Add docs for built-in widgets

CHANGELOG.md

@@ -29,6 +29,7 @@ The rules for this file:
 
 <!-- New added features -->
 
+- Added built-in widgets documentation (PR #63)
 - Added batching and parallel support for com distance widget (PR #64)
 
 ### Fixed

docs/source/built_in_widgets.rst

@@ -0,0 +1,92 @@
+Built-in Analysis Widgets
+=========================
+
+Here is a list of built-in analysis widgets and whether they support batching
+and can run in parallel:
+
+.. list-table::
+   :widths: 20 60 10 10
+   :header-rows: 1
+
+   * - Widget
+     - Description
+     - Batching
+     - Parallel
+   * - :mod:`~mdadash.backend.analyses.acf`
+     - Autocorrelation Function (ACF)
+     - —
+     - ✅
+   * - :mod:`~mdadash.backend.analyses.com_distance`
+     - Distance between two center-of-masses
+     - ✅
+     - ✅
+   * - :mod:`~mdadash.backend.analyses.contacts`
+     - Contacts within a cutoff
+     - ✅
+     - ✅
+   * - :mod:`~mdadash.backend.analyses.custom_code`
+     - Custom user-defined code
+     - —
+     - —
+   * - :mod:`~mdadash.backend.analyses.dssp`
+     - DSSP Analysis
+     - ✅
+     - ✅
+   * - :mod:`~mdadash.backend.analyses.energies`
+     - Widgets for various simulation energies
+     - —
+     - —
+   * - :mod:`~mdadash.backend.analyses.helix_analysis`
+     - Helix Analysis
+     - ✅
+     - ✅
+   * - :mod:`~mdadash.backend.analyses.hydrogen_bonds`
+     - 	Number of Hydrogen bonds
+     - ✅
+     - ✅
+   * - :mod:`~mdadash.backend.analyses.janin`
+     - Janin plot (Dihedral angles analysis)
+     - —
+     - —
+   * - :mod:`~mdadash.backend.analyses.msd`
+     - MSD Analysis
+     - —
+     - ✅
+   * - :mod:`~mdadash.backend.analyses.native_contacts`
+     - Native Contacts Analysis
+     - ✅
+     - ✅
+   * - :mod:`~mdadash.backend.analyses.ramachandran`
+     - Ramachandran plot (Dihedral angles analysis)
+     - —
+     - —
+   * - :mod:`~mdadash.backend.analyses.rmsd`
+     - RMSD Analysis
+     - ✅
+     - ✅
+   * - :mod:`~mdadash.backend.analyses.rog`
+     - Radii of Gyration
+     - ✅
+     - ✅
+
+.. raw:: html
+
+  <p style="text-align: center;">✅ Supported, ❌ Not supported, — Not applicable</p>
+
+.. toctree::
+   :hidden:
+
+   ACF <autosummary/mdadash.backend.analyses.acf>
+   COMDistance <autosummary/mdadash.backend.analyses.com_distance>
+   Contacts <autosummary/mdadash.backend.analyses.contacts>
+   Custom Code <autosummary/mdadash.backend.analyses.custom_code>
+   DSSP <autosummary/mdadash.backend.analyses.dssp>
+   Energies <autosummary/mdadash.backend.analyses.energies>
+   Helix Analysis <autosummary/mdadash.backend.analyses.helix_analysis>
+   Hydrogen bonds <autosummary/mdadash.backend.analyses.hydrogen_bonds>
+   Janin Plot <autosummary/mdadash.backend.analyses.janin>
+   MSD Analysis <autosummary/mdadash.backend.analyses.msd>
+   Native Contacts <autosummary/mdadash.backend.analyses.native_contacts>
+   Ramachandran Plot <autosummary/mdadash.backend.analyses.ramachandran>
+   RMSD <autosummary/mdadash.backend.analyses.rmsd>
+   ROG <autosummary/mdadash.backend.analyses.rog>

docs/source/conf.py

@@ -22,11 +22,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "mdadash"
-copyright = (
-    "2026, MDAnalysis. "
-    "Project structure based on the "
-    "MDAnalysis Cookiecutter version 0.1"
-)
+copyright = "2026, MDAnalysis. Project based on the MDAnalysis Cookiecutter version 0.1"
 author = "Pardhav Maradani"
 
