/**
* Internal - makes a map of the highlights for reaction mapping.
*
* @param reactants reaction reactants
* @param products reaction products
* @return the highlight map
*/
private Map<IChemObject, Color> makeHighlightAtomMap(
List<IAtomContainer> reactants, List<IAtomContainer> products) {
Map<IChemObject, Color> colorMap = new HashMap<>();
Map<Integer, Color> mapToColor = new HashMap<>();
int colorIdx = -1;
for (IAtomContainer mol : reactants) {
int prevPalletIdx = colorIdx;
for (IAtom atom : mol.atoms()) {
int mapidx = accessAtomMap(atom);
if (mapidx > 0) {
if (prevPalletIdx == colorIdx) {
colorIdx++; // select next color
if (colorIdx >= atomMapColors.length)
throw new IllegalArgumentException(
"Not enough colors to highlight atom mapping, please provide mode");
}
Color color = atomMapColors[colorIdx];
colorMap.put(atom, color);
mapToColor.put(mapidx, color);
}
}
if (colorIdx > prevPalletIdx) {
for (IBond bond : mol.bonds()) {
IAtom a1 = bond.getAtom(0);
IAtom a2 = bond.getAtom(1);
Color c1 = colorMap.get(a1);
Color c2 = colorMap.get(a2);
if (c1 != null && c1 == c2) colorMap.put(bond, c1);
}
}
}
for (IAtomContainer mol : products) {
for (IAtom atom : mol.atoms()) {
int mapidx = accessAtomMap(atom);
if (mapidx > 0) {
colorMap.put(atom, mapToColor.get(mapidx));
}
}
for (IBond bond : mol.bonds()) {
IAtom a1 = bond.getAtom(0);
IAtom a2 = bond.getAtom(1);
Color c1 = colorMap.get(a1);
Color c2 = colorMap.get(a2);
if (c1 != null && c1 == c2) colorMap.put(bond, c1);
}
}
return colorMap;
}
/**
* Hide the atoms and bonds of a contracted abbreviation. If the abbreviations is attached we
* remap the attachment symbol to display the name. If there are no attachments the symbol we be
* added later ({@see #generateSgroups}).
*
* @param container molecule
* @param sgroup abbreviation group display shortcut
*/
private static void contractAbbreviation(
IAtomContainer container, Map<IAtom, String> symbolRemap, Sgroup sgroup) {
final Set<IBond> crossing = sgroup.getBonds();
final Set<IAtom> atoms = sgroup.getAtoms();
// only do 0,1 attachments for now
if (crossing.size() > 1) return;
for (IAtom atom : atoms) {
StandardGenerator.hide(atom);
}
for (IBond bond : container.bonds()) {
if (atoms.contains(bond.getAtom(0)) || atoms.contains(bond.getAtom(1)))
StandardGenerator.hide(bond);
}
for (IBond bond : crossing) {
StandardGenerator.unhide(bond);
IAtom a1 = bond.getAtom(0);
IAtom a2 = bond.getAtom(1);
StandardGenerator.unhide(a1);
if (atoms.contains(a1)) symbolRemap.put(a1, sgroup.getSubscript());
StandardGenerator.unhide(a2);
if (atoms.contains(a2)) symbolRemap.put(a2, sgroup.getSubscript());
}
}
private double caclModelScale(Collection<IAtomContainer> mols) {
List<IBond> bonds = new ArrayList<>();
for (IAtomContainer mol : mols) {
for (IBond bond : mol.bonds()) {
bonds.add(bond);
}
}
return calcModelScaleForBondLength(medianBondLength(bonds));
}
/**
* Eliminates one bond of this atom from the molecule
*
* @param atom The atom one bond is eliminated of
* @param molecule The molecule that contains the atom
*/
private void breakBond(IAtom atom, IAtomContainer molecule) {
Iterator<IBond> bonds = molecule.bonds().iterator();
while (bonds.hasNext()) {
IBond bond = (IBond) bonds.next();
if (bond.contains(atom)) {
molecule.removeElectronContainer(bond);
break;
}
}
}
/**
* This method calculate the number of bonds of a given type in an atomContainer
*
* @param container AtomContainer
* @return The number of bonds of a certain type.
