Installation (Requires Python 3.9 and above)

Use the following command:

pip install nrgrank

Using NRGRank in a python script:

from nrgrank import process_target, process_ligands, nrgrank_main

Preparatory steps

1. Preprocessing the target

Required Arguments

Argument	Description	Possible value(s)
target_mol2_path	Path to target mol2 file	Absolute path
binding_site_file_path	Path to binding site file generated by GetCleft	Absolute path

Optional Arguments

Flag	Description	Possible value(s)
create_new_dir	A new folder will be created to store generated files	True,False
overwrite	Allows overwriting existing files	True,False

Example command

target_save_dir = process_target(target_mol2_path='foo/bar/target.mol2', binding_site_file_path='foo/bar/bd_site_sph_1.pdb')

2. Preparing the ligands

All ligands for one screen must be in the same mol2 file

Required Arguments

For running on a single mol2 file:

Flag	Description	Possible value(s)
ligand_path	Path to ligand mol2 file	Absolute path
conformers_per_molecule	Number of conformers per molecule	Int

Optional Arguments

Flag	Description	Possible value(s)
overwrite	Allows overwriting existing files	True,False
ligand_type	Assign a specific ligand type recognised by NRGRank. Can be useful for benchmarking.	(str)
output_dir	Folder where generated files will be stored	Absolute path

Example commands:

ligand_save_dir = process_ligands(ligand_path='foo/bar/ligands.mol2', conformers_per_molecule=1)

---

NRGRank

Required Flags

Flag	Description	Possible value(s)
target_name	Target name that is used to name the output file	(str)
preprocessed_target_path	Path to preprocessed_target folder (can be path returned from process_target)	Absolute path
preprocessed_ligand_path	Path to preprocessed_ligands folder (can be path returned from process_ligands)	Absolute path
result_folder_path	Path to folder where result file will be written	Absolute path

Optional Flags

Flag	Description	Possible value(s)
ligand_type	Type of ligand. Useful when benchmarking with DUD-E	active,decoy,ligand
ligand_slice	List of 2 numbers containing the index of the first and last ligand to be screened	(list)
write_info	Write a .txt file containing information about the run	True,False
write_csv	Write a the result csv	True,False
unique_run_id	Adds a unique id to the output	(str,int)
result_csv_and_pose_name	changes the name of written result csv and folder for ligand poses	(str)

Example commands:

result_file_path, result_csv_lines = nrgrank_main(target_name='target', 
                   preprocessed_target_path='foo/bar/preprocessed_target', 
                   preprocessed_ligand_path='foo/bar/preprocessed_ligands_1_conf',
                   result_folder_path='foo/bar/results')

Returns the path to the result file and the lines contained in the result csv