@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));
}
/** @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 testFingerprinter_int_int() throws java.lang.Exception {
ShortestPathFingerprinter fingerprinter = new ShortestPathFingerprinter(1024);
Assert.assertNotNull(fingerprinter);
IAtomContainer mol = TestMoleculeFactory.makeIndole();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
BitSet bs = fingerprinter.getBitFingerprint(mol).asBitSet();
IAtomContainer frag1 = TestMoleculeFactory.makePyrrole();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(frag1);
BitSet bs1 = fingerprinter.getBitFingerprint(frag1).asBitSet();
Assert.assertTrue(FingerprinterTool.isSubset(bs, bs1));
}
@Test
public void testGenerateFingerprintMultiphtalene() throws InvalidSmilesException, Exception {
String smiles = "C1=CC2=CC=C3C4=CC5=CC6=CC=CC=C6C=C5C=C4C=CC3=C2C=C1";
SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer molecule = smilesParser.parseSmiles(smiles);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
ShortestPathFingerprinter fingerprint = new ShortestPathFingerprinter(1024);
BitSet fingerprint1;
fingerprint1 = fingerprint.getBitFingerprint(molecule).asBitSet();
org.junit.Assert.assertEquals(15, fingerprint1.cardinality());
}
/**
* 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);
}
/**
* Get the expected set of molecules.
*
* @return The IAtomContainerSet
*/
private IAtomContainerSet getExpectedProducts() {
IAtomContainerSet setOfProducts = builder.newInstance(IAtomContainerSet.class);
IAtomContainer molecule = builder.newInstance(IAtomContainer.class);
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.getAtom(0).setFormalCharge(1);
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.addBond(0, 1, IBond.Order.SINGLE);
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.addBond(1, 2, IBond.Order.SINGLE);
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.addBond(2, 3, IBond.Order.SINGLE);
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.addBond(3, 4, IBond.Order.SINGLE);
molecule.addAtom(builder.newInstance(IAtom.class, "C"));
molecule.addBond(4, 5, IBond.Order.SINGLE);
try {
addExplicitHydrogens(molecule);
} catch (Exception e) {
e.printStackTrace();
}
molecule.getAtom(0).setFormalCharge(0);
molecule.addSingleElectron(new SingleElectron(molecule.getAtom(0)));
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
makeSureAtomTypesAreRecognized(molecule);
} catch (CDKException e) {
e.printStackTrace();
}
setOfProducts.addAtomContainer(molecule);
return setOfProducts;
}
@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());
}
/**
* A unit test for JUnit with C=CCCl # C=CC[Cl+*]
*
* @cdk.inchi InChI=1/C3H7Cl/c1-2-3-4/h2-3H2,1H3
*/
@Test
public void testCompareIonized() throws Exception {
IAtomContainer molA = builder.newInstance(IAtomContainer.class);
molA.addAtom(builder.newInstance(IAtom.class, "C"));
molA.addAtom(builder.newInstance(IAtom.class, "C"));
molA.addBond(0, 1, IBond.Order.SINGLE);
molA.addAtom(builder.newInstance(IAtom.class, "C"));
molA.addBond(1, 2, IBond.Order.SINGLE);
molA.addAtom(builder.newInstance(IAtom.class, "Cl"));
molA.addBond(2, 3, IBond.Order.SINGLE);
addExplicitHydrogens(molA);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molA);
lpcheck.saturate(molA);
double resultA =
((DoubleResult) descriptor.calculate(molA.getAtom(3), molA).getValue()).doubleValue();
IAtomContainer molB = builder.newInstance(IAtomContainer.class);
molB.addAtom(builder.newInstance(IAtom.class, "C"));
molB.addAtom(builder.newInstance(IAtom.class, "C"));
molB.addBond(0, 1, IBond.Order.SINGLE);
