diff --git a/doc/source/index.rst b/doc/source/index.rst
index beb448decf2f2dcc80c3b161dcc4109ce499c42e..d3b584c5f7f0d6b70dc869ac0053b4cbd46a23dc 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -11,12 +11,14 @@ Welcome to PyCGTOOL's documentation!
 
    self
    tutorial
+   mapping-only
    Module Documentation <modules>
 
 
 .. toctree::
    :maxdepth: 2
 
+:doc:`tutorial`
 
 Features
 --------
@@ -121,16 +123,30 @@ Advanced Usage
 
 Modes
 ~~~~~
+
 PyCGTOOL performs several other functions which may be useful in the testing and use of coarse-grained models.
 
-Mapping-only mode performs a coarse-grain mapping on a single frame and may be used to generate initial coordinates for a coarse-grain simulation, whether the model being used was created by PyCGTOOL or not.  In this respect it functions similarly to the MARTINI tool MARTINIZE.  This mode may be invoked by::
+Mapping Only
+............
+
+Mapping-only mode simply converts an input atomistic coordinate file into its coarse-grained representation.
+For full detail see: :doc:`mapping-only`.
+
+This mode may be invoked by::
 
    pycgtool.py -g <GRO file> -m <MAP file>
 
-Measure-only mode may be used to aid in the testing of a coarse-grained model by making measurements of bonds from a true coarse-grained simulation trajectory.  These bond measurements may be compared directly to those collected from the pseudo-coarse-grained trajectory used to generate the model.  This mode may be invoked by::
+
+Measure Only
+............
+
+Measure-only mode may be used to aid in the testing of a coarse-grained model by making measurements of bonds from a true coarse-grained simulation trajectory.
+These bond measurements may be compared directly to those collected from the pseudo-coarse-grained trajectory used to generate the model.
+This mode may be invoked by::
 
    pycgtool.py -g <GRO file> -x <XTC file> -b <BND file>
 
+
 Advanced Options
 ~~~~~~~~~~~~~~~~
 By passing the flag ``--advanced`` to PyCGTOOL several advanced options are accessible.  The arrow keys may be used to navigate through the menu.  Enter selects an option to be edited, or if the option is boolean toggles it.  Once you have edited an option press enter again.  When all options are satisfactory, press q to proceed.
diff --git a/doc/source/mapping-only.rst b/doc/source/mapping-only.rst
new file mode 100644
index 0000000000000000000000000000000000000000..976ae608a94de7d73580e7b61e2496fc2bf34a77
--- /dev/null
+++ b/doc/source/mapping-only.rst
@@ -0,0 +1,22 @@
+Mapping Only Mode
+=================
+
+PyCGTOOL may be used in mapping only mode to simply convert an all-atom (AA) coordinate file into its coarse-grained (CG) representation.
+In this respect it functions similarly to the MARTINI tool `Martinize`.
+The main uses of the functionality are:
+
+- Enable direct comparison between AA and CG simulations
+- Use a pre-equilibrated AA coordinate file as the starting point for a CG simulation
+
+In order to perform the AA to CG mapping, a PyCGTOOL mapping file is required.
+For guidance on the creation of this file see the full :doc:`tutorial`.
+
+To perform a mapping from a single snapshot `.gro` file use the command::
+
+    pycgtool.py -g <GRO file> -m <MAP file>
+
+To perform a mapping of a complete `.xtc` trajectory use the command::
+
+    pycgtool.py -g <GRO file> -x <XTC file> -m <MAP file>
+
+But note that mapping an entire trajectory requires that the optional dependency `MDTraj` is installed.
diff --git a/doc/source/pycgtool.functionalforms.rst b/doc/source/pycgtool.functionalforms.rst
new file mode 100644
index 0000000000000000000000000000000000000000..c69160b61d63f9d1c4655e0bb6683ab201c9fa1c
--- /dev/null
+++ b/doc/source/pycgtool.functionalforms.rst
@@ -0,0 +1,7 @@
+pycgtool.functionalforms module
+===============================
+
+.. automodule:: pycgtool.functionalforms
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/pycgtool.rst b/doc/source/pycgtool.rst
index 4f6aded4de1272c48919e24e4e18eb4a5a95fa78..17932f881cba72b0a66a656b274581f6b5c5c135 100644
--- a/doc/source/pycgtool.rst
+++ b/doc/source/pycgtool.rst
@@ -16,6 +16,7 @@ Submodules
    pycgtool.bondset
    pycgtool.forcefield
    pycgtool.frame
+   pycgtool.functionalforms
    pycgtool.interface
    pycgtool.mapping
    pycgtool.pycgtool