*/
@Override
public DescriptorValue calculate(IAtomContainer container) {
if (order.equals("")) {
int bondCount = 0;
for (IBond bond : container.bonds()) {
boolean hasHydrogen = false;
for (int i = 0; i < bond.getAtomCount(); i++) {
if (bond.getAtom(i).getSymbol().equals("H")) {
hasHydrogen = true;
break;
}
}
if (!hasHydrogen) bondCount++;
}
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new IntegerResult(bondCount),
getDescriptorNames(),
null);
}
int bondCount = 0;
for (IBond bond : container.bonds()) {
if (bondMatch(bond.getOrder(), order)) {
bondCount += 1;
}
}
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
new IntegerResult(bondCount),
getDescriptorNames());
}
private IRenderingElement generate(IAtomContainer molecule, RendererModel model, int atomNum)
throws CDKException {
// tag the atom and bond ids
String molId = molecule.getProperty(MarkedElement.ID_KEY);
if (molId != null) {
int atomId = 0, bondid = 0;
for (IAtom atom : molecule.atoms())
setIfMissing(atom, MarkedElement.ID_KEY, molId + "atm" + ++atomId);
for (IBond bond : molecule.bonds())
setIfMissing(bond, MarkedElement.ID_KEY, molId + "bnd" + ++bondid);
}
if (annotateAtomNum) {
for (IAtom atom : molecule.atoms()) {
if (atom.getProperty(StandardGenerator.ANNOTATION_LABEL) != null)
throw new UnsupportedOperationException("Multiple annotation labels are not supported.");
atom.setProperty(StandardGenerator.ANNOTATION_LABEL, Integer.toString(atomNum++));
}
} else if (annotateAtomVal) {
for (IAtom atom : molecule.atoms()) {
if (atom.getProperty(StandardGenerator.ANNOTATION_LABEL) != null)
throw new UnsupportedOperationException("Multiple annotation labels are not supported.");
atom.setProperty(
StandardGenerator.ANNOTATION_LABEL, atom.getProperty(CDKConstants.COMMENT));
}
} else if (annotateAtomMap) {
for (IAtom atom : molecule.atoms()) {
if (atom.getProperty(StandardGenerator.ANNOTATION_LABEL) != null)
throw new UnsupportedOperationException("Multiple annotation labels are not supported.");
int mapidx = accessAtomMap(atom);
if (mapidx > 0) {
atom.setProperty(StandardGenerator.ANNOTATION_LABEL, Integer.toString(mapidx));
}
}
}
ElementGroup grp = new ElementGroup();
for (IGenerator<IAtomContainer> gen : gens) grp.add(gen.generate(molecule, model));
// cleanup
if (annotateAtomNum || annotateAtomMap) {
for (IAtom atom : molecule.atoms()) {
atom.removeProperty(StandardGenerator.ANNOTATION_LABEL);
}
}
return grp;
}
private boolean checkForNullBonds(IAtomContainer mol) {
for (IBond b : mol.bonds()) {
if (b == null) {
LOGGER.info("Null bonds for: " + mol.getID());
return true;
}
if (b.getAtomCount() < 2) {
LOGGER.info("bond with less than two atoms: " + mol.getID());
return true;
}
if (b.getAtom(0) == null || b.getAtom(1) == null) {
LOGGER.info("Bond with one or two atoms null: " + mol.getID());
return true;
}
}
return false;
}
/**
* Hide the repeated atoms and bonds of a multiple group. We hide al atoms that belong to the
* group unless they are defined in the parent atom list. Any bond to those atoms that is not a
* crossing bond or one connecting atoms in the parent list is hidden.
*
* @param container molecule
* @param sgroup multiple group display shortcut
*/
private static void hideMultipleParts(IAtomContainer container, Sgroup sgroup) {
final Set<IBond> crossing = sgroup.getBonds();
final Set<IAtom> atoms = sgroup.getAtoms();
final Set<IAtom> parentAtoms = sgroup.getValue(SgroupKey.CtabParentAtomList);
for (IBond bond : container.bonds()) {
if (parentAtoms.contains(bond.getAtom(0)) && parentAtoms.contains(bond.getAtom(1))) continue;
if (atoms.contains(bond.getAtom(0)) || atoms.contains(bond.getAtom(1)))
StandardGenerator.hide(bond);
}
for (IAtom atom : atoms) {
if (!parentAtoms.contains(atom)) StandardGenerator.hide(atom);
}
for (IBond bond : crossing) {
StandardGenerator.unhide(bond);
}
}
protected synchronized BitSet getStructureKeyBits(IAtomContainer ac) {
// quick workaround for aromatic compounds, to avoid matching non-aromatic keys
// TODO remove this when isoTester/keys processing is fixed
// isoTester is fixed, but CDK isomorphism tester still needs the workaround, should be fixed in
// CDK nightly Mar 2010
for (IBond bond : ac.bonds())
if (bond.getFlag(CDKConstants.ISAROMATIC)) {
for (IAtom a : bond.atoms()) a.setFlag(CDKConstants.ISAROMATIC, true);
// in e.g. triazole the atoms are not set as aromatics, but bonds are!
if (cleanKekuleBonds) bond.setOrder(Order.SINGLE);
}
// end of the workaround
BitSet keys = new BitSet(nKeys);
boolean res;
for (int i = 0; i < nKeys; i++) {
isoTester.setSequence(smartsQueries.get(i), sequences.get(i));
res = isoTester.hasIsomorphism(ac);
keys.set(i, res);
}
return (keys);
}
/** @throws BioclipseException */
private void calculateInchi() throws BioclipseException {
try {
IAtomContainer clone = (IAtomContainer) getAtomContainer().clone();
// remove aromaticity flags
for (IAtom atom : clone.atoms()) atom.setFlag(CDKConstants.ISAROMATIC, false);
for (IBond bond : clone.bonds()) bond.setFlag(CDKConstants.ISAROMATIC, false);
if (factory == null) {
factory = InChIGeneratorFactory.getInstance();
}
InChIGenerator gen = factory.getInChIGenerator(clone);
INCHI_RET status = gen.getReturnStatus();
if (status == INCHI_RET.OKAY || status == INCHI_RET.WARNING) {
InChI inchi = new InChI();
inchi.setValue(gen.getInchi());
inchi.setKey(gen.getInchiKey());
cachedInchi = inchi;
} else {
throw new InvalidParameterException(
"Error while generating InChI (" + status + "): " + gen.getMessage());
}
} catch (Exception e) {
throw new BioclipseException("Could not create InChI: " + e.getMessage(), e);
}
}
/**
* 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);
}
}
/**
* Create a stereo encoder for cumulative double bonds.
*
* @param container the container
* @param graph adjacency list representation of the container
* @return a stereo encoder
*/
@Override
public StereoEncoder create(IAtomContainer container, int[][] graph) {
int n = container.getAtomCount();
BondMap map = new BondMap(n);
List<StereoEncoder> encoders = new ArrayList<StereoEncoder>(1);
// index double bonds by their atoms
for (IBond bond : container.bonds()) {
if (isDoubleBond(bond)) map.add(bond);
}
Set<IAtom> visited = new HashSet<IAtom>(n);
// find atoms which are connected between two double bonds
for (IAtom a : map.atoms()) {
List<IBond> bonds = map.bonds(a);
if (bonds.size() == 2) {
// (s)tart/(e)nd of cumulated system: -s=a=e-
IAtom s = bonds.get(0).getConnectedAtom(a);
IAtom e = bonds.get(1).getConnectedAtom(a);
// need the parents to re-use the double bond encoder
IAtom sParent = a;
IAtom eParent = a;
visited.add(a);
visited.add(s);
visited.add(e);
int size = 2;
// expand out from 'l'
while (s != null && map.cumulated(s)) {
IAtom p = map.bonds(s).get(0).getConnectedAtom(s);
IAtom q = map.bonds(s).get(1).getConnectedAtom(s);
sParent = s;
s = visited.add(p) ? p : visited.add(q) ? q : null;
size++;
}
// expand from 'r'
while (e != null && map.cumulated(e)) {
IAtom p = map.bonds(e).get(0).getConnectedAtom(e);
IAtom q = map.bonds(e).get(1).getConnectedAtom(e);
eParent = e;
e = visited.add(p) ? p : visited.add(q) ? q : null;
size++;
}
// s and e are null if we had a cumulative cycle...
if (s != null && e != null) {
// system has now be expanded, size is the number of double
// bonds. For odd numbers we use E/Z whilst for even are
// axial M/P.
