Class SearchHit

    • Constructor Detail

      • SearchHit

        public SearchHit​(int[] singleHit)
        Constructor: creates a hit object from a single (1 dimensional) hit mapping array.
        singleHit - the 1D hit mapping array
      • SearchHit

        public SearchHit​(int[][] groupHit)
        Constructor: creates a hit object from a group (2 dimensional) hit mapping array.

        Warning: The given array is not copied for efficiency reasons. Do not modify it after passing to this constructor.

        groupHit - the 2D hit mapping array
    • Method Detail

      • hashCode

        public int hashCode()
        hashCode in class Object
      • getSingleHit

        public int[] getSingleHit()
        Returns the single hit view of the hit object.

        The single hit is a simple array of int values so that the i-th element is the index of the target atom that is matched to the i-th query atom. In case of an R-group query, this array corresponds to the root of the query.

        Special matching atom indexes:

        The hit array may contain special codes that are not valid indexes of the target structure. These special values are defined as follows.
        • In case of explicit query H atoms matching to implied H atoms in the target, a negative number is returned. The absolute value of this number equals with the atom index of the heavy atom bearing the implicit hydrogen, or Integer.MIN_VALUE in case of 0 heavy atom index.
        • The same method is used for explicit LP (lone pair) atoms in the query. The hit contains the negated number of the target heavy atom with the matching lone pair, or Integer.MIN_VALUE for 0 index. SearchConstants.HIT_LP is set for isolated lone pairs (in which case there is no such target heavy atom).
        • Multicenter atoms (e.g. of multicenter coordinate bonds) are not returned, the match array always contains SearchConstants.HIT_MULTICENTER for these atoms.
        • In case of defined or undefined R-atom matching on a group of atoms: only one representative matched atom is set in the match array, or SearchConstants.HIT_R_EMPTY_MATCH denoting the match to an empty group.
        • Unmapable atoms (e.g. polymer star atoms) are denoted by SearchConstants.HIT_UNMAPABLE in the match array.
        • Excluded query atoms receive the special SearchConstants.HIT_EXCLUDEDQ value.
        • All Superatom S-groups are treated as expanded during the search, so atom indices are returned accordingly.
        the single hit view of the hit object
        See Also:
      • getGroupHit

        public int[][] getGroupHit()
        Returns the group hit view of the hit object.

        The group hit is an array of int arrays so that the i-th array contains the indexes of all target atoms that is matched to the i-th query atom. In contrast with the single hit, group hits allow multiple target atoms matching a single query atom. This can be the case if the query contains R-atoms or homology groups, because they may match several atoms in the target at once. In case of undefined R-atoms, empty match is denoted by an empty array (see SearchConstants.UNDEF_R_MATCHING_GROUP_H_EMPTY).

        In group hits, the same special matching atom indexes are used as in single hits. See getSingleHit() for their description.

        Warning: For efficiency reasons, this method directly returns the internal array representation. Make a deep copy of the result if you would like to modify it.

        the group hit view of the hit object
        See Also: