<!--
* @Date: 2024-05-06 17:19:11
* @LastEditors: BHM-Bob 2262029386@qq.com
* @LastEditTime: 2025-02-05 19:23:44
* @Description:
-->
<h1 style="text-align:center;">LazyDock: Lazy Dock, Easy Life</h1>
<p style="text-align:center;">
<img src="https://static.pepy.tech/badge/lazydock" alt="Downloads" style="display:inline-block; margin-left:auto; margin-right:auto;" />
<img src="https://img.shields.io/pypi/dm/lazydock" alt="Downloads" style="display:inline-block; margin-left:auto; margin-right:auto;" />
<img src="https://img.shields.io/github/downloads/BHM-Bob/LazyDock/total?label=GitHub%20all%20releases%20downloads" alt="Downloads" style="display:inline-block; margin-left:auto; margin-right:auto;" />
</p>
<p style="text-align:center;">
<a href="https://github.com/BHM-Bob/LazyDock/"><img src="https://img.shields.io/github/repo-size/BHM-Bob/LazyDock" alt="repo size" style="display:inline-block; margin-left:auto; margin-right:auto;" /></a>
<a href="https://github.com/BHM-Bob/LazyDock/"><img src="https://img.shields.io/github/languages/code-size/BHM-Bob/LazyDock" alt="code size" style="display:inline-block; margin-left:auto; margin-right:auto;" /></a>
<a href="https://github.com/BHM-Bob/LazyDock/releases"><img src="https://img.shields.io/github/v/release/BHM-Bob/LazyDock?label=GitHub%20Release" alt="GitHub release (latest by date)" style="display:inline-block; margin-left:auto; margin-right:auto;" /></a>
<a href="https://github.com/BHM-Bob/LazyDock/releases"><img src="https://img.shields.io/github/commit-activity/m/BHM-Bob/LazyDock" alt="GitHub Commit Activity" style="display:inline-block; margin-left:auto; margin-right:auto;" /></a>
<a><img src="https://img.shields.io/github/last-commit/BHM-Bob/LazyDock?label=GitHub%20Last%20Commit" alt="GitHub last commit" style="display:inline-block; margin-left:auto; margin-right:auto;" /></a>
</p>
<p style="text-align:center;">
<a href="https://pypi.org/project/lazydock/"><img src="https://img.shields.io/pypi/status/lazydock?label=PyPI%20Status" alt="PyPI Status" style="display:inline-block; margin-left:auto; margin-right:auto;" /></a>
<a href="https://pypi.org/project/lazydock/"><img src="https://img.shields.io/pypi/v/lazydock?label=PyPI%20Release" alt="PyPI" style="display:inline-block; margin-left:auto; margin-right:auto;" /></a>
<a href="https://pypi.org/project/lazydock/"><img src="https://img.shields.io/pypi/pyversions/lazydock" alt="python versions" style="display:inline-block; margin-left:auto; margin-right:auto;" /></a>
</p>
<p style="text-align:center;">
<img alt="GitHub language count" src="https://img.shields.io/github/languages/count/BHM-Bob/LazyDock">
<a href="https://github.com/BHM-Bob/LazyDock/"><img src="https://img.shields.io/readthedocs/ba-py" alt="docs" style="display:inline-block; margin-left:auto; margin-right:auto;" /></a>
<a href="https://github.com/BHM-Bob/LazyDock/"><img src="https://img.shields.io/github/license/BHM-Bob/LazyDock" alt="license" style="display:inline-block; margin-left:auto; margin-right:auto;" /></a>
</p>
<p style="text-align:center;">
<a href="https://github.com/BHM-Bob/BA_PY/"><img src="https://img.shields.io/badge/Windows-support-<COLOR>.svg" alt="windows" style="display:inline-block; margin-left:auto; margin-right:auto;" /></a>
<a href="https://github.com/BHM-Bob/BA_PY/"><img src="https://img.shields.io/badge/Linux-support-<COLOR>.svg" alt="linux" style="display:inline-block; margin-left:auto; margin-right:auto;" /></a>
</p>
<h2 style="text-align:center;">Get start</h2>
## install
#### install lazydock python package itself
- pypi
```bash
pip install lazydock -U
```
- source
```bash
pip install git+https://github.com/BHM-Bob/BA_PY.git
```
```bash
pip install git+https://gitee.com/BHM-Bob/BA_PY.git
```
- dependencies
1. mbapy: **coding base**.
2. pygame: needed by `mbapy.BaseInfo`, part of coding base.
3. nicegui: needed by `lazydock.pml_plugin` to run web ui.
4. openbabel-wheel: needed by `lazydock.scripts.prepare_gmx.py` to center molecule, can be commented out if installed openbabel software.
5. networkx: needed by `lazydock.gmx.thirdparty.cgenff_charmm2gmx.py`, can be changed to other version if compatible.
6. DuIvyTools: needed by `lazydock.scripts.run_gmx` & `ana_gmx` to visualize gmx output.
7. lazydock_md_task: needed by `lazydock.scripts.ana_gmx` to run MD-TASK.
8. compas: needed by `lazydock.pml.align_to_axis` to calculate bonding box.
9. md-davis: needed by `lazydock.scripts.ana_gmx` to run MD-DaVis.
#### install lazydock-pymol-plugin
In pymol plugin installation GUI, install `path-to-site-packages/lazydock_pymol_plugin/__init__.py`.
#### install plip for lazydock
```bash
pip install plip -U --no-deps
```
#### install MD-TASK for lazydock
Now all needed functionality of MD-TASK for lazydock is included in lazydock_md_task package. Already installed by requirements.
#### install MD-DaVis for lazydock
```bash
pip install md-davis -U --no-deps
```
#### install gmx_MMPBSA for lazydock
```bash
conda install -c conda-forge "mpi4py==4.0.1" "ambertools<=23.3" pocl
pip install gmx_MMPBSA -U --no-deps
```
Version are from gmx_MMPBSA's docs.
## Docs
- [read the docs: lazydock.rtfd.io](https://lazydock.rtfd.io)
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"description": "<!--\n * @Date: 2024-05-06 17:19:11\n * @LastEditors: BHM-Bob 2262029386@qq.com\n * @LastEditTime: 2025-02-05 19:23:44\n * @Description: \n-->\n\n\n<h1 style=\"text-align:center;\">LazyDock: Lazy Dock, Easy Life</h1>\n\n<p style=\"text-align:center;\">\n<img src=\"https://static.pepy.tech/badge/lazydock\" alt=\"Downloads\" style=\"display:inline-block; margin-left:auto; margin-right:auto;\" />\n<img src=\"https://img.shields.io/pypi/dm/lazydock\" alt=\"Downloads\" style=\"display:inline-block; margin-left:auto; margin-right:auto;\" />\n<img src=\"https://img.shields.io/github/downloads/BHM-Bob/LazyDock/total?label=GitHub%20all%20releases%20downloads\" alt=\"Downloads\" style=\"display:inline-block; margin-left:auto; margin-right:auto;\" />\n</p>\n\n<p style=\"text-align:center;\">\n<a href=\"https://github.com/BHM-Bob/LazyDock/\"><img src=\"https://img.shields.io/github/repo-size/BHM-Bob/LazyDock\" alt=\"repo size\" style=\"display:inline-block; margin-left:auto; margin-right:auto;\" /></a>\n<a href=\"https://github.com/BHM-Bob/LazyDock/\"><img src=\"https://img.shields.io/github/languages/code-size/BHM-Bob/LazyDock\" alt=\"code size\" style=\"display:inline-block; margin-left:auto; margin-right:auto;\" /></a>\n<a href=\"https://github.com/BHM-Bob/LazyDock/releases\"><img src=\"https://img.shields.io/github/v/release/BHM-Bob/LazyDock?label=GitHub%20Release\" alt=\"GitHub release (latest by date)\" style=\"display:inline-block; margin-left:auto; margin-right:auto;\" /></a>\n<a href=\"https://github.com/BHM-Bob/LazyDock/releases\"><img src=\"https://img.shields.io/github/commit-activity/m/BHM-Bob/LazyDock\" alt=\"GitHub Commit Activity\" style=\"display:inline-block; margin-left:auto; margin-right:auto;\" /></a>\n<a><img src=\"https://img.shields.io/github/last-commit/BHM-Bob/LazyDock?label=GitHub%20Last%20Commit\" alt=\"GitHub last commit\" style=\"display:inline-block; margin-left:auto; margin-right:auto;\" /></a>\n</p>\n\n<p style=\"text-align:center;\">\n<a href=\"https://pypi.org/project/lazydock/\"><img src=\"https://img.shields.io/pypi/status/lazydock?label=PyPI%20Status\" alt=\"PyPI Status\" style=\"display:inline-block; margin-left:auto; margin-right:auto;\" /></a>\n<a href=\"https://pypi.org/project/lazydock/\"><img src=\"https://img.shields.io/pypi/v/lazydock?label=PyPI%20Release\" alt=\"PyPI\" style=\"display:inline-block; margin-left:auto; margin-right:auto;\" /></a>\n<a href=\"https://pypi.org/project/lazydock/\"><img src=\"https://img.shields.io/pypi/pyversions/lazydock\" alt=\"python versions\" style=\"display:inline-block; margin-left:auto; margin-right:auto;\" /></a>\n</p>\n\n<p style=\"text-align:center;\">\n<img alt=\"GitHub language count\" src=\"https://img.shields.io/github/languages/count/BHM-Bob/LazyDock\">\n<a href=\"https://github.com/BHM-Bob/LazyDock/\"><img src=\"https://img.shields.io/readthedocs/ba-py\" alt=\"docs\" style=\"display:inline-block; margin-left:auto; margin-right:auto;\" /></a>\n<a href=\"https://github.com/BHM-Bob/LazyDock/\"><img src=\"https://img.shields.io/github/license/BHM-Bob/LazyDock\" alt=\"license\" style=\"display:inline-block; margin-left:auto; margin-right:auto;\" /></a>\n</p>\n\n<p style=\"text-align:center;\">\n<a href=\"https://github.com/BHM-Bob/BA_PY/\"><img src=\"https://img.shields.io/badge/Windows-support-<COLOR>.svg\" alt=\"windows\" style=\"display:inline-block; margin-left:auto; margin-right:auto;\" /></a>\n<a href=\"https://github.com/BHM-Bob/BA_PY/\"><img src=\"https://img.shields.io/badge/Linux-support-<COLOR>.svg\" alt=\"linux\" style=\"display:inline-block; margin-left:auto; margin-right:auto;\" /></a>\n</p>\n\n\n<h2 style=\"text-align:center;\">Get start</h2>\n\n## install \n#### install lazydock python package itself \n- pypi\n```bash\npip install lazydock -U\n```\n- source\n```bash\npip install git+https://github.com/BHM-Bob/BA_PY.git\n```\n```bash\npip install git+https://gitee.com/BHM-Bob/BA_PY.git\n```\n- dependencies\n 1. mbapy: **coding base**.\n 2. pygame: needed by `mbapy.BaseInfo`, part of coding base.\n 3. nicegui: needed by `lazydock.pml_plugin` to run web ui.\n 4. openbabel-wheel: needed by `lazydock.scripts.prepare_gmx.py` to center molecule, can be commented out if installed openbabel software.\n 5. networkx: needed by `lazydock.gmx.thirdparty.cgenff_charmm2gmx.py`, can be changed to other version if compatible.\n 6. 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