// \ /
// s = = = = e
// / \
if (isOdd(size)) {
StereoEncoder encoder =
GeometricDoubleBondEncoderFactory.newEncoder(
container, s, sParent, e, eParent, graph);
if (encoder != null) {
encoders.add(encoder);
}
} else {
StereoEncoder encoder = axialEncoder(container, s, e);
if (encoder != null) {
encoders.add(encoder);
}
}
}
}
}
return encoders.isEmpty() ? StereoEncoder.EMPTY : new MultiStereoEncoder(encoders);
}
private static void markRingAtomsAndBondsAromatic(IAtomContainer container) {
for (IAtom atom : container.atoms()) atom.setFlag(CDKConstants.ISAROMATIC, true);
for (IBond bond : container.bonds()) bond.setFlag(CDKConstants.ISAROMATIC, true);
}
/** 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);
}
}
}
}
}
/** Checks whether all bonds have exactly two atoms. */
public static boolean hasGraphRepresentation(IAtomContainer molecule) {
for (IBond bond : molecule.bonds()) if (bond.getAtomCount() != 2) return false;
return true;
}
@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;
}
/**
* Search if the setOfAtomContainer contains the atomContainer
*
* @param set ISetOfAtomContainer object where to search
* @param atomContainer IAtomContainer to search
* @return True, if the atomContainer is contained
*/
private boolean existAC(IAtomContainerSet set, IAtomContainer atomContainer) {
IAtomContainer acClone = null;
try {
acClone = (IMolecule) atomContainer.clone();
if (!lookingSymmetry) {
/*remove all aromatic flags*/
for (IAtom atom : acClone.atoms()) atom.setFlag(CDKConstants.ISAROMATIC, false);
for (IBond bond : acClone.bonds()) bond.setFlag(CDKConstants.ISAROMATIC, false);
}
} catch (CloneNotSupportedException e1) {
e1.printStackTrace();
}
for (int i = 0; i < acClone.getAtomCount(); i++)
// if(acClone.getAtom(i).getID() == null)
acClone.getAtom(i).setID("" + acClone.getAtomNumber(acClone.getAtom(i)));
if (lookingSymmetry) {
try {
CDKHueckelAromaticityDetector.detectAromaticity(acClone);
} catch (CDKException e) {
e.printStackTrace();
}
} else {
if (!lookingSymmetry) {
/*remove all aromatic flags*/
for (IAtom atom : acClone.atoms()) atom.setFlag(CDKConstants.ISAROMATIC, false);
for (IBond bond : acClone.bonds()) bond.setFlag(CDKConstants.ISAROMATIC, false);
}
}
for (int i = 0; i < set.getAtomContainerCount(); i++) {
IAtomContainer ss = set.getAtomContainer(i);
for (int j = 0; j < ss.getAtomCount(); j++)
// if(ss.getAtom(j).getID() == null)
ss.getAtom(j).setID("" + ss.getAtomNumber(ss.getAtom(j)));
try {
if (!lookingSymmetry) {
QueryAtomContainer qAC =
QueryAtomContainerCreator.createSymbolChargeIDQueryContainer(acClone);
if (UniversalIsomorphismTester.isIsomorph(ss, qAC)) {
QueryAtomContainer qAC2 =
QueryAtomContainerCreator.createSymbolAndBondOrderQueryContainer(acClone);
if (UniversalIsomorphismTester.isIsomorph(ss, qAC2)) return true;
}
} else {
QueryAtomContainer qAC =
QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(acClone);
CDKHueckelAromaticityDetector.detectAromaticity(ss);
if (UniversalIsomorphismTester.isIsomorph(ss, qAC)) return true;
}
} catch (CDKException e1) {
System.err.println(e1);
logger.error(e1.getMessage());
logger.debug(e1);
}
}
return false;
}
@Test
public void unionMolecules() throws IOException, CDKException {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer mol1 = sp.parseSmiles("OOC1=CC=CC=C1");
IAtomContainer mol2 = sp.parseSmiles("c1ccc(cc1)c2ccccc2");
int i = 0;
for (IAtom atom1 : mol1.atoms()) {
atom1.setID(String.valueOf((i++)));
}
int j = 0;
for (IAtom atom2 : mol2.atoms()) {
atom2.setID(String.valueOf((j++)));
}
MoleculeSanityCheck.aromatizeMolecule(mol1);
MoleculeSanityCheck.aromatizeMolecule(mol2);
Isomorphism isomorphism = new Isomorphism(mol1, mol2, Algorithm.DEFAULT, true, false, false);
