/HEML

Primary LanguagePython

HEML

Installing

pip install -e .

In the current directory. This will give you the following scripts in your enviroment:

  • get_charges.py - uses ChargeFW2 to compute the charges on a pdb with default paramters
  • process_charges.py - constructs input files for CPET calculations. Added optionality for processing.
  • run_topology.py - runs cpet topology calculations on a folder
  • run_box_calc.py - runs cpet box field calculations on a folder
  • dist_and_compress_each_protein.py - specify code for analyzing MD trajectories
  • run_sweep.py - runs a sweep of parameters for compression along with statistics to pick the best clustering hyperparameters.
  • dist_on_topo.py - runs a compression on the current folder

For Computing Fields/Boxs on an MD trajectory:

1) Run``split_movies.py`` to separate your frames. If you need to remove solvent molecules, run ``remove_solvent_from_pdb.py`` subsequently.

2) Setup an``./options.json`` file with the following entries:
  • cpet_loc - currently CPET is a dependency and can be found at https://github.com/matthew-hennefarth/CPET. We are in the process of creating a pythonic variant that can be installed via pip
  • chargefw2_loc - another dependency for computing electric fields.
  • processed_pdb_folder - finalized location for pdb files.
  • charges_folder - where raw charges are located.
  • processed_charges_folder - where finalized charges are to be output.
  • cpet_folder- location for output cpet calculations and input files.
  1. You can now run get_charges.py and this will generate files in the pqr format in the destination (charges_folder).
  2. Process the charges and generate the cpet input files via process_charges.py
  3. Run your box or topology calculation using run_topology.py or run_box_calc.py
  4. We have implemented helper methods to build your own compression workflows but you can use the dist_on_topo.py script to compress the current folder

If you use any of the scripts/utilities in this package it would be goated if you cited the following

  1. Todo: add HEML
  2. Todo: add Proto