| Name | mdpertool JSON |
| Version |
0.0.1.dev1
JSON |
| download |
| home_page | https://github.com/bio-otto/MDPerTool_GUI |
| Summary | A Software Tool for Investigation of Allosteric Communication within Protein Structures via Energy Dissipation in Molecular Dynamics Simulations |
| upload_time | 2024-04-20 12:43:22 |
| maintainer | None |
| docs_url | None |
| author | Halil I. Ozdemir |
| requires_python | >=3.7 |
| license | MIT License Copyright (c) 2020 Halil İbrahim ÖZDEMİR 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. |
| keywords |
allostery
energy dissipation
dynamics
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
<h1 align="left"><span style="" text-align="left">MDPERTOOL: Perturbation based Allosteric Pathway Finder</span>
<a href="http://compbio.bioe.eng.marmara.edu.tr/" target="_parent">
<img src="https://github.com/Bio-Otto/MDPerTool_GUI/blob/master/mdpertool/gui/icons/big_icons/logo_for_contacts.png" style="position:fixed; bottom:-15px; width: 150px; height: 120px;" width="150" height="120" align="right"/>
</a>
</h1>
<div align="center">
<img src="https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg" alt="Awesome Badge"/>
<a href="http://compbio.bioe.eng.marmara.edu.tr/"><img src="https://img.shields.io/static/v1?label=&labelColor=505050&message=ozbek-lab&color=%230076D6&style=flat&logo=google-chrome&logoColor=%230076D6" alt="website"/></a>
<!-- <img src="http://hits.dwyl.com/abhisheknaiidu/awesome-github-profile-readme.svg" alt="Hits Badge"/> -->
<img src="https://img.shields.io/static/v1?label=%F0%9F%8C%9F&message=If%20Useful&style=style=flat&color=BC4E99" alt="Star Badge"/>
<a href="https://twitter.com/LabOzbek" ><img src="https://img.shields.io/twitter/follow/pemoshh.svg?style=social" /> </a>
<br>
<i>A Software Tool for Investigation of Allosteric Communication within Protein Structures via Energy Dissipation in Molecular Dynamics Simulations</i>
<a href="https://github.com/Bio-Otto/MDPerTool_GUI/stargazers"><img src="https://img.shields.io/github/stars/Bio-Otto/Bio-Otto" alt="Stars Badge"/></a>
<a href="https://github.com/Bio-Otto/MDPerTool_GUI/members"><img src="https://img.shields.io/github/forks/Bio-Otto/Bio-Otto" alt="Forks Badge"/></a>
<a href="https://github.com/Bio-Otto/MDPerTool_GUI/pulls"><img src="https://img.shields.io/github/issues-pr/Bio-Otto/Bio-Otto" alt="Pull Requests Badge"/></a>
<a href="https://github.com/Bio-Otto/MDPerTool_GUI/issues"><img src="https://img.shields.io/github/issues/Bio-Otto/Bio-Otto" alt="Issues Badge"/></a>
<a href="https://github.com/Bio-Otto/MDPerTool_GUI/contributors"><img alt="GitHub contributors" src="https://img.shields.io/github/contributors/Bio-Otto/MDPerTool_GUI?color=2b9348"></a>
<a href="https://github.com/Bio-Otto/MDPerTool_GUI/blob/master/LICENSE"><img src="https://img.shields.io/badge/License-MIT-yellow.svg" alt="License Badge"/></a>
[](https://badge.fury.io/gh/Bio-Otto%2FMDPerTool_GUI)
[]()
<img alt="Awesome GitHub Profile Readme" src="https://github.com/Bio-Otto/MDPerTool_GUI/blob/master/mdpertool/gui/icons/MDPerTool.gif"> </img>
<p align="center">
<a href="http://compbio.bioe.eng.marmara.edu.tr/" target="_parent">
<img src="https://github.com/Bio-Otto/Example_MD_Scripts/blob/master/PoweredByOzbekLab.png" style="position:fixed; bottom:0px; width: 250px; height: 40px;" width="250" height="40" /></a>
<img src="https://github.com/Bio-Otto/MDPerTool_GUI/blob/master/mdpertool/gui/icons/orange-logo-linux.png" width="40" title="Available on Ubuntu 20.10">
<img src="https://github.com/Bio-Otto/MDPerTool_GUI/blob/master/mdpertool/gui/icons/windows-logo.png" width="40" title="Available on Windows">
</p>
### Installation
Open your favorite Terminal and run the commands below:
```diff
# For Windows Users
$ git clone https://github.com/Bio-Otto/MDPerTool_GUI.git
$ cd MDPerTool_GUI
$ conda env create -f envs/winx64_env.yml
$ conda activate mdpertool
$ cd mdpertool
$ python ui_main.py
```
```diff
# For linux Users
$ git clone https://github.com/Bio-Otto/MDPerTool_GUI.git
$ cd MDPerTool_GUI
$ conda env create -f envs/linux64_env.yml
$ conda activate mdpertool
$ cd mdpertool
$ python ui_main.py
```
### For terminal usage just type;
```sh
$ python no_gui.py -p pdb_file -wdcd True -pert_res 'SER345' -speed_factor 4
```
* __-p__ --> User gives the absolute path of the pdb file.
