From dfc5049104eccb8f9c02dd63d28c8e0135698670 Mon Sep 17 00:00:00 2001
From: James Graham <j.graham@soton.ac.uk>
Date: Tue, 20 Apr 2021 21:16:04 +0100
Subject: [PATCH] docs: clean docs files no longer necessary

---
 .readthedocs.yml                           | 12 ----
 docs/Makefile                              | 20 -------
 docs/conf.py                               | 68 ----------------------
 docs/file-formats.md                       | 27 ++++++---
 docs/make.bat                              | 35 -----------
 docs/{mapping-only.rst => mapping-only.md} | 17 +++---
 6 files changed, 29 insertions(+), 150 deletions(-)
 delete mode 100644 .readthedocs.yml
 delete mode 100644 docs/Makefile
 delete mode 100644 docs/conf.py
 delete mode 100644 docs/make.bat
 rename docs/{mapping-only.rst => mapping-only.md} (70%)

diff --git a/.readthedocs.yml b/.readthedocs.yml
deleted file mode 100644
index b3423e0..0000000
--- a/.readthedocs.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-version: 2
-
-sphinx:
-  configuration: docs/conf.py
-
-python:
-  version: 3.7
-  install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - docs
diff --git a/docs/Makefile b/docs/Makefile
deleted file mode 100644
index d4bb2cb..0000000
--- a/docs/Makefile
+++ /dev/null
@@ -1,20 +0,0 @@
-# Minimal makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line, and also
-# from the environment for the first two.
-SPHINXOPTS    ?=
-SPHINXBUILD   ?= sphinx-build
-SOURCEDIR     = .
-BUILDDIR      = _build
-
-# Put it first so that "make" without argument is like "make help".
-help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
-
-.PHONY: help Makefile
-
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/conf.py b/docs/conf.py
deleted file mode 100644
index 522a3b2..0000000
--- a/docs/conf.py
+++ /dev/null
@@ -1,68 +0,0 @@
-# Configuration file for the Sphinx documentation builder.
-#
-# This file only contains a selection of the most common options. For a full
-# list see the documentation:
-# https://www.sphinx-doc.org/en/master/usage/configuration.html
-
-# -- Path setup --------------------------------------------------------------
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
-
-
-# -- Project information -----------------------------------------------------
-
-project = 'PyCGTOOL'
-copyright = '2016, James Graham'
-author = 'James Graham'
-
-# The full version, including alpha/beta/rc tags
-release = '2.0.0'
-
-# -- General configuration ---------------------------------------------------
-
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
-extensions = [
-    'autoapi.extension',
-    'sphinx_rtd_theme',
-    'sphinx.ext.viewcode',
-    'myst_parser',
-]
-
-source_suffix = ['.rst', '.md']
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
-
-myst_enable_extensions = ['deflist']
-
-
-# -- Options for HTML output -------------------------------------------------
-
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-#
-html_theme = 'sphinx_rtd_theme'
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
-
-
-# -- Sphinx AudoAPI options --------------------------------------------------
-
-autoapi_type = 'python'
-autoapi_dirs = ['../pycgtool']
diff --git a/docs/file-formats.md b/docs/file-formats.md
index 587e487..4e3c3ce 100644
--- a/docs/file-formats.md
+++ b/docs/file-formats.md
@@ -3,7 +3,7 @@
 ## Mapping Definition File
 An example of mapping definition file for the monosaccharide allose taken from `test/data/sugar.map` is shown below.
 
-Molecule names (as present in the gro coordinate file) are used as section headers inside square brackets.
+Molecule names (as present in the coordinate file) are used as section headers inside square brackets.
 Each of the following lines describes a single coarse-grained bead mapping.
 The items on a line are:
 - the name of the bead
@@ -13,8 +13,8 @@ The items on a line are:
 
