", 7);
valencesTable.put("Fr", 1);
valencesTable.put("Ra", 2);
valencesTable.put("Cu", 2);
valencesTable.put("Mn", 2);
valencesTable.put("Co", 2);
// do all ring perception
AllRingsFinder arf = new AllRingsFinder();
IRingSet allRings;
try {
allRings = arf.findAllRings(atomContainer);
} catch (CDKException e) {
logger.debug(e.toString());
throw new CDKException(e.toString(), e);
}
// sets SSSR information
SSSRFinder finder = new SSSRFinder(atomContainer);
IRingSet sssr = finder.findEssentialRings();
for (IAtom atom : atomContainer.atoms()) {
// add a property to each ring atom that will be an array of
// Integers, indicating what size ring the given atom belongs to
// Add SSSR ring counts
if (allRings.contains(atom)) { // it's in a ring
atom.setFlag(CDKConstants.ISINRING, true);
// lets find which ring sets it is a part of
List<Integer> ringsizes = new ArrayList<Integer>();
IRingSet currentRings = allRings.getRings(atom);
int min = 0;
for (int i = 0; i < currentRings.getAtomContainerCount(); i++) {
int size = currentRings.getAtomContainer(i).getAtomCount();
if (min > size) min = size;
ringsizes.add(size);
}
atom.setProperty(CDKConstants.RING_SIZES, ringsizes);
atom.setProperty(CDKConstants.SMALLEST_RINGS, sssr.getRings(atom));
} else {
atom.setFlag(CDKConstants.ISINRING, false);
}
// determine how many rings bonds each atom is a part of
int hCount;
if (atom.getImplicitHydrogenCount() == CDKConstants.UNSET) hCount = 0;
else hCount = atom.getImplicitHydrogenCount();
List<IAtom> connectedAtoms = atomContainer.getConnectedAtomsList(atom);
int total = hCount + connectedAtoms.size();
for (IAtom connectedAtom : connectedAtoms) {
if (connectedAtom.getSymbol().equals("H")) {
hCount++;
}
}
atom.setProperty(CDKConstants.TOTAL_CONNECTIONS, total);
atom.setProperty(CDKConstants.TOTAL_H_COUNT, hCount);
if (valencesTable.get(atom.getSymbol()) != null) {
int formalCharge =
atom.getFormalCharge() == CDKConstants.UNSET ? 0 : atom.getFormalCharge();
atom.setValency(valencesTable.get(atom.getSymbol()) - formalCharge);
}
}
for (IBond bond : atomContainer.bonds()) {
if (allRings.getRings(bond).getAtomContainerCount() > 0) {
bond.setFlag(CDKConstants.ISINRING, true);
}
}
for (IAtom atom : atomContainer.atoms()) {
List<IAtom> connectedAtoms = atomContainer.getConnectedAtomsList(atom);
int counter = 0;
IAtom any;
for (IAtom connectedAtom : connectedAtoms) {
any = connectedAtom;
if (any.getFlag(CDKConstants.ISINRING)) {
counter++;
}
}
atom.setProperty(CDKConstants.RING_CONNECTIONS, counter);
}
// check for atomaticity
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(atomContainer);
CDKHueckelAromaticityDetector.detectAromaticity(atomContainer);
} catch (CDKException e) {
logger.debug(e.toString());
throw new CDKException(e.toString(), e);
}
}
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());
}
public String perceiveSybylAtomTypes(IMolecule mol)
throws InvocationTargetException {
ICDKMolecule cdkmol;
try {
cdkmol = cdk.asCDKMolecule(mol);
}
catch (BioclipseException e) {
System.out.println("Error converting cdk10 to cdk");
e.printStackTrace();
throw new InvocationTargetException(e);
}
IAtomContainer ac = cdkmol.getAtomContainer();
CDKAtomTypeMatcher cdkMatcher
= CDKAtomTypeMatcher.getInstance(ac.getBuilder());
AtomTypeMapper mapper
= AtomTypeMapper.getInstance(
