@@ -8,6 +8,7 @@ python ipynbtest.py "sliced_sequential_ensembles.ipynb" || testfail=1
 python ipynbtest.py "toy_bootstrapping.ipynb" || testfail=1
 python ipynbtest.py "toy_tis.ipynb" || testfail=1
 python ipynbtest.py "repex_networks.ipynb" || testfail=1
+python ipynbtest.py "multistate_system_setup.ipynb" || testfail=1
 python ipynbtest.py "langevin_integrator_check.ipynb" || testfail=1
 python ipynbtest.py "sliced_sequential_ensembles.ipynb" || testfail=1
 # needs to run after alanine since it need the trajectory.nc file
 
@@ -0,0 +1 @@
+*.nc
@@ -0,0 +1,85 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "%matplotlib inline\n",
+    "import matplotlib.pyplot as plt\n",
+    "import openpathsampling as paths\n",
+    "import numpy as np\n",
+    "\n",
+    "from openpathsampling.analysis.tis_analysis import sampleset_sample_generator\n",
+    "\n",
+    "storage = paths.storage.Storage(\"mstis.nc\", mode=\"r\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "collapsed": false,
+    "scrolled": true
+   },
+   "outputs": [
+    {
+     "ename": "TypeError",
+     "evalue": "object.__new__(): not enough arguments",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-2-6388b15d781e>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmstis\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mstorage\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnetworks\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+      "\u001b[0;32m/Users/dwhs/Dropbox/msm-tis/openpathsampling/storage/object_storage.pyc\u001b[0m in \u001b[0;36minner\u001b[0;34m(self, idx, *args, **kwargs)\u001b[0m\n\u001b[1;32m   1204\u001b[0m         \u001b[0;31m# the class method directly it is not bound yet and so we need to include the self! Took me some time to\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1205\u001b[0m         \u001b[0;31m# understand and figure that out\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1206\u001b[0;31m         \u001b[0mobj\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mn_idx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1207\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0mobj\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1208\u001b[0m             \u001b[0;31m# update cache there might have been a change due to naming\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m/Users/dwhs/Dropbox/msm-tis/openpathsampling/storage/object_storage.pyc\u001b[0m in \u001b[0;36minner\u001b[0;34m(self, idx, *args, **kwargs)\u001b[0m\n\u001b[1;32m   1272\u001b[0m             \u001b[0;32mreturn\u001b[0m \u001b[0mNone\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1273\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1274\u001b[0;31m             \u001b[0mobj\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mn_idx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1275\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1276\u001b[0m         \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mhasattr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'idx'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m/Users/dwhs/Dropbox/msm-tis/openpathsampling/storage/object_storage.pyc\u001b[0m in \u001b[0;36mload\u001b[0;34m(self, idx)\u001b[0m\n\u001b[1;32m    546\u001b[0m         '''\n\u001b[1;32m    547\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 548\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload_json\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0midx_dimension\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0;34m'_json'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0midx\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    549\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    550\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mclear_cache\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m/Users/dwhs/Dropbox/msm-tis/openpathsampling/storage/object_storage.pyc\u001b[0m in \u001b[0;36mload_json\u001b[0;34m(self, name, idx)\u001b[0m\n\u001b[1;32m    921\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    922\u001b[0m         \u001b[0msimplified\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0myaml\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mjson_string\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 923\u001b[0;31m         \u001b[0mobj\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msimplifier\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbuild\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msimplified\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    924\u001b[0m         \u001b[0msetattr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'json'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mjson_string\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    925\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m/Users/dwhs/Dropbox/msm-tis/openpathsampling/storage/storage.pyc\u001b[0m in \u001b[0;36mbuild\u001b[0;34m(self, obj)\u001b[0m\n\u001b[1;32m    571\u001b[0m                 \u001b[0;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    572\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 573\u001b[0;31m         \u001b[0;32mreturn\u001b[0m \u001b[0msuper\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mStorableObjectJSON\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbuild\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+      "\u001b[0;32m/Users/dwhs/Dropbox/msm-tis/openpathsampling/todict.pyc\u001b[0m in \u001b[0;36mbuild\u001b[0;34m(self, obj)\u001b[0m\n\u001b[1;32m    212\u001b[0m                 \u001b[0;32mif\u001b[0m \u001b[0mobj\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'_cls'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mclass_list\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    213\u001b[0m                     \u001b[0mattributes\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbuild\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'_dict'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 214\u001b[0;31m                     \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mclass_list\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mobj\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'_cls'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfrom_dict\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mattributes\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    215\u001b[0m                 \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    216\u001b[0m                     \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'Cannot create obj of class \"'\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mobj\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'_cls'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m+\u001b[0m \u001b[0;34m'\". Class is not registered as creatable!'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m/Users/dwhs/Dropbox/msm-tis/openpathsampling/analysis/network.py\u001b[0m in \u001b[0;36mfrom_dict\u001b[0;34m(dct)\u001b[0m\n\u001b[1;32m     62\u001b[0m     \u001b[0;34m@\u001b[0m\u001b[0mstaticmethod\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     63\u001b[0m     \u001b[0;32mdef\u001b[0m \u001b[0mfrom_dict\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdct\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 64\u001b[0;31m         \u001b[0mnetwork\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mMSTISNetwork\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__new__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     65\u001b[0m         \u001b[0mnetwork\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfrom_state\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mdct\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'from_state'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     66\u001b[0m         \u001b[0mnetwork\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmovers\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mdct\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'movers'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;31mTypeError\u001b[0m: object.__new__(): not enough arguments"
+     ]
+    }
+   ],
+   "source": [
+    "mstis = storage.networks.load(0)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "print mstis"
+   ]
+  }
+ ],
+ "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": "2.7.9"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}
@@ -25,13 +25,15 @@ def __call__(self, x, y):
 
