/**
* Constructs an AtomContainer with a copy of the atoms and electronContainers of another
* AtomContainer (A shallow copy, i.e., with the same objects as in the original AtomContainer).
*
* @param container An AtomContainer to copy the atoms and electronContainers from
*/
public AtomContainer(IAtomContainer container) {
this.atomCount = container.getAtomCount();
this.bondCount = container.getBondCount();
this.lonePairCount = container.getLonePairCount();
this.singleElectronCount = container.getSingleElectronCount();
this.atoms = new IAtom[this.atomCount];
this.bonds = new IBond[this.bondCount];
this.lonePairs = new ILonePair[this.lonePairCount];
this.singleElectrons = new ISingleElectron[this.singleElectronCount];
stereoElements = new HashSet<IStereoElement>(atomCount / 2);
for (IStereoElement element : container.stereoElements()) {
addStereoElement(element);
}
for (int f = 0; f < container.getAtomCount(); f++) {
atoms[f] = container.getAtom(f);
container.getAtom(f).addListener(this);
}
for (int f = 0; f < this.bondCount; f++) {
bonds[f] = container.getBond(f);
container.getBond(f).addListener(this);
}
for (int f = 0; f < this.lonePairCount; f++) {
lonePairs[f] = container.getLonePair(f);
container.getLonePair(f).addListener(this);
}
for (int f = 0; f < this.singleElectronCount; f++) {
singleElectrons[f] = container.getSingleElectron(f);
container.getSingleElectron(f).addListener(this);
}
}
/**
* Returns the ring that is formed by the atoms in the given vector.
*
* @param vec The vector that contains the atoms of the ring
* @param mol The molecule this ring is a substructure of
* @return The ring formed by the given atoms
*/
private IRing prepareRing(List vec, IAtomContainer mol) {
// add the atoms in vec to the new ring
int atomCount = vec.size();
IRing ring = mol.getBuilder().newInstance(IRing.class, atomCount);
IAtom[] atoms = new IAtom[atomCount];
vec.toArray(atoms);
ring.setAtoms(atoms);
// add the bonds in mol to the new ring
try {
IBond b;
for (int i = 0; i < atomCount - 1; i++) {
b = mol.getBond(atoms[i], atoms[i + 1]);
if (b != null) {
ring.addBond(b);
} else {
logger.error("This should not happen.");
}
}
b = mol.getBond(atoms[0], atoms[atomCount - 1]);
if (b != null) {
ring.addBond(b);
} else {
logger.error("This should not happen either.");
}
} catch (Exception exc) {
logger.debug(exc);
}
logger.debug("found Ring ", ring);
return ring;
}
/**
* Adds all atoms and electronContainers of a given atomcontainer to this container.
*
* @param atomContainer The atomcontainer to be added
*/
public void add(IAtomContainer atomContainer) {
for (int f = 0; f < atomContainer.getAtomCount(); f++) {
if (!contains(atomContainer.getAtom(f))) {
addAtom(atomContainer.getAtom(f));
}
}
for (int f = 0; f < atomContainer.getBondCount(); f++) {
if (!contains(atomContainer.getBond(f))) {
addBond(atomContainer.getBond(f));
}
}
for (int f = 0; f < atomContainer.getLonePairCount(); f++) {
if (!contains(atomContainer.getLonePair(f))) {
addLonePair(atomContainer.getLonePair(f));
}
}
for (int f = 0; f < atomContainer.getSingleElectronCount(); f++) {
if (!contains(atomContainer.getSingleElectron(f))) {
addSingleElectron(atomContainer.getSingleElectron(f));
}
}
for (IStereoElement se : atomContainer.stereoElements()) stereoElements.add(se);
notifyChanged();
}
/**
* A unit test suite for JUnit.
*
* @return The test suite
*/
@Test
public void testCDKConstants_REACTIVE_CENTER() throws Exception {
IReactionProcess type = new RadicalSiteHrBetaReaction();
IAtomContainerSet setOfReactants = getExampleReactants();
IAtomContainer molecule = setOfReactants.getAtomContainer(0);
/* manually put the reactive center */
molecule.getAtom(3).setFlag(CDKConstants.REACTIVE_CENTER, true);
molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER, true);
molecule.getAtom(6).setFlag(CDKConstants.REACTIVE_CENTER, true);
molecule.getBond(5).setFlag(CDKConstants.REACTIVE_CENTER, true);
List<IParameterReact> paramList = new ArrayList<IParameterReact>();
IParameterReact param = new SetReactionCenter();
param.setParameter(Boolean.TRUE);
paramList.add(param);
type.setParameterList(paramList);
/* initiate */
IReactionSet setOfReactions = type.initiate(setOfReactants, null);
IAtomContainer reactant = setOfReactions.getReaction(0).getReactants().getAtomContainer(0);
Assert.assertTrue(molecule.getAtom(6).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getAtom(6).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(molecule.getAtom(0).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getAtom(0).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(molecule.getAtom(3).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getAtom(3).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(molecule.getBond(5).getFlag(CDKConstants.REACTIVE_CENTER));
Assert.assertTrue(reactant.getBond(5).getFlag(CDKConstants.REACTIVE_CENTER));
}
public static void checkAverageBondLength(IAtomContainer ac) {
double avlength = GeometryTools.getBondLengthAverage3D(ac);
for (int i = 0; i < ac.getBondCount(); i++) {
double distance =
ac.getBond(i).getAtom(0).getPoint3d().distance(ac.getBond(i).getAtom(1).getPoint3d());
Assert.assertTrue(
"Unreasonable bond length (" + distance + ") for bond " + i,
distance >= avlength / 2 && distance <= avlength * 2);
}
}
/** @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());
;
}
void expandNode(Node node) {
// System.out.println(node.toString(target));
QuerySequenceElement el = sequence.get(node.sequenceElNum);
if (el.center == null) // This node describers a bond that closes a ring
{
// Checking whether this bond is present in the target
IAtom tAt0 = node.atoms[query.getAtomNumber(el.atoms[0])];
IAtom tAt1 = node.atoms[query.getAtomNumber(el.atoms[1])];
IBond tBo = target.getBond(tAt0, tAt1);
if (tBo != null)
if (el.bonds[0].matches(tBo)) {
node.sequenceElNum++;
// stack.push(node);
if (node.sequenceElNum == sequence.size()) {
// The node is not added in the stack if the end of the sequence is reached
isomorphismFound = true;
if (FlagStoreIsomorphismNode) isomorphismNodes.add(node);
} else stack.push(node);
}
} else {
targetAt.clear();
IAtom tAt = node.atoms[el.centerNum];
List<IAtom> conAt = target.getConnectedAtomsList(tAt);
for (int i = 0; i < conAt.size(); i++) {
if (!containsAtom(node.atoms, conAt.get(i))) targetAt.add(conAt.get(i));
}
if (el.atoms.length <= targetAt.size()) generateNodes(node);
}
}
/**
* Helper method, used to help construct a configuration.
*
* @param bond
* @param container
* @return the array position of the bond in the container
*/
private int getBondPosition(IBond bond, IAtomContainer container) {
for (int i = 0; i < container.getBondCount(); i++) {
if (bond.equals(container.getBond(i))) {
return i;
}
}
return -1;
}
/**
* (Z)-1,2-difluoroethene
*
* @cdk.inchi InChI=1/C2H2F2/c3-1-2-4/h1-2H/b2-1-
*/
@Test
public void z_1_2_difluoroethene() throws Exception {
IAtomContainer ac = new AtomContainer();
ac.addAtom(new Atom("F"));
ac.addAtom(new Atom("C"));
ac.addAtom(new Atom("C"));
ac.addAtom(new Atom("F"));
ac.addBond(0, 1, SINGLE);
ac.addBond(1, 2, DOUBLE);
ac.addBond(2, 3, SINGLE);
ac.addStereoElement(
new DoubleBondStereochemistry(
ac.getBond(1), new IBond[] {ac.getBond(0), ac.getBond(2)}, TOGETHER));
Graph g = convert(ac);
assertThat(g.toSmiles(), is("F/C=C\\F"));
}
/**
* Returns bond map between sourceAtomCount and targetAtomCount molecules based on the atoms
*
* @param ac1 sourceAtomCount molecule
