A method of generating a molecular structure includes generating, based on a predetermined number of a plurality of nodes, all possible two-dimensional (2D) graphs and a plurality of edges representing connections between the plurality of nodes and, for each 2D graph from among the generated 2D graphs, generating all possible molecular structures based on the 2D graph by substituting each of the plurality of nodes with a polygonal ring structure including carbon atoms and substituting the edges with bonds between polygonal ring structures. Also, a method includes substituting at least one of carbon atoms included in the polygonal ring structures with an atom other than a carbon atom.