| Name | posebusters JSON |
| Version |
0.2.16
JSON |
| download |
| home_page | None |
| Summary | PoseBusters: Plausibility checks for generated molecule poses. |
| upload_time | 2024-07-10 12:50:44 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | ~=3.8 |
| license | None |
| keywords |
posebusters
docking
tests
metric
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
PoseBusters: Plausibility checks for generated molecule poses.
### Paper in [Chemical Science](https://pubs.rsc.org/en/content/articlelanding/2024/sc/d3sc04185a) and preprint on [arXiv](https://arxiv.org/abs/2308.05777)
## Installation
```bash
# install with pip from PyPI
pip install posebusters
```
<!-- # install with conda from conda-forge
conda install posebusters -c conda-forge -->
## Usage
<!-- ### Command line usage -->
```bash
# Check generated molecule pose.
bust molecule_pred.sdf
bust molecule_a.sdf molecule_b.sdf
bust molecule_*.sdf
# Check new ligand generated for a given protein.
bust ligand_pred.sdf -p mol_cond.pdb
# Check re-docked ligand (a pose that should recover the ligand in a given protein-ligand crystal complex).
bust ligand_pred.sdf -l mol_true.sdf -p protein.pdb
# Check any of the three by providing a csv with files to check together
bust -t file_table.csv
```
<!-- ### Python API
```python
from dockbusters import DockBuster
# check re-docked ligand
DockBuster().bust(ligand_pred_file, ligand_crystal_file, protein_crystal_file)
# check docked ligand
DockBuster().bust(ligand_pred_file, protein_crystal_file)
# check molecule
DockBuster().bust(ligand_pred_file, protein_crystal_file)
``` -->
## Documentation
Documentation is available at [https://posebusters.readthedocs.io](https://posebusters.readthedocs.io).
For more information about the tests and for a study using PoseBusters to compare docking methods, refer to our [paper](https://pubs.rsc.org/en/content/articlelanding/2024/sc/d3sc04185a) or [preprint](https://arxiv.org/abs/2308.05777):
```
@article{buttenschoen2023posebusters,
title = {{{PoseBusters}}: {{AI-based}} Docking Methods Fail to Generate Physically Valid Poses or Generalise to Novel Sequences},
shorttitle = {{{PoseBusters}}},
author = {Buttenschoen, Martin and Morris, Garrett M. and Deane, Charlotte M.},
year = "2023",
publisher = "The Royal Society of Chemistry",
doi = "10.1039/D3SC04185A",
url = "http://dx.doi.org/10.1039/D3SC04185A",
}
```
The data used for the paper is available at [https://zenodo.org/record/8278563](https://zenodo.org/record/8278563).
## Feedback & Contact
We welcome all feedback. For code issues, please open an issue. For other inquiries contact us by email.
## Thanks
This program uses software written by other people. Notably:
- RDKit - [https://github.com/rdkit/rdkit](https://github.com/rdkit/rdkit)
- Pandas - [https://github.com/pandas-dev/pandas](https://github.com/pandas-dev/pandas)
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