* @param ac2 targetAtomCount molecule
* @param mapping mappings between sourceAtomCount and targetAtomCount molecule atoms
* @return bond map between sourceAtomCount and targetAtomCount molecules based on the atoms
*/
private synchronized Map<IBond, IBond> makeBondMapOfAtomMap(
IAtomContainer ac1, IAtomContainer ac2, AtomAtomMapping mapping) {
Map<IBond, IBond> bondbondMappingMap = Collections.synchronizedMap(new HashMap<IBond, IBond>());
for (Map.Entry<IAtom, IAtom> map1 : mapping.getMappingsByAtoms().entrySet()) {
for (Map.Entry<IAtom, IAtom> map2 : mapping.getMappingsByAtoms().entrySet()) {
if (map1.getKey() != map2.getKey()) {
IBond bond1 = ac1.getBond(map1.getKey(), map2.getKey());
IBond bond2 = ac2.getBond(map1.getValue(), map2.getValue());
if (bond1 != null && bond2 != null && !bondbondMappingMap.containsKey(bond1)) {
bondbondMappingMap.put(bond1, bond2);
}
}
}
}
// System.out.println("Mol Map size:" + bondbondMappingMap.size());
return bondbondMappingMap;
}
/** A unit test for JUnit */
@Test
public void testAlanin() throws Exception {
HydrogenPlacer hydrogenPlacer = new HydrogenPlacer();
IAtomContainer mol1 = new AtomContainer();
SmilesGenerator sg = new SmilesGenerator();
mol1.addAtom(new Atom("N", new Point2d(1, 0)));
// 1
mol1.addAtom(new Atom("C", new Point2d(1, 2)));
// 2
mol1.addAtom(new Atom("F", new Point2d(1, 2)));
// 3
mol1.addAtom(new Atom("C", new Point2d(0, 0)));
// 4
mol1.addAtom(new Atom("C", new Point2d(1, 4)));
// 5
mol1.addAtom(new Atom("O", new Point2d(1, 5)));
// 6
mol1.addAtom(new Atom("O", new Point2d(1, 6)));
// 7
mol1.addBond(0, 1, IBond.Order.SINGLE);
// 1
mol1.addBond(1, 2, IBond.Order.SINGLE, IBond.Stereo.UP);
// 2
mol1.addBond(1, 3, IBond.Order.SINGLE, IBond.Stereo.DOWN);
// 3
mol1.addBond(1, 4, IBond.Order.SINGLE);
// 4
mol1.addBond(4, 5, IBond.Order.SINGLE);
// 5
mol1.addBond(4, 6, IBond.Order.DOUBLE);
// 6
addExplicitHydrogens(mol1);
hydrogenPlacer.placeHydrogens2D(mol1, 1.0);
IsotopeFactory ifac = IsotopeFactory.getInstance(mol1.getBuilder());
ifac.configureAtoms(mol1);
String smiles1 = null;
if (standAlone) {
display(mol1);
}
smiles1 = sg.createSMILES(mol1, true, new boolean[mol1.getBondCount()]);
if (standAlone) {
System.err.println("SMILES 1: " + smiles1);
}
Assert.assertNotNull(smiles1);
Assert.assertEquals("[H]OC(=O)[C@](F)(N([H])[H])C([H])([H])[H]", smiles1);
mol1.getBond(1).setStereo(IBond.Stereo.DOWN);
mol1.getBond(2).setStereo(IBond.Stereo.UP);
smiles1 = sg.createSMILES(mol1, true, new boolean[mol1.getBondCount()]);
if (standAlone) {
System.err.println("SMILES 1: " + smiles1);
}
Assert.assertNotNull(smiles1);
Assert.assertEquals("[H]OC(=O)[C@](F)(C([H])([H])[H])N([H])[H]", smiles1);
}
protected void process(
IAtomContainer target,
List<Integer> unmapped_atoms_molB,
int mappingSize,
List<Integer> i_bond_setB,
List<String> c_bond_setB,
List<Integer> mapped_atoms,
int counter) {
int unmapped_numB = unmapped_atoms_molB.size();
boolean bond_considered = false;
boolean normal_bond = true;
for (int atomIndex = 0; atomIndex < target.getBondCount(); atomIndex++) {
Integer indexI = target.getAtomNumber(target.getBond(atomIndex).getAtom(0));
Integer indexJ = target.getAtomNumber(target.getBond(atomIndex).getAtom(1));
IBond bond = target.getBond(atomIndex);
Integer order = (bond.getOrder().ordinal() + 1);
for (int b = 0; b < unmapped_numB; b++) {
if (unmapped_atoms_molB.get(b).equals(indexI)) {
normal_bond =
unMappedAtomsEqualsIndexI(
target, mappingSize, atomIndex, counter, mapped_atoms, indexI, indexJ, order);
bond_considered = true;
} else if (unmapped_atoms_molB.get(b) == indexJ) {
normal_bond =
unMappedAtomsEqualsIndexJ(
target, mappingSize, atomIndex, counter, mapped_atoms, indexI, indexJ, order);
bond_considered = true;
}
if (normal_bond && bond_considered) {
markNormalBonds(atomIndex, i_bond_setB, c_bond_setB, indexI, indexJ, order);
normal_bond = true;
break;
}
}
bond_considered = false;
}
}
/**
* This is a mock test where we don't want aromatic bonds to have a configuration.
* (Z)-1,2-difluoroethene is not aromatic but a 'real' example would be porphyrins.
