Installation and Usage Guide

1. Downloading easyPARM

To download the easyPARM code, clone the repository from GitHub using the following command:

git clone https://github.com/Abdelazim-Abdelgawwad/easyPARM.git

Alternatively, you can visit the repository directly: easyPARM GitHub Repository.

2. Installation

2.1 Prerequisites

To successfully install and run easyPARM, ensure that the following prerequisites are met:

Python 3 or higher: easyPARM requires Python version 3 or above to function properly. Download the latest version from the official Python website.
Required Python Packages: Install the necessary dependencies by running:
```
pip install periodictable scipy biopython
```
- periodictable: Provides access to the periodic table of elements, essential for metal-specific calculations.
- scipy: Used for various numerical computations related to force fields and molecular mechanics.
- biopython: Provides tools for computational biology, which may be required for certain functionalities in easyPARM.

2.2 Granting Execution Permissions

If the installation files such as .sh scripts (e.g., easyPARM.sh, 01_easyPARM.sh, 04_parmch2_frcmod.sh, and readit) do not have executable permissions, update their permissions with:

chmod +x file_name

Replace file_name with the actual script name.

3. Running easyPARM

Once the installation is complete, you can run easyPARM using one of the following methods:

3.1 Running the Script Directly

To run easyPARM.sh, follow these steps carefully:

Navigate to your working directory.
Execute the script from the easyPARM directory using:
```
../easyPARM.sh
```
After running the command, you should see an output like this:
```
Running in directory: /full/path/to/working_directory
Script directory: /full/path/to/scripts_of_easyPARM
```
⚠️ Important: Always verify that both paths are correct before proceeding.
If they are incorrect, check your current location and script path.

3.2 Setting Up an Alias for Easy Access

To run easyPARM from any location in your terminal, create an alias by adding the following line to your ~/.bashrc or ~/.bash_profile file:

alias easyPARM='/full/path/to/easyPARM.sh'

After adding the alias, apply the changes by running:

source ~/.bashrc   # or source ~/.bash_profile

Now, you can simply run:

easyPARM

from any terminal location.

4. Troubleshooting

4.1 Checking Dependencies

If you encounter issues related to missing packages, reinstall the required dependencies:

pip install --upgrade periodictable scipy biopython

4.2 Debugging Execution Issues

If the scripts fail to execute:

Ensure they have the correct permissions:
```
chmod +x easyPARM.sh
```
Check for missing dependencies using:
```
python3 -m pip check
```

For additional support, please consult the GitHub Issues Page or contact the development team.