Hello. I'm facing some trouble running the library feature of the Pyrod software (https://github.com/wolberlab/pyrod). I have completed the super pharmacophore formation analysis by the "Trajectory Pharmacophore Combo". The next step would be the library function, which aims to "Generate a combinatorial pharmacophore library based on an input pharmacophore." accorging to the Pyrod website. When I run the library function, it returns the following message:

(pyrod) pyrod library.cfg /home/lammol/miniconda3/envs/pyrod/lib/python3.8/site-packages/Bio/Application/__init__.py:40: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated. Due to the ongoing maintenance burden of keeping command line application wrappers up to date, we have decided to deprecate and eventually remove these modules. We instead now recommend building your command line and invoking it directly with the subprocess module. warnings.warn( |X| )__) )_) )___) )) )___) )____))_) _ )____)_____))__) \---__|____/|___|___----- ~~~~~~~~~\ oo oo oo oo /~~~~~~~~~ ~~~~~~~~~~~~~~~~~~ ~~~~~~ ~~ ~~~~ PyRod v0.7.5 ~~~~~ ~~~~ ~~ ~~~~ Tracing water molecules in molecular dynamics simulations. Starting library generation. 0 pharmacophores will be written taking about 0 B of space.

In other words, it is not generating the a combinatorial pharmacophore library as it should. I have already tried several approaches. Could someone help me?

Sincerely,

José Augusto Leoncio Gomide.