*
* @cdk.inchi InChI=1/C2H2F2/c3-1-2-4/h1-2H/b2-1-
*/
@Test
public void z_1_2_difluoroethene_aromatic() throws Exception {
IAtomContainer ac = new AtomContainer();
ac.addAtom(new Atom("F"));
ac.addAtom(new Atom("C"));
ac.addAtom(new Atom("C"));
ac.addAtom(new Atom("F"));
ac.addBond(0, 1, SINGLE);
ac.addBond(1, 2, DOUBLE);
ac.addBond(2, 3, SINGLE);
ac.getBond(1).setFlag(CDKConstants.ISAROMATIC, true);
ac.addStereoElement(
new DoubleBondStereochemistry(
ac.getBond(1), new IBond[] {ac.getBond(0), ac.getBond(2)}, TOGETHER));
Graph g = convert(ac);
assertThat(g.toSmiles(), is("F[CH]:[CH]F"));
}
/**
* Generate Compatibility Graph Nodes Bond Insensitive
*
* @return
* @throws IOException
*/
private int compatibilityGraph() throws IOException {
int comp_graph_nodes_List_size = compGraphNodes.size();
// System.out.println("Source atom count " + source.getAtomCount());
// System.out.println("target atom count " + target.getAtomCount());
// System.out.println("Expected " + (source.getAtomCount() * target.getAtomCount())
// + " Found Compatibilty: " + ((compGraphNodes.size() / 3) * 2));
// System.out.println("compGraphNodes " + compGraphNodes);
for (int a = 0; a < comp_graph_nodes_List_size; a += 3) {
for (int b = a; b < comp_graph_nodes_List_size; b += 3) {
if ((a != b)
&& (!Objects.equals(compGraphNodes.get(a), compGraphNodes.get(b)))
&& (!Objects.equals(compGraphNodes.get(a + 1), compGraphNodes.get(b + 1)))) {
IBond reactantBond;
IBond productBond;
// System.out.println("a " + compGraphNodes.get(a) + " b " +
// compGraphNodes.get(b));
// exists a bond in molecule 2, so that molecule 1 pair is connected?
reactantBond =
source.getBond(
source.getAtom(compGraphNodes.get(a)), source.getAtom(compGraphNodes.get(b)));
productBond =
target.getBond(
target.getAtom(compGraphNodes.get(a + 1)),
target.getAtom(compGraphNodes.get(b + 1)));
if (reactantBond != null && productBond != null) {
addEdges(reactantBond, productBond, a, b);
} else if (reactantBond == null && productBond == null) {
dEdges.add((a / 3) + 1);
dEdges.add((b / 3) + 1);
}
}
}
}
cEdgesSize = cEdges.size();
dEdgesSize = dEdges.size();
return 0;
}
/**
* compatibilityGraphCEdgeZero is used to build up of the edges of the compatibility graph BIS
*
* @return
* @throws IOException
*/
private int compatibilityGraphCEdgeZero() throws IOException {
int compGraphNodesCZeroListSize = compGraphNodesCZero.size();
for (int a = 0; a < compGraphNodesCZeroListSize; a += 4) {
int index_a = compGraphNodesCZero.get(a);
int index_aPlus1 = compGraphNodesCZero.get(a + 1);
for (int b = a + 4; b < compGraphNodesCZeroListSize; b += 4) {
int index_b = compGraphNodesCZero.get(b);
int index_bPlus1 = compGraphNodesCZero.get(b + 1);
// if element atomCont !=jIndex and atoms on the adjacent sides of the bonds are not equal
if ((a != b) && (index_a != index_b) && (index_aPlus1 != index_bPlus1)) {
IBond reactantBond;
IBond productBond;
reactantBond = source.getBond(source.getAtom(index_a), source.getAtom(index_b));
productBond = target.getBond(target.getAtom(index_aPlus1), target.getAtom(index_bPlus1));
if (reactantBond != null && productBond != null) {
addZeroEdges(reactantBond, productBond, a, b);
} else if (reactantBond == null
&& productBond == null
&& source.getAtomCount() < 50
&& target.getAtomCount() < 50) {
// 50 unique condition to speed up the AAM
dEdges.add((a / 4) + 1);
dEdges.add((b / 4) + 1);
}
}
}
}
// Size of C and D edges of the compatibility graph
cEdgesSize = cEdges.size();
dEdgesSize = dEdges.size();
return 0;
}
private void processBondsBlock(int lineCount, IAtomContainer container) throws IOException {
for (int i = 0; i < lineCount; i++) {
String line = input.readLine();
int atom1 = Integer.parseInt(line.substring(10, 13).trim()) - 1;
int atom2 = Integer.parseInt(line.substring(16, 19).trim()) - 1;
if (container.getBond(container.getAtom(atom1), container.getAtom(atom2)) == null) {
IBond bond =
container.getBuilder().newBond(container.getAtom(atom1), container.getAtom(atom2));
int order = Integer.parseInt(line.substring(23).trim());
bond.setOrder(BondManipulator.createBondOrder((double) order));
container.addBond(bond);
} // else: bond already present; CTX store the bonds twice
}
}
/**
* Removes all atoms and electronContainers of a given atomcontainer from this container.