isomorphism.setChemFilters(false, false, false);
int combinations = 1;
List<String> acSet = new ArrayList<String>();
if (isomorphism.getFirstAtomMapping() != null) {
for (AtomAtomMapping mapping : isomorphism.getAllAtomMapping()) {
IAtomContainer union = new AtomContainer();
for (IAtom atom : mol1.atoms()) {
union.addAtom(atom);
}
for (IBond bond : mol1.bonds()) {
union.addBond(bond);
}
for (IBond bond : mol2.bonds()) {
IAtom a1 = bond.getAtom(0);
IAtom a2 = bond.getAtom(1);
if (!mapping.getMappingsByAtoms().containsValue(a1)
&& !mapping.getMappingsByAtoms().containsValue(a2)) {
if (!union.contains(a1)) {
union.addAtom(a1);
}
if (!union.contains(a2)) {
union.addAtom(a2);
}
union.addBond(bond);
} else if (mapping.getMappingsByAtoms().containsValue(a1)
&& !mapping.getMappingsByAtoms().containsValue(a2)) {
if (!union.contains(a2)) {
union.addAtom(a2);
}
union.addBond(
new Bond(
a2,
getKey(a1, mapping.getMappingsByAtoms()),
bond.getOrder(),
bond.getStereo()));
} else if (!mapping.getMappingsByAtoms().containsValue(a1)
&& mapping.getMappingsByAtoms().containsValue(a2)) {
if (!union.contains(a1)) {
union.addAtom(a1);
}
union.addBond(
new Bond(
a1,
getKey(a2, mapping.getMappingsByAtoms()),
bond.getOrder(),
bond.getStereo()));
}
}
/*check if this combination is chemically valid*/
if (isChemicallyValid(union)) {
String molSMILES = getSMILES(union).toString();
if (!acSet.contains(molSMILES)) {
acSet.add(molSMILES);
}
}
}
}
// for (String container : acSet) {
// System.out.println("\n-------------" + " Combination " + combinations++ +
// "--------------------");
// System.out.println("Query SMILES " + getSMILES(mol1).toString() + ", count " +
// mol1.getAtomCount());
// System.out.println("Target SMILES " + getSMILES(mol2).toString() + ", count " +
// mol2.getAtomCount());
// System.out.println("Union SMILES " + container + ", count " +
// sp.parseSmiles(container).getAtomCount());
// }
}
@TestMethod(value = "testCalculate_IAtomContainer")
public DescriptorValue calculate(
IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset) {
IAtomContainer varAtomContainer;
try {
varAtomContainer = (IAtomContainer) atomContainer.clone();
} catch (CloneNotSupportedException e) {
return getDummyDescriptorValue(e);
}
int atomPosition = atomContainer.getAtomNumber(atom);
IAtom clonedAtom = varAtomContainer.getAtom(atomPosition);
DoubleArrayResult rdfProtonCalculatedValues = new DoubleArrayResult(gsr_desc_length);
if (!atom.getSymbol().equals("H")) {
return getDummyDescriptorValue(new CDKException("Invalid atom specified"));
}
///////////////////////// FIRST SECTION OF MAIN METHOD: DEFINITION OF MAIN VARIABLES
///////////////////////// AND AROMATICITY AND PI-SYSTEM AND RINGS DETECTION
Molecule mol = new Molecule(varAtomContainer);
if (varAtomContainer != acold) {
acold = varAtomContainer;
// DETECTION OF pi SYSTEMS
varAtomContainerSet = ConjugatedPiSystemsDetector.detect(mol);
if (precalculatedringset == null)
try {
varRingSet = (new AllRingsFinder()).findAllRings(varAtomContainer);
} catch (CDKException e) {
return getDummyDescriptorValue(e);
}
else varRingSet = precalculatedringset;
try {
GasteigerMarsiliPartialCharges peoe = new GasteigerMarsiliPartialCharges();
peoe.assignGasteigerMarsiliSigmaPartialCharges(mol, true);
} catch (Exception ex1) {
return getDummyDescriptorValue(ex1);
}
}
if (checkAromaticity) {
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(varAtomContainer);
CDKHueckelAromaticityDetector.detectAromaticity(varAtomContainer);
} catch (CDKException e) {
return getDummyDescriptorValue(e);
}
}
IRingSet rsAtom;
Ring ring;
IRingSet ringsWithThisBond;
// SET ISINRING FLAGS FOR BONDS
