Mol2db
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 the following algorithm:
- find the first atom in the rigid component as the first atom with only 1 unique position
- expand through bonds to any atoms that have the same or fewer unique positions. bonded atoms with more unique positions are recursively added as branches
- for each branch, repeat the examining of bonded atoms and examine unique positions
this would appear to have flaws if the atom positions downstream overlap, especially since a distance tolerance is used to consider things overlapped.
confhier.c puts the conformations into the hierarchy. the potential problem here is that only one atom in each conformation in used to determine if the conformation differs from a previous one. when there are some atoms in a conformation that are the same while others are different, the results will be random based on atom ordering in the mol2 files, and can be incorrect.