void setRoot(IAtom atom) {
        setMol(atom.getContainer());
        numMapped = 1;
        int aidx = atom.getIndex();
        avisit[aidx] = true;
        amap[0] = aidx;
    }
void setRoot ( IAtom atom ) { setMol ( atom . getContainer ( ) ) ; numMapped = 1 ; int aidx = atom . getIndex ( ) ; avisit [ aidx ] = true ; amap [ 0 ] = aidx ; }
Set the molecule to be matched and the 'root' atom at which the match
must start (e.g. query atom 0). It is presumed the root atom has already
been tested against the query atom and matched.

@param atom the root atom.