*
* @param atomContainer The atomcontainer to be removed
*/
public void remove(IAtomContainer atomContainer) {
for (int f = 0; f < atomContainer.getAtomCount(); f++) {
removeAtom(atomContainer.getAtom(f));
}
for (int f = 0; f < atomContainer.getBondCount(); f++) {
removeBond(atomContainer.getBond(f));
}
for (int f = 0; f < atomContainer.getLonePairCount(); f++) {
removeLonePair(atomContainer.getLonePair(f));
}
for (int f = 0; f < atomContainer.getSingleElectronCount(); f++) {
removeSingleElectron(atomContainer.getSingleElectron(f));
}
}
@Test
public void testSplit() throws CDKException {
IAtomContainer mol = smilesParser.parseSmiles("C1CC1C2CCC2");
SpanningTree st = new SpanningTree(mol);
IRingSet rings = st.getAllRings();
IBond splitBond = null;
for (int i = 0; i < mol.getBondCount(); i++) {
if (rings.getRings(mol.getBond(i)).getAtomContainerCount() == 0) {
splitBond = mol.getBond(i);
break;
}
}
List<IAtomContainer> frags = FragmentUtils.splitMolecule(mol, splitBond);
SmilesGenerator sg = new SmilesGenerator();
Set<String> uniqueFrags = new HashSet<String>();
for (IAtomContainer frag : frags) {
uniqueFrags.add(sg.createSMILES(frag));
}
Assert.assertEquals(2, uniqueFrags.size());
// You can put the fragments back together with a ring closure and dot
// [CH]12CC1.[CH]12CCC1
Assert.assertThat(uniqueFrags, hasItems("[CH]1CC1", "[CH]1CCC1"));
}
/** {@inheritDoc} */
@Override
@TestMethod("testIsStereoMisMatch")
public synchronized boolean isStereoMisMatch() {
boolean flag = false;
IAtomContainer reactant = getQuery();
IAtomContainer product = getTarget();
int stereoMisMatchScore = 0;
if (getMappingCount() > 0) {
AtomAtomMapping firstAtomMCS = getMCSList().iterator().next();
for (IAtom indexI : firstAtomMCS.getMappingsByAtoms().keySet()) {
IAtom indexJ = firstAtomMCS.getMappingsByAtoms().get(indexI);
for (IAtom indexIPlus : firstAtomMCS.getMappingsByAtoms().keySet()) {
IAtom indexJPlus = firstAtomMCS.getMappingsByAtoms().get(indexIPlus);
if (!indexI.equals(indexIPlus) && !indexJ.equals(indexJPlus)) {
IAtom sourceAtom1 = indexI;
IAtom sourceAtom2 = indexIPlus;
IBond rBond = reactant.getBond(sourceAtom1, sourceAtom2);
IAtom targetAtom1 = indexJ;
IAtom targetAtom2 = indexJPlus;
IBond pBond = product.getBond(targetAtom1, targetAtom2);
if ((rBond != null && pBond != null) && (rBond.getStereo() != pBond.getStereo())) {
stereoMisMatchScore++;
}
}
}
}
}
if (stereoMisMatchScore > 0) {
flag = true;
}
return flag;
}
public List<IBond> generateBondMapping(IAtomContainer container, List<IAtom> atomMapping) {
if (query == null) return null;
List<IBond> v = new ArrayList<IBond>();
for (int i = 0; i < query.getBondCount(); i++) {
IAtom qa0 = query.getBond(i).getAtom(0);
IAtom qa1 = query.getBond(i).getAtom(1);
IAtom a0 = atomMapping.get(query.getAtomNumber(qa0));
IAtom a1 = atomMapping.get(query.getAtomNumber(qa1));
v.add(container.getBond(a0, a1));
}
return (v);
}
private synchronized IQuery build(IAtomContainer queryMolecule) {
VFQueryBuilder result = new VFQueryBuilder();
for (IAtom atom : queryMolecule.atoms()) {
AtomMatcher matcher = createAtomMatcher(queryMolecule, atom);
if (matcher != null) {
result.addNode(matcher, atom);
}
}
for (int i = 0; i < queryMolecule.getBondCount(); i++) {
IBond bond = queryMolecule.getBond(i);
IAtom atomI = bond.getAtom(0);
IAtom atomJ = bond.getAtom(1);
result.connect(
result.getNode(atomI), result.getNode(atomJ), createBondMatcher(queryMolecule, bond));
}
return result;
}
@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);
}
@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);
}
private List<List<Integer>> getAtomMappings(List bondMapping, IAtomContainer atomContainer) {
List<List<Integer>> atomMapping = new ArrayList<List<Integer>>();
// loop over each mapping
for (Object aBondMapping : bondMapping) {
List list = (List) aBondMapping;
List<Integer> tmp = new ArrayList<Integer>();
IAtom atom1 = null;
IAtom atom2 = null;
// loop over this mapping
for (Object aList : list) {
RMap map = (RMap) aList;
int bondID = map.getId1();
// get the atoms in this bond
IBond bond = atomContainer.getBond(bondID);
atom1 = bond.getAtom(0);
atom2 = bond.getAtom(1);
Integer idx1 = atomContainer.getAtomNumber(atom1);
Integer idx2 = atomContainer.getAtomNumber(atom2);
if (!tmp.contains(idx1)) tmp.add(idx1);
if (!tmp.contains(idx2)) tmp.add(idx2);
}
if (tmp.size() > 0) atomMapping.add(tmp);
// If there is only one bond, check if it matches both ways.
if (list.size() == 1 && atom1.getAtomicNumber() == atom2.getAtomicNumber()) {
List<Integer> tmp2 = new ArrayList<Integer>();
tmp2.add(tmp.get(0));
tmp2.add(tmp.get(1));
atomMapping.add(tmp2);
}
}
return atomMapping;
}
/**
* Generated coordinates for a given ring, which is fused to another ring. The rings share exactly
* one bond.
