/**
* Perform a SMARTS match and check whether the query is present in the target molecule.
*
* <p>This function simply checks whether the query pattern matches the specified molecule.
* However the function will also, internally, save the mapping of query atoms to the target
* molecule
*
* @param atomContainer The target moleculoe
* @param forceInitialization If true, then the molecule is initialized (ring perception,
* aromaticity etc). If false, the molecule is only initialized if it is different (in terms
* of object reference) than one supplied in a previous call to this method.
* @return true if the pattern is found in the target molecule, false otherwise
* @throws CDKException if there is an error in ring, aromaticity or isomorphism perception
* @see #getMatchingAtoms()
* @see #countMatches()
* @see #matches(org.openscience.cdk.interfaces.IAtomContainer)
*/
@TestMethod("testQueryTool, testQueryToolSingleAtomCase, testQuery")
public boolean matches(IAtomContainer atomContainer, boolean forceInitialization)
throws CDKException {
if (this.atomContainer == atomContainer) {
if (forceInitialization) initializeMolecule();
} else {
this.atomContainer = atomContainer;
initializeMolecule();
}
// First calculate the recursive smarts
initializeRecursiveSmarts(this.atomContainer);
// lets see if we have a single atom query
if (query.getAtomCount() == 1) {
// lets get the query atom
IQueryAtom queryAtom = (IQueryAtom) query.getAtom(0);
matchingAtoms = new ArrayList<List<Integer>>();
for (IAtom atom : this.atomContainer.atoms()) {
if (queryAtom.matches(atom)) {
List<Integer> tmp = new ArrayList<Integer>();
tmp.add(this.atomContainer.getAtomNumber(atom));
matchingAtoms.add(tmp);
}
}
} else {
List bondMapping =
new UniversalIsomorphismTester().getSubgraphMaps(this.atomContainer, query);
matchingAtoms = getAtomMappings(bondMapping, this.atomContainer);
}
return matchingAtoms.size() != 0;
}
/**
* Initializes recursive smarts atoms in the query.
*
* <p>We loop over the SMARTS atoms in the query and associate the target molecule with each of
* the SMARTS atoms that need it
*
* @param atomContainer
* @throws CDKException
*/
private void initializeRecursiveSmarts(IAtomContainer atomContainer) throws CDKException {
for (IAtom atom : query.atoms()) {
initializeRecursiveSmartsAtom(atom, atomContainer);
}
}