Iterator<IBond> bondsInContainer = varAtomContainer.bonds().iterator();
while (bondsInContainer.hasNext()) {
IBond bond = bondsInContainer.next();
ringsWithThisBond = varRingSet.getRings(bond);
if (ringsWithThisBond.getAtomContainerCount() > 0) {
bond.setFlag(CDKConstants.ISINRING, true);
}
}
// SET ISINRING FLAGS FOR ATOMS
IRingSet ringsWithThisAtom;
for (int w = 0; w < varAtomContainer.getAtomCount(); w++) {
ringsWithThisAtom = varRingSet.getRings(varAtomContainer.getAtom(w));
if (ringsWithThisAtom.getAtomContainerCount() > 0) {
varAtomContainer.getAtom(w).setFlag(CDKConstants.ISINRING, true);
}
}
IAtomContainer detected = varAtomContainerSet.getAtomContainer(0);
// neighboors[0] is the atom joined to the target proton:
List<IAtom> neighboors = mol.getConnectedAtomsList(clonedAtom);
IAtom neighbour0 = neighboors.get(0);
// 2', 3', 4', 5', 6', and 7' atoms up to the target are detected:
List<IAtom> atomsInSecondSphere = mol.getConnectedAtomsList(neighbour0);
List<IAtom> atomsInThirdSphere;
List<IAtom> atomsInFourthSphere;
List<IAtom> atomsInFifthSphere;
List<IAtom> atomsInSixthSphere;
List<IAtom> atomsInSeventhSphere;
// SOME LISTS ARE CREATED FOR STORING OF INTERESTING ATOMS AND BONDS DURING DETECTION
ArrayList<Integer> singles = new ArrayList<Integer>(); // list of any bond not rotatable
ArrayList<Integer> doubles = new ArrayList<Integer>(); // list with only double bonds
ArrayList<Integer> atoms = new ArrayList<Integer>(); // list with all the atoms in spheres
// atoms.add( Integer.valueOf( mol.getAtomNumber(neighboors[0]) ) );
ArrayList<Integer> bondsInCycloex =
new ArrayList<Integer>(); // list for bonds in cycloexane-like rings
// 2', 3', 4', 5', 6', and 7' bonds up to the target are detected:
IBond secondBond; // (remember that first bond is proton bond)
IBond thirdBond; //
IBond fourthBond; //
IBond fifthBond; //
IBond sixthBond; //
IBond seventhBond; //
// definition of some variables used in the main FOR loop for detection of interesting atoms and
// bonds:
boolean theBondIsInA6MemberedRing; // this is like a flag for bonds which are in cycloexane-like
// rings (rings with more than 4 at.)
IBond.Order bondOrder;
int bondNumber;
int sphere;
// THIS MAIN FOR LOOP DETECT RIGID BONDS IN 7 SPHERES:
for (IAtom curAtomSecond : atomsInSecondSphere) {
secondBond = mol.getBond(neighbour0, curAtomSecond);
if (mol.getAtomNumber(curAtomSecond) != atomPosition
&& getIfBondIsNotRotatable(mol, secondBond, detected)) {
sphere = 2;
bondOrder = secondBond.getOrder();
bondNumber = mol.getBondNumber(secondBond);
theBondIsInA6MemberedRing = false;
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomSecond),
atoms,
sphere,
theBondIsInA6MemberedRing);
atomsInThirdSphere = mol.getConnectedAtomsList(curAtomSecond);
if (atomsInThirdSphere.size() > 0) {
for (IAtom curAtomThird : atomsInThirdSphere) {
thirdBond = mol.getBond(curAtomThird, curAtomSecond);
// IF THE ATOMS IS IN THE THIRD SPHERE AND IN A CYCLOEXANE-LIKE RING, IT IS STORED IN
// THE PROPER LIST:
if (mol.getAtomNumber(curAtomThird) != atomPosition
&& getIfBondIsNotRotatable(mol, thirdBond, detected)) {
sphere = 3;
bondOrder = thirdBond.getOrder();
bondNumber = mol.getBondNumber(thirdBond);
theBondIsInA6MemberedRing = false;
// if the bond is in a cyclohexane-like ring (a ring with 5 or more atoms, not
// aromatic)
// the boolean "theBondIsInA6MemberedRing" is set to true
if (!thirdBond.getFlag(CDKConstants.ISAROMATIC)) {
if (!curAtomThird.equals(neighbour0)) {
rsAtom = varRingSet.getRings(thirdBond);
for (int f = 0; f < rsAtom.getAtomContainerCount(); f++) {
ring = (Ring) rsAtom.getAtomContainer(f);
if (ring.getRingSize() > 4 && ring.contains(thirdBond)) {
theBondIsInA6MemberedRing = true;
}
}
}