*
* @param ring The ring to be placed
* @param sharedAtoms The atoms of this ring, also members of another ring, which are already
* placed
* @param sharedAtomsCenter The geometric center of these atoms
* @param ringCenterVector A vector pointing the the center of the new ring
* @param bondLength The standard bondlength
*/
public void placeFusedRing(
IRing ring,
IAtomContainer sharedAtoms,
Point2d sharedAtomsCenter,
Vector2d ringCenterVector,
double bondLength) {
logger.debug("RingPlacer.placeFusedRing() start");
Point2d ringCenter = new Point2d(sharedAtomsCenter);
double radius = getNativeRingRadius(ring, bondLength);
double newRingPerpendicular = Math.sqrt(Math.pow(radius, 2) - Math.pow(bondLength / 2, 2));
ringCenterVector.normalize();
logger.debug("placeFusedRing->: ringCenterVector.length()" + ringCenterVector.length());
ringCenterVector.scale(newRingPerpendicular);
ringCenter.add(ringCenterVector);
IAtom bondAtom1 = sharedAtoms.getAtom(0);
IAtom bondAtom2 = sharedAtoms.getAtom(1);
Vector2d bondAtom1Vector = new Vector2d(bondAtom1.getPoint2d());
Vector2d bondAtom2Vector = new Vector2d(bondAtom2.getPoint2d());
Vector2d originRingCenterVector = new Vector2d(ringCenter);
bondAtom1Vector.sub(originRingCenterVector);
bondAtom2Vector.sub(originRingCenterVector);
double occupiedAngle = bondAtom1Vector.angle(bondAtom2Vector);
double remainingAngle = (2 * Math.PI) - occupiedAngle;
double addAngle = remainingAngle / (ring.getRingSize() - 1);
logger.debug("placeFusedRing->occupiedAngle: " + Math.toDegrees(occupiedAngle));
logger.debug("placeFusedRing->remainingAngle: " + Math.toDegrees(remainingAngle));
logger.debug("placeFusedRing->addAngle: " + Math.toDegrees(addAngle));
IAtom startAtom;
double centerX = ringCenter.x;
double centerY = ringCenter.y;
double xDiff = bondAtom1.getPoint2d().x - bondAtom2.getPoint2d().x;
double yDiff = bondAtom1.getPoint2d().y - bondAtom2.getPoint2d().y;
double startAngle;
;
int direction = 1;
// if bond is vertical
if (xDiff == 0) {
logger.debug("placeFusedRing->Bond is vertical");
// starts with the lower Atom
if (bondAtom1.getPoint2d().y > bondAtom2.getPoint2d().y) {
startAtom = bondAtom1;
} else {
startAtom = bondAtom2;
}
// changes the drawing direction
if (centerX < bondAtom1.getPoint2d().x) {
direction = 1;
} else {
direction = -1;
}
}
// if bond is not vertical
else {
// starts with the left Atom
if (bondAtom1.getPoint2d().x > bondAtom2.getPoint2d().x) {
startAtom = bondAtom1;
} else {
startAtom = bondAtom2;
}
// changes the drawing direction
if (centerY - bondAtom1.getPoint2d().y
> (centerX - bondAtom1.getPoint2d().x) * yDiff / xDiff) {
direction = 1;
} else {
direction = -1;
}
}
startAngle =
GeometryTools.getAngle(
startAtom.getPoint2d().x - ringCenter.x, startAtom.getPoint2d().y - ringCenter.y);
IAtom currentAtom = startAtom;
// determine first bond in Ring
// int k = 0;
// for (k = 0; k < ring.getElectronContainerCount(); k++) {
// if (ring.getElectronContainer(k) instanceof IBond) break;
// }
IBond currentBond = sharedAtoms.getBond(0);
Vector atomsToDraw = new Vector();
for (int i = 0; i < ring.getBondCount() - 2; i++) {
currentBond = ring.getNextBond(currentBond, currentAtom);
currentAtom = currentBond.getConnectedAtom(currentAtom);
atomsToDraw.addElement(currentAtom);
}
addAngle = addAngle * direction;
try {
logger.debug("placeFusedRing->startAngle: " + Math.toDegrees(startAngle));
logger.debug("placeFusedRing->addAngle: " + Math.toDegrees(addAngle));
logger.debug("placeFusedRing->startAtom is: " + (molecule.getAtomNumber(startAtom) + 1));
logger.debug("AtomsToDraw: " + atomPlacer.listNumbers(molecule, atomsToDraw));
} catch (Exception exc) {
logger.debug("Caught an exception while logging in RingPlacer");
