MCCE4-Tools Installation

Tools for processing MCCE4 simulation outputs.
A concise description is provided in the file tools.info in MCCE4-Tools/mcce4_tools.
Of note: The tool glossary provide a quick way to find out the actual key/values pertaining to a step. Usage: glossary Step1, glossary Step2, etc.

Installation Steps:

Navigate to a directory of your choice (referred to as ‘clone_dir’).

Clone this repo, MCCE4-Tools & cd into it (copy and paste this command into your terminal):

   git clone https://github.com/GunnerLab/MCCE4-Tools.git; cd MCCE4-Tools;

Add the clone’s path to your .bashrc (.bash_profile) file, save it, then “dot” or “source” the file. Change ‘clone_dir’ in the pathname below to your current directory, which you may find using the bash command pwd
```
   export PATH="clone_dir/MCCE4-Tools/mcce4_tools:$PATH"
```
If all went well, all the command line tools are discoverable (but not runable yet). You can verify their location by running the which command, e.g.:
```
   which getpdb
```
Next, check your defined environments by running this command: conda env list.
You do not have an ‘mc4’ environment if it’s not listed in the screen output; in this case, create a NEW environment named ‘mc4’:
```
   conda env create -f mct4.yml
```
Otherwise, update your existing ‘mc4’ environment (which you should have if you have installed MCCE4-Alpha):
```
    conda env update -n mc4 -f mc4.yml
```
Test a tool
- Activate your environment, e.g. conda activate mc4
- Type getpdb and press Enter: the cli usage should display

NOTES:

Although pymol is necessary for certain tools, it is not included in mc4.yml due to licensing; installation details for PyMOL 3.1 (Version 3.1.6.1) is here

🎉 Congrats! Now that you’ve installed both MCCE4-Alpha and 🛠️MCCE4-Tools , please proceed to the Quick Start Tutorial. Exercises 4 and 5 requires installation of MCCE4-Tools.