Our group ran into the problem of fixing a constraint on big data mol2 files. The GOLD docking software ran into problems if the specific atoms that were constant in each molecule of our data file (~97,116 mol2 structures) were not selected to bind into the region of our protein active site. The scripts are designed for lengths that fit minimized energy mol2 generated files with SYBYL and the TRIPOS force field. Examples were demonstrated on github and the code can be downloaded.
Input: 97,116 Molecules
Time of Renumbering Atoms :3.25 minutes
Sorting back the Atoms: 2,4 minues
Python Compiler: 3.5