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posecheck

(★ 100)

Pose checks for 3D Structure-based Drug Design methods

파일 탐색기

최종 버전 다운로드 (.zip)

- - publish.yaml
  - tests.yaml
- reduce
- smina.static
- - 1a2g.pdb
  - 1a2g_ligand.sdf
- crossdocked_split_by_name.pkl
- posecheck_logo.png
- split_by_name.pt
- - conf.py
  - index.rst
  - posecheck_logo.png
- make.bat
- Makefile
- requirements.txt
- - __init__.py
  - datasets.py
- - __init__.py
  - biopython.py
  - chem.py
  - clashes.py
  - constants.py
  - docking.py
  - docking_utils.py
  - interactions.py
  - loading.py
  - strain.py
  - validators.py
- .DS_Store
- __init__.py
- docking_eval.py
- eval.py
- posecheck.py
- __init__.py
- test_biopython.py
- test_chem.py
- test_clashes.py
- test_hydride.py
- test_interactions.py
- test_loading.py
- test_posecheck.py
- test_strain.py
.gitignore
.readthedocs.yaml
changelog.md
LICENSE
MANIFEST.in
README.md
requirements.txt
setup.py

# 설치 가이드

1. 코드 내려받기

git clone https://github.com/cch1999/posecheck

깃허브에서 프로젝트 코드 전체를 내 컴퓨터로 내려받습니다.

cd posecheck

방금 내려받은 프로젝트 폴더 안으로 이동합니다.

2. 공식 설치 스크립트

쉬움 추천

사전 준비물

Python 3 pip 명령어를 쓰려면 Python이 필요합니다.

pip install posecheck

PyPI에 배포된 패키지를 바로 설치합니다. 소스 클론이 필요 없습니다.

✅ 설치 후 새 터미널을 열고, 프로그램의 버전 확인 명령(예: --version)으로 정상 설치됐는지 확인하세요.

이 레포의 README에 적힌 실제 명령어를 그대로 가져왔습니다.

3. Python

쉬움

사전 준비물

Git GitHub에서 프로젝트 코드를 내려받으려면 필요합니다.
Python 3 설치 시 'Add Python to PATH' 옵션을 꼭 체크하세요 (Windows).

pip install posecheck

PyPI에 배포된 패키지를 바로 설치합니다. 소스 클론이 필요 없습니다.

✅ 에러 메시지 없이 실행되고 터미널에 안내 문구가 출력되면 정상입니다.

이 레포의 README에 적힌 실제 명령어를 그대로 가져왔습니다.

// repository documentation

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# PoseCheck: Benchmarking Generated Poses

[![arXiv](https://img.shields.io/badge/arXiv-2308.07413-b31b1b.svg)](https://arxiv.org/abs/2308.07413)
![version](https://img.shields.io/badge/version-1.3.1-blue)
[![python](https://img.shields.io/badge/-Python_3.9_%7C_3.10_%7C_3.11-blue?logo=python&logoColor=white)](https://github.com/pre-commit/pre-commit)
[![build](https://github.com/cch1999/posecheck/actions/workflows/tests.yaml/badge.svg?branch=main)](https://github.com/cch1999/posecheck/actions/workflows/tests.yaml)
[![Documentation Status](https://readthedocs.org/projects/posecheck/badge/?version=latest)](https://posecheck.readthedocs.io/en/latest/?badge=latest)
[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)

![PoseCheck Logo](https://raw.githubusercontent.com/cch1999/posecheck/main/data/posecheck_logo.png)

[Paper](https://arxiv.org/abs/2308.07413) | [Documentation](https://posecheck.readthedocs.io/en/latest/)

## What is PoseCheck?

PoseCheck is a package for analysing the quality of generated protein-ligand complexes from 3D target-conditioned generative models.

## Installation

```bash
pip install posecheck
```

## Example usage

We provide a simple top level API to easily interact with the whole of the benchmark. Just define the `PoseCheck` object once at the top of your existing testing code and test molecules by loading them in iteratively. You can also use all the testing functions manually as well (see Docs for more info).

```python
from posecheck import PoseCheck

# Initialize the PoseCheck object
pc = PoseCheck()

# Load a protein from a PDB file (will run reduce in the background)
pc.load_protein_from_pdb("data/examples/1a2g.pdb")

# Load ligands from an SDF file
pc.load_ligands_from_sdf("data/examples/1a2g_ligand.sdf")
# Alternatively, load RDKit molecules directly
# pc.load_ligands_from_mols([rdmol])

# Check for clashes
clashes = pc.calculate_clashes()
print(f"Number of clashes in example molecule: {clashes[0]}")

# Check for strain
strain = pc.calculate_strain_energy()
print(f"Strain energy of example molecule: {strain[0]}")

# Check for interactions
interactions = pc.calculate_interactions()
print(f"Interactions of example molecule: {interactions}")
```

## Tips

- Reading and processing all the PDB files using `reduce` can take a while for a large test set. If you are running `PoseCheck` frequently, it might be worth pre-processing all proteins yourself using `prot = posecheck.utils.loading.load_protein_from_pdb(pdb_path)` and setting this directly within `PoseCheck` using `pc.protein = prot`.

## Data from the paper

The data for the paper can be found at the following Zenodo link and should be placed in the `data` directory.

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10208912.svg)](https://zenodo.org/records/10208912)

## Cite

```bibtex
@article{harris2023benchmarking,
  title={Benchmarking Generated Poses: How Rational is Structure-based Drug Design with Generative Models?},
  author={Harris, Charles and Didi, Kieran and Jamasb, Arian R and Joshi, Chaitanya K and Mathis, Simon V and Lio, Pietro and Blundell, Tom},
  journal={arXiv preprint arXiv:2308.07413},
  year={2023}
}
```

## Acknowledgements

PoseCheck relies on several other codebases to function. Here are the links to them:

- [RDKit](https://github.com/rdkit/rdkit): A collection of cheminformatics and machine learning tools.
- [ProLIF](https://github.com/chemosim-lab/ProLIF): Protein-Ligand Interaction Fingerprints generator.
- [Seaborn](https://github.com/mwaskom/seaborn): Statistical data visualization library.
- [NumPy](https://github.com/numpy/numpy): The fundamental package for scientific computing with Python.
- [DataMol](https://github.com/datamol-org/datamol): A minimalist and practical chemoinformatics library for python.
- [Pandas](https://github.com/pandas-dev/pandas): Powerful data structures for data analysis, time series, and statistics.
- [Reduce](https://github.com/rlabduke/reduce): A program for adding hydrogens to a Protein DataBank (PDB) molecular structure file.

There is also the similar package [PoseBusters](https://github.com/maabuu/posebusters) which provides additional tests to us and is recommended if you are benchmarking protein-ligand docking models.