/**
* Modules for cleaning a molecule
*
* @param molecule
* @return cleaned AtomContainer
*/
@TestMethod("testCheckAndCleanMolecule")
public static IAtomContainer checkAndCleanMolecule(IAtomContainer molecule) {
boolean isMarkush = false;
for (IAtom atom : molecule.atoms()) {
if (atom.getSymbol().equals("R")) {
isMarkush = true;
break;
}
}
if (isMarkush) {
System.err.println("Skipping Markush structure for sanity check");
}
// Check for salts and such
if (!ConnectivityChecker.isConnected(molecule)) {
// lets see if we have just two parts if so, we assume its a salt and just work
// on the larger part. Ideally we should have a check to ensure that the smaller
// part is a metal/halogen etc.
IMoleculeSet fragments = ConnectivityChecker.partitionIntoMolecules(molecule);
if (fragments.getMoleculeCount() > 2) {
System.err.println("More than 2 components. Skipped");
} else {
IMolecule frag1 = fragments.getMolecule(0);
IMolecule frag2 = fragments.getMolecule(1);
if (frag1.getAtomCount() > frag2.getAtomCount()) {
molecule = frag1;
} else {
molecule = frag2;
}
}
}
configure(molecule);
return molecule;
}
/**
* Generates a shortest path based BitSet fingerprint for the given AtomContainer.
*
* @param ac The AtomContainer for which a fingerprint is generated
* @exception CDKException if there error in aromaticity perception or other CDK functions
* @return A {@link BitSet} representing the fingerprint
*/
@Override
public IBitFingerprint getBitFingerprint(IAtomContainer ac) throws CDKException {
IAtomContainer atomContainer = null;
try {
atomContainer = (IAtomContainer) ac.clone();
} catch (CloneNotSupportedException ex) {
logger.error("Failed to clone the molecule:", ex);
}
Aromaticity.cdkLegacy().apply(atomContainer);
BitSet bitSet = new BitSet(fingerprintLength);
if (!ConnectivityChecker.isConnected(atomContainer)) {
IAtomContainerSet partitionedMolecules =
ConnectivityChecker.partitionIntoMolecules(atomContainer);
for (IAtomContainer container : partitionedMolecules.atomContainers()) {
addUniquePath(container, bitSet);
}
} else {
addUniquePath(atomContainer, bitSet);
}
return new BitSetFingerprint(bitSet);
}
/**
* Returns unique unmapped fragments in the target molecule.
*
* @return unique fragments in the target molecule
* @throws CloneNotSupportedException
*/
public synchronized IAtomContainerSet getUniqueFragmentsInTarget()
throws CloneNotSupportedException {
IAtomContainer ac = (IAtomContainer) target.clone();
List<IAtom> commonAtoms = Collections.synchronizedList(new ArrayList<IAtom>());
for (IAtom atom : mapping.values()) {
commonAtoms.add(ac.getAtom(getTargetIndex(atom)));
}
for (IAtom atom : commonAtoms) {
ac.removeAtomAndConnectedElectronContainers(atom);
}
// now we probably have a set of disconnected components
// so lets get a set of individual atom containers for
// corresponding to each component
return ConnectivityChecker.partitionIntoMolecules(ac);
}
/**
* Choose any possible quadruple of the set of atoms in ac and establish all of the possible
* bonding schemes according to Faulon's equations.
*/
public static List sample(IMolecule ac) {
logger.debug("RandomGenerator->mutate() Start");
List structures = new ArrayList();
int nrOfAtoms = ac.getAtomCount();
double a11 = 0, a12 = 0, a22 = 0, a21 = 0;
double b11 = 0, lowerborder = 0, upperborder = 0;
double b12 = 0;
double b21 = 0;
double b22 = 0;
double[] cmax = new double[4];
double[] cmin = new double[4];
IAtomContainer newAc = null;
IAtom ax1 = null, ax2 = null, ay1 = null, ay2 = null;
IBond b1 = null, b2 = null, b3 = null, b4 = null;
// int[] choices = new int[3];
/* We need at least two non-zero bonds in order to be successful */
int nonZeroBondsCounter = 0;
for (int x1 = 0; x1 < nrOfAtoms; x1++) {
for (int x2 = x1 + 1; x2 < nrOfAtoms; x2++) {
for (int y1 = x2 + 1; y1 < nrOfAtoms; y1++) {
for (int y2 = y1 + 1; y2 < nrOfAtoms; y2++) {
nonZeroBondsCounter = 0;
ax1 = ac.getAtom(x1);
ay1 = ac.getAtom(y1);
ax2 = ac.getAtom(x2);
ay2 = ac.getAtom(y2);
/* Get four bonds for these four atoms */
b1 = ac.getBond(ax1, ay1);
if (b1 != null) {
a11 = BondManipulator.destroyBondOrder(b1.getOrder());
nonZeroBondsCounter++;
} else {
a11 = 0;
}
b2 = ac.getBond(ax1, ay2);
if (b2 != null) {
a12 = BondManipulator.destroyBondOrder(b2.getOrder());
nonZeroBondsCounter++;
} else {
a12 = 0;
}
b3 = ac.getBond(ax2, ay1);
if (b3 != null) {
a21 = BondManipulator.destroyBondOrder(b3.getOrder());
nonZeroBondsCounter++;
} else {
a21 = 0;
}
b4 = ac.getBond(ax2, ay2);
if (b4 != null) {
a22 = BondManipulator.destroyBondOrder(b4.getOrder());
nonZeroBondsCounter++;
} else {
a22 = 0;
}
if (nonZeroBondsCounter > 1) {
/* Compute the range for b11 (see Faulons formulae for details) */
cmax[0] = 0;
cmax[1] = a11 - a22;
cmax[2] = a11 + a12 - 3;
cmax[3] = a11 + a21 - 3;
cmin[0] = 3;
cmin[1] = a11 + a12;
cmin[2] = a11 + a21;
cmin[3] = a11 - a22 + 3;
lowerborder = MathTools.max(cmax);
upperborder = MathTools.min(cmin);
for (b11 = lowerborder; b11 <= upperborder; b11++) {
if (b11 != a11) {
b12 = a11 + a12 - b11;
b21 = a11 + a21 - b11;
b22 = a22 - a11 + b11;
logger.debug("Trying atom combination : " + x1 + ":" + x2 + ":" + y1 + ":" + y2);
try {
newAc = (IAtomContainer) ac.clone();
change(newAc, x1, y1, x2, y2, b11, b12, b21, b22);
if (ConnectivityChecker.isConnected(newAc)) {
structures.add(newAc);
} else {
logger.debug("not connected");
}
} catch (CloneNotSupportedException e) {
logger.error("Cloning exception: " + e.getMessage());
logger.debug(e);
}
}
}
}
}
}
}
}
return structures;
}
/**
* Initiates the process for the given mechanism. The atoms to apply are mapped between reactants
* and products.
*
* @param atomContainerSet
* @param atomList The list of atoms taking part in the mechanism. Only allowed two atoms. The
* first atom is the atom which contains the ISingleElectron and the second third is the atom
* which will be removed the first atom
* @param bondList The list of bonds taking part in the mechanism. Only allowed one bond. It is
* the bond which is moved
* @return The Reaction mechanism
*/
@TestMethod(value = "testInitiate_IAtomContainerSet_ArrayList_ArrayList")
public IReaction initiate(
IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)
throws CDKException {
CDKAtomTypeMatcher atMatcher = CDKAtomTypeMatcher.getInstance(atomContainerSet.getBuilder());
if (atomContainerSet.getAtomContainerCount() != 1) {
throw new CDKException("RadicalSiteIonizationMechanism only expects one IMolecule");
}
if (atomList.size() != 3) {
throw new CDKException("RadicalSiteIonizationMechanism expects three atoms in the ArrayList");
}
if (bondList.size() != 2) {
throw new CDKException(
"RadicalSiteIonizationMechanism only expect one bond in the ArrayList");
}
IAtomContainer molecule = atomContainerSet.getAtomContainer(0);
IAtomContainer reactantCloned;
try {
reactantCloned = (IAtomContainer) molecule.clone();
} catch (CloneNotSupportedException e) {
throw new CDKException("Could not clone IMolecule!", e);
}
IAtom atom1 = atomList.get(0); // Atom containing the ISingleElectron
IAtom atom1C = reactantCloned.getAtom(molecule.getAtomNumber(atom1));
IAtom atom2 = atomList.get(1); // Atom
IAtom atom2C = reactantCloned.getAtom(molecule.getAtomNumber(atom2));
IAtom atom3 = atomList.get(2); // Atom to be saved
IAtom atom3C = reactantCloned.getAtom(molecule.getAtomNumber(atom3));
IBond bond1 = bondList.get(0); // Bond to increase the order
int posBond1 = molecule.getBondNumber(bond1);
IBond bond2 = bondList.get(1); // Bond to remove
