pocketvina 0.2.0__tar.gz

pocketvina-0.2.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Ahmet Sarigun
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pocketvina-0.2.0/MANIFEST.in

@@ -0,0 +1,30 @@
+# sdist = the wheel's files (package data in pyproject.toml) + what rebuilding the engine and the tests need
+include LICENSE README.md pyproject.toml setup.py MANIFEST.in
+# the engine: prebuilt binary, OpenCL kernel sources, and its C++ sources (make -C pocketvina; Boost not included)
+include pocketvina/Makefile pocketvina/PocketVina-GPU
+graft pocketvina/OpenCL
+graft pocketvina/lib
+graft pocketvina/main
+# the notebook viewer (package data) and the site's original viewer.js it is compared with (viewer/README.md)
+graft pocketvina/viewer
+# python -m pytest tests (the tests also read the example inputs and run the Colab notebook)
+graft tests
+graft example
+include notebooks/*.ipynb notebooks/*.py
+# never shipped, also if a file finder (e.g. setuptools_scm in the build environment) or the SOURCES.txt of an older
+# build (pocketvina.egg-info/, read again by every build) adds what git tracks: Boost and P2Rank trees of older source
+# installs, the OpenCL kernel binaries of older versions (now compiled at first use into a per-user cache), and the
+# folders and files that are not part of the package (benchmarks, scratch folders, web UI, container files)
+prune pocketvina/boost_1_77_0
+prune pocketvina/p2rank_2.5
+prune pocketvina/QuickVina2-GPU-2-1
+exclude pocketvina/*.bin
+prune benchmark
+prune scripts_test
+prune test
+prune fastapi
+prune app
+prune doc
+prune .github
+exclude Dockerfile .dockerignore .gitignore pocketvina.def
+global-exclude *.py[cod]