molB.addAtom(builder.newInstance(IAtom.class, "C"));
molB.addBond(1, 2, IBond.Order.SINGLE);
molB.addAtom(builder.newInstance(IAtom.class, "Cl"));
molB.getAtom(3).setFormalCharge(1);
molB.addSingleElectron(3);
molB.addLonePair(3);
molB.addLonePair(3);
molB.addBond(2, 3, IBond.Order.SINGLE);
addExplicitHydrogens(molB);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molB);
lpcheck.saturate(molB);
Assert.assertEquals(1, molB.getAtom(3).getFormalCharge(), 0.00001);
Assert.assertEquals(1, molB.getSingleElectronCount(), 0.00001);
Assert.assertEquals(2, molB.getLonePairCount(), 0.00001);
double resultB =
((DoubleResult) descriptor.calculate(molB.getAtom(3), molB).getValue()).doubleValue();
Assert.assertNotSame(resultA, resultB);
}
@Test
public void testRegression() throws Exception {
IAtomContainer mol1 = TestMoleculeFactory.makeIndole();
IAtomContainer mol2 = TestMoleculeFactory.makePyrrole();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol1);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol2);
ShortestPathFingerprinter fingerprinter = new ShortestPathFingerprinter();
IBitFingerprint bs1 = fingerprinter.getBitFingerprint(mol1);
Assert.assertEquals(
"Seems the fingerprint code has changed. This will cause a number of other tests to fail too!",
22,
bs1.cardinality());
IBitFingerprint bs2 = fingerprinter.getBitFingerprint(mol2);
Assert.assertEquals(
"Seems the fingerprint code has changed. This will cause a number of other tests to fail too!",
11,
bs2.cardinality());
}
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]);
}
}
@Test
public void testFingerprinterBitSetSize() throws Exception {
ShortestPathFingerprinter fingerprinter = new ShortestPathFingerprinter(1024);
Assert.assertNotNull(fingerprinter);
IAtomContainer mol = TestMoleculeFactory.makeIndole();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
BitSet bs = fingerprinter.getBitFingerprint(mol).asBitSet();
Assert.assertEquals(1024, bs.length()); // highest set bit
Assert.assertEquals(1024, bs.size()); // actual bit set size
}
@Test
public void testgetBitFingerprint_IAtomContainer() throws java.lang.Exception {
ShortestPathFingerprinter fingerprinter = new ShortestPathFingerprinter();
IAtomContainer mol = TestMoleculeFactory.makeIndole();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
IBitFingerprint bs = fingerprinter.getBitFingerprint(mol);
Assert.assertNotNull(bs);
Assert.assertEquals(fingerprinter.getSize(), bs.size());
}
/**
* This method calculates the ionization potential of an atom.
*
* @param atom The IAtom to ionize.
* @param container Parameter is the IAtomContainer.
* @return The ionization potential. Not possible the ionization.
*/
@Override
public DescriptorValue calculate(IAtom atom, IAtomContainer container) {
double value = 0;
// FIXME: for now I'll cache a few modified atomic properties, and restore them at the end of
// this method
String originalAtomtypeName = atom.getAtomTypeName();
Integer originalNeighborCount = atom.getFormalNeighbourCount();
Integer originalValency = atom.getValency();
IAtomType.Hybridization originalHybrid = atom.getHybridization();
Double originalBondOrderSum = atom.getBondOrderSum();
Order originalMaxBondOrder = atom.getMaxBondOrder();
if (!isCachedAtomContainer(container)) {
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(container);
LonePairElectronChecker lpcheck = new LonePairElectronChecker();
lpcheck.saturate(container);
} catch (CDKException e) {
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new DoubleResult(Double.NaN),
getDescriptorNames(),
e);
}
}
try {
