Fix two missing classes

docs-source/python-api/app.rst.jinja2

+.. _app :
+
 Application Layer
 =================
 

docs-source/python-api/index.rst

@@ -3,6 +3,15 @@
 OpenMM Python API
 =================
 
+The Python API provides information about the classes and methods available in OpenMM for Python developers.
+
+OpenMM consists of two parts. First, there is a set of :ref:`libraries <library>` for performing many types of computations needed for molecular simulations: force evaluation, numerical integration, energy minimization, etc.
+
+Second, there is an :ref:`application layer <app>`, a set of Python libraries providing a high level interface for running simulations. This layer is targeted at computational biologists or other people who want to run simulations, and who may or may not be programmers.
+
+See the user guide for more details.
+
+
 .. toctree::
    :maxdepth: 2
 

docs-source/python-api/library.rst.jinja2

-Library API
-===========
+.. _library :
+
+Library Layer
+=============
 
 
 Core Objects

docs-source/python-api/render.py

@@ -8,9 +8,11 @@ from glob import glob
 import inspect
 
 import jinja2
-import simtk.openmm.openmm
+import simtk.openmm
 import simtk.openmm.app
 
+
+
 def fullname(klass):
     return klass.__module__ + '.' + klass.__name__
 
@@ -32,16 +34,17 @@ def library_template_variables():
         'library_extras': [],
     }
 
-    mm_klasses = inspect.getmembers(simtk.openmm.openmm, predicate=inspect.isclass)
+    mm_klasses = inspect.getmembers(simtk.openmm, predicate=inspect.isclass)
+
 
     # gather all Force subclasses
     for name, klass in mm_klasses:
-        if issubclass(klass, mm.Force):
+        if issubclass(klass, simtk.openmm.openmm.Force):
             data['forces'].append(fullname(klass))
 
     # gather all Integrator subclasses
     for _, klass in mm_klasses:
-        if issubclass(klass, mm.Integrator):
+        if issubclass(klass, simtk.openmm.openmm.Integrator):
             data['integrators'].append(fullname(klass))
 
     # gather all extra subclasses in simtk.openmm.openmm
@@ -81,7 +84,6 @@ def app_template_variables():
         'fileclasses': [],
         'app_extras': [],
     }
-
     app_klasses = inspect.getmembers(simtk.openmm.app, predicate=inspect.isclass)
 
     # gather all Reporters