"org/openscience/cdk/dict/data/cdk-sybyl-mappings.owl" );
IAtomType[] sybylTypes = new IAtomType[ac.getAtomCount()];
int atomCounter = 0;
int a=0;
for (IAtom atom : ac.atoms()) {
IAtomType type;
try {
type = cdkMatcher.findMatchingAtomType(ac, atom);
}
catch (CDKException e) {
type = null;
}
if (type==null) {
// logger.debug("AT null for atom: " + atom);
type = atom.getBuilder().newAtomType(atom.getSymbol());
type.setAtomTypeName("X");
}
AtomTypeManipulator.configure(atom, type);
a++;
}
try {
CDKHueckelAromaticityDetector.detectAromaticity(ac);
// System.out.println("Arom: "
// + CDKHueckelAromaticityDetector.detectAromaticity(ac) );
}
catch (CDKException e) {
logger.debug("Failed to perceive aromaticity: " + e.getMessage());
}
for (IAtom atom : ac.atoms()) {
String mappedType = mapper.mapAtomType(atom.getAtomTypeName());
if ("C.2".equals(mappedType)
&& atom.getFlag(CDKConstants.ISAROMATIC)) {
mappedType = "C.ar";
}
else if ("N.pl3".equals(mappedType)
&& atom.getFlag(CDKConstants.ISAROMATIC)) {
mappedType = "N.ar";
}
try {
sybylTypes[atomCounter] = factory.getAtomType(mappedType);
}
catch (NoSuchAtomTypeException e) {
// yes, setting null's here is important
sybylTypes[atomCounter] = null;
}
atomCounter++;
}
StringBuffer result = new StringBuffer();
// now that full perception is finished, we can set atom type names:
for (int i = 0; i < sybylTypes.length; i++) {
if (sybylTypes[i] != null) {
ac.getAtom(i).setAtomTypeName(sybylTypes[i].getAtomTypeName());
}
else {
ac.getAtom(i).setAtomTypeName("X");
}
result.append(i).append(':').append(ac.getAtom(i).getAtomTypeName())
/*.append("\n")*/;
}
return result.toString();
}
/**
* Loads one or more files into IAtomContainer objects.
*
* <p>This method does not need knowledge of the format since it is autodetected. Note that if
* aromaticity detection or atom typing is specified and fails for a specific molecule, that
* molecule will be set to <i>null</i>
*
* @param filenames An array of String's containing the filenames of the structures we want to
* load
* @param doAromaticity If true, then aromaticity perception is performed
* @param doTyping If true, atom typing and configuration is performed. This will use the internal
* CDK atom typing scheme
* @return An array of AtoContainer's
* @throws CDKException if there is an error when reading a file
*/
public static IAtomContainer[] loadMolecules(
String[] filenames, boolean doAromaticity, boolean doTyping, boolean doIsotopes)
throws CDKException, IOException {
Vector<IAtomContainer> v = new Vector<IAtomContainer>();
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
try {
int i;
int j;
for (i = 0; i < filenames.length; i++) {
File input = new File(filenames[i]);
ReaderFactory readerFactory = new ReaderFactory();
ISimpleChemObjectReader reader = readerFactory.createReader(new FileReader(input));
if (reader == null) { // see if it's a SMI file
if (filenames[i].endsWith(".smi")) {
reader = new SMILESReader(new FileReader(input));
}
}
IChemFile content = (IChemFile) reader.read(builder.newInstance(IChemFile.class));
if (content == null) continue;
List<IAtomContainer> c = ChemFileManipulator.getAllAtomContainers(content);
// we should do this loop in case we have files
// that contain multiple molecules
v.addAll(c);
}
} catch (Exception e) {
e.printStackTrace();
throw new CDKException(e.toString());
}
// convert the vector to a simple array
IAtomContainer[] retValues = new IAtomContainer[v.size()];
for (int i = 0; i < v.size(); i++) {
retValues[i] = v.get(i);
}
// before returning, lets make see if we
// need to perceive aromaticity and atom typing
if (doAromaticity) {
for (int i = 0; i < retValues.length; i++) {
try {
CDKHueckelAromaticityDetector.detectAromaticity(retValues[i]);
} catch (CDKException e) {
retValues[i] = null;
}
}
}
if (doTyping) {
for (int i = 0; i < retValues.length; i++) {
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(retValues[i]);
} catch (CDKException e) {
retValues[i] = null;
}
}
}
if (doIsotopes) {
IsotopeFactory ifac = IsotopeFactory.getInstance(DefaultChemObjectBuilder.getInstance());
for (IAtomContainer retValue : retValues) {
ifac.configureAtoms(retValue);
}
}
return retValues;
}
@TestMethod(value = "testCalculate_IAtomContainer")
public DescriptorValue calculate(
IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset) {
IAtomContainer varAtomContainer;
try {
varAtomContainer = (IAtomContainer) atomContainer.clone();
} catch (CloneNotSupportedException e) {
return getDummyDescriptorValue(e);
}
int atomPosition = atomContainer.getAtomNumber(atom);
IAtom clonedAtom = varAtomContainer.getAtom(atomPosition);
DoubleArrayResult rdfProtonCalculatedValues = new DoubleArrayResult(gsr_desc_length);
if (!atom.getSymbol().equals("H")) {
return getDummyDescriptorValue(new CDKException("Invalid atom specified"));
}
///////////////////////// FIRST SECTION OF MAIN METHOD: DEFINITION OF MAIN VARIABLES
///////////////////////// AND AROMATICITY AND PI-SYSTEM AND RINGS DETECTION
Molecule mol = new Molecule(varAtomContainer);
if (varAtomContainer != acold) {
acold = varAtomContainer;
// DETECTION OF pi SYSTEMS
varAtomContainerSet = ConjugatedPiSystemsDetector.detect(mol);
if (precalculatedringset == null)
try {
varRingSet = (new AllRingsFinder()).findAllRings(varAtomContainer);
} catch (CDKException e) {
return getDummyDescriptorValue(e);
}
else varRingSet = precalculatedringset;
try {
GasteigerMarsiliPartialCharges peoe = new GasteigerMarsiliPartialCharges();
peoe.assignGasteigerMarsiliSigmaPartialCharges(mol, true);
} catch (Exception ex1) {
return getDummyDescriptorValue(ex1);
}
}
if (checkAromaticity) {
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(varAtomContainer);
CDKHueckelAromaticityDetector.detectAromaticity(varAtomContainer);
} catch (CDKException e) {
return getDummyDescriptorValue(e);
}
}
IRingSet rsAtom;
Ring ring;
IRingSet ringsWithThisBond;
// SET ISINRING FLAGS FOR BONDS
Iterator<IBond> bondsInContainer = varAtomContainer.bonds().iterator();
while (bondsInContainer.hasNext()) {
IBond bond = bondsInContainer.next();
ringsWithThisBond = varRingSet.getRings(bond);
if (ringsWithThisBond.getAtomContainerCount() > 0) {
bond.setFlag(CDKConstants.ISINRING, true);
}
}
// SET ISINRING FLAGS FOR ATOMS
IRingSet ringsWithThisAtom;
for (int w = 0; w < varAtomContainer.getAtomCount(); w++) {
ringsWithThisAtom = varRingSet.getRings(varAtomContainer.getAtom(w));
if (ringsWithThisAtom.getAtomContainerCount() > 0) {
varAtomContainer.getAtom(w).setFlag(CDKConstants.ISINRING, true);
}
}
IAtomContainer detected = varAtomContainerSet.getAtomContainer(0);
// neighboors[0] is the atom joined to the target proton:
List<IAtom> neighboors = mol.getConnectedAtomsList(clonedAtom);
IAtom neighbour0 = neighboors.get(0);
// 2', 3', 4', 5', 6', and 7' atoms up to the target are detected:
List<IAtom> atomsInSecondSphere = mol.getConnectedAtomsList(neighbour0);
List<IAtom> atomsInThirdSphere;
List<IAtom> atomsInFourthSphere;
List<IAtom> atomsInFifthSphere;
List<IAtom> atomsInSixthSphere;
List<IAtom> atomsInSeventhSphere;
// SOME LISTS ARE CREATED FOR STORING OF INTERESTING ATOMS AND BONDS DURING DETECTION
ArrayList<Integer> singles = new ArrayList<Integer>(); // list of any bond not rotatable
ArrayList<Integer> doubles = new ArrayList<Integer>(); // list with only double bonds
ArrayList<Integer> atoms = new ArrayList<Integer>(); // list with all the atoms in spheres
// atoms.add( Integer.valueOf( mol.getAtomNumber(neighboors[0]) ) );
ArrayList<Integer> bondsInCycloex =
new ArrayList<Integer>(); // list for bonds in cycloexane-like rings
// 2', 3', 4', 5', 6', and 7' bonds up to the target are detected:
IBond secondBond; // (remember that first bond is proton bond)
IBond thirdBond; //
IBond fourthBond; //
IBond fifthBond; //
IBond sixthBond; //
IBond seventhBond; //
// definition of some variables used in the main FOR loop for detection of interesting atoms and
// bonds:
boolean theBondIsInA6MemberedRing; // this is like a flag for bonds which are in cycloexane-like
// rings (rings with more than 4 at.)
IBond.Order bondOrder;
int bondNumber;
int sphere;
// THIS MAIN FOR LOOP DETECT RIGID BONDS IN 7 SPHERES:
for (IAtom curAtomSecond : atomsInSecondSphere) {
secondBond = mol.getBond(neighbour0, curAtomSecond);
if (mol.getAtomNumber(curAtomSecond) != atomPosition
&& getIfBondIsNotRotatable(mol, secondBond, detected)) {
sphere = 2;
bondOrder = secondBond.getOrder();
bondNumber = mol.getBondNumber(secondBond);
theBondIsInA6MemberedRing = false;
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomSecond),
atoms,
sphere,
theBondIsInA6MemberedRing);
atomsInThirdSphere = mol.getConnectedAtomsList(curAtomSecond);
if (atomsInThirdSphere.size() > 0) {
for (IAtom curAtomThird : atomsInThirdSphere) {
thirdBond = mol.getBond(curAtomThird, curAtomSecond);
// IF THE ATOMS IS IN THE THIRD SPHERE AND IN A CYCLOEXANE-LIKE RING, IT IS STORED IN
// THE PROPER LIST:
if (mol.getAtomNumber(curAtomThird) != atomPosition
&& getIfBondIsNotRotatable(mol, thirdBond, detected)) {
sphere = 3;
bondOrder = thirdBond.getOrder();
bondNumber = mol.getBondNumber(thirdBond);
theBondIsInA6MemberedRing = false;
// if the bond is in a cyclohexane-like ring (a ring with 5 or more atoms, not
// aromatic)
// the boolean "theBondIsInA6MemberedRing" is set to true
if (!thirdBond.getFlag(CDKConstants.ISAROMATIC)) {
if (!curAtomThird.equals(neighbour0)) {
rsAtom = varRingSet.getRings(thirdBond);
for (int f = 0; f < rsAtom.getAtomContainerCount(); f++) {
ring = (Ring) rsAtom.getAtomContainer(f);
if (ring.getRingSize() > 4 && ring.contains(thirdBond)) {
theBondIsInA6MemberedRing = true;
}
}
}
}
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomThird),
atoms,
sphere,
theBondIsInA6MemberedRing);
theBondIsInA6MemberedRing = false;
atomsInFourthSphere = mol.getConnectedAtomsList(curAtomThird);
if (atomsInFourthSphere.size() > 0) {
for (IAtom curAtomFourth : atomsInFourthSphere) {
fourthBond = mol.getBond(curAtomThird, curAtomFourth);
if (mol.getAtomNumber(curAtomFourth) != atomPosition
&& getIfBondIsNotRotatable(mol, fourthBond, detected)) {
sphere = 4;
bondOrder = fourthBond.getOrder();
bondNumber = mol.getBondNumber(fourthBond);
theBondIsInA6MemberedRing = false;
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomFourth),
atoms,
sphere,
theBondIsInA6MemberedRing);
atomsInFifthSphere = mol.getConnectedAtomsList(curAtomFourth);
if (atomsInFifthSphere.size() > 0) {
for (IAtom curAtomFifth : atomsInFifthSphere) {
fifthBond = mol.getBond(curAtomFifth, curAtomFourth);
if (mol.getAtomNumber(curAtomFifth) != atomPosition
&& getIfBondIsNotRotatable(mol, fifthBond, detected)) {
sphere = 5;
bondOrder = fifthBond.getOrder();
bondNumber = mol.getBondNumber(fifthBond);
theBondIsInA6MemberedRing = false;
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomFifth),
atoms,
sphere,
theBondIsInA6MemberedRing);
atomsInSixthSphere = mol.getConnectedAtomsList(curAtomFifth);
if (atomsInSixthSphere.size() > 0) {
for (IAtom curAtomSixth : atomsInSixthSphere) {
sixthBond = mol.getBond(curAtomFifth, curAtomSixth);
if (mol.getAtomNumber(curAtomSixth) != atomPosition
&& getIfBondIsNotRotatable(mol, sixthBond, detected)) {
sphere = 6;
bondOrder = sixthBond.getOrder();
bondNumber = mol.getBondNumber(sixthBond);
theBondIsInA6MemberedRing = false;
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomSixth),
atoms,
sphere,
theBondIsInA6MemberedRing);
atomsInSeventhSphere = mol.getConnectedAtomsList(curAtomSixth);
if (atomsInSeventhSphere.size() > 0) {
for (IAtom curAtomSeventh : atomsInSeventhSphere) {
seventhBond = mol.getBond(curAtomSeventh, curAtomSixth);
if (mol.getAtomNumber(curAtomSeventh) != atomPosition
&& getIfBondIsNotRotatable(mol, seventhBond, detected)) {
sphere = 7;
bondOrder = seventhBond.getOrder();
bondNumber = mol.getBondNumber(seventhBond);
theBondIsInA6MemberedRing = false;
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomSeventh),
atoms,
sphere,
theBondIsInA6MemberedRing);
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
// Variables
double[] values; // for storage of results of other methods
double distance;
double sum;
double smooth = -20;
double partial;
int position;
double limitInf;
double limitSup;
double step;
//////////////////////// THE FOUTH DESCRIPTOR IS gS(r), WHICH TAKES INTO ACCOUNT SINGLE BONDS IN
// RIGID SYSTEMS
Vector3d a_a = new Vector3d();
Vector3d a_b = new Vector3d();
Vector3d b_a = new Vector3d();
Vector3d b_b = new Vector3d();
Point3d middlePoint = new Point3d();
double angle = 0;
if (singles.size() > 0) {
double dist0;
double dist1;
IAtom singleBondAtom0;
IAtom singleBondAtom1;
distance = 0;
position = 0;
IBond theSingleBond = null;
limitInf = 0;
limitSup = Math.PI / 2;
step = (limitSup - limitInf) / 7;
smooth = -1.15;
int counter = 0;
for (double ghs = 0; ghs < limitSup; ghs = ghs + step) {
sum = 0;
for (int sing = 0; sing < singles.size(); sing++) {
angle = 0;
partial = 0;
Integer thisSingleBond = singles.get(sing);
position = thisSingleBond;
theSingleBond = mol.getBond(position);
middlePoint = theSingleBond.get3DCenter();
singleBondAtom0 = theSingleBond.getAtom(0);
singleBondAtom1 = theSingleBond.getAtom(1);
dist0 = calculateDistanceBetweenTwoAtoms(singleBondAtom0, atom);
dist1 = calculateDistanceBetweenTwoAtoms(singleBondAtom1, atom);
a_a.set(middlePoint.x, middlePoint.y, middlePoint.z);
if (dist1 > dist0)
a_b.set(
singleBondAtom0.getPoint3d().x,
singleBondAtom0.getPoint3d().y,
singleBondAtom0.getPoint3d().z);
else
a_b.set(
singleBondAtom1.getPoint3d().x,
singleBondAtom1.getPoint3d().y,
singleBondAtom1.getPoint3d().z);
b_a.set(middlePoint.x, middlePoint.y, middlePoint.z);
b_b.set(atom.getPoint3d().x, atom.getPoint3d().y, atom.getPoint3d().z);
values = calculateDistanceBetweenAtomAndBond(atom, theSingleBond);
angle = calculateAngleBetweenTwoLines(a_a, a_b, b_a, b_b);
// System.out.println("ANGLe: "+angle+ " "+ mol.getAtomNumber(atomsInSingleBond[0]) +" "
// +mol.getAtomNumber(atomsInSingleBond[1]));
partial =
(1 / (Math.pow(values[0], 2))) * Math.exp(smooth * (Math.pow((ghs - angle), 2)));
sum += partial;
}
// gSr_function.add(new Double(sum));
rdfProtonCalculatedValues.add(sum);
logger.debug("RDF gSr prob.: " + sum + " at distance " + ghs);
counter++;
}
} else {
return getDummyDescriptorValue(new CDKException("Some error occurred. Please report"));
}
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
rdfProtonCalculatedValues,
getDescriptorNames());
}
/**
* Search if the setOfAtomContainer contains the atomContainer
*
* @param set ISetOfAtomContainer object where to search
* @param atomContainer IAtomContainer to search
* @return True, if the atomContainer is contained
*/
private boolean existAC(IAtomContainerSet set, IAtomContainer atomContainer) {
IAtomContainer acClone = null;
try {
acClone = (IMolecule) atomContainer.clone();
if (!lookingSymmetry) {
/*remove all aromatic flags*/
for (IAtom atom : acClone.atoms()) atom.setFlag(CDKConstants.ISAROMATIC, false);
for (IBond bond : acClone.bonds()) bond.setFlag(CDKConstants.ISAROMATIC, false);
}
} catch (CloneNotSupportedException e1) {
e1.printStackTrace();
}
for (int i = 0; i < acClone.getAtomCount(); i++)
// if(acClone.getAtom(i).getID() == null)
acClone.getAtom(i).setID("" + acClone.getAtomNumber(acClone.getAtom(i)));
if (lookingSymmetry) {
try {
CDKHueckelAromaticityDetector.detectAromaticity(acClone);
} catch (CDKException e) {
e.printStackTrace();
}
} else {
if (!lookingSymmetry) {
/*remove all aromatic flags*/
for (IAtom atom : acClone.atoms()) atom.setFlag(CDKConstants.ISAROMATIC, false);
for (IBond bond : acClone.bonds()) bond.setFlag(CDKConstants.ISAROMATIC, false);
}
}
for (int i = 0; i < set.getAtomContainerCount(); i++) {
IAtomContainer ss = set.getAtomContainer(i);
for (int j = 0; j < ss.getAtomCount(); j++)
// if(ss.getAtom(j).getID() == null)
ss.getAtom(j).setID("" + ss.getAtomNumber(ss.getAtom(j)));
try {
if (!lookingSymmetry) {
QueryAtomContainer qAC =
QueryAtomContainerCreator.createSymbolChargeIDQueryContainer(acClone);
if (UniversalIsomorphismTester.isIsomorph(ss, qAC)) {
QueryAtomContainer qAC2 =
QueryAtomContainerCreator.createSymbolAndBondOrderQueryContainer(acClone);
if (UniversalIsomorphismTester.isIsomorph(ss, qAC2)) return true;
}
} else {
QueryAtomContainer qAC =
QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(acClone);
CDKHueckelAromaticityDetector.detectAromaticity(ss);
if (UniversalIsomorphismTester.isIsomorph(ss, qAC)) return true;
}
} catch (CDKException e1) {
System.err.println(e1);
logger.error(e1.getMessage());
logger.debug(e1);
}
}
return false;
}