value = IonizationPotentialTool.predictIP(container, atom);
} catch (CDKException e) {
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new DoubleResult(Double.NaN),
getDescriptorNames(),
e);
}
// restore original props
atom.setAtomTypeName(originalAtomtypeName);
atom.setFormalNeighbourCount(originalNeighborCount);
atom.setValency(originalValency);
atom.setHybridization(originalHybrid);
atom.setMaxBondOrder(originalMaxBondOrder);
atom.setBondOrderSum(originalBondOrderSum);
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new DoubleResult(value),
getDescriptorNames());
}
/** @cdk.inchi InChI=1/C4H5N/c1-2-4-5-3-1/h1-5H */
@Test
public void xtestPyrrole() throws Exception {
IAtomContainer enol = new AtomContainer();
// atom block
IAtom atom1 = new Atom(Elements.CARBON);
atom1.setHybridization(Hybridization.SP2);
IAtom atom2 = new Atom(Elements.CARBON);
atom2.setHybridization(Hybridization.SP2);
IAtom atom3 = new Atom(Elements.CARBON);
atom3.setHybridization(Hybridization.SP2);
IAtom atom4 = new Atom(Elements.CARBON);
atom4.setHybridization(Hybridization.SP2);
IAtom atom5 = new Atom(Elements.NITROGEN);
atom5.setHybridization(Hybridization.SP2);
atom5.setImplicitHydrogenCount(1);
// bond block
IBond bond1 = new Bond(atom1, atom2);
IBond bond2 = new Bond(atom2, atom3);
IBond bond3 = new Bond(atom3, atom4);
IBond bond4 = new Bond(atom4, atom5);
IBond bond5 = new Bond(atom5, atom1);
enol.addAtom(atom1);
enol.addAtom(atom2);
enol.addAtom(atom3);
enol.addAtom(atom4);
enol.addAtom(atom5);
enol.addBond(bond1);
enol.addBond(bond2);
enol.addBond(bond3);
enol.addBond(bond4);
enol.addBond(bond5);
// perceive atom types
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(enol);
// now have the algorithm have a go at it
enol = fbot.kekuliseAromaticRings(enol);
Assert.assertNotNull(enol);
// Assert.assertTrue(fbot.isOK(enol));
// now check whether it did the right thing
Assert.assertEquals(CDKConstants.BONDORDER_DOUBLE, enol.getBond(0).getOrder());
;
Assert.assertEquals(CDKConstants.BONDORDER_SINGLE, enol.getBond(1).getOrder());
;
Assert.assertEquals(CDKConstants.BONDORDER_DOUBLE, enol.getBond(2).getOrder());
;
Assert.assertEquals(CDKConstants.BONDORDER_SINGLE, enol.getBond(3).getOrder());
;
Assert.assertEquals(CDKConstants.BONDORDER_SINGLE, enol.getBond(4).getOrder());
;
}
private void fixHydrogenIsotopes(IAtomContainer molecule, IsotopeFactory isotopeFactory) {
for (IAtom atom : AtomContainerManipulator.getAtomArray(molecule)) {
if (atom instanceof IPseudoAtom) {
IPseudoAtom pseudo = (IPseudoAtom) atom;
if ("D".equals(pseudo.getLabel())) {
IAtom newAtom = molecule.getBuilder().newInstance(IAtom.class, atom);
newAtom.setSymbol("H");
newAtom.setAtomicNumber(1);
isotopeFactory.configure(newAtom, isotopeFactory.getIsotope("H", 2));
AtomContainerManipulator.replaceAtomByAtom(molecule, atom, newAtom);
} else if ("T".equals(pseudo.getLabel())) {
IAtom newAtom = molecule.getBuilder().newInstance(IAtom.class, atom);
newAtom.setSymbol("H");
newAtom.setAtomicNumber(1);
isotopeFactory.configure(newAtom, isotopeFactory.getIsotope("H", 3));
AtomContainerManipulator.replaceAtomByAtom(molecule, atom, newAtom);
}
}
}
}
/**
* Test of ShortestPathFingerprinter method
*
* @throws InvalidSmilesException
* @throws CDKException
*/
@Test
public void testGenerateFingerprintIsSubset() throws InvalidSmilesException, CDKException {
String smilesT = "NC(=O)C1=C2C=CC(Br)=CC2=C(Cl)C=C1";
String smilesQ = "CC1=C2C=CC(Br)=CC2=C(Cl)C=C1";
SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer moleculeQ = smilesParser.parseSmiles(smilesQ);
IAtomContainer moleculeT = smilesParser.parseSmiles(smilesT);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(moleculeQ);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(moleculeT);
ShortestPathFingerprinter fingerprint = new ShortestPathFingerprinter(1024);
BitSet fingerprintQ;
BitSet fingerprintT;
fingerprintQ = fingerprint.getBitFingerprint(moleculeQ).asBitSet();
fingerprintT = fingerprint.getBitFingerprint(moleculeT).asBitSet();
org.junit.Assert.assertTrue(FingerprinterTool.isSubset(fingerprintT, fingerprintQ));
}
static Graph convert(
IAtomContainer ac,
boolean perceiveAromaticity,
boolean isomeric,
boolean aromatic,
boolean atomClasses)
throws Exception {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(ac);
CDKHydrogenAdder.getInstance(SilentChemObjectBuilder.getInstance()).addImplicitHydrogens(ac);
if (perceiveAromaticity) Aromaticity.cdkLegacy().apply(ac);
return new CDKToBeam(isomeric, aromatic, atomClasses).toBeamGraph(ac);
}
/**
* Test of ShortestPathFingerprinter method
*
* @throws InvalidSmilesException
* @throws CDKException
* @throws FileNotFoundException
*/
@Test
public void testGenerateFingerprintIsNotASubset1()
throws InvalidSmilesException, CDKException, FileNotFoundException, FileNotFoundException {
String smilesT = "O[C@H]1[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@@H]1O";
String smilesQ = "OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(O)=O";
SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
smilesParser.kekulise(false);
IAtomContainer moleculeQ = smilesParser.parseSmiles(smilesQ);
IAtomContainer moleculeT = smilesParser.parseSmiles(smilesT);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(moleculeQ);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(moleculeT);
ShortestPathFingerprinter fingerprint = new ShortestPathFingerprinter(1024);
BitSet fingerprintQ;
BitSet fingerprintT;
fingerprintQ = fingerprint.getBitFingerprint(moleculeQ).asBitSet();
fingerprintT = fingerprint.getBitFingerprint(moleculeT).asBitSet();
org.junit.Assert.assertFalse(FingerprinterTool.isSubset(fingerprintT, fingerprintQ));
}
@Test
public void testAtomPermutation2() throws CDKException {
IAtomContainer pamine = TestMoleculeFactory.makeCyclopentane();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(pamine);
ShortestPathFingerprinter fp = new ShortestPathFingerprinter();
IBitFingerprint bs1 = fp.getBitFingerprint(pamine);
AtomContainerAtomPermutor acp = new AtomContainerAtomPermutor(pamine);
while (acp.hasNext()) {
IAtomContainer container = acp.next();
IBitFingerprint bs2 = fp.getBitFingerprint(container);
Assert.assertTrue(bs1.equals(bs2));
}
}
/**
* Test of ShortestPathFingerprinter method
*
* @throws InvalidSmilesException
* @throws CDKException
*/
@Test
public void testGenerateFingerprint() throws InvalidSmilesException, CDKException {
String smiles = "CCCCC1C(=O)N(N(C1=O)C1=CC=CC=C1)C1=CC=CC=C1";
SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer molecule = smilesParser.parseSmiles(smiles);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
Aromaticity.cdkLegacy().apply(molecule);
ShortestPathFingerprinter fingerprint = new ShortestPathFingerprinter(1024);
BitSet fingerprint1;
fingerprint1 = fingerprint.getBitFingerprint(molecule).asBitSet();
org.junit.Assert.assertEquals(125, fingerprint1.cardinality());
org.junit.Assert.assertEquals(1024, fingerprint1.size());
}
/**
* Layout all rings in the given RingSet that are connected to a given Ring
*
* @param rs The RingSet to be searched for rings connected to Ring
* @param ring The Ring for which all connected rings in RingSet are to be layed out.
