/**
* Performs a breadthFirstSearch in an AtomContainer starting with a particular sphere, which
* usually consists of one start atom, and searches for a pi system.
*
* @param container The AtomContainer to be searched
* @param sphere A sphere of atoms to start the search with
* @param path A ArrayList which stores the atoms belonging to the pi system
* @throws org.openscience.cdk.exception.CDKException Description of the Exception
*/
private void breadthFirstSearch(IAtomContainer container, List<IAtom> sphere, List<IAtom> path)
throws CDKException {
IAtom atom;
IAtom nextAtom;
List<IAtom> newSphere = new ArrayList<IAtom>();
// logger.debug("Start of breadthFirstSearch");
for (int i = 0; i < sphere.size(); i++) {
atom = sphere.get(i);
// logger.debug("BreadthFirstSearch around atom " + (atomNr + 1));
List<IBond> bonds = container.getConnectedBondsList(atom);
for (IBond bond : bonds) {
nextAtom = bond.getConnectedAtom(atom);
if ((!nextAtom.getFlag(CDKConstants.ISAROMATIC) && !nextAtom.getFlag(CDKConstants.ISINRING))
& !nextAtom.getFlag(CDKConstants.VISITED)) {
// logger.debug("BDS> AtomNr:"+container.getAtomNumber(nextAtom)+"
// maxBondOrder:"+container.getMaximumBondOrder(nextAtom)+"
// Aromatic:"+nextAtom.getFlag(CDKConstants.ISAROMATIC)+"
// FormalCharge:"+nextAtom.getFormalCharge()+" Charge:"+nextAtom.getCharge()+"
// Flag:"+nextAtom.getFlag(CDKConstants.VISITED));
path.add(nextAtom);
// logger.debug("BreadthFirstSearch is meeting new atom " + (nextAtomNr + 1));
nextAtom.setFlag(CDKConstants.VISITED, true);
if (container.getConnectedBondsCount(nextAtom) > 1) {
newSphere.add(nextAtom);
}
} else {
nextAtom.setFlag(CDKConstants.VISITED, true);
}
}
}
if (newSphere.size() > 0) {
breadthFirstSearch(container, newSphere, path);
}
}
private boolean getIfBondIsNotRotatable(Molecule mol, IBond bond, IAtomContainer detected) {
boolean isBondNotRotatable = false;
int counter = 0;
IAtom atom0 = bond.getAtom(0);
IAtom atom1 = bond.getAtom(1);
if (detected != null) {
if (detected.contains(bond)) counter += 1;
}
if (atom0.getFlag(CDKConstants.ISINRING)) {
if (atom1.getFlag(CDKConstants.ISINRING)) {
counter += 1;
} else {
if (atom1.getSymbol().equals("H")) counter += 1;
else counter += 0;
}
}
if (atom0.getSymbol().equals("N") && atom1.getSymbol().equals("C")) {
if (getIfACarbonIsDoubleBondedToAnOxygen(mol, atom1)) counter += 1;
}
if (atom0.getSymbol().equals("C") && atom1.getSymbol().equals("N")) {
if (getIfACarbonIsDoubleBondedToAnOxygen(mol, atom0)) counter += 1;
}
if (counter > 0) isBondNotRotatable = true;
return isBondNotRotatable;
}
/**
* Initiate process. It is needed to call the addExplicitHydrogensToSatisfyValency from the class
* tools.HydrogenAdder.
*
* @param reactants reactants of the reaction
* @param agents agents of the reaction (Must be in this case null)
* @exception CDKException Description of the Exception
*/
@TestMethod("testInitiate_IMoleculeSet_IMoleculeSet")
public IReactionSet initiate(IMoleculeSet reactants, IMoleculeSet agents) throws CDKException {
logger.debug("initiate reaction: HeterolyticCleavagePBReaction");
if (reactants.getMoleculeCount() != 1) {
throw new CDKException("HeterolyticCleavagePBReaction only expects one reactant");
}
if (agents != null) {
throw new CDKException("HeterolyticCleavagePBReaction don't expects agents");
}
IReactionSet setOfReactions =
DefaultChemObjectBuilder.getInstance().newInstance(IReactionSet.class);
IMolecule reactant = reactants.getMolecule(0);
/* if the parameter hasActiveCenter is not fixed yet, set the active centers*/
IParameterReact ipr = super.getParameterClass(SetReactionCenter.class);
if (ipr != null && !ipr.isSetParameter()) setActiveCenters(reactant);
Iterator<IBond> bondis = reactant.bonds().iterator();
while (bondis.hasNext()) {
IBond bondi = bondis.next();
IAtom atom1 = bondi.getAtom(0);
IAtom atom2 = bondi.getAtom(1);
if (bondi.getFlag(CDKConstants.REACTIVE_CENTER)
&& bondi.getOrder() != IBond.Order.SINGLE
&& atom1.getFlag(CDKConstants.REACTIVE_CENTER)
&& atom2.getFlag(CDKConstants.REACTIVE_CENTER)
&& (atom1.getFormalCharge() == CDKConstants.UNSET ? 0 : atom1.getFormalCharge()) == 0
&& (atom2.getFormalCharge() == CDKConstants.UNSET ? 0 : atom2.getFormalCharge()) == 0
&& reactant.getConnectedSingleElectronsCount(atom1) == 0
&& reactant.getConnectedSingleElectronsCount(atom2) == 0) {
/**/
for (int j = 0; j < 2; j++) {
ArrayList<IAtom> atomList = new ArrayList<IAtom>();
