From 7f34bfe33febb2c3f680f09c076bfcbd41ce712f Mon Sep 17 00:00:00 2001
From: David Dotson <dotsdl@gmail.com>
Date: Sun, 4 Jan 2015 13:50:09 -0700
Subject: [PATCH] Finished tags/categories doc.

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 docs/tags-categories.rst | 67 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 67 insertions(+)
 create mode 100644 docs/tags-categories.rst

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+==========================
+Differentiating Containers
+==========================
+**Sims** and **Groups** can be used to develop "fire-and-forget" analysis
+routines. Large numbers of Containers can be fed to an analysis code to give
+that code access to all trajectory and intermediate data, with individual
+Containers handled according to their characteristics. To make it possible to
+write code that tailors its approach according to the Container it encounters,
+we can use tags and categories.
+
+Tags are individual strings that describe a Container. Using our **Sim**
+``marklar`` as an example, we can add many tags at once ::
+
+    >>> s.tags.add('TIP4P', 'ADK', 'kinases', 'globular', 'equilibrium')
+    >>> s.tags
+    <Tags(['ADK', 'TIP4P', 'equilibrium', 'globular', 'kinases'])>
+
+They can be iterated through as well ::
+
+    >>> for tag in s.tags:
+    >>>     print tag
+    kinases
+    globular
+    ADK
+    TIP4P
+    equilibrium
+
+Categories are key-value pairs of strings. They are particularly useful as
+switches for analysis code. For example, if we are simulating two different
+states of a protein (say, "open" and "closed"), we can make a category that
+reflects this. In this case, we categorize ``marklar`` as "open" ::
+    
+    >>> s.categories['state'] = 'open'
+    >>> s.categories
+    <Categories({'state': 'open'})>
+
+Perhaps we've written some analysis code that will take both "open" and "closed"
+simulation trajectories as input but needs to handle them differently. It can
+see what variety of **Sim** it is working with using ::
+
+    >>> s.categories['state']
+    'open'
+
+Future: Querying
+================
+Tags and categories are two elements of Containers that will be :doc:`queryable
+<Coordinator>`.
+
+Reference: Tags
+===============
+The class :class:`MDSynthesis.Core.Aggregators.Tags` is the interface used
+by Containers to access their tags. It is not intended to be used on its own,
+but is shown here to give a detailed view of its methods.
+
+.. autoclass:: MDSynthesis.Core.Aggregators.Tags
+    :members:
+    :inherited-members:
+
+Reference: Categories
+=====================
+The class :class:`MDSynthesis.Core.Aggregators.Categories` is the interface
+used by Containers to access their categories. It is not intended to be used on
+its own, but is shown here to give a detailed view of its methods.
+
+.. autoclass:: MDSynthesis.Core.Aggregators.Categories
+    :members:
+    :inherited-members: