Usage
=====

This section provides detailed instructions on how to use FastConformation, including how to run the GUI and various CLI tools provided by the package.

Installing on Linux
===================

To install FastConformation on a Linux system, follow these steps:

1. Open a terminal.
2. Run the installation script by typing:

   .. code-block:: bash

      bash ./install.sh

   Running the installation script will open the GUI.

3. To run the GUI again after exiting, type:

   .. code-block:: bash

      poetry run run_gui

   Or you can also run it as:

   .. code-block:: bash

      fast_conformation/fast_conf-conda/bin/python -m fast_conformation.gui.run_gui

Installing on Windows (WSL)
===========================

To run FastConformation on Windows using WSL, ensure that WSL and Miniconda are installed. You can install WSL by following these steps:

1. Open PowerShell, Windows Command Prompt, or Terminal in administrator mode (Right-click > Run as administrator).
2. Type the following command to install WSL:

   .. code-block:: bash

      wsl --install

3. Restart your machine.

Running FastConformation on Windows
===============================

1. Download the `install.sh` file from the GitHub repository.
2. Open the terminal and type `WSL` to enter the WSL environment.
3. Navigate to the WSL file system by typing:

   .. code-block:: bash

      cd ~/

4. Move the downloaded `install.sh` file to this directory:

   .. code-block:: bash

      mv /location/of/file/install.sh ~/

   Replace `/location/of/file/` with the path to where your `install.sh` file is located.

5. Run the installation script by typing:

   .. code-block:: bash

      bash ./install.sh

   Running the installation script will open the GUI.

6. To run the GUI again after exiting, type:

   .. code-block:: bash

      fast_conformation/fast_conf-conda/bin/python -m fast_conformation.gui.run_gui

   Note that you must be in the WSL file system (`~/`) to run this command successfully.

Running the GUI
===============

Once FastConformation is installed, you can access its graphical user interface (GUI) by running the following command:

.. code-block:: bash

   run_gui

Alternatively, you can start the GUI using:

.. code-block:: bash

   fast_conformation/fast_conf-conda/bin/python -m fast_conformation.gui.run_gui

This GUI allows you to perform MSA generation, AF2 prediction, and analysis to predict different protein conformations using MSA subsampling.

Using the Command-Line Interface (CLI)
======================================

FastConformation provides several CLI tools for different tasks, including MSA generation, prediction, and analysis. Below is a list of available commands with brief descriptions.

First, run 

```bash
fast_conf_init
```

The parameters for each command can either be included in the config file or via the command line. Visit the CLI guide page of the documentation for more information.
Sample config files and sample results are available via this link [Download Sample Files](https://drive.google.com/drive/folders/1ev5HfWVyMTBw3FRtKWxYaswuaIXvC1FS?usp=drive_link).

**MSA Generation:**

- **jackhmmer_msa**: Generate MSA using `jackhmmer`.

  .. code-block:: bash

     jackhmmer_msa --config_file <path_to_config>

- **mmseqs2_msa**: Generate MSA using `mmseqs2`.

  .. code-block:: bash

     mmseqs2_msa --config_file <path_to_config>


**Prediction:**

- **predict_ensemble**: Run ensemble predictions.

  .. code-block:: bash

     predict_ensemble --config_file <path_to_config>

- **fast_conf_init**: Create a sample config file.

  .. code-block:: bash

     fast_conf_init

**Analysis:**

- **rmsd_mode1d**: Analyze RMSD in 1D mode.

  .. code-block:: bash

     rmsd_mode1d --config_file <path_to_config>

- **rmsd_mode2d**: Analyze RMSD in 2D mode.

  .. code-block:: bash

     rmsd_mode2d --config_file <path_to_config>

- **tmscore_mode1d**: Analyze TM-score in 1D mode.

  .. code-block:: bash

     tmscore_mode1d --config_file <path_to_config>

- **tmscore_mode2d**: Analyze TM-score in 2D mode.

  .. code-block:: bash

     tmscore_mode2d --config_file <path_to_config>

- **pca_clustering**: Perform PCA clustering on the predicted structures.

  .. code-block:: bash

     pca_clustering --config_file <path_to_config>

- **rmsf_plddt**: Calculate RMSF and pLDDT for the predicted structures.

  .. code-block:: bash

     rmsf_plddt --config_file <path_to_config>

- **save_traj**: Save trajectories from the analysis.

  .. code-block:: bash

     save_traj --config_file <path_to_config>

For more detailed instructions on how to use each tool, refer to the respective CLI documentation sections provided in this guide.

Additional Notes
================

- Ensure that all necessary configuration files are correctly set up as described in their respective sections.
- For more detailed instructions and examples, visit the specific CLI documentation sections.