int posBond2 = molecule.getBondNumber(bond2);
BondManipulator.increaseBondOrder(reactantCloned.getBond(posBond1));
reactantCloned.removeBond(reactantCloned.getBond(posBond2));
List<ISingleElectron> selectron = reactantCloned.getConnectedSingleElectronsList(atom1C);
reactantCloned.removeSingleElectron(selectron.get(selectron.size() - 1));
atom1C.setHybridization(null);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
IAtomType type = atMatcher.findMatchingAtomType(reactantCloned, atom1C);
if (type == null) return null;
atom2C.setHybridization(null);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
type = atMatcher.findMatchingAtomType(reactantCloned, atom2C);
if (type == null) return null;
reactantCloned.addSingleElectron(new SingleElectron(atom3C));
atom3C.setHybridization(null);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
type = atMatcher.findMatchingAtomType(reactantCloned, atom3C);
if (type == null) return null;
IReaction reaction = DefaultChemObjectBuilder.getInstance().newInstance(IReaction.class);
reaction.addReactant(molecule);
/* mapping */
for (IAtom atom : molecule.atoms()) {
IMapping mapping =
DefaultChemObjectBuilder.getInstance()
.newInstance(
IMapping.class, atom, reactantCloned.getAtom(molecule.getAtomNumber(atom)));
reaction.addMapping(mapping);
}
IAtomContainerSet moleculeSetP = ConnectivityChecker.partitionIntoMolecules(reactantCloned);
for (int z = 0; z < moleculeSetP.getAtomContainerCount(); z++)
reaction.addProduct((IAtomContainer) moleculeSetP.getAtomContainer(z));
return reaction;
}
@TestMethod("testDetectAromaticity_IAtomContainer")
public static boolean detectAromaticity(IAtomContainer atomContainer) throws CDKException {
SpanningTree spanningTree = new SpanningTree(atomContainer);
IAtomContainer ringSystems = spanningTree.getCyclicFragmentsContainer();
if (ringSystems.getAtomCount() == 0) {
// If there are no rings, then there cannot be any aromaticity
return false;
}
// disregard all atoms we know that cannot be aromatic anyway
for (IAtom atom : ringSystems.atoms())
if (!atomIsPotentiallyAromatic(atom))
ringSystems.removeAtomAndConnectedElectronContainers(atom);
// FIXME: should not really mark them here
Iterator<IAtom> atoms = ringSystems.atoms().iterator();
while (atoms.hasNext()) atoms.next().setFlag(CDKConstants.ISINRING, true);
Iterator<IBond> bonds = ringSystems.bonds().iterator();
while (bonds.hasNext()) bonds.next().setFlag(CDKConstants.ISINRING, true);
boolean foundSomeAromaticity = false;
Iterator<IAtomContainer> isolatedRingSystems =
ConnectivityChecker.partitionIntoMolecules(ringSystems).atomContainers().iterator();
while (isolatedRingSystems.hasNext()) {
IAtomContainer isolatedSystem = isolatedRingSystems.next();
IRingSet singleRings = new SSSRFinder(isolatedSystem).findSSSR();
Iterator<IAtomContainer> singleRingsIterator = singleRings.atomContainers().iterator();
int maxRingSize = 20;
boolean atLeastOneRingIsSprouted = false;
boolean allRingsAreAromatic = true;
// test single rings in SSSR
while (singleRingsIterator.hasNext()) {
IAtomContainer singleRing = singleRingsIterator.next();
if (singleRing.getAtomCount() > maxRingSize) maxRingSize = singleRing.getAtomCount();
if (isRingSystemSproutedWithNonRingDoubleBonds(atomContainer, singleRing)) {
// OK, this ring is not aromatic
atLeastOneRingIsSprouted = true;
allRingsAreAromatic = false;
} else {
// possibly aromatic
boolean ringIsAromatic = isHueckelValid(singleRing);
foundSomeAromaticity |= ringIsAromatic;
allRingsAreAromatic &= ringIsAromatic;
if (ringIsAromatic) markRingAtomsAndBondsAromatic(singleRing);
}
}
// OK, what about the one larger ring (if no aromaticity found in SSSR)?
if (!allRingsAreAromatic
&& !atLeastOneRingIsSprouted
&& singleRings.getAtomContainerCount() <= 3) {
// every ring system consisting of more than two rings is too difficult
Iterator<IAtomContainer> allRingsIterator =
new AllRingsFinder()
.findAllRingsInIsolatedRingSystem(isolatedSystem)
.atomContainers()
.iterator();
while (allRingsIterator.hasNext()) {
// there should be exactly three rings, of which only one has a size larger
// than the two previous ones
IAtomContainer ring = allRingsIterator.next();
if (ring.getAtomCount() <= maxRingSize) {
// possibly aromatic
boolean ringIsAromatic = isHueckelValid(ring);
foundSomeAromaticity |= ringIsAromatic;
if (ringIsAromatic) markRingAtomsAndBondsAromatic(ring);
}
}
}
}
return foundSomeAromaticity;
}