pocketvina-0.2.0/PKG-INFO

@@ -0,0 +1,142 @@
+Metadata-Version: 2.4
+Name: pocketvina
+Version: 0.2.0
+Summary: GPU-accelerated protein-ligand docking with automated pocket detection, exploring through multi-pocket conditioning.
+Author-email: Ahmet Sarigun <Ahmet.Sariguen@mdc-berlin.de>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/BIMSBbioinfo/PocketVina
+Project-URL: Source, https://github.com/BIMSBbioinfo/PocketVina
+Project-URL: Documentation, https://bioinformatics.mdc-berlin.de/PocketVina/
+Keywords: docking,virtual screening,GPU,OpenCL,P2Rank,AutoDock Vina
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Environment :: GPU
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: pandas<3
+Requires-Dist: rdkit
+Requires-Dist: openbabel-wheel
+Requires-Dist: pyarrow
+Requires-Dist: duckdb
+Requires-Dist: click
+Requires-Dist: tqdm
+Requires-Dist: tomli; python_version < "3.11"
+Requires-Dist: posebusters
+Requires-Dist: py3Dmol
+Requires-Dist: molviewspec; python_version >= "3.10"
+Provides-Extra: bust
+Provides-Extra: viz
+Provides-Extra: meeko
+Requires-Dist: meeko; python_version >= "3.10" and extra == "meeko"
+Requires-Dist: meeko<0.8; python_version < "3.10" and extra == "meeko"
+Requires-Dist: scipy; extra == "meeko"
+Requires-Dist: gemmi; extra == "meeko"
+Provides-Extra: app
+Requires-Dist: flask; extra == "app"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: ruff==0.17.3; extra == "dev"
+Requires-Dist: nbclient; extra == "dev"
+Requires-Dist: nbformat; extra == "dev"
+Requires-Dist: ipykernel; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: myst-parser; extra == "docs"
+Requires-Dist: furo; extra == "docs"
+Requires-Dist: sphinx-click; extra == "docs"
+Dynamic: license-file
+
+<h1 align="center">PocketVina</h1>
+
+<p align="center">
+  <a href="https://www.arxiv.org/abs/2506.20043"><img src="https://img.shields.io/badge/arXiv-preprint-B31B1B?style-for-the-badge&logo=arXiv"/></a>
+  <a href="https://zenodo.org/records/15733460"><img src="https://img.shields.io/badge/Zenodo-Dataset & Raw Results-1682D4?style-for-the-badge&logo=zenodo"/></a>
+  <a href="https://hub.docker.com/r/asarigun/pocketvina"><img src="https://img.shields.io/badge/Docker-Image-2496ED?style-for-the-badge&logo=docker"/></a>
+  <a href="https://www.youtube.com/watch?v=n8-YKOTvHGs"><img src="https://img.shields.io/badge/YouTube-UI Demo-FF0000?style-for-the-badge&logo=youtube"/></a>
+  <!--<a href="ADD LINK"><img src="https://img.shields.io/badge/PyPI%20-package%20-3775A9?style-for-the-badge&logo=PyPI"/></a>-->
+  <a href="https://isocpp.org/"><img src="https://img.shields.io/badge/C++-11.4.0-00599C?style-for-the-badge&logo=cplusplus"/></a>
+  <a href="https://gcc.gnu.org/"><img src="https://img.shields.io/badge/C-11.4.0-3C2179?style-for-the-badge&logo=c"/></a>
+  <a href="https://adoptium.net/"><img src="https://img.shields.io/badge/Java-17+-007396?style-for-the-badge&logo=openjdk"/></a>
+  <a href="https://www.python.org/downloads/release/"><img src="https://img.shields.io/badge/Python-3.9+-3776AB?style-for-the-badge&logo=python"/></a>
+  <a href="https://developer.nvidia.com/cuda-toolkit"><img src="https://img.shields.io/badge/CUDA-11.5+-76B900?style-for-the-badge&logo=nvidia"/></a>
+  <a href="https://www.khronos.org/opencl/"><img src="https://img.shields.io/badge/OpenCL-3.0-4FC08D?style-for-the-badge&logo=opencl"/></a>
+  <a href="LICENSE"><img src="https://img.shields.io/badge/License-MIT-blue?style-for-the-badge&logo=legal"/></a>
+  <a href="https://colab.research.google.com/github/BIMSBbioinfo/PocketVina/blob/main/notebooks/quickstart_colab.ipynb"><img src="https://img.shields.io/badge/Google_Colab-Tutorial-F9AB00?style-for-the-badge&logo=googlecolab"/></a>
+  <a href="https://bioinformatics.mdc-berlin.de/PocketVina/"><img src="https://img.shields.io/badge/Docs-Documentation-0A7BBB?style-for-the-badge&logo=readme"/></a>
+</p>
+
+<p align="center">
+    GPU-accelerated protein-ligand docking with automated pocket detection, exploring through multi-pocket conditioning.
+</p>
+
+<p align="center">
+  <img src="doc/assets/pocketvina.gif" width="98%" />
+</p>
+
+PocketVina finds the pockets of each protein with P2Rank and docks every ligand into the best pockets on the GPU.
+
+## Installation
+
+```bash
+pip install pocketvina
+```
+
+PocketVina runs on Linux with an NVIDIA GPU and needs Java 17+ for P2Rank. Other ways to install (conda, Docker) are
+in the [documentation](https://bioinformatics.mdc-berlin.de/PocketVina/installation.html).
+
+## Citations
+
+If you use PocketVina, please cite our [preprint](https://arxiv.org/abs/2506.20043):
+
+```bibtex
+@misc{sarigun2025pocketvinaenablesscalablehighly,
+      title={PocketVina Enables Scalable and Highly Accurate Physically Valid Docking through Multi-Pocket Conditioning},
+      author={Ahmet Sarigun and Bora Uyar and Vedran Franke and Altuna Akalin},
+      year={2025},
+      eprint={2506.20043},
+      archivePrefix={arXiv},
+      primaryClass={q-bio.QM},
+      url={https://arxiv.org/abs/2506.20043},
+}
+```
+
+PocketVina builds on P2Rank, QuickVina2-GPU, AutoDock Vina, PoseBusters, Mol\* and RDKit. Please cite them too: their
+papers are on the [citing page](https://bioinformatics.mdc-berlin.de/PocketVina/citing.html).
+
+## Getting started
+
+- [Quick start](https://bioinformatics.mdc-berlin.de/PocketVina/quickstart.html): dock the example proteins and ligands, then look at the results in 3D
+- [Google Colab notebook](https://colab.research.google.com/github/BIMSBbioinfo/PocketVina/blob/main/notebooks/quickstart_colab.ipynb)
+- [Command line](https://bioinformatics.mdc-berlin.de/PocketVina/cli.html)
+- [Large screens on a cluster (SLURM)](https://bioinformatics.mdc-berlin.de/PocketVina/hpc.html)
+
+## Benchmarks
+
+The benchmark data and results are on [Zenodo](https://zenodo.org/records/15733460). The code to reproduce them is in
+[benchmark/](benchmark/).
+
+## Documentation
+
+The [documentation](https://bioinformatics.mdc-berlin.de/PocketVina/) was generated with
+[Sphinx](https://www.sphinx-doc.org) from the Markdown pages in [docs/](docs/index.md), using MyST-Parser and the
+Furo theme. To build it locally:
+
+```bash
+pip install -r docs/requirements.txt
+sphinx-build docs docs/_build/html
+```
+
+## Contact
+
+For questions and bug reports, open an [issue](https://github.com/BIMSBbioinfo/PocketVina/issues) or start a
+[discussion](https://github.com/BIMSBbioinfo/PocketVina/discussions).
+
+## License
+
+PocketVina is released under the MIT License ([LICENSE](LICENSE)). The docking engine is based on AutoDock Vina and
+QuickVina2-GPU-2.1 and keeps their Apache License 2.0. The bundled Mol\* viewer is MIT licensed.

