From 91730d948a3026b2ea5cf9ba4d15da46e167f4ed Mon Sep 17 00:00:00 2001
From: James Graham <J.A.Graham@soton.ac.uk>
Date: Tue, 21 Feb 2017 12:01:41 +0000
Subject: [PATCH] Added more detail on mapping-only-mode to documentation
---
doc/source/index.rst | 20 ++++++++++++++++++--
doc/source/mapping-only.rst | 22 ++++++++++++++++++++++
doc/source/pycgtool.functionalforms.rst | 7 +++++++
doc/source/pycgtool.rst | 1 +
4 files changed, 48 insertions(+), 2 deletions(-)
create mode 100644 doc/source/mapping-only.rst
create mode 100644 doc/source/pycgtool.functionalforms.rst
diff --git a/doc/source/index.rst b/doc/source/index.rst
index beb448d..d3b584c 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 0000000..976ae60
--- /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 0000000..c69160b
--- /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 4f6aded..17932f8 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
--
GitLab