/**
* 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();
}
}
public String getSMILES(IAtomContainer molecule) throws CDKException {
String smiles = "";
if (molecule.getAtomCount() == 0) {
return smiles;
}
SmilesGenerator sg = new SmilesGenerator(true);
AllRingsFinder arf = new AllRingsFinder();
IRingSet findAllRings = arf.findAllRings(molecule);
sg.setRings(findAllRings);
sg.setRingFinder(arf);
smiles = sg.createSMILES(molecule, false, new boolean[molecule.getBondCount()]);
return smiles;
}
/**
* 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);
}
}