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 paramtersprocess_charges.py
- constructs input files for CPET calculations. Added optionality for processing.run_topology.py
- runs cpet topology calculations on a folderrun_box_calc.py
- runs cpet box field calculations on a folderdist_and_compress_each_protein.py
- specify code for analyzing MD trajectoriesrun_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.
- You can now run
get_charges.py
and this will generate files in the pqr format in the destination (charges_folder
). - Process the charges and generate the cpet input files via
process_charges.py
- Run your box or topology calculation using
run_topology.py
orrun_box_calc.py
- 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
- Todo: add HEML
- Todo: add Proto