Formats and AtomGroup methods

.gitignore

@@ -22,4 +22,18 @@ doc/build
 *.so
 
 # Ignore generated docs
-doc/source/scripts/generated/*
+# *.txt
+
+# ignore generated files
+*.vmd
+*.dcd
+*.xyz
+*.pdb
+*.trr
+*.ndx
+*.xtc
+
+# example files
+doc/source/examples/*
+!doc/source/examples/*.ipynb
+!doc/source/examples/analysis/*.ipynb

doc/source/_static/custom.css

@@ -5,8 +5,8 @@
 /* MDAnalysis gray: #808080 */
 /* MDAnalysis white: #FFFFFF */
 /* MDAnalysis black: #000000 */
-/* Darker orange: e76900 */
-/* Even darker orange: #a24900 */
+/* Very light orange: #FFEBD0 */
+/* Code orange: #ca6500 */
 /* RTD dark grey: #343131 */
 /* RTD light grey: #e6e6e6 */
 
@@ -203,4 +203,18 @@ dl.field-list > dt::after {
 
 .rst-content code:not(.xref).literal {
     color: #ca6500;
-}
+}
+/* override table width restrictions */
+@media screen and (min-width: 767px) {
+
+    .wy-table-responsive table td, .wy-table-responsive table th {
+       /* !important prevents the common CSS stylesheets from overriding
+          this as on RTD they are loaded after this stylesheet */
+       white-space: normal !important;
+    }
+
+    .wy-table-responsive {
+       overflow: visible !important;
+       max-width: 100% !important;
+    }
+ }

doc/source/advanced_topology.rst

@@ -8,9 +8,9 @@ Advanced topology concepts
 .. _adding-residue-label:
 
 Adding a Residue or Segment to a Universe
------------------------------------------
+=========================================
 
-To add a :class:`~MDAnalysis.core.groups.Residue` or :code:`~MDAnalysis.core.groups.Segment` to a topology, use the :meth:`Universe.add_Residue <MDAnalysis.core.universe.Universe.add_Residue>` or :meth:`Universe.add_Segment <MDAnalysis.core.universe.Universe.add_Segment>` methods.
+To add a :class:`~MDAnalysis.core.groups.Residue` or :class:`~MDAnalysis.core.groups.Segment` to a topology, use the :meth:`Universe.add_Residue <MDAnalysis.core.universe.Universe.add_Residue>` or :meth:`Universe.add_Segment <MDAnalysis.core.universe.Universe.add_Segment>` methods.
 
 .. code-block::
 
@@ -39,7 +39,7 @@ Another example is `creating custom segments for protein domains <examples/const
 .. _molecule-label:
 
 Molecules
----------
+=========
 
 In MDAnalysis, a molecule is a GROMACS-only concept that is relevant in some analysis methods. A group of atoms is considered a "molecule" if it is defined by the :code:`[ moleculetype ]` section in a `GROMACS topology <http://manual.gromacs.org/documentation/2019/reference-manual/file-formats.html#top>`_. Molecules are only defined if a Universe is created from a GROMACS topology file (i.e. with a .tpr extension). Unlike fragments, they are not accessible directly from atoms.
 
@@ -53,9 +53,15 @@ In MDAnalysis, a molecule is a GROMACS-only concept that is relevant in some ana
         cls=self.__class__.__name__, attr=attr))
     AttributeError: AtomGroup has no attribute molecules
 
-However, the order (:code:`molnum`) and name (:code:`moltype`) of each molecule is accessible as :ref:`topology attributes <topology-attributes>`::
+However, the order (:code:`molnum`) and name (:code:`moltype`) of each molecule is accessible as :ref:`topology attributes <topology-attributes-label>`::
 
     >>> tpr.atoms.molnums
     array([    0,     0,     0, ..., 11086, 11087, 11088])
     >>> tpr.atoms.moltypes
-    array(['AKeco', 'AKeco', 'AKeco', ..., 'NA+', 'NA+', 'NA+'], dtype=object)
+    array(['AKeco', 'AKeco', 'AKeco', ..., 'NA+', 'NA+', 'NA+'], dtype=object)
+
+
+.. _custom-topologyattrs-label:
+
+Adding custom TopologyAttrs
+===========================

doc/source/analysis.rst

@@ -1,6 +1,41 @@
 .. -*- coding: utf-8 -*-
-.. analysis:
+.. _analysis-label:
 
 =====================
 Analysis
-=====================
+=====================
+
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Alignments, distances, and contacts
+
+   examples/analysis/alignments.ipynb
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Hydrogen bonding
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Dimensionality reduction
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Structure
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Volumetric analysis
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Membranes and membrane proteins
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Nucleic acids
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Polymers