run cli program over all files in folder

@echo off
setlocal enableDelayedExpansion

set MYDIR=D:\Vytauto\Shared\methyl_transferases_docking4\010\0*.mol2
for /F %%x in ('dir /B/D %MYDIR%') do (
  echo %%x
  babel %%x %%x.pdbqt
)