}
atomPlacer.populatePolygonCorners(atomsToDraw, ringCenter, startAngle, addAngle, radius);
}
private static IAtomContainer change(
IAtomContainer ac,
int x1,
int y1,
int x2,
int y2,
double b11,
double b12,
double b21,
double b22) {
IAtom ax1 = null, ax2 = null, ay1 = null, ay2 = null;
IBond b1 = null, b2 = null, b3 = null, b4 = null;
try {
ax1 = ac.getAtom(x1);
ax2 = ac.getAtom(x2);
ay1 = ac.getAtom(y1);
ay2 = ac.getAtom(y2);
} catch (Exception exc) {
logger.debug(exc);
}
b1 = ac.getBond(ax1, ay1);
b2 = ac.getBond(ax1, ay2);
b3 = ac.getBond(ax2, ay1);
b4 = ac.getBond(ax2, ay2);
if (b11 > 0) {
if (b1 == null) {
logger.debug("no bond " + x1 + "-" + y1 + ". Adding it with order " + b11);
b1 = ac.getBuilder().newBond(ax1, ay1, BondManipulator.createBondOrder(b11));
ac.addBond(b1);
} else {
b1.setOrder(BondManipulator.createBondOrder(b11));
logger.debug("Setting bondorder for " + x1 + "-" + y1 + " to " + b11);
}
} else if (b1 != null) {
ac.removeBond(b1);
logger.debug("removing bond " + x1 + "-" + y1);
}
if (b12 > 0) {
if (b2 == null) {
logger.debug("no bond " + x1 + "-" + y2 + ". Adding it with order " + b12);
b2 = ac.getBuilder().newBond(ax1, ay2, BondManipulator.createBondOrder(b12));
ac.addBond(b2);
} else {
b2.setOrder(BondManipulator.createBondOrder(b12));
logger.debug("Setting bondorder for " + x1 + "-" + y2 + " to " + b12);
}
} else if (b2 != null) {
ac.removeBond(b2);
logger.debug("removing bond " + x1 + "-" + y2);
}
if (b21 > 0) {
if (b3 == null) {
logger.debug("no bond " + x2 + "-" + y1 + ". Adding it with order " + b21);
b3 = ac.getBuilder().newBond(ax2, ay1, BondManipulator.createBondOrder(b21));
ac.addBond(b3);
} else {
b3.setOrder(BondManipulator.createBondOrder(b21));
logger.debug("Setting bondorder for " + x2 + "-" + y1 + " to " + b21);
}
} else if (b3 != null) {
ac.removeBond(b3);
logger.debug("removing bond " + x2 + "-" + y1);
}
if (b22 > 0) {
if (b4 == null) {
logger.debug("no bond " + x2 + "-" + y2 + ". Adding it with order " + b22);
b4 = ac.getBuilder().newBond(ax2, ay2, BondManipulator.createBondOrder(b22));
ac.addBond(b4);
} else {
b4.setOrder(BondManipulator.createBondOrder(b22));
logger.debug("Setting bondorder for " + x2 + "-" + y2 + " to " + b22);
}
} else if (b4 != null) {
ac.removeBond(b4);
logger.debug("removing bond " + x2 + "-" + y2);
}
return ac;
}
/** Recursive function to produce valid configurations for {@link #getAllConfigurations()}. */
private void findConfigurationsRecursively(
List<Integer> rGroupNumbers,
List<List<Integer>> occurrences,
List<Integer> occurIndexes,
List<Integer[]> distributions,
List<List<RGroup>> substitutes,
int level,
List<IAtomContainer> result)
throws CDKException {
if (level == rGroupNumbers.size()) {
if (!checkIfThenConditionsMet(rGroupNumbers, distributions)) return;
// Clone the root to get a scaffold to plug the substitutes into.
IAtomContainer root = this.getRootStructure();
IAtomContainer rootClone = null;
try {
rootClone = (IAtomContainer) root.clone();
} catch (CloneNotSupportedException e) {
// Abort with CDK exception
throw new CDKException("clone() failed; could not perform R-group substitution.");
}
for (int rgpIdx = 0; rgpIdx < rGroupNumbers.size(); rgpIdx++) {
int rNum = rGroupNumbers.get(rgpIdx);
int pos = 0;
List<RGroup> mapped = substitutes.get(rgpIdx);
for (RGroup substitute : mapped) {
IAtom rAtom = this.getRgroupQueryAtoms(rNum).get(pos);
if (substitute != null) {
IAtomContainer rgrpClone = null;
try {
rgrpClone = (IAtomContainer) (substitute.getGroup().clone());
} catch (CloneNotSupportedException e) {
throw new CDKException("clone() failed; could not perform R-group substitution.");
}
// root cloned, substitute cloned. These now need to be attached to each other..