*/
void placeConnectedRings(IRingSet rs, IRing ring, int handleType, double bondLength) {
IRingSet connectedRings = rs.getConnectedRings(ring);
IRing connectedRing;
IAtomContainer sharedAtoms;
int sac;
Point2d oldRingCenter, sharedAtomsCenter, tempPoint;
Vector2d tempVector, oldRingCenterVector, newRingCenterVector;
// logger.debug(rs.reportRingList(molecule));
for (IAtomContainer container : connectedRings.atomContainers()) {
connectedRing = (IRing) container;
if (!connectedRing.getFlag(CDKConstants.ISPLACED)) {
// logger.debug(ring.toString(molecule));
// logger.debug(connectedRing.toString(molecule));
sharedAtoms = AtomContainerManipulator.getIntersection(ring, connectedRing);
sac = sharedAtoms.getAtomCount();
logger.debug("placeConnectedRings-> connectedRing: " + (ring.toString()));
if ((sac == 2 && handleType == FUSED)
|| (sac == 1 && handleType == SPIRO)
|| (sac > 2 && handleType == BRIDGED)) {
sharedAtomsCenter = GeometryTools.get2DCenter(sharedAtoms);
oldRingCenter = GeometryTools.get2DCenter(ring);
tempVector = (new Vector2d(sharedAtomsCenter));
newRingCenterVector = new Vector2d(tempVector);
newRingCenterVector.sub(new Vector2d(oldRingCenter));
oldRingCenterVector = new Vector2d(newRingCenterVector);
logger.debug(
"placeConnectedRing -> tempVector: "
+ tempVector
+ ", tempVector.length: "
+ tempVector.length());
logger.debug("placeConnectedRing -> bondCenter: " + sharedAtomsCenter);
logger.debug(
"placeConnectedRing -> oldRingCenterVector.length(): "
+ oldRingCenterVector.length());
logger.debug(
"placeConnectedRing -> newRingCenterVector.length(): "
+ newRingCenterVector.length());
tempPoint = new Point2d(sharedAtomsCenter);
tempPoint.add(newRingCenterVector);
placeRing(connectedRing, sharedAtoms, sharedAtomsCenter, newRingCenterVector, bondLength);
connectedRing.setFlag(CDKConstants.ISPLACED, true);
placeConnectedRings(rs, connectedRing, handleType, bondLength);
}
}
}
}
@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);
}
/**
* set the active center for this molecule. The active center will be those which correspond with
* [A*]-B=C .
*
* <pre>
* A: Atom with single electron
* -: Single bond
* B: Atom
* =: Double bond
* C: Atom
* </pre>
*
* @param reactant The molecule to set the activity
* @throws CDKException
*/
private void setActiveCenters(IAtomContainer reactant) throws CDKException {
if (AtomContainerManipulator.getTotalNegativeFormalCharge(reactant)
!= 0 /*|| AtomContainerManipulator.getTotalPositiveFormalCharge(reactant) != 0*/) return;
Iterator<IAtom> atoms = reactant.atoms().iterator();
while (atoms.hasNext()) {
IAtom atomi = atoms.next();
if (reactant.getConnectedSingleElectronsCount(atomi) == 1) {
Iterator<IBond> bondis = reactant.getConnectedBondsList(atomi).iterator();
while (bondis.hasNext()) {
IBond bondi = bondis.next();
if (bondi.getOrder() == IBond.Order.SINGLE) {
IAtom atomj = bondi.getConnectedAtom(atomi);
if ((atomj.getFormalCharge() == CDKConstants.UNSET ? 0 : atomj.getFormalCharge()) == 0
&& reactant.getConnectedSingleElectronsCount(atomj) == 0) {
Iterator<IBond> bondjs = reactant.getConnectedBondsList(atomj).iterator();
while (bondjs.hasNext()) {
IBond bondj = bondjs.next();
if (bondj.equals(bondi)) continue;
if (bondj.getOrder() == IBond.Order.DOUBLE) {
IAtom atomk = bondj.getConnectedAtom(atomj);
if ((atomk.getFormalCharge() == CDKConstants.UNSET ? 0 : atomk.getFormalCharge())
== 0
&& reactant.getConnectedSingleElectronsCount(atomk) == 0) {
atomi.setFlag(CDKConstants.REACTIVE_CENTER, true);
atomj.setFlag(CDKConstants.REACTIVE_CENTER, true);
atomk.setFlag(CDKConstants.REACTIVE_CENTER, true);
bondi.setFlag(CDKConstants.REACTIVE_CENTER, true);
bondj.setFlag(CDKConstants.REACTIVE_CENTER, true);
}
}
}
}
}
}
}
}
}
@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);
}
/**
* Get the Ethene structure.
