jhprinz · Jul 11, 2016 · Jul 11, 2016 · Jul 12, 2016 · Jul 12, 2016 · Jul 12, 2016
diff --git a/devtools/conda-recipe/meta.yaml b/devtools/conda-recipe/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: openpathsampling-dev
-  version: "0.9.1"
+  version: "0.9.2"
 
 source:
 #  git_url: ../../.git

diff --git a/docs/conf.py b/docs/conf.py
@@ -96,9 +96,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.9.1'
+version = '0.9.2'
 # The full version, including alpha/beta/rc tags.
-release = '0.9.1'
+release = '0.9.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/docs/examples/miscellaneous/committors.rst b/docs/examples/miscellaneous/committors.rst
@@ -1,10 +1,12 @@
+.. basic_committor::
+
 Basic Committor/Shooting Point Analysis
 =======================================
 
 This notebook shows some basics on how to use the committor simulation and
-how to use the shooting point analysis.
-
-.. note:: A more details example of a committor analyis is coming soon.
+how to use the shooting point analysis. A more detailed example, showing how
+to perform a committor analysis on alanine dipeptide based on the results of
+a TPS simulation, is included in :ref:`this example <ad_committor>`.
 
 -----
 

diff --git a/docs/examples/miscellaneous/committors_alanine_dipeptide.rst b/docs/examples/miscellaneous/committors_alanine_dipeptide.rst
@@ -0,0 +1,46 @@
+.. ad_committor::
+
+Committor Simulation and Analysis for Alanine Dipeptide
+=======================================================
+
+This sequence of notebooks provides an example of how to calculate the
+committor for a real biomolecular system (alanine dipeptide).
+
+The first notebook deals with selecting the snapshots to use as starting
+points for the committor. In this particular case, we didn't care about the
+statistics of those points, so we select them directly from ``storage``.
+This is because these points were being harvested as part of an approach to
+estimate the committor at any given point. If you need the statistics of
+those points within the TPS ensemble, e.g., for the transition state
+ensemble, then you should select your points differently (by looping over
+``storage.steps`` and taking the ``active`` sample set).
+
+The second notebook runs the committor simulation. The third notebook
+prepares the analysis data in a way that was needed for this particular
+project, where each "shot" of the committor was treated as a separate
+"experiment." While this approach is not normally needed, if you already
+have data that can easily be put into this format, the fourth notebook shows
+how it can be used to construct a :class:`.ShootingPointAnalysis` object.
+That notebook also proceeds to demonstrate the kinds of analysis that object
+can perform.
+
+-----
+
+.. notebook:: examples/misc/alanine_dipeptide_committor/1_select_snapshots.ipynb
+   :skip_exceptions:
+
+-----
+
+.. notebook:: examples/misc/alanine_dipeptide_committor/2_committor_simulation.ipynb
+   :skip_exceptions:
+
+-----
+
+.. notebook:: examples/misc/alanine_dipeptide_committor/3_committor_analysis.ipynb
+   :skip_exceptions:
+
+-----
+
+.. notebook:: examples/misc/alanine_dipeptide_committor/4_analysis_help.ipynb
+   :skip_exceptions:
+
diff --git a/examples/misc/README.md b/examples/misc/README.md
@@ -6,6 +6,9 @@ aspects of OpenPathSampling.
 * [`committors.ipynb`](http://github.com/openpathsampling/openpathsampling/blob/master/examples/misc/committors.ipynb)
   How to use OPS for committor analysis, and to analyze the shooting points
   from a path sampling simulation.
+* [`alanine_dipeptide_committor`](http://github.com/openpathsampling/openpathsampling/blob/master/examples/misc/alanine_dipeptide_committor/)
+  A sequence of several files to perform a committor simulation and analyze
+  it for a real system.
 * [`custom_strategy_repex_shoot_repex.ipynb`](http://github.com/openpathsampling/openpathsampling/blob/master/examples/misc/custom_strategy_repex_shoot_repex.ipynb)
   How to make a custom move strategy and custom mover, and then compare
   measures of replica travel between two different move schemes.

diff --git a/examples/misc/alanine_dipeptide_committor/1_select_snapshots.ipynb b/examples/misc/alanine_dipeptide_committor/1_select_snapshots.ipynb
@@ -0,0 +1,201 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Select Snapshots\n",
+    "\n",
+    "This notebook will take an old (and large) TPS simulation file, select some snapshots to use as input data.\n",
+    "\n",
+    "Note: this first version is quick and dirty. There might be some points to consider to select better snapshots. But this is just intended to get initial data to our colleagues."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "import openpathsampling as paths\n",
+    "import random"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "CPU times: user 20.7 s, sys: 6.48 s, total: 27.2 s\n",
+      "Wall time: 2min 10s\n"
+     ]
+    }
+   ],
+   "source": [
+    "%%time\n",
+    "storage = paths.Storage(\"alanine_dipeptide_tps.nc\", \"r\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "17.95GB\n"
+     ]
+    }
+   ],
+   "source": [
+    "print storage.file_size_str"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "946650\n"
+     ]
+    }
+   ],
+   "source": [
+    "n_snapshots = len(storage.snapshots)\n",
+    "print n_snapshots"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "stateA = storage.volumes['C_7eq']\n",
+    "stateB = storage.volumes['alpha_R']"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Now we do the main calculation: every snapshot must not be in a state, and we never re-use a snapshot. (In other words, randomly chosen without replacement.)\n",
+    "\n",
+    "In addition, OPS snapshots are always listed in pairs, with velocities reversed. (The data is only stored once, but both can be accessed directly from the snapshot storage.) Because of this, we'll make sure we only take the even-numbered snapshots."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "CPU times: user 16.4 s, sys: 452 ms, total: 16.8 s\n",
+      "Wall time: 1min 1s\n"
+     ]
+    }
+   ],
+   "source": [
+    "%%time\n",
+    "snapshots = []\n",
+    "while len(snapshots) < 1000:\n",
+    "    random_choice = random.randint(0, (n_snapshots/2)-1)\n",
+    "    snap = storage.snapshots[random_choice*2]\n",
+    "    if not stateA(snap) and not stateB(snap) and snap not in snapshots:\n",
+    "        snapshots.append(snap)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "new_store = paths.Storage(\"snapshots.nc\", \"w\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "new_store.save(snapshots);"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "# save the old engine because we'll re-use its topology later\n",
+    "new_store.save(storage.engines[0]);"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "new_store.sync()\n",
+    "new_store.close()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 2",
+   "language": "python",
+   "name": "python2"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 1
+}