Workflow for the template-based combinatorial enumeration of virtual compound libraries. An appropriate lipid template structure is selected from a pre-defined list of templates for the specified lipid abbreviation. 2D structures of lipid templates are stored internally as MDL MOL strings and annotated with information regarding atom numbers and atomic coordinates for attachment points, number of existing carbon atoms in chains, head group name, etc. After an appropriate template has been identified and chains selected for the specified lipid abbreviation, a virtual compound library is generated by the combinatorial enumeration of all selected chains at appropriate attachment points on the template. A SD file is written out containing structure data along with abbreviation, systematic name, lipid category, main class, sub class, etc.