Merge branch 'master' of https://github.com/SimTk/openmm

wrappers/python/src/swig_doxygen/OpenMM.i

@@ -64,6 +64,14 @@ using namespace OpenMM;
 
 %include OpenMM_headers.i
 
+%pythoncode %{
+  # when we import * from the python module, we only want to import the
+  # actual classes, and not the swigregistration methods, which have already
+  # been