MCCE4-Tools (alpha)

• Tools for processing MCCE4 simulation outputs.
• A concise description is provided in the file tools.info in MCCE4-Tools/mcce4_tools. If you are reading this document online, you can view this file here.

Installation Steps:

1. Navigate to a directory of your choice (referred to as 'clone_dir'):
2. Clone this repo, MCCE4-Tools & cd into it (cpy and paste this command into your terminal):

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

3. Add the clone's path to your .bashrc (.bash_profile) file, save it, then "dot" or source the file:

 # CHANGE 'clone_dir' to your path!

 export PATH="clone_dir/MCCE4-Tools/mcce4_tools:$PATH"

4. 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

5. To run the tools, either: - Activate an appropriate environment associated with python 3.10 (and that includes the packages in the environment file, MCCE4-Tools/mc4.yml). - Alternatively, you can create one with the provided MCCE4-Tools/mc4.yml file:
   • Choose one of these two options to create the environment:
     1. Option 1: Create a NEW environment named 'mc4' if you do not have one already. To find out, run the command: conda env list. You do not have an 'mc4' environment if it's not listed in its output:

      conda env create -f mc4.yml

     2. Option 2: Update your existing 'mc4' environment (which you have already created if you have installed MCCE4-Alpha):

      conda env update -n mc4 -f mc4.yml

6. 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

7. Setup to access the codebase programmatically: * Activate your environment, e.g. conda activate mc4 * Go into the clone directory (cd MCCE4-Tools) * Install the clone codebase as an editable package in your activated environment: bash pip install -e . * Test the package: Open the Python interpreter, then test an import statement from the package: ```python from mcce4_tools.mcce4 import constants print(dir(constants))

   OR

   import mcce4_tools.mcce4 as mct dir(mct.constants) ```

Keeping your toolbase up-to-date:

As this is repo is frequently updated, your installation must be kept up to date. Please, run the following commands before using any of its command line tools or accessing its codebase programmatically:

here=$(pwd);
clone=$(dirname $(dirname "$(python3 -c "import os, sys; print(os.path.realpath(sys.argv[1]))" "$(which ms_protonation)")")); cd "$clone";
git pull;
cd "$here";

Command line tools descriptions:

• A concise description is viewable from your clone's tools.info file:

 cat MCCE4-Tools/mcce4_tools/tools.info

The notebooks folder

This folder contain examples of usage of the codebase instead of, or in addition to, the command-line tools.

Currently, the ms_protonation_analysis notebook is a walk-through of the processing pipeline used in the ms_protonation tool.
As this tool requires a parameter file at the command line; two files with a '.crgms' extension are provided as examples.