 # The short X.Y version

docs/source/index.rst

@@ -13,13 +13,12 @@ Source code and contributing instructions for this project can be found in the `
    :caption: Contents:
 
    getting_started
+   built_in_widgets
    api
 
 
-
 Indices and tables
 ==================
 
 * :ref:`genindex`
 * :ref:`modindex`
-* :ref:`search`

mdadash/backend/analyses/__init__.py

@@ -1,5 +1,5 @@
 """
-Module that has all the analyses widgets
+Module for all the built-in analyses widgets
 """
 
 from . import (

mdadash/backend/analyses/acf.py

@@ -19,6 +19,93 @@
 
 
 class ACFAnalysis(WidgetBase):
+    """
+
+    **Autocorrelation Function**
+
+    This widget calculates time-lag autocorrelation for different physical properties.
+
+    The following physical properties are supported:
+
+    * velocity
+    * position
+    * force
+
+    A custom :class:`SlidingWindowACF` is used to calculate autocorrelation of chosen
+    physical property for each new frame against the time-lag buffer / window of past frames.
+
+    .. important::
+        To correctly compute positional ACF using this widget, you must supply
+        coordinates in the unwrapped convention, also known as no-jump. That is,
+        when atoms pass the periodic boundary, they must not be wrapped back into
+        the primary simulation cell. You can enable NoJump for the universe in the
+        Universe Configuration section in the Settings page of the dashboard.
+
+    **Inputs**
+
+    Run mode
+        The mode in which the widget is run - `serial` or `parallel`
+            Default: ``serial``
+
+    Physical property
+        The physical property to analyze - `velocity`, `position` or `force`
+            Default: ``velocity``
+
+    Selection
+        The MDAnalysis selection phrase to run this analysis on
+            Default: ``all``
+
+    Dimension type
+        The desired dimensions to include in the ACF -
+        `xyz`, `xy`, `yz`, `xz`, `x`, `y` or `z`
+
+            Default: ``xyz``
+
+    Centered
+        Use mean subtacted values to calculate ACF
+            Default: ``False``
+
+        .. caution::
+            A running updated mean based on data processed so far is used.
+            The number of data samples must be much greater than the lag-time
+            window for this to be accurate
+
+    Show running integral
+        Show running integral of the ACF
+            Default: ``False``
+
+        .. tip::
+            Using this option with the `velocity` physical property, i.e., (VACF)
+            can be used to observe the diffusion coefficient value in the output plot
+
+    Show particle ACFs
+        Show ACFs for individual particles of the selection in the plot
+            Default: ``False``
+
+        .. caution::
+            Enabling this option for large selections can slow down the
+            analysis and generation of the plot data
+
+    Normalize
+        Normalize the computed ACF values
+            Default: ``False``
+
+    Custom title
+        Custom title for the output plot
+            Default: ''
+
+    **Output**
+
+    Here is an example output plot of this widget:
+
+    .. figure:: /_static/images/acf_output.jpg
+        :alt: ACF output
+
+    .. tip::
+        This widget can run in parallel
+
+    """
+
     name = "ACF"
     description = "Autocorrelation Function"
 
@@ -227,9 +314,13 @@ def apply_parallel_results(self, values):
 
 
 class SlidingWindowACF:
-    """Sliding Window ACF
+    """
+
+    **Sliding Window ACF**
 
-    Calculate ACF for a sliding window of frames
+    This class computes the ACF of a physical property for each new frame
+    against the time-lag buffer / window of past N frames. The total number
+    of computations for each frame is O(N).
 