*
* @return The IMolecule
* @throws CDKException
*/
private IMolecule getEthene() throws Exception {
IMolecule molecule = builder.newMolecule();
molecule.addAtom(builder.newAtom("C"));
molecule.addAtom(builder.newAtom("C"));
molecule.addBond(0, 1, IBond.Order.DOUBLE);
molecule.addAtom(builder.newAtom("H"));
molecule.addAtom(builder.newAtom("H"));
molecule.addAtom(builder.newAtom("H"));
molecule.addAtom(builder.newAtom("H"));
molecule.addBond(0, 2, IBond.Order.SINGLE);
molecule.addBond(0, 3, IBond.Order.SINGLE);
molecule.addBond(1, 4, IBond.Order.SINGLE);
molecule.addBond(1, 5, IBond.Order.SINGLE);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
LonePairElectronChecker lpcheck = new LonePairElectronChecker();
lpcheck.saturate(molecule);
return molecule;
}
@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);
}
@Test
public void checkUniqueMolecularDescriptorNames() throws Exception {
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
List<DescriptorSpecification> specs = engine.getDescriptorSpecifications();
// we work with a simple molecule with 3D coordinates
String filename = "data/mdl/lobtest2.sdf";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
ISimpleChemObjectReader reader = new MDLV2000Reader(ins);
ChemFile content = (ChemFile) reader.read(new ChemFile());
List cList = ChemFileManipulator.getAllAtomContainers(content);
IAtomContainer ac = (IAtomContainer) cList.get(0);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(ac);
engine.process(ac);
int ncalc = 0;
List<String> descNames = new ArrayList<String>();
for (DescriptorSpecification spec : specs) {
DescriptorValue value = (DescriptorValue) ac.getProperty(spec);
if (value == null) continue;
ncalc++;
String[] names = value.getNames();
descNames.addAll(Arrays.asList(names));
}
List<String> dups = new ArrayList<String>();
Set<String> uniqueNames = new HashSet<String>();
for (String name : descNames) {
if (!uniqueNames.add(name)) dups.add(name);
}
Assert.assertEquals(specs.size(), ncalc);
Assert.assertEquals(descNames.size(), uniqueNames.size());
if (dups.size() != 0) {
System.out.println("Following names were duplicated");
for (String dup : dups) {
System.out.println("dup = " + dup);
}
}
}
/**
* The method calculates the sigma electronegativity of a given atom It is needed to call the
* addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
*
* @param atom The IAtom for which the DescriptorValue is requested
* @param ac AtomContainer
* @return return the sigma electronegativity
*/
@TestMethod(value = "testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtom atom, IAtomContainer ac) {
IAtomContainer clone;
IAtom localAtom;
try {
clone = (IAtomContainer) ac.clone();
localAtom = clone.getAtom(ac.getAtomNumber(atom));
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(clone);
} catch (CDKException e) {
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new DoubleResult(Double.NaN),
descriptorNames,
e);
} catch (CloneNotSupportedException e) {
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new DoubleResult(Double.NaN),
descriptorNames,
e);
}
if (maxIterations != -1 && maxIterations != 0)
electronegativity.setMaxIterations(maxIterations);
double result = electronegativity.calculateSigmaElectronegativity(clone, localAtom);
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new DoubleResult(result),
descriptorNames);
}
/**
* 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);
}
}
