AD_Help

#!/usr/bin/env bash

echo """
Help for Automated Antibody Docking 2

Note: This code is evolving rapidly. The help herein might be out of date. Some executables might 
      not work yet or might not work well.

WD = working directory

The general workflow goes like:

- AD_Setup <WD>
  - Checks for very basic content in the working directory and writes information to the directory
    if certain information is missing.
  - Optional, but recommened unless you are very familiar with how the code works.
- AD_Validate <WD>
  - Checks that all the needed files are present in the working directory. 
  - Optional.
  - This is always called by AD_Evaluate.
- AD_Evaluate <WD>
  - Generates the docking input files from the files you placed in the working directory.
  - Strongly recommended unless you are doing something unusual.
  - If this finishes successfully, then the specified number of docking run replicas should work.
- AD_Run_AD <WD>
  - Sets up and runs the specified number of docking run replicas.
  - Recommended for most users.
  - If you need very specialized control over how the docking happens, there are other options.
- AD_Analyze <WD>
  - Runs some analyses on the docking run replicas.
  - Recommended for most users.
  - This is probably convenient even if you plan to do custom analyses, but you don't have to use it.

If you are running everything in serial:

- AD_Run_Core_Serial <WD>
  - Runs the following in serial:
    - AD_Evaluate <WD>
    - AD_Run_AD <WD>
    - AD_Analyze <WD>
  - This is what gets run when you test your docker image.

You can run these at any time:

- AD_Help
  - You probably ran this in order to be reading these words.
- AD_Get_Status <WD>
  - This will attempt to determine the status of a project, including its replicas.

If you need fine control, see the contents of these directories:

- 0.configure
- 1.prepare_antibody
- 2.prepare_glycan
- 3.prepare_docking_directories
- 4.run_docking
- 5.analyze_results
- 6.check_status

These should be run before trying to use any of the code in this tree. Most folks will probably need 
to preface them with './', for example, "./Compile". The installation step is recommended for most
users because the executables expect the other executables to be on the user's PATH.

- Compile
  - This will compile any binaries needed for AAD2.
  - It produces binaries, as needed, inside the directories mentioned just above.
- Install </install/dir>
  - This will copy all the executable files into the installation directory ("/install/dir").
  - If the installation directory is not specified, the executables will be installed into the AAD2
    top-level directory, e.g., into a "/path/to/AAD2/bin" directory.
"""