 All items on a line are whitespace separated.
 Multiple molecules may be specified in their own sections.
-It is not recommended to provide a mapping for water since MARTINI water combines four molecules into a single bead which is not yet supported by PyCGTOOL.
-Note that bead charges in the MARTINI framework are by convention integers and are used only for formally charged functional groups.  An example of a molecule mapping using charges can be found in `test/data/dppc.map`.
+It is not recommended to provide a mapping for water since MARTINI water combines four molecules into a single bead which is not possible to map directly.
+Note that bead charges in the MARTINI framework are by convention integers and are used only for formally charged functional groups.
 
 ```
 ; comments begin with a semicolon
@@ -26,15 +26,26 @@ C4 P3 C4 O4
 C5 P2 C5 C6 O6
 O5 P4 O5
 
-[SOL]
-W P4 OW HW1 HW2
+[DPPC]
+NC3 Q0  1 NC3
+PO4 Qa -1 PO4
+GL1 Na GL1
+GL2 Na GL2
+C1A C1 C1A
+C2A C3 C2A
+C3A C1 C3A
+C4A C1 C4A
+C1B C1 C1B
+C2B C3 C2B
+C3B C1 C3B
+C4B C1 C4B
 ```
 
-The Martini 3.0 force field has now introduced the use of virtual sites for polycylic compounds or polysaccharides in order to improve numerical stability for highly constrained structures.
+The Martini force field has introduced in version 3 the use of virtual sites for polycylic compounds or polysaccharides in order to improve numerical stability for highly constrained structures.
 Below is an example of how virtual sites can be included in the mapping file for naphthalene (see `/test/data/martini3/naphthalene.map`).
 Similar to the previously described mapping syntax, a virtual site is defined with a prefix of ``@v`` as follows `@v [name] [type] [charge] [constructing beads]`.
 The constructing beads refer to a list of space delimited coarse grained bead names from which the position of the virtual site will be calculated.
-Currently virtual sites can be constructed from either the center of geometry or mass of the constructing sites via the `--virtual_map_center` flag.
+Currently virtual sites can be constructed from either the center of geometry or mass of the constructing sites via the `--virtual-map-center` flag.
 
 ```
 [ NAPH ]
@@ -54,7 +65,7 @@ Each line is a list of bead names, using the names defined in the mapping file.
 Two bead names on a line defines a bond length, three defines an angle, and four defines a dihedral.
 
 If no angles are defined for a molecule, PyCGTOOL will construct all angles from the list of bonds. 
-This may also be enabled for dihedrals via the `--generate_dihedrals` flag, but is not recommended as in most cases coarse-grained models do not require dihedrals. 
+This may also be enabled for dihedrals via the `--generate-dihedrals` flag, but is not recommended as in most cases coarse-grained models do not require dihedrals. 
 Additionally, any angles inside a triangle of bond lengths are excluded from the output as they often cause simulation stability issues when used in conjunction with LINCS.
 
 ```
diff --git a/docs/make.bat b/docs/make.bat
deleted file mode 100644
index 2119f51..0000000
--- a/docs/make.bat
+++ /dev/null
@@ -1,35 +0,0 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=.
-set BUILDDIR=_build
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.http://sphinx-doc.org/
-	exit /b 1
-)
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
-popd
diff --git a/docs/mapping-only.rst b/docs/mapping-only.md
similarity index 70%
rename from docs/mapping-only.rst
rename to docs/mapping-only.md
index aee79af..1abffb5 100644
--- a/docs/mapping-only.rst
+++ b/docs/mapping-only.md
@@ -1,5 +1,4 @@
-Mapping Only Mode
-=================
+# 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`.
@@ -9,12 +8,16 @@ The main uses of the functionality are:
 - 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`.
+For guidance on the creation of this file see the full [tutorial](tutorial).
 
-To perform a mapping from a single snapshot file (e.g. PDB, GRO, etc.) use the command::
+To perform a mapping from a single snapshot file (e.g. PDB, GRO, etc.) use the command:
 
-    pycgtool <topology file> -m <MAP file>
+```
+pycgtool <topology file> -m <MAP file>
+```
 
-To perform a mapping of a complete trajectory (e.g. XTC, DCD, etc.) use the command::
+To perform a mapping of a complete trajectory (e.g. XTC, DCD, etc.) use the command:
 
-    pycgtool <topology file> <trajectory file> -m <MAP file>
+```
+pycgtool <topology file> <trajectory file> -m <MAP file>
+```
-- 
GitLab