Merge pull request #1524 from peastman/unitdocs

Added units classes to Python API docs

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

@@ -21,6 +21,9 @@ Representation and Manipulation
     :template: class.rst
 
     ~simtk.openmm.app.topology.Topology
+    ~simtk.openmm.app.topology.Chain
+    ~simtk.openmm.app.topology.Residue
+    ~simtk.openmm.app.topology.Atom
     ~simtk.openmm.app.modeller.Modeller
 
 Simulation
@@ -53,3 +56,14 @@ Extras
     {% for extra in app_extras %}
     ~{{ extra }}
     {% endfor %}
+
+Units
+~~~~~~
+.. autosummary::
+    :toctree: generated/
+    :template: class.rst
+    :nosignatures:
+
+    {% for unit in units %}
+    ~{{ unit }}
+    {% endfor %}

docs-source/api-python/render.py

@@ -32,6 +32,7 @@ def library_template_variables():
         'integrators': [],
         'forces': [],
         'library_extras': [],
+        'units': [],
     }
 
     mm_klasses = inspect.getmembers(simtk.openmm, predicate=inspect.isclass)
@@ -65,6 +66,11 @@ def library_template_variables():
         if full not in exclude and not klass.__name__[0].islower():
             data['library_extras'].append(full)
 
+    # gather units related classes
+    unit_klasses = inspect.getmembers(simtk.unit, predicate=inspect.isclass)
+    for name, klass in unit_klasses:
+        data['units'].append(fullname(klass))
+
     return data
 
 
@@ -93,11 +99,14 @@ def app_template_variables():
 
     # gather all classes with "File" in the name
     for name, klass in app_klasses:
-        if 'File' in name:
+        if 'File' in name or 'CharmmParameterSet' in name:
             data['fileclasses'].append(fullname(klass))
 
     # gather all extra subclasses in simtk.openmm.app
     exclude = ['simtk.openmm.app.topology.Topology',
+               'simtk.openmm.app.topology.Chain',
+               'simtk.openmm.app.topology.Residue',
+               'simtk.openmm.app.topology.Atom',
                'simtk.openmm.app.modeller.Modeller',
                'simtk.openmm.app.forcefield.ForceField',
                'simtk.openmm.app.simulation.Simulation']