rootClone.add(rgrpClone);
Map<Integer, IBond> rAttachmentPoints = this.getRootAttachmentPoints().get(rAtom);
if (rAttachmentPoints != null) {
// Loop over attachment points of the R# atom
for (int apo = 0; apo < rAttachmentPoints.size(); apo++) {
IBond bond = rAttachmentPoints.get(apo + 1);
// Check how R# is attached to bond
int whichAtomInBond = 0;
if (bond.getAtom(1).equals(rAtom)) whichAtomInBond = 1;
IAtom subsAt = null;
if (apo == 0) subsAt = substitute.getFirstAttachmentPoint();
else subsAt = substitute.getSecondAttachmentPoint();
// Do substitution with the clones
IBond cloneBond = rootClone.getBond(getBondPosition(bond, root));
if (subsAt != null) {
IAtom subsCloneAtom =
rgrpClone.getAtom(getAtomPosition(subsAt, substitute.getGroup()));
cloneBond.setAtom(subsCloneAtom, whichAtomInBond);
}
}
}
// Optional: shift substitutes 2D for easier visual checking
if (rAtom.getPoint2d() != null
&& substitute != null
&& substitute.getFirstAttachmentPoint() != null
&& substitute.getFirstAttachmentPoint().getPoint2d() != null) {
Point2d pointR = rAtom.getPoint2d();
Point2d pointC = substitute.getFirstAttachmentPoint().getPoint2d();
double xDiff = pointC.x - pointR.x;
double yDiff = pointC.y - pointR.y;
for (IAtom subAt : rgrpClone.atoms()) {
if (subAt.getPoint2d() != null) {
subAt.getPoint2d().x -= xDiff;
subAt.getPoint2d().y -= yDiff;
}
}
}
} else {
// Distribution flag is 0, this means the R# group will not be substituted.
// Any atom connected to this group should be given the defined RestH value.
IAtom discarded = rootClone.getAtom(getAtomPosition(rAtom, root));
for (IBond r0Bond : rootClone.bonds()) {
if (r0Bond.contains(discarded)) {
for (IAtom atInBond : r0Bond.atoms()) {
atInBond.setProperty(
CDKConstants.REST_H, this.getRGroupDefinitions().get(rNum).isRestH());
}
}
}
}
pos++;
}
}
// Remove R# remnants from the clone, bonds and atoms that may linger.
boolean confHasRGroupBonds = true;
while (confHasRGroupBonds) {
for (IBond cloneBond : rootClone.bonds()) {
boolean removeBond = false;
if (cloneBond.getAtom(0) instanceof IPseudoAtom
&& isValidRgroupQueryLabel(((IPseudoAtom) cloneBond.getAtom(0)).getLabel()))
removeBond = true;
else if (cloneBond.getAtom(1) instanceof IPseudoAtom
&& isValidRgroupQueryLabel(((IPseudoAtom) cloneBond.getAtom(1)).getLabel()))
removeBond = true;
if (removeBond) {
rootClone.removeBond(cloneBond);
confHasRGroupBonds = true;
break;
}
confHasRGroupBonds = false;
}
}
boolean confHasRGroupAtoms = true;
while (confHasRGroupAtoms) {
for (IAtom cloneAt : rootClone.atoms()) {
if (cloneAt instanceof IPseudoAtom)
if (isValidRgroupQueryLabel(((IPseudoAtom) cloneAt).getLabel())) {
rootClone.removeAtom(cloneAt);
confHasRGroupAtoms = true;
break;
}
confHasRGroupAtoms = false;
}
}
// Add to result list
result.add(rootClone);
} else {
for (int idx = 0; idx < occurrences.get(level).size(); idx++) {
occurIndexes.set(level, idx);
// With an occurrence picked 0..n for this level's R-group, now find
// all possible distributions (positional alternatives).
int occurrence = occurrences.get(level).get(idx);
int positions = this.getRgroupQueryAtoms(rGroupNumbers.get(level)).size();
Integer[] candidate = new Integer[positions];
for (int j = 0; j < candidate.length; j++) {
candidate[j] = 0;
}
List<Integer[]> rgrpDistributions = new ArrayList<Integer[]>();
findDistributions(occurrence, candidate, rgrpDistributions, 0);
for (Integer[] distribution : rgrpDistributions) {
distributions.set(level, distribution);
RGroup[] mapping = new RGroup[distribution.length];
List<List<RGroup>> mappedSubstitutes = new ArrayList<List<RGroup>>();
mapSubstitutes(
this.getRGroupDefinitions().get(rGroupNumbers.get(level)),
0,
distribution,
mapping,
mappedSubstitutes);
for (List<RGroup> mappings : mappedSubstitutes) {
substitutes.set(level, mappings);
findConfigurationsRecursively(
rGroupNumbers,
occurrences,
occurIndexes,
distributions,
substitutes,
level + 1,
result);
}
}
}
}
}
/**
* 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(IAtomContainer 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;
}