Merge a1240e2 into 8aef814

devtools/ci/ipythontests.sh

@@ -11,6 +11,8 @@ ipynbtest.py "mstis.ipynb" || testfail=1
 date
 ipynbtest.py "mstis_analysis.ipynb" || testfail=1
 date
+ipynbtest.py "srtis.ipynb" || testfail=1
+date
 ipynbtest.py "repex_networks.ipynb" || testfail=1
 date
 ipynbtest.py "mistis_setup.ipynb" || testfail=1

examples/ipython/README.md

@@ -35,26 +35,32 @@ See below for a complete list of available notebooks.
 
 ## Examples
 
-#### MSTIS example (3 parts)
+#### MSTIS example (4 parts)
 
 This is the main example illustrating the usage of OpenPathSampling for a
 Multi-State Transition Interface Sampling in a 2D toy potential with 3
 states and using a simple Langevin integrator
 
 
 - [`mstis_bootstrap.ipynb`](http://github.com/choderalab/openpathsampling/blob/master/examples/ipython/mstis_bootstrap.ipynb)
-    [Part 1] of the MSTIS (Multi State TIS) testing notebooks. This will
+    [Part 1] of the MSTIS (Multiple State TIS) testing notebooks. This will
     setup the general system and create initial pathways to be used in later
     parts. Contains an example on how to use bootstrapping.
 - [`mstis.ipynb`](http://github.com/choderalab/openpathsampling/blob/master/examples/ipython/mstis.ipynb)
-    [Part 2] of the MSTIS (Multi State TIS) testing notebooks. This uses the
+    [Part 2] of the MSTIS (Multiple State TIS) testing notebooks. This uses the
     previously generated initial pathways and generates data to be analyzed
     later.
 - [`mstis_analysis.ipynb`](http://github.com/choderalab/openpathsampling/blob/master/examples/ipython/mstis_analysis.ipynb)
-    [Part 3] of the MSTIS (Multi State TIS) testing notebooks. This takes
+    [Part 3] of the MSTIS (Multiple State TIS) testing notebooks. This takes
     the previously generated data and does a complete analysis on them.
     Including different visualizations, rate computations, flow analysis,
     etc.
+- [`srtis.ipynb`](http://github.com/choderalab/openpathsampling/blob/master/examples/ipython/srtis.ipynb)
+    [Part 4] of the MSTIS (Multiple State TIS) testing notebooks. This takes
+    the same network as used in `mstis.ipynb`, but uses it in a
+    single-replica TIS scheme. This notebook also includes some analysis of
+    the SRTIS results.
+
 
 #### MISTIS example (2 parts)
 

examples/ipython/move_strategies_and_schemes.ipynb

@@ -43,7 +43,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {
     "collapsed": false
    },
@@ -90,16 +90,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 8,
    "metadata": {
     "collapsed": false
    },
    "outputs": [],
    "source": [
-    "# move_decision_tree = paths.DefaultScheme(network).move_decision_tree()\n",
-    "scheme = paths.DefaultScheme(network)\n",
-    "scheme.movers = {} # TODO: this will be removed, and lines on either side combined, when all is integrated\n",
-    "move_decision_tree = scheme.move_decision_tree()\n",
+    "move_decision_tree = paths.DefaultScheme(network).move_decision_tree()\n",
     "all_ensembles = network.all_ensembles"
    ]
   },