 class ToyPlot(object):
     def __init__(self):
-        range_x = np.arange(-1.1, 1.1, 0.05)
-        range_y = np.arange(-1.1, 0.9, 0.05)
+        range_x = np.arange(-1.1, 1.1, 0.01)
+        range_y = np.arange(-1.1, 1.1, 0.01)
         self.extent = [range_x[0], range_x[-1], range_y[0], range_y[-1]]
         self.X, self.Y = np.meshgrid(range_x, range_y)
         pylab.rcParams['figure.figsize'] = 9, 6
         self.repcolordict = {0 : 'k-', 1 : 'r-', 2 : 'g-', 3 : 'b-', 
-                             4 : 'r-', 5 : 'k-'}
+                             4 : 'r-'}
+
+        self.contour_range = np.arange(0.0, 1.5, 0.1)
 
         self._states = None
         self._pes = None
@@ -46,9 +48,9 @@ def add_pes(self, pes):
     def add_states(self, states):
         if self._states is None:
             state = states[0]
-            self._states = np.vectorize(CallableVolume(state))(self.X, self.Y)
+            self._states = np.vectorize(CallableVolume(state))(self.X, -self.Y)
             for state in states[1:]:
-                self._states += np.vectorize(CallableVolume(state))(self.X, self.Y)
+                self._states += np.vectorize(CallableVolume(state))(self.X, -self.Y)
 
     def add_interfaces(self, ifaces):
         if self._interfaces is None:
@@ -83,7 +85,7 @@ def plot(self, trajectories=[], bold=[]):
                        aspect='auto')
         if self._pes is not None:
             plt.contour(self.X, self.Y, self._pes, 
-                        levels=np.arange(0.0, 1.5, 0.1), colors='k')
+                        levels=self.contour_range, colors='k')
         if self._interfaces is not None:
             for iface in self._interfaces:
                 plt.contour(self.X, self.Y, iface, 
@@ -98,7 +100,7 @@ def plot(self, trajectories=[], bold=[]):
                     zorder=1)
         for traj in trajectories:
             plt.plot(traj.xyz()[:,0,0], traj.xyz()[:,0,1],
-                     self.repcolordict[trajectories.index(traj)],
+                     self.repcolordict[trajectories.index(traj) % 5],
                      zorder=2)
 
     def reset(self):
 
@@ -9,7 +9,8 @@
     ReversedTrajectoryEnsemble, SequentialEnsemble, VolumeEnsemble,
     SequentialEnsemble, IntersectionEnsemble, UnionEnsemble,
     SymmetricDifferenceEnsemble, RelativeComplementEnsemble,
-    SingleFrameEnsemble, MinusInterfaceEnsemble, TISEnsemble
+    SingleFrameEnsemble, MinusInterfaceEnsemble, TISEnsemble,
+    OptionalEnsemble
 )
 
 from snapshot import Snapshot, Configuration, Momentum
@@ -26,7 +27,7 @@
     PartialAcceptanceSequentialMover, ReplicaIDChangeMover, SequentialMover,
     ConditionalMover, FilterByReplica, RestrictToLastSampleMover,
     CollapseMove, PathSimulatorMover, PathReversalSet,
-    NeighborEnsembleReplicaExchange
+    NeighborEnsembleReplicaExchange, OneWayShootingMover
 )
 
 
@@ -62,6 +63,10 @@
 from analysis.tis_analysis import TISTransition, RETISTransition, Transition, \
     TPSTransition
 
+from analysis.network import (
+    MSTISNetwork
+)
+
 from analysis.replica_network import (
     ReplicaNetwork, trace_ensembles_for_replica,
     trace_replicas_for_ensemble, condense_repeats,