Methods such as SpaceLight and FTrees have been developed to search nonenumerated chemical spaces. However, these tools can only use small molecules as queries and do not allow structure-based virtual screening as such. Here, we describe a software called SpaceHASTEN that enables users to dock non-enumerated chemical spaces using reasonable computational resources. It is significantly different to the previously published methods V-SYNTHES and Chemical Space Docking for structure-based virtual screening of non-enumerated chemical spaces, as SpaceHASTEN uses the concept of chemical similarity of whole molecules, instead of a fragment-based approach, to navigate the vast chemical space.