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Merged
richardjgowers merged 1 commit into from
Jan 26, 2017
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WIP: New topology docs (#1078) #1176

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7 changes: 3 additions & 4 deletions package/doc/sphinx/source/documentation_pages/overview.rst
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.. _overview-label:

==========================
Overview over MDAnalysis
==========================
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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
---------------------
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2 changes: 1 addition & 1 deletion package/doc/sphinx/source/documentation_pages/selections.rst
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.. _selection-commands-label:

====================
Selection Commands
Selection commands
====================

Once you have the :meth:`~MDAnalysis.core.universe.Universe` object, you can
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15 changes: 15 additions & 0 deletions package/doc/sphinx/source/documentation_pages/topology.rst
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.. -*- 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.
1 change: 1 addition & 0 deletions package/doc/sphinx/source/index.rst
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:numbered:

./documentation_pages/overview
./documentation_pages/topology
./documentation_pages/selections
./documentation_pages/analysis_modules
./documentation_pages/topology_modules
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