     """
 

mdadash/backend/analyses/com_distance.py

@@ -18,9 +18,72 @@
 
 
 class COMDistance(WidgetBase):
-    """COM Distance
+    """
+
+    **COM Distance**
+
+    This widget shows the distance between two center-of-masses (COMs).
+
+    **Inputs**
+
+    Run frequency
+        .. compound::
+            The frequency with which the widget is run - `every-frame` or `batch`
+                Default: ``every-frame``
+
+    Run mode
+        The mode in which the widget is run - `serial` or `parallel`
+            Default: ``serial``
+
+    Selection 1
+        First MDAnalysis selection phrase
+            Default: ``protein``
+
+    Selection 2
+        Second MDAnalysis selection phrase
+            Default: ``resid 1``
+
+    Periodic
+        Select with periodic boundary conditions
+            Default: ``True``
+
+    Updating
+        Update selection during each timestep
+            Default: ``False``
+
+    Custom title
+        Custom title for the plot
+            Default: ''
+
+    Max values
+        Max values to show in plot
+            Default: ``100``
+
+    Max distance
+        Max distance for alert check
+            Default: ``50.0``
+
+    Alert if distance > 'Max distance
+        Create an alert if the above condition is met
+            Default: ``False``
+
+    Pause simulation if distance > 'Max distance'
+        Pause the simulation if the above condition is met
+            Default: ``False``
+
+    X-axis
+        X-axis value - `time` or `step`
+            Default: ``time``
+
+    **Output**
+
+    Here is an example output plot of this widget:
+
+    .. figure:: /_static/images/com_distance_output.jpg
+        :alt: COM Distance output
 
-    Distance between two center-of-masses (COMs)
+    .. tip::
+        This widget supports batching and can run in parallel
 
     """
 

mdadash/backend/analyses/contacts.py

@@ -17,16 +17,64 @@
 
 
 class Contacts(WidgetBase):
-    """
+    r"""
 
     **Contacts within a cutoff**
 
-    This widget uses `MDAnalysis.lib.distances.capped_distance`_ to calculate number
-    of contacts with a given cutoff between two groups.
+    This widget uses `MDAnalysis.lib.distances.capped_distance`_ to caclulate
+    `number of contacts within a cutoff`_ between two contacting groups.
+
+    .. _number of contacts within a cutoff: https://userguide.mdanalysis.org/
+        stable/examples/analysis/distances_and_contacts/contacts_within_cutoff.html
 
     .. _MDAnalysis.lib.distances.capped_distance: https://docs.mdanalysis.org/stable/
         documentation_pages/lib/distances.html#MDAnalysis.lib.distances.capped_distance
 
+    **Inputs**
+
+    Run frequency
+        .. compound::
+            The frequency with which the widget is run - `every-frame` or `batch`
+                Default: ``every-frame``
+
+    Run mode
+        The mode in which the widget is run - `serial` or `parallel`
+            Default: ``serial``
+
+    Contacting Group 1
+        MDAnalysis selection phrase of first group
+            Default: ``(resname ASP GLU) and (name OE* OD*)``
+
+    Contacting Group 2
+        MDAnalysis selection phrase of second group
+            Default: ``(resname ARG LYS) and (name NH* NZ)``
+
+    Radius
+        Radius within which contacts exist
+            Default: ``4.5``
+
+    Custom title
+        Custom title for the plot
+            Default: ''
+
+    Max values
+        Max values to show in plot
+            Default: ``100``
+
+    X-axis
+        X-axis value - `time` or `step`
+            Default: ``time``
+
+    **Output**
+
+    Here is an example output plot of this widget:
+
+    .. figure:: /_static/images/contacts_output.jpg
+        :alt: Contacts output
+
+    .. tip::
+        This widget supports batching and can run in parallel
+
     """
 
     name = "Contacts"