I have a bunch of pdb files and I need to make some computation on them. I have found a python module (http://gecco.org.chemie.uni-frankfurt.de/liquid/index.html) for PyMol which does exactly what I want - the pdb file is loaded into pymol, then I run a plugin from pymol UI which computes and saves a file with the data. The problem is that I have a thousands of these pdb files, I wonder if I can automatize this process. The only input to the plugin's python script is some kind of pymol-specific coordinates, is it possible to run a plugin without computational costly molecule visualisation or so? The only thing I need is to find the right input for the plugin script (without even opening the pymol in the best case) because it takes the information about molecule only if molecule is opened in pymol. I wil appreciate any suggestion.