edits for documentation

docs/mdpath_classes/mdpath.rst

@@ -1,5 +1,6 @@
 .. automodule:: mdpath.mdpath
    :members:
+   :functions:
    :undoc-members:
    :show-inheritance:
    :noindex:  # Avoid indexing this module in the API section

docs/mdpath_classes/mdpath_tools.rst

@@ -1,5 +1,6 @@
 .. automodule:: mdpath.mdpath_tools
    :members:
+   :functions:
    :undoc-members:
    :show-inheritance:
    :noindex:  # Avoid indexing this module in the API section

mdpath/mdpath.py

@@ -12,6 +12,9 @@
 This is the main script of MDPath. It is used to run MDPath from the command line.
 MDPath can be called from the comadline using 'mdapth' after instalation
 Use the -h flag to see the available options.
+
+Functions
+----------
 """
 
 import os
@@ -35,6 +38,20 @@
 
 
 def main():
+    """Main function for running MDPath from the command line.
+    It can be called using 'mdpath' after installation.
+    
+    Command-line inputs:
+    -top: Topology file of your MD simulation
+    -traj: Trajectory file of your MD simulation
+    -cpu: Amount of cores used in multiprocessing (default: half of available cores)
+    -lig: Protein ligand interacting residues (default: False)
+    -bs: How often bootstrapping should be performed (default: False)
+    -fardist: Default distance for faraway residues (default: 12.0)
+    -closedist: Default distance for close residues (default: 12.0)
+    -graphdist: Default distance for residues making up the graph (default: 5.0)
+    -numpath: Default number of top paths considered for clustering (default: 500).
+    """
     parser = argparse.ArgumentParser(
         prog="mdpath",
         description="Calculate signal transduction paths in your MD trajectories",

mdpath/mdpath_tools.py

@@ -1,3 +1,12 @@
+"""MDPath Tools
+=============================
+This module contains the command-line interface (CLI) functions for editing and visualizing the results of MDPath analysis.
+All functions can be called from the command line after installation of the package.
+
+Functions
+-----------
+"""
+
 import os
 import argparse
 import pandas as pd
@@ -15,6 +24,28 @@
 
 
 def edit_3D_visualization_json():
+    """Edit the 3D visualization JSONS to your visualization needs from the command line.
+    
+    This function provides a command-line interface (CLI) for editing 3D visualization JSON files.
+    It supports various operations such as recoloring, scaling, and flatting the radius of the entries in the JSON file.
+    It cann be called using 'mdpath_json_editor' after installation.
+    
+    Command-line inputs:
+    -json (str): The path to the JSON file to edit for 3D visualization. 
+    -scale (float): The factor to multiply the radius of path cylinders with. 
+    -recolor (str): The path to the color file for 3D visualization colors.
+    -flat (float): Sets every radius of path cylinders to the input value.
+    -clusterscale (float): The maximum radius for the cluster-based scaling.
+    
+    Note: Only one operation can be performed at a time. If multiple operations are specified, an error will be displayed.
+    
+    Command-line usage:
+    $ mdpath_json_editor -json <path_to_json_file> -scale <scaling_factor_float>
+    $ mdpath_json_editor -json <path_to_json_file> -recolor <path_to_color_json_file>
+    $ mdpath_json_editor -json <path_to_json_file> -flat <flat_radius_value_float>
+    $ mdpath_json_editor -json <path_to_json_file> -clusterscale <scaling_factor_float>
+    """
+
     parser = argparse.ArgumentParser(
         prog="mdpath_json_edit",
         description="Edit the 3D visualization JSONS to your visualization needs.",
@@ -157,6 +188,20 @@ def edit_3D_visualization_json():
 
 
 def path_comparison():
+    """Compare Pathways of different simulations.
+    
+    This function provides a command-line interface (CLI) for morphing the 3d visualization of a simulation to fit ontop of the coordinates of another simulatuion.
+    This enables easy comparison of the pathways of different simulations.
+    It cann be called using 'mdpath_compare' after installation.
+    
+    Command-line inputs:
+    - atop: The path to the file containing the residue coordinates that are used as a template.
+    - bcluster: The path to the file containing the cluster that is morphed ontop.
+
+
+    Command-line usage:
+    $ mdpath_compare -atop <path_to_atop_file> -bcluster <path_to_bcluster_file>
+    """
     parser = argparse.ArgumentParser(
         prog="mdpath_compare",
         description="Compare Pathways of different simulations",
@@ -195,6 +240,24 @@ def path_comparison():
 
 
 def multitraj_analysis():
+    """
+    Merge and analyze multiple trajectories.
+
+    This function provides a command-line interface (CLI) for merging and analyzing multiple trajectories.
+    It requires the topology file of the MD simulation and a list of multiple pathways from previous analysis.
+    The function calculates various properties of the merged pathways, clusters them, and saves the results in JSON files.
+    It cann be called using 'mdpath_multitraj' after installation.
+    
+
+    Command-line inputs:
+        -top: Topology file of your MD simulation.
+        -multitraj: List of multiple pathways from previous analysis.
+        -cpu: Amount of cores used in multiprocessing.
+        -closedist: Default distance for close residues.
+
+    Command-line usage:
+    $ mdpath_multitraj -top <path_to_topology_file> -multitraj <path_to_multitraj_file> -cpu <number_of_cores> -closedist <default_distance>
+    """
     parser = argparse.ArgumentParser(
         prog="mdpath_multitraj",
         description="Merge and analyze multiple trajectories.",
@@ -276,9 +339,28 @@ def multitraj_analysis():
 
 
 def gpcr_2D_vis():
+    """
+    Create a 2D Visualization of Paths through a GPCR using the Ballesteros-Weinstein-System for numbering(querries gpcrdb.org for numbering).
+
+    This function provides a command-line interface (CLI) for creating a 2D visualization of paths through a GPCR.
+    It queries gpcrdb.org for the Ballesteros-Weinstein-System numbering and assigns generic numbers to the protein atoms.
+    Then a 2D visualization of the GPCR paths is created based on the updated cluster pathways and the specified cutoff percentage.
+    
+    Command-line inputs:
+    -top: Topology file of your MD simulation
+    -clust: Pickle file with cluster pathways dictionary
+    -cut: Percentage of the top paths to visualize (default is 0 = all paths are drawn)
+    -num: Path to write the numbered structure file to (default is "./numbered_structure.pdb")
+
+
+    Note: This function requires access to the internet to query gpcrdb.org for the Ballesteros-Weinstein-System numbering.
+
+    Example usage:
+    $ mdpath_gpcr_image -top <path_to_topology_file> -clust <path_to_cluster_pathways.pickl> -cut <cutoff_float> -num <path_where_to_save_numberd_structure>
+    """
     parser = argparse.ArgumentParser(
         prog="mdpath_gpcr",
-        description="Create a 2D Visualization of Paths throught a GPCR.",
+        description="Create a 2D Visualization of Paths through a GPCR.",
         formatter_class=argparse.RawTextHelpFormatter,
     )
     parser.add_argument(
@@ -290,7 +372,7 @@ def gpcr_2D_vis():
     parser.add_argument(
         "-clust",
         dest="cluster_pathways",
-        help="Picle file with cluster pathways dict.",
+        help="Pickle file with cluster pathways dict.",
         required=True,
     )
     parser.add_argument(