if (j == 0) {
atomList.add(atom1);
atomList.add(atom2);
} else {
atomList.add(atom2);
atomList.add(atom1);
}
ArrayList<IBond> bondList = new ArrayList<IBond>();
bondList.add(bondi);
IMoleculeSet moleculeSet = reactant.getBuilder().newInstance(IMoleculeSet.class);
moleculeSet.addMolecule(reactant);
IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList);
if (reaction == null) continue;
else setOfReactions.addReaction(reaction);
}
}
}
return setOfReactions;
}
public boolean matches(IAtom atom) {
if (atom.getSymbol().equals(this.getSymbol()) && atom.getFlag(CDKConstants.ISAROMATIC)) {
return true;
} else {
return false;
}
}
@Test
public void testConfigure_IAtom_IAtomType() {
IAtom atom = new NNAtom(Elements.CARBON);
IAtomType atomType = new NNAtomType(Elements.CARBON);
atomType.setFlag(CDKConstants.IS_HYDROGENBOND_ACCEPTOR, true);
AtomTypeManipulator.configure(atom, atomType);
Assert.assertEquals(
atomType.getFlag(CDKConstants.IS_HYDROGENBOND_ACCEPTOR),
atom.getFlag(CDKConstants.IS_HYDROGENBOND_ACCEPTOR));
}
@Test
public void testRingFlags1() throws Exception {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer molecule = sp.parseSmiles("c1ccccc1");
new SSSRFinder(molecule).findSSSR();
int count = 0;
Iterator atoms = molecule.atoms().iterator();
while (atoms.hasNext()) {
IAtom atom = (IAtom) atoms.next();
if (atom.getFlag(CDKConstants.ISINRING)) count++;
}
Assert.assertEquals("All atoms in benzene were not marked as being in a ring", 6, count);
}
/**
* 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);
}
}
/**
* Initiate process. It is needed to call the addExplicitHydrogensToSatisfyValency from the class
* tools.HydrogenAdder.
*
* @exception CDKException Description of the Exception
* @param reactants reactants of the reaction.
* @param agents agents of the reaction (Must be in this case null).
*/
@TestMethod("testInitiate_IAtomContainerSet_IAtomContainerSet")
public IReactionSet initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
throws CDKException {
logger.debug("initiate reaction: RearrangementRadicalReaction");
if (reactants.getAtomContainerCount() != 1) {
throw new CDKException("RearrangementRadicalReaction only expects one reactant");
}
if (agents != null) {
throw new CDKException("RearrangementRadicalReaction don't expects agents");
}
IReactionSet setOfReactions =
DefaultChemObjectBuilder.getInstance().newInstance(IReactionSet.class);
IAtomContainer reactant = reactants.getAtomContainer(0);
/* if the parameter hasActiveCenter is not fixed yet, set the active centers*/
IParameterReact ipr = super.getParameterClass(SetReactionCenter.class);
if (ipr != null && !ipr.isSetParameter()) setActiveCenters(reactant);
Iterator<IAtom> atoms = reactants.getAtomContainer(0).atoms().iterator();
while (atoms.hasNext()) {
IAtom atomi = atoms.next();
if (atomi.getFlag(CDKConstants.REACTIVE_CENTER)
&& reactant.getConnectedSingleElectronsCount(atomi) == 1) {
Iterator<IBond> bondis = reactant.getConnectedBondsList(atomi).iterator();
while (bondis.hasNext()) {
IBond bondi = bondis.next();
if (bondi.getFlag(CDKConstants.REACTIVE_CENTER)
&& bondi.getOrder() == IBond.Order.SINGLE) {
IAtom atomj = bondi.getConnectedAtom(atomi);
if (atomi.getFlag(CDKConstants.REACTIVE_CENTER)
&& (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.getFlag(CDKConstants.REACTIVE_CENTER)
&& bondj.getOrder() == IBond.Order.DOUBLE) {
IAtom atomk = bondj.getConnectedAtom(atomj);
if (atomk.getFlag(CDKConstants.REACTIVE_CENTER)
&& (atomk.getFormalCharge() == CDKConstants.UNSET
? 0
: atomk.getFormalCharge())
== 0
&& reactant.getConnectedSingleElectronsCount(atomk) == 0) {
ArrayList<IAtom> atomList = new ArrayList<IAtom>();
atomList.add(atomi);
atomList.add(atomj);
atomList.add(atomk);
ArrayList<IBond> bondList = new ArrayList<IBond>();
bondList.add(bondi);
bondList.add(bondj);
IAtomContainerSet moleculeSet =
reactant.getBuilder().newInstance(IAtomContainerSet.class);
moleculeSet.addAtomContainer(reactant);
IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList);
if (reaction == null) continue;
else setOfReactions.addReaction(reaction);
}
}
}
}
}
}
}
}
return setOfReactions;
}
/**
* 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();
}
private boolean isRingAtom(IAtom atom) {
return atom.getFlag(CDKConstants.ISINRING);
}
private boolean isAliphaticAtom(IAtom atom) {
return atom.getFlag(CDKConstants.ISALIPHATIC);
}