Merge branch 'gui_development'

README.md

@@ -1,78 +1,84 @@
+# MDPERTOOL: Perturbation-based Allosteric Pathway Finder
 
-<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"/>
+<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;" 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>
+	<a href="https://anaconda.org/bio-otto/mdpertool"><img src="https://img.shields.io/conda/v/bio-otto/mdpertool.svg" alt="Conda Build"/></a>
+    <img src="https://anaconda.org/bio-otto/mdpertool/badges/platforms.svg" alt="Platforms"/>
+    <img src="https://anaconda.org/bio-otto/mdpertool/badges/downloads.svg" alt="Download Counter"/>
+    <img src="https://anaconda.org/bio-otto/mdpertool/badges/license.svg" alt="License"/>
+    <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="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>
+    <a href="https://twitter.com/LabOzbek"><img src="https://img.shields.io/twitter/follow/pemoshh.svg?style=social" alt="Twitter Follow"/></a>
+    <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>
+
+</div>
 
 <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>
-[![Version](https://badge.fury.io/gh/Bio-Otto%2FMDPerTool_GUI.svg)](https://badge.fury.io/gh/Bio-Otto%2FMDPerTool_GUI)
-[![GitHub Release](https://img.shields.io/github/release/Bio-Otto/MDPerTool_GUI.svg?style=flat)]()
+![MDPerTool Animation](https://github.com/Bio-Otto/MDPerTool_GUI/blob/master/mdpertool/gui/icons/MDPerTool.gif)
 
-<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
 
-### Installation
+To install MDPERTOOL using Conda, simply run the following commands:
 
-Open your favorite Terminal and run the commands below:
+```sh
+conda install bio-otto::mdpertool
+```
+This will install MDPERTOOL and all of its dependencies. Once the installation is completed, you can access the Command Line Interface by typing 'mdpertool' in your terminal.
 
+---
 
-```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
-```
+### Manual Installation
 
+To manually install MDPERTOOL, follow the instructions below:
+
+#### For Windows Users
+```cmd
+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
+```
+<p align="right">
+	<img src="https://github.com/Bio-Otto/MDPerTool_GUI/blob/master/mdpertool/gui/icons/windows-logo.png" width="60" title="Available on Windows">
+</p>
 
-### For terminal usage just type; 
 
+#### For Linux Users
 ```sh
-$ python no_gui.py -p pdb_file -wdcd True -pert_res 'SER345' -speed_factor 4
+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
 ```
+<p align="right">
+    <img src="https://github.com/Bio-Otto/MDPerTool_GUI/blob/master/mdpertool/gui/icons/orange-logo-linux.png" width="35" title="Available on Ubuntu 20.10">
+</p>
+
+---
 
-* __-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.
+## 🖥️ Terminal Usage
 
+For terminal usage, run:
 
+```sh
+python no_gui.py -p pdb_file -wdcd True -pert_res 'SER345' -speed_factor 4
+```
 
-### Dependencies
 
+## 📦 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.
@@ -86,38 +92,41 @@ $ python no_gui.py -p pdb_file -wdcd True -pert_res 'SER345' -speed_factor 4
 * __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.
+And of course MDPERTOOL itself is an open source public repository.
 
-### Also you can check full functional parameters with: 
+#### Also you can check full functional parameters with: 
 
 ```sh
-$ python no_gui.py -h
+python no_gui.py -h
 ```
 
 For Molecular Dynamic Simulation production
 
 ```sh
-$ no_gui.py -p <pdb file> -pff <charmm36> -wff <tip5p> -wdcd <True>
+python 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
+
+
+  - Automated topology builder
+  - Residue base energy decomposition
+  - DCD and XTC file format support
+  - Easy to installation using Conda 
 
 
 ### Features of MDPERTOOL v0.0.1
 
-MDPERTOOL includes the following features. 
+This version of mdpertool includes the following features. 
 
 <table align="center">
     <thead>
         <tr>
             <th align="left">Feature</th>
-            <th align="center">README</th>
+            <th align="center">Documentation</th>
         </tr>
     </thead>
     <tbody>
@@ -141,27 +150,27 @@ MDPERTOOL includes the following features.
 
 </table><p></p></div>
 
+---
 
-### Development
-
-Want to contribute?
-Get a branch and Join us to make MDPERTOOL even greater!
+## 🚀 Development
 
-### Todos
+Want to contribute? Get a branch and join us to make MDPERTOOL even greater!
 
- - Write MORE Tests
- - Add Night Mode
-
-
-License
-----
 
-MIT
+## 📋 Todos
 
+ - Write MORE Tests
+ - Add Light Mode
 
-**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)
+## 📝 License
 
+MDPERTOOL is licensed under the MIT License. See the LICENSE file for more details.
 
-[MDPERTOOL]: <https://github.com/Bio-Otto/MDPERTOOL_v01>
+Free Software, Hell Yeah!
+<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" 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>