completing user-guide

README.md

@@ -18,7 +18,7 @@ Table of contents
 =================
 - [Installation](#installation)
 - [Basic examples](#basic-examples)
-- [How to contribute](#how-to-contribute)
+- [How to contribute?](#how-to-contribute)
 - [License](#license)
 - [Copyright](#copyright)
 - [Acknowledgements](#acknowledgements)

docs/conf.py

@@ -48,6 +48,8 @@
     'sphinx.ext.napoleon',
     'sphinx.ext.intersphinx',
     'sphinx.ext.extlinks',
+    'sphinx.ext.autosectionlabel',
+    'sphinxemoji.sphinxemoji',
 ]
 
 autosummary_generate = True
@@ -244,7 +246,7 @@ def setup(app):
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'prolint2', 'ProLint2 Documentation', author, 'prolint2', 'Lipid-protein interaction nalysis.', 'Miscellaneous'),
+    (master_doc, 'prolint2', 'ProLint2 Documentation', author, 'prolint2', 'Lipid-protein interaction analysis.', 'Miscellaneous'),
 ]
 
 # -- Extension configuration -------------------------------------------------

docs/index.rst

@@ -41,6 +41,15 @@ ProLint2 is an efficient and user-friendly framework for the automated analysis
 ..  figure:: _static/fvg.png
     :align: center
 
+Table of contents
+=================
+- :ref:`Installation`
+- :ref:`Basic examples`
+- :ref:`How to contribute?`
+- :ref:`License`
+- :ref:`Copyright`
+- :ref:`Acknowledgements`
+
 Installation
 ============
 To install **prolint2** we recommend creating a new conda environment as follows:
@@ -60,47 +69,41 @@ Basic examples
 ==============
 
 Using the Prolint2's API:
--------------------------
 
 .. code-block:: python
 
-      from prolint2 import PL2
-      from prolint2.sampledata import GIRK
+    from prolint2 import Universe
+    from prolint2.sampledata import GIRKDataSample
+    GIRK = GIRKDataSample()
 
-      target_system = PL2(GIRK.coordinates, GIRK.trajectory) 
+    u = Universe(GIRK.coordinates, GIRK.trajectory)
 
-      target_system.contacts.compute(cutoff=7)
-      target_system.contacts.export('results.csv')
+    contacts = u.compute_contacts(cutoff=7) # cutoff in Angstroms
 
       
 Using the Prolint2's command-line interface:
---------------------------------------------
 
 .. code-block:: none
 
-      prolint2 coordinates.gro trajectory.xtc -c 7 -e results.csv
+      prolint2 coordinates.gro trajectory.xtc -c 7 
 
 You can find more details on how to use **prolint2** in the `usage page`_.
 
-Contents
-========
-
 .. toctree::
-   :maxdepth: 1
+    :hidden:
+    :maxdepth: 1
 
-   source/user_guide.rst
-   api
-   source/contributor_guide.rst
-   source/tutorials.rst
-   source/database.rst
+    source/user_guide.rst
+    api
+    source/contributor_guide.rst
+    source/tutorials.rst
+    source/database.rst
 
-.. Indices and tables
-.. ==================
-
-.. * :ref:`genindex`
-.. * :ref:`modindex`
-.. * :ref:`search`
+How to contribute?
+==================
+If you find a bug in the source code, you can help us by submitting an issue `here`_. Even better, you can submit a Pull Request with a fix. 
 
+We really appreciate your feedback!
 
 License 
 =======
@@ -120,3 +123,5 @@ The respository structure of **ProLint2** is based on the `Computational Molecul
 .. _`MIT License`: https://opensource.org/licenses/MIT
 .. _`github.com/Prolint/prolint2`: https://github.com/ProLint/prolint2
 .. _`usage page`: source/user_guide.html
+.. _`here`: https://github.com/ProLint/prolint2/issues
+

docs/source/user_guide.rst

@@ -1,7 +1,7 @@
 User Guide
 ==========
 
-This page details how to use **prolint2** to analyze molecular dynamics trajectories of membrane proteins. On the `Prolint's resources page`_ you can get some simple membrane protein systems that you can use to test the tools before moving on with your own systems.
+**prolint2** is designed to be flexible and adaptable to your specific research needs. You can adjust various parameters within the tools to fine-tune the analysis and visualization processes. We hope this user guide helps you make the most of **prolint2** for your lipid-protein interaction analysis. If you encounter any issues, have questions, or wish to contribute to the project, please don't hesitate to reach out to the us through `our GitHub repo`_. Happy analyzing! |:rocket:|
 
 .. toctree::
    :maxdepth: 2
@@ -26,4 +26,6 @@ This page details how to use **prolint2** to analyze molecular dynamics trajecto
    user_guide/calling_prolint.rst
    user_guide/selection_interface.rst
 
-.. _`Prolint's resources page`: https://www.prolint.ca/resources/data
+.. _`Prolint's resources page`: https://www.prolint.ca/resources/data
+.. _`GitHub`: https://www.prolint.ca/resources/data
+.. _`our GitHub repo`: https://github.com/ProLint/prolint2