Installation (Requires Python 3.9 and above)
Use the following command:
pip install nrgrank
To install nrgrank with rdkit for generating conformers:
pip install "nrgrank[rdkit]"
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 |
The name of the target. Used for naming the output CSV file when csv_and_pose_name is not specified |
(str) |
preprocessed_target_path |
Path to the preprocessed target folder (e.g., output from process_target()) |
Absolute path |
preprocessed_ligand_path |
Path to the preprocessed ligand folder (e.g., output from process_ligand()) |
Absolute path |
result_folder_path |
Directory path where the docking results will be stored | Absolute path |
Optional Flags
| Flag | Description | Possible value(s) |
|---|---|---|
result_csv_and_pose_name |
Custom name for CSV and pose files. If not given, defaults to target_name |
(str) |
ligand_type |
Type of ligand being processed. Useful when benchmarking with DUD-E | "ligand", "active", "decoy" |
ligand_slice |
Slice range of ligands to process | list[int] or None |
write_info |
Write informational remarks to output (e.g., .txt log) | True, False |
write_file |
Output result file(s) | True, False |
output_dictionary |
Output results as a Python dictionary | True, False |
file_separator |
Separator character for the result file (CSV/TSV) | ",", "\t" |
output_header |
Write a header row in the CSV file | True, False |
save_time |
Save time taken per molecule for docking | True, False |
normalise_score |
Normalise docking score by number of atoms in molecule | True, False |
unique_run_id |
Unique identifier to avoid file name conflicts and used to name ligand poses | (str) |
user_config |
Arbitrary keyword arguments for overriding default docking parameters | key=value pairs |
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
1 maintainer
Metadata
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Release files for nrgrank 1.0.14
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
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| nrgrank-1.0.14.tar.gz | 49.0 kB | Details |
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|---|---|---|---|---|
| nrgrank-1.0.14-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 97.7 kB
Release files / nrgrank-1.0.14.tar.gz
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