CompuCell3D · maciekswat · Aug 24, 2024 · Aug 25, 2024 · Aug 31, 2024 · Aug 31, 2024
diff --git a/docs/curvature.rst b/docs/curvature.rst
@@ -1,3 +1,4 @@
+.. _curvature-plugin:
 Curvature Plugin
 ----------------
 

diff --git a/docs/example_compartmental_elongated_cells_tutorial.rst b/docs/example_compartmental_elongated_cells_tutorial.rst
diff --git a/docs/focal_point_plasticity.rst b/docs/focal_point_plasticity.rst
@@ -1,3 +1,4 @@
+.. _fpp-plugin:
 FocalPointPlasticity Plugin
 ---------------------------
 
@@ -122,6 +123,34 @@ example):
    </Plugin>
 
 
+The total number of links a given cell can form is computed as a sum of ``<MaxNumberOfJunctions>`` values coming from ``<Parameters>``
+or ``<InternalParameters>`` sections where a given cell type appears. In the example above ``Center`` can form maximum of 2 internal links (between compartments)
+
+CompuCell3D gives you ability to override this default algorithm by adding additional tag that control the total number of links:
+
+
+.. code-block:: xml
+
+   <Plugin Name="FocalPointPlasticity">
+
+       <MaxTotalNumberOfLinks CellType="Center">1</MaxTotalNumberOfLinks>
+       <InternalMaxTotalNumberOfLinks CellType="Center">1</InternalMaxTotalNumberOfLinks>
+
+
+       <Parameters Type1="Top" Type2="Top">
+          <Lambda>10.0</Lambda>
+        ...
+
+In this example we are limiting the maximum number of links ``Center`` cells can form with Center cells of another cluster to 1
+``<MaxTotalNumberOfLinks CellType="Center">1</MaxTotalNumberOfLinks>`` and do the same for number of links the ``Center`` cells can form
+with cells that are members of the same cluster: ``<InternalMaxTotalNumberOfLinks CellType="Center">1</InternalMaxTotalNumberOfLinks>``
+
+
+
+where we can override this default algorithm. This feature can be useful when working with "elongated" compartmental cells where
+you do not want Center cells to form more than two links
+
+
 We can also specify link constituent law and change it to different form
 that "spring relation". To do this we use the following syntax inside
 FocalPointPlasticity CC3DML plugin:

diff --git a/docs/images/elongated_cells_tutorial/img001.png b/docs/images/elongated_cells_tutorial/img001.png
diff --git a/docs/images/elongated_cells_tutorial/img002.png b/docs/images/elongated_cells_tutorial/img002.png
diff --git a/docs/images/elongated_cells_tutorial/img003.png b/docs/images/elongated_cells_tutorial/img003.png
diff --git a/docs/images/elongated_cells_tutorial/img004.png b/docs/images/elongated_cells_tutorial/img004.png
diff --git a/docs/images/elongated_cells_tutorial/img005.png b/docs/images/elongated_cells_tutorial/img005.png
diff --git a/docs/images/elongated_cells_tutorial/img006.png b/docs/images/elongated_cells_tutorial/img006.png
diff --git a/docs/images/elongated_cells_tutorial/img007.png b/docs/images/elongated_cells_tutorial/img007.png
diff --git a/docs/images/elongated_cells_tutorial/img008.png b/docs/images/elongated_cells_tutorial/img008.png
diff --git a/docs/images/elongated_cells_tutorial/img009.png b/docs/images/elongated_cells_tutorial/img009.png
diff --git a/docs/images/elongated_cells_tutorial/img010.png b/docs/images/elongated_cells_tutorial/img010.png
diff --git a/docs/images/elongated_cells_tutorial/img011.png b/docs/images/elongated_cells_tutorial/img011.png
diff --git a/docs/images/elongated_cells_tutorial/img012.png b/docs/images/elongated_cells_tutorial/img012.png
diff --git a/docs/images/elongated_cells_tutorial/img013.png b/docs/images/elongated_cells_tutorial/img013.png
diff --git a/docs/images/elongated_cells_tutorial/img014.png b/docs/images/elongated_cells_tutorial/img014.png
diff --git a/docs/images/elongated_cells_tutorial/img015.png b/docs/images/elongated_cells_tutorial/img015.png
diff --git a/docs/images/elongated_cells_tutorial/img016.png b/docs/images/elongated_cells_tutorial/img016.png
diff --git a/docs/images/elongated_cells_tutorial/img017.png b/docs/images/elongated_cells_tutorial/img017.png
diff --git a/docs/index.rst b/docs/index.rst
@@ -73,6 +73,14 @@ or watch the `CompuCell3D Workshop Python tutorial videos <https://www.youtube.c
     maboss
 
 
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+   :caption: Real-world Examples
+
+   section_real_world_examples
+
+
 .. toctree::
     :caption: Screenshots, Restarts, Parameter Scans
     :hidden:

diff --git a/docs/section_real_world_examples → docs/section_real_world_examples.rst b/docs/section_real_world_examples → docs/section_real_world_examples.rst
@@ -4,6 +4,7 @@ Real-World Examples Section
 .. toctree::
     :maxdepth: 1
 
+    example_compartmental_elongated_cells_tutorial
     example_cell_sorting
     example_epithelial_mesenchymal_transition
     example_contact_inhibited_cell_growth