* __-wdcd__ --> The program uses dcd as default output format. Users can change it to XTC file format using ```-wdcd False -wxtc True``` argument.
* __-pert_res__ --> Users should enter the residue(s) to be perturbed.
* __-speed_factor__ --> Users should indicate the velocity rescale factor.
### Dependencies
* __OpenMM__ - A high performance toolkit for molecular simulation.
* __Networkx__ - NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
* __Pandas__ - pandas is a fast, powerful, flexible and easy to use open source data analysis and manipulation tool
* __Numpy__ - The fundamental package for scientific computing with Python
* __Pymol (Open Source)__ - PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.
* __Matplotlib__ - Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python.
* __Pyqtgraph__ - Scientific Graphics and GUI Library for Python
* __PySide2__ - Python bindings for the Qt cross-platform application and UI framework
* __ProDy__ - Protein Dynamics and Sequence Analysis
* __Parmed__ - Parameter/topology editor and molecular simulator
And of course MDPERTOOL v0.0.1 itself is an open source [public repository][MDPERTOOL] on GitHub.
### Also you can check full functional parameters with:
```sh
$ python no_gui.py -h
```
For Molecular Dynamic Simulation production
```sh
$ no_gui.py -p <pdb file> -pff <charmm36> -wff <tip5p> -wdcd <True>
```
MDPerTool applies Energy Dissipation Concept using OpenMM Molecular Dynamic Toolkit, which also supports the CUDA platform.
# New Features!
- Automated Topology Builder
- Residue Decomposition
- DCD and XTC file format support
### Features of MDPERTOOL v0.0.1
MDPERTOOL includes the following features.
<table align="center">
<thead>
<tr>
<th align="left">Feature</th>
<th align="center">README</th>
</tr>
</thead>
<tbody>
<tr>
<td align="left">Each Residue Decomposition</td>
<td align="center">[plugins/dropbox/README.md][MDPERTOOL]</td>
</tr>
<tr>
<td align="left">Molecular Dynamic Simulation</td>
<td align="center">[plugins/github/README.md][MDPERTOOL]</td>
</tr>
<tr>
<td align="left">Energy Dissipation Network</td>
<td align="center">[plugins/googledrive/README.md][MDPERTOOL]</td>
</tr>
<tr>
<td align="left">Free Energy Calculations</td>
<td align="center">[plugins/onedrive/README.md][MDPERTOOL]</td>
</tr>
</tbody>
</table><p></p></div>
### Development
Want to contribute?
Get a branch and Join us to make MDPERTOOL even greater!
### Todos
- Write MORE Tests
- Add Night Mode
License
----
MIT
**Free Software, Hell Yeah!**
[//]: # (These are reference links used in the body of this note and get stripped out when the markdown processor does its job. There is no need to format nicely because it shouldn't be seen. Thanks SO - http://stackoverflow.com/questions/4823468/store-comments-in-markdown-syntax)
[MDPERTOOL]: <https://github.com/Bio-Otto/MDPERTOOL_v01>
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"description": "\r\n<h1 align=\"left\"><span style=\"\" text-align=\"left\">MDPERTOOL: Perturbation based Allosteric Pathway Finder</span>\r\n<a href=\"http://compbio.bioe.eng.marmara.edu.tr/\" target=\"_parent\">\r\n<img src=\"https://github.com/Bio-Otto/MDPerTool_GUI/blob/master/mdpertool/gui/icons/big_icons/logo_for_contacts.png\" style=\"position:fixed; bottom:-15px; width: 150px; height: 120px;\" width=\"150\" height=\"120\" align=\"right\"/>\r\n</a>\r\n\r\n</h1>\r\n<div align=\"center\">\r\n<img src=\"https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg\" alt=\"Awesome Badge\"/>\r\n<a href=\"http://compbio.bioe.eng.marmara.edu.tr/\"><img src=\"https://img.shields.io/static/v1?label=&labelColor=505050&message=ozbek-lab&color=%230076D6&style=flat&logo=google-chrome&logoColor=%230076D6\" alt=\"website\"/></a>\r\n<!-- <img src=\"http://hits.dwyl.com/abhisheknaiidu/awesome-github-profile-readme.svg\" alt=\"Hits Badge\"/> -->\r\n<img src=\"https://img.shields.io/static/v1?label=%F0%9F%8C%9F&message=If%20Useful&style=style=flat&color=BC4E99\" alt=\"Star Badge\"/>\r\n<a href=\"https://twitter.com/LabOzbek\" ><img src=\"https://img.shields.io/twitter/follow/pemoshh.svg?style=social\" /> </a>\r\n<br>\r\n\r\n<i>A Software Tool for Investigation of Allosteric Communication within Protein Structures via Energy Dissipation in Molecular Dynamics Simulations</i>\r\n\r\n<a href=\"https://github.com/Bio-Otto/MDPerTool_GUI/stargazers\"><img src=\"https://img.shields.io/github/stars/Bio-Otto/Bio-Otto\" alt=\"Stars Badge\"/></a>\r\n<a href=\"https://github.com/Bio-Otto/MDPerTool_GUI/members\"><img src=\"https://img.shields.io/github/forks/Bio-Otto/Bio-Otto\" alt=\"Forks Badge\"/></a>\r\n<a href=\"https://github.com/Bio-Otto/MDPerTool_GUI/pulls\"><img src=\"https://img.shields.io/github/issues-pr/Bio-Otto/Bio-Otto\" alt=\"Pull Requests Badge\"/></a>\r\n<a href=\"https://github.com/Bio-Otto/MDPerTool_GUI/issues\"><img src=\"https://img.shields.io/github/issues/Bio-Otto/Bio-Otto\" alt=\"Issues Badge\"/></a>\r\n<a href=\"https://github.com/Bio-Otto/MDPerTool_GUI/contributors\"><img alt=\"GitHub contributors\" src=\"https://img.shields.io/github/contributors/Bio-Otto/MDPerTool_GUI?color=2b9348\"></a>\r\n<a href=\"https://github.com/Bio-Otto/MDPerTool_GUI/blob/master/LICENSE\"><img src=\"https://img.shields.io/badge/License-MIT-yellow.svg\" alt=\"License Badge\"/></a>\r\n[](https://badge.fury.io/gh/Bio-Otto%2FMDPerTool_GUI)\r\n[]()\r\n\r\n<img alt=\"Awesome GitHub Profile Readme\" src=\"https://github.com/Bio-Otto/MDPerTool_GUI/blob/master/mdpertool/gui/icons/MDPerTool.gif\"> </img>\r\n\r\n<p align=\"center\">\r\n <a href=\"http://compbio.bioe.eng.marmara.edu.tr/\" target=\"_parent\">\r\n <img src=\"https://github.com/Bio-Otto/Example_MD_Scripts/blob/master/PoweredByOzbekLab.png\" style=\"position:fixed; bottom:0px; width: 250px; height: 40px;\" width=\"250\" height=\"40\" /></a>\r\n <img src=\"https://github.com/Bio-Otto/MDPerTool_GUI/blob/master/mdpertool/gui/icons/orange-logo-linux.png\" width=\"40\" title=\"Available on Ubuntu 20.10\">\r\n <img src=\"https://github.com/Bio-Otto/MDPerTool_GUI/blob/master/mdpertool/gui/icons/windows-logo.png\" width=\"40\" title=\"Available on Windows\">\r\n</p>\r\n\r\n### Installation\r\n\r\nOpen your favorite Terminal and run the commands below:\r\n\r\n\r\n```diff\r\n# For Windows Users \r\n$ git clone https://github.com/Bio-Otto/MDPerTool_GUI.git\r\n$ cd MDPerTool_GUI\r\n$ conda env create -f envs/winx64_env.yml\r\n$ conda activate mdpertool\r\n$ cd mdpertool\r\n$ python ui_main.py\r\n```\r\n```diff\r\n# For linux Users\r\n$ git clone https://github.com/Bio-Otto/MDPerTool_GUI.git\r\n$ cd MDPerTool_GUI\r\n$ conda env create -f envs/linux64_env.yml\r\n$ conda activate mdpertool\r\n$ cd mdpertool\r\n$ python ui_main.py\r\n```\r\n\r\n\r\n### For terminal usage just type; \r\n\r\n```sh\r\n$ python no_gui.py -p pdb_file -wdcd True -pert_res 'SER345' -speed_factor 4\r\n```\r\n\r\n* __-p__ --> User gives the absolute path of the pdb file. \r\n* __-wdcd__ --> The program uses dcd as default output format. Users can change it to XTC file format using ```-wdcd False -wxtc True``` argument.\r\n* __-pert_res__ --> Users should enter the residue(s) to be perturbed.\r\n* __-speed_factor__ --> Users should indicate the velocity rescale factor.\r\n\r\n\r\n\r\n### Dependencies\r\n\r\n\r\n* __OpenMM__ - A high performance toolkit for molecular simulation. \r\n* __Networkx__ - NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.\r\n\r\n* __Pandas__ - pandas is a fast, powerful, flexible and easy to use open source data analysis and manipulation tool\r\n* __Numpy__ - The fundamental package for scientific computing with Python \r\n* __Pymol (Open Source)__ - PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schr\u00f6dinger.\r\n* __Matplotlib__ - Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python.\r\n* __Pyqtgraph__ - Scientific Graphics and GUI Library for Python\r\n* __PySide2__ - Python bindings for the Qt cross-platform application and UI framework\r\n* __ProDy__ - Protein Dynamics and Sequence Analysis\r\n* __Parmed__ - Parameter/topology editor and molecular simulator\r\n\r\nAnd of course MDPERTOOL v0.0.1 itself is an open source [public repository][MDPERTOOL] on GitHub.\r\n\r\n### Also you can check full functional parameters with: \r\n\r\n```sh\r\n$ python no_gui.py -h\r\n```\r\n\r\nFor Molecular Dynamic Simulation production\r\n\r\n```sh\r\n$ no_gui.py -p <pdb file> -pff <charmm36> -wff <tip5p> -wdcd <True>\r\n```\r\n\r\nMDPerTool applies Energy Dissipation Concept using OpenMM Molecular Dynamic Toolkit, which also supports the CUDA platform.\r\n\r\n# New Features!\r\n\r\n - Automated Topology Builder\r\n - Residue Decomposition\r\n - DCD and XTC file format support \r\n \r\n\r\n### Features of MDPERTOOL v0.0.1\r\n\r\nMDPERTOOL includes the following features. \r\n\r\n<table align=\"center\">\r\n <thead>\r\n <tr>\r\n <th align=\"left\">Feature</th>\r\n <th align=\"center\">README</th>\r\n </tr>\r\n </thead>\r\n <tbody>\r\n <tr>\r\n <td align=\"left\">Each Residue Decomposition</td>\r\n <td align=\"center\">[plugins/dropbox/README.md][MDPERTOOL]</td>\r\n </tr>\r\n <tr>\r\n <td align=\"left\">Molecular Dynamic Simulation</td>\r\n <td align=\"center\">[plugins/github/README.md][MDPERTOOL]</td>\r\n </tr>\r\n <tr>\r\n <td align=\"left\">Energy Dissipation Network</td>\r\n <td align=\"center\">[plugins/googledrive/README.md][MDPERTOOL]</td>\r\n </tr>\r\n <tr>\r\n <td align=\"left\">Free Energy Calculations</td>\r\n <td align=\"center\">[plugins/onedrive/README.md][MDPERTOOL]</td>\r\n </tr>\r\n </tbody>\r\n\r\n</table><p></p></div>\r\n\r\n\r\n### Development\r\n\r\nWant to contribute?\r\nGet a branch and Join us to make MDPERTOOL even greater!\r\n\r\n### Todos\r\n\r\n - Write MORE Tests\r\n - Add Night Mode\r\n \r\n\r\nLicense\r\n----\r\n\r\nMIT\r\n\r\n\r\n**Free Software, Hell Yeah!**\r\n\r\n[//]: # (These are reference links used in the body of this note and get stripped out when the markdown processor does its job. There is no need to format nicely because it shouldn't be seen. Thanks SO - http://stackoverflow.com/questions/4823468/store-comments-in-markdown-syntax)\r\n\r\n\r\n[MDPERTOOL]: <https://github.com/Bio-Otto/MDPERTOOL_v01>\r\n",
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