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Inductive Logic Programming (ILP) is a combination of inductive learning and first-order logic aiming to learn first-order hypotheses from training examples. ILP has a serious bottleneck in an intractably enormous hypothesis search space. Thismakes existing approaches perform poorly on large-scale real-world datasets. In this research, we propose a technique to make the system handle an enormous search space efficiently by deriving qualitative information into search heuristics. Currently, heuristic functions used in ILP systems are based only on quantitative information, e.g. number of examples covered and length of candidates. We focus on a kind of data consisting of several parts. The approach aims to find hypotheses describing each class by using both individual and relational features of parts. The data can be found in denoting chemical compound structure for Structure-Activity Relationship studies (SAR). We apply the proposed method to extract rules describing chemical activity from their structures. The experiments are conducted on a real-world dataset. The results are compared to existing ILP methods using ten-fold cross validation.