}
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomThird),
atoms,
sphere,
theBondIsInA6MemberedRing);
theBondIsInA6MemberedRing = false;
atomsInFourthSphere = mol.getConnectedAtomsList(curAtomThird);
if (atomsInFourthSphere.size() > 0) {
for (IAtom curAtomFourth : atomsInFourthSphere) {
fourthBond = mol.getBond(curAtomThird, curAtomFourth);
if (mol.getAtomNumber(curAtomFourth) != atomPosition
&& getIfBondIsNotRotatable(mol, fourthBond, detected)) {
sphere = 4;
bondOrder = fourthBond.getOrder();
bondNumber = mol.getBondNumber(fourthBond);
theBondIsInA6MemberedRing = false;
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomFourth),
atoms,
sphere,
theBondIsInA6MemberedRing);
atomsInFifthSphere = mol.getConnectedAtomsList(curAtomFourth);
if (atomsInFifthSphere.size() > 0) {
for (IAtom curAtomFifth : atomsInFifthSphere) {
fifthBond = mol.getBond(curAtomFifth, curAtomFourth);
if (mol.getAtomNumber(curAtomFifth) != atomPosition
&& getIfBondIsNotRotatable(mol, fifthBond, detected)) {
sphere = 5;
bondOrder = fifthBond.getOrder();
bondNumber = mol.getBondNumber(fifthBond);
theBondIsInA6MemberedRing = false;
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomFifth),
atoms,
sphere,
theBondIsInA6MemberedRing);
atomsInSixthSphere = mol.getConnectedAtomsList(curAtomFifth);
if (atomsInSixthSphere.size() > 0) {
for (IAtom curAtomSixth : atomsInSixthSphere) {
sixthBond = mol.getBond(curAtomFifth, curAtomSixth);
if (mol.getAtomNumber(curAtomSixth) != atomPosition
&& getIfBondIsNotRotatable(mol, sixthBond, detected)) {
sphere = 6;
bondOrder = sixthBond.getOrder();
bondNumber = mol.getBondNumber(sixthBond);
theBondIsInA6MemberedRing = false;
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomSixth),
atoms,
sphere,
theBondIsInA6MemberedRing);
atomsInSeventhSphere = mol.getConnectedAtomsList(curAtomSixth);
if (atomsInSeventhSphere.size() > 0) {
for (IAtom curAtomSeventh : atomsInSeventhSphere) {
seventhBond = mol.getBond(curAtomSeventh, curAtomSixth);
if (mol.getAtomNumber(curAtomSeventh) != atomPosition
&& getIfBondIsNotRotatable(mol, seventhBond, detected)) {
sphere = 7;
bondOrder = seventhBond.getOrder();
bondNumber = mol.getBondNumber(seventhBond);
theBondIsInA6MemberedRing = false;
checkAndStore(
bondNumber,
bondOrder,
singles,
doubles,
bondsInCycloex,
mol.getAtomNumber(curAtomSeventh),
atoms,
sphere,
theBondIsInA6MemberedRing);
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
// Variables
double[] values; // for storage of results of other methods
double distance;
double sum;
double smooth = -20;
double partial;
int position;
double limitInf;
double limitSup;
double step;
//////////////////////// THE FOUTH DESCRIPTOR IS gS(r), WHICH TAKES INTO ACCOUNT SINGLE BONDS IN
// RIGID SYSTEMS
Vector3d a_a = new Vector3d();
Vector3d a_b = new Vector3d();
Vector3d b_a = new Vector3d();
Vector3d b_b = new Vector3d();
Point3d middlePoint = new Point3d();
double angle = 0;
if (singles.size() > 0) {
double dist0;
double dist1;
IAtom singleBondAtom0;
IAtom singleBondAtom1;
distance = 0;
position = 0;
IBond theSingleBond = null;
limitInf = 0;
limitSup = Math.PI / 2;
step = (limitSup - limitInf) / 7;
smooth = -1.15;
int counter = 0;
for (double ghs = 0; ghs < limitSup; ghs = ghs + step) {
sum = 0;
for (int sing = 0; sing < singles.size(); sing++) {
angle = 0;
partial = 0;
Integer thisSingleBond = singles.get(sing);
position = thisSingleBond;
theSingleBond = mol.getBond(position);
middlePoint = theSingleBond.get3DCenter();
singleBondAtom0 = theSingleBond.getAtom(0);
singleBondAtom1 = theSingleBond.getAtom(1);
dist0 = calculateDistanceBetweenTwoAtoms(singleBondAtom0, atom);
dist1 = calculateDistanceBetweenTwoAtoms(singleBondAtom1, atom);
a_a.set(middlePoint.x, middlePoint.y, middlePoint.z);
if (dist1 > dist0)
a_b.set(
singleBondAtom0.getPoint3d().x,
singleBondAtom0.getPoint3d().y,
singleBondAtom0.getPoint3d().z);
else
a_b.set(
singleBondAtom1.getPoint3d().x,
singleBondAtom1.getPoint3d().y,
singleBondAtom1.getPoint3d().z);
b_a.set(middlePoint.x, middlePoint.y, middlePoint.z);
b_b.set(atom.getPoint3d().x, atom.getPoint3d().y, atom.getPoint3d().z);
values = calculateDistanceBetweenAtomAndBond(atom, theSingleBond);
angle = calculateAngleBetweenTwoLines(a_a, a_b, b_a, b_b);
// System.out.println("ANGLe: "+angle+ " "+ mol.getAtomNumber(atomsInSingleBond[0]) +" "
// +mol.getAtomNumber(atomsInSingleBond[1]));
partial =
(1 / (Math.pow(values[0], 2))) * Math.exp(smooth * (Math.pow((ghs - angle), 2)));
sum += partial;
}
// gSr_function.add(new Double(sum));
rdfProtonCalculatedValues.add(sum);
logger.debug("RDF gSr prob.: " + sum + " at distance " + ghs);
counter++;
}
} else {
return getDummyDescriptorValue(new CDKException("Some error occurred. Please report"));
}
return new DescriptorValue(
getSpecification(),
getParameterNames(),
getParameters(),
rdfProtonCalculatedValues,
getDescriptorNames());
}
/**
* This makes atom map1 of matching atoms out of atom map1 of matching bonds as produced by the
* get(Subgraph|Ismorphism)Map methods. Added by Asad since CDK one doesn't pick up the correct
* changes
*
* @param list The list produced by the getMap method.
* @param sourceGraph first molecule. Must not be an IQueryAtomContainer.
* @param targetGraph second molecule. May be an IQueryAtomContainer.
* @return The mapping found projected on sourceGraph. This is atom List of CDKRMap objects
* containing Ids of matching atoms.
*/
private synchronized List<List<CDKRMap>> makeAtomsMapOfBondsMapSingleBond(
List<CDKRMap> list, IAtomContainer sourceGraph, IAtomContainer targetGraph) {
if (list == null) {
return null;
}
Map<IBond, IBond> bondMap = new HashMap<IBond, IBond>(list.size());
for (CDKRMap solBondMap : list) {
int id1 = solBondMap.getId1();
int id2 = solBondMap.getId2();
IBond qBond = sourceGraph.getBond(id1);
IBond tBond = targetGraph.getBond(id2);
bondMap.put(qBond, tBond);
}
List<CDKRMap> result1 = new ArrayList<CDKRMap>();
List<CDKRMap> result2 = new ArrayList<CDKRMap>();
for (IBond qbond : sourceGraph.bonds()) {
if (bondMap.containsKey(qbond)) {
IBond tbond = bondMap.get(qbond);
CDKRMap map00 = null;
CDKRMap map01 = null;
CDKRMap map10 = null;
CDKRMap map11 = null;
if ((qbond.getAtom(0).getSymbol().equals(tbond.getAtom(0).getSymbol()))
&& (qbond.getAtom(1).getSymbol().equals(tbond.getAtom(1).getSymbol()))) {
map00 =
new CDKRMap(
sourceGraph.getAtomNumber(qbond.getAtom(0)),
targetGraph.getAtomNumber(tbond.getAtom(0)));
map11 =
new CDKRMap(
sourceGraph.getAtomNumber(qbond.getAtom(1)),
targetGraph.getAtomNumber(tbond.getAtom(1)));
if (!result1.contains(map00)) {
result1.add(map00);
}
if (!result1.contains(map11)) {
result1.add(map11);
}
}
if ((qbond.getAtom(0).getSymbol().equals(tbond.getAtom(1).getSymbol()))
&& (qbond.getAtom(1).getSymbol().equals(tbond.getAtom(0).getSymbol()))) {
map01 =
new CDKRMap(
sourceGraph.getAtomNumber(qbond.getAtom(0)),
targetGraph.getAtomNumber(tbond.getAtom(1)));
map10 =
new CDKRMap(
sourceGraph.getAtomNumber(qbond.getAtom(1)),
targetGraph.getAtomNumber(tbond.getAtom(0)));
if (!result2.contains(map01)) {
result2.add(map01);
}
if (!result2.contains(map10)) {
result2.add(map10);
}
}
}
}
List<List<CDKRMap>> result = new ArrayList<List<CDKRMap>>();
if (result1.size() == result2.size()) {
result.add(result1);
result.add(result2);
} else if (result1.size() > result2.size()) {
result.add(result1);
} else {
result.add(result2);
}
return result;
}