# Protein Dynamic Network Pathway Runner (PDNPR)
PDNPR is a tool for visualizing protein dynamic network paths, combining libraries such as PyMOL, NetworkX and MDTraj to achieve trajectory extraction, network construction, path analysis and visualization from molecular dynamics.
<!-- ## Code get
```sh
git clone https://github.com/Spencer-JRWang/PDNPR
```
## Environment configuration
### Dependency package
Create and configure the required environment using Conda.
### Create Conda environment:
- Build environment
```sh
conda env create -f environment.yml
```
- Activate environment
```sh
conda activate PDNPR -->
<!-- ``` -->
## Run PDNPR
1. Call PDNPR:
- use PDNPR GUI
```python
from PDNPR import GUI
```
- use PDNPR package
```python
from PDNPR.PDNPR import pdnpr
pdnpr(step, start_AA, end_AA, edge_cutoff, md_file, pdb_file)
```
2. Set parameters
- On the GUI screen, enter the following parameters:
- Step: retrieves the frame stride.
- Start Amino Acid: indicates the start amino acid number.
- End Amino Acid: indicates the number of the end amino acid.
- Edge Cutoff: specifies the threshold of the edge weight.
- Select file
- Click the run button to select the Molecular Dynamics trajectory file (XTC file) and Protein structure file (PDB file).
- Run the task
- The output area displays progress and information.
- The task consists of the following steps:
- Extract frames
- Generating network
- Merge networks
- Calculate the shortest path
- Generate and save PyMOL images
- View results
- After completion of the task, the output area will display the information of the shortest path, save the image and pse file, and automatically open the generated image file.
<!-- ## Running example
## GUI
<p align="center">
<img src="https://github.com/Spencer-JRWang/PDNPR/blob/main/Example/Output/run.png" alt="Figure_run" width="300" />
</p>
### Shortest route
```txt
shortest route: 915 -> 936 -> 935 -> 809 -> 808 -> 840 -> 841 -> 709 -> 708 -> 747 -> 743 -> 88
```
### PyMoL Figure
<p align="center">
<img src="Example/Output/pymol_fig.png" alt="Figure_mol" width="500" />
</p>
## package
```python
from PDNPR import pdnpr
pdnpr(step, start_AA, end_AA, edge_cutoff, md_file, pdb_file)
``` -->
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"description": "\n# Protein Dynamic Network Pathway Runner (PDNPR)\n\nPDNPR is a tool for visualizing protein dynamic network paths, combining libraries such as PyMOL, NetworkX and MDTraj to achieve trajectory extraction, network construction, path analysis and visualization from molecular dynamics.\n\n<!-- ## Code get\n```sh\ngit clone https://github.com/Spencer-JRWang/PDNPR\n```\n\n## Environment configuration\n\n### Dependency package\nCreate and configure the required environment using Conda.\n\n\n### Create Conda environment:\n- Build environment\n```sh\nconda env create -f environment.yml\n```\n\n- Activate environment\n```sh\nconda activate PDNPR -->\n<!-- ``` -->\n\n## Run PDNPR\n1. Call PDNPR:\n\n- use PDNPR GUI\n```python\nfrom PDNPR import GUI\n```\n\n- use PDNPR package\n```python\nfrom PDNPR.PDNPR import pdnpr\npdnpr(step, start_AA, end_AA, edge_cutoff, md_file, pdb_file)\n```\n\n2. Set parameters\n- On the GUI screen, enter the following parameters:\n - Step: retrieves the frame stride.\n - Start Amino Acid: indicates the start amino acid number.\n - End Amino Acid: indicates the number of the end amino acid.\n - Edge Cutoff: specifies the threshold of the edge weight.\n - Select file\n - Click the run button to select the Molecular Dynamics trajectory file (XTC file) and Protein structure file (PDB file).\n\n- Run the task\n - The output area displays progress and information. \n - The task consists of the following steps:\n - Extract frames\n - Generating network\n - Merge networks\n - Calculate the shortest path\n - Generate and save PyMOL images\n - View results\n - After completion of the task, the output area will display the information of the shortest path, save the image and pse file, and automatically open the generated image file.\n\n<!-- ## Running example\n## GUI\n<p align=\"center\">\n <img src=\"https://github.com/Spencer-JRWang/PDNPR/blob/main/Example/Output/run.png\" alt=\"Figure_run\" width=\"300\" />\n</p>\n\n### Shortest route\n```txt\nshortest route: 915 -> 936 -> 935 -> 809 -> 808 -> 840 -> 841 -> 709 -> 708 -> 747 -> 743 -> 88\n```\n\n### PyMoL Figure\n<p align=\"center\">\n <img src=\"Example/Output/pymol_fig.png\" alt=\"Figure_mol\" width=\"500\" />\n</p>\n\n## package\n```python\nfrom PDNPR import pdnpr\npdnpr(step, start_AA, end_AA, edge_cutoff, md_file, pdb_file)\n``` -->\n",
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