Locates all matches of the fragment in the molecule that result in distinguishable sets of molecule atoms. Multiple matches involving the same atoms, e.g. with a benzene ring, are counted and listed only once. If count mode is different from 'existence', then an atom mapping from fragment to molecule is collected and can be retrieved with getMatchList().
Optionaloptions: SSSearcherFindFragmentInMoleculeOptionscount of sub-structure matches of fragment in molecule
If the match count mode is one of 'firstMatch', 'overlapping', 'rigorous' then this method returns an array of all counted matches, i.e. int arrays mapping fragment atoms to molecule atoms. Atoms being part of a matched bridge bond are naturally not covered by the mapping. Atoms being part of a matching bridge bond are available with getBridgeBondAtomList(). Note: If some query fragment atoms are marked as exclude group, then the respective matchlist values are -1.
list of distinct counted matches.
Returns whether the current fragment is in the target molecule.
Set the fragment to search.
Molecule instance to set as fragment. It has to be
flagged with setFragment(true) first.
Set the target molecule in which the search will be done.
Molecule instance to set as target molecule.
Basic substructure searcher.