pocketvina-0.2.0/README.md

@@ -0,0 +1,89 @@
+<h1 align="center">PocketVina</h1>
+
+<p align="center">
+  <a href="https://www.arxiv.org/abs/2506.20043"><img src="https://img.shields.io/badge/arXiv-preprint-B31B1B?style-for-the-badge&logo=arXiv"/></a>
+  <a href="https://zenodo.org/records/15733460"><img src="https://img.shields.io/badge/Zenodo-Dataset & Raw Results-1682D4?style-for-the-badge&logo=zenodo"/></a>
+  <a href="https://hub.docker.com/r/asarigun/pocketvina"><img src="https://img.shields.io/badge/Docker-Image-2496ED?style-for-the-badge&logo=docker"/></a>
+  <a href="https://www.youtube.com/watch?v=n8-YKOTvHGs"><img src="https://img.shields.io/badge/YouTube-UI Demo-FF0000?style-for-the-badge&logo=youtube"/></a>
+  <!--<a href="ADD LINK"><img src="https://img.shields.io/badge/PyPI%20-package%20-3775A9?style-for-the-badge&logo=PyPI"/></a>-->
+  <a href="https://isocpp.org/"><img src="https://img.shields.io/badge/C++-11.4.0-00599C?style-for-the-badge&logo=cplusplus"/></a>
+  <a href="https://gcc.gnu.org/"><img src="https://img.shields.io/badge/C-11.4.0-3C2179?style-for-the-badge&logo=c"/></a>
+  <a href="https://adoptium.net/"><img src="https://img.shields.io/badge/Java-17+-007396?style-for-the-badge&logo=openjdk"/></a>
+  <a href="https://www.python.org/downloads/release/"><img src="https://img.shields.io/badge/Python-3.9+-3776AB?style-for-the-badge&logo=python"/></a>
+  <a href="https://developer.nvidia.com/cuda-toolkit"><img src="https://img.shields.io/badge/CUDA-11.5+-76B900?style-for-the-badge&logo=nvidia"/></a>
+  <a href="https://www.khronos.org/opencl/"><img src="https://img.shields.io/badge/OpenCL-3.0-4FC08D?style-for-the-badge&logo=opencl"/></a>
+  <a href="LICENSE"><img src="https://img.shields.io/badge/License-MIT-blue?style-for-the-badge&logo=legal"/></a>
+  <a href="https://colab.research.google.com/github/BIMSBbioinfo/PocketVina/blob/main/notebooks/quickstart_colab.ipynb"><img src="https://img.shields.io/badge/Google_Colab-Tutorial-F9AB00?style-for-the-badge&logo=googlecolab"/></a>
+  <a href="https://bioinformatics.mdc-berlin.de/PocketVina/"><img src="https://img.shields.io/badge/Docs-Documentation-0A7BBB?style-for-the-badge&logo=readme"/></a>
+</p>
+
+<p align="center">
+    GPU-accelerated protein-ligand docking with automated pocket detection, exploring through multi-pocket conditioning.
+</p>
+
+<p align="center">
+  <img src="doc/assets/pocketvina.gif" width="98%" />
+</p>
+
+PocketVina finds the pockets of each protein with P2Rank and docks every ligand into the best pockets on the GPU.
+
+## Installation
+
+```bash
+pip install pocketvina
+```
+
+PocketVina runs on Linux with an NVIDIA GPU and needs Java 17+ for P2Rank. Other ways to install (conda, Docker) are
+in the [documentation](https://bioinformatics.mdc-berlin.de/PocketVina/installation.html).
+
+## Citations
+
+If you use PocketVina, please cite our [preprint](https://arxiv.org/abs/2506.20043):
+
+```bibtex
+@misc{sarigun2025pocketvinaenablesscalablehighly,
+      title={PocketVina Enables Scalable and Highly Accurate Physically Valid Docking through Multi-Pocket Conditioning},
+      author={Ahmet Sarigun and Bora Uyar and Vedran Franke and Altuna Akalin},
+      year={2025},
+      eprint={2506.20043},
+      archivePrefix={arXiv},
+      primaryClass={q-bio.QM},
+      url={https://arxiv.org/abs/2506.20043},
+}
+```
+
+PocketVina builds on P2Rank, QuickVina2-GPU, AutoDock Vina, PoseBusters, Mol\* and RDKit. Please cite them too: their
+papers are on the [citing page](https://bioinformatics.mdc-berlin.de/PocketVina/citing.html).
+
+## Getting started
+
+- [Quick start](https://bioinformatics.mdc-berlin.de/PocketVina/quickstart.html): dock the example proteins and ligands, then look at the results in 3D
+- [Google Colab notebook](https://colab.research.google.com/github/BIMSBbioinfo/PocketVina/blob/main/notebooks/quickstart_colab.ipynb)
+- [Command line](https://bioinformatics.mdc-berlin.de/PocketVina/cli.html)
+- [Large screens on a cluster (SLURM)](https://bioinformatics.mdc-berlin.de/PocketVina/hpc.html)
+
+## Benchmarks
+
+The benchmark data and results are on [Zenodo](https://zenodo.org/records/15733460). The code to reproduce them is in
+[benchmark/](benchmark/).
+
+## Documentation
+
+The [documentation](https://bioinformatics.mdc-berlin.de/PocketVina/) was generated with
+[Sphinx](https://www.sphinx-doc.org) from the Markdown pages in [docs/](docs/index.md), using MyST-Parser and the
+Furo theme. To build it locally:
+
+```bash
+pip install -r docs/requirements.txt
+sphinx-build docs docs/_build/html
+```
+
+## Contact
+
+For questions and bug reports, open an [issue](https://github.com/BIMSBbioinfo/PocketVina/issues) or start a
+[discussion](https://github.com/BIMSBbioinfo/PocketVina/discussions).
+
+## License
+
+PocketVina is released under the MIT License ([LICENSE](LICENSE)). The docking engine is based on AutoDock Vina and
+QuickVina2-GPU-2.1 and keeps their Apache License 2.0. The bundled Mol\* viewer is MIT licensed.

