mol2db is a program developed to combine multimol2 files into the Flexibase format read by DOCK.
The purpose of this page is to document how mol2db works and any changes made to mol2db, and is not necessarily a guide to preparing files to run or running them through mol2db.
ui.c reads the inhier parameter file and sets variables
hiergen.c uses the multiple conformations to construct the hierarchy data structure by examining connected atoms first, and if the connected atoms have the same number of unique positions they are considered to be in the same group. this would appear to have flaws.