diff --git a/package/doc/sphinx/source/documentation_pages/overview.rst b/package/doc/sphinx/source/documentation_pages/overview.rst index f0afff09433..faa5f225114 100644 --- a/package/doc/sphinx/source/documentation_pages/overview.rst +++ b/package/doc/sphinx/source/documentation_pages/overview.rst @@ -1,3 +1,5 @@ +.. _overview-label: + ========================== Overview over MDAnalysis ========================== @@ -134,10 +136,7 @@ as described in :ref:`selection-commands-label`. Examples ======== -The easiest way to get started with MDAnalysis is to read this -introduction and the chapter on :ref:`selection-commands-label` and then -explore the package interactively in IPython_ or another interactive -Python interpreter. +The easiest way to get started with MDAnalysis is to read this introduction and the chapters on :ref:`topology-label` and :ref:`selection-commands-label`, then explore the package interactively in IPython_ or another interactive Python interpreter. Included trajectories --------------------- diff --git a/package/doc/sphinx/source/documentation_pages/selections.rst b/package/doc/sphinx/source/documentation_pages/selections.rst index 5d70cdcbded..77851225050 100644 --- a/package/doc/sphinx/source/documentation_pages/selections.rst +++ b/package/doc/sphinx/source/documentation_pages/selections.rst @@ -2,7 +2,7 @@ .. _selection-commands-label: ==================== - Selection Commands + Selection commands ==================== Once you have the :meth:`~MDAnalysis.core.universe.Universe` object, you can diff --git a/package/doc/sphinx/source/documentation_pages/topology.rst b/package/doc/sphinx/source/documentation_pages/topology.rst new file mode 100644 index 00000000000..ecf61b0af17 --- /dev/null +++ b/package/doc/sphinx/source/documentation_pages/topology.rst @@ -0,0 +1,15 @@ +.. -*- coding: utf-8 -*- +.. _topology-label: + +===================== + The topology system +===================== + +As shown briefly in :ref:`overview-label`, the :class:`~MDAnalysis.core.universe.Universe` class is the primary object and core interface to molecular dynamics data in MDAnalysis. +When loading topology information from a file, as with :: + + >>> from MDAnalysis import Universe + >>> from MDAnalysis.tests.datafiles import PSF + >>> u = Universe(PSF) + +the file is read, the contents parsed, and a :class:`~MDAnalysis.core.topology.Topology` object is constructed from these contents. diff --git a/package/doc/sphinx/source/index.rst b/package/doc/sphinx/source/index.rst index 1830fe69a18..27b33473d65 100644 --- a/package/doc/sphinx/source/index.rst +++ b/package/doc/sphinx/source/index.rst @@ -75,6 +75,7 @@ Contents :numbered: ./documentation_pages/overview + ./documentation_pages/topology ./documentation_pages/selections ./documentation_pages/analysis_modules ./documentation_pages/topology_modules