pocketvina-0.2.0/example/ligands.txt

@@ -0,0 +1,10 @@
+molecule_name,smiles
+molecule1,CNC(=O)C1=CC=CC=C1SC2=CC3=C(C=C2)C(=N[NH]3)\C=C\C4=CC=CC=N4
+molecule2,CC1=NC(=C(O)C2=C1C=C(OC3=CC=CC=C3)C=C2)C(=O)NCC(O)=O
+molecule3,C[N]1C=NC2=C(F)C(=C(C=C12)C(=O)NOCCO)NC3=CC=C(Br)C=C3Cl
+molecule4,COC(=O)C1=CC=C\2C(=C1)NC(=O)C2=C(NC3=CC=C(C=C3)N(C)C(=O)CN4CCN(C)CC4)/C5=CC=CC=C5
+molecule5,CN(C)C/C=C/C(=O)NC1=CC2=C(NC3=CC=C(F)C(=C3)Cl)N=CN=C2C=C1OC4CCOC4
+molecule6,COC1=C(Cl)C=C(Cl)C(=C1)NC2=C(C=NC3=CC(=C(OC)C=C23)OCCCN4CCN(C)CC4)C#N
+molecule7,CC1=NC(=CC(=N1)N2CCN(CCO)CC2)NC3=NC=C(S3)C(=O)NC4=C(Cl)C=CC=C4C
+molecule8,COC1CC(CCC1O[P](C)(C)=O)CC(C)C2CC(=O)C(C)\C=C(C)\C(O)C(OC)C(=O)C(C)CC(C)/C=C/C=C/C=C(C)/C(CC3CCC(C)C(O)(O3)C(=O)C(=O)N4CCCCC4C(=O)O2)OC
+molecule9,COC1=C(OCCCN2CCOCC2)C=C3C(=NC=NC3=C1)NC4=CC=C(F)C(=C4)Cl

pocketvina-0.2.0/example/protein_files.txt

@@ -0,0 +1,2 @@
+Path/to/PocketVina/example/proteins/2W83.pdb
+Path/to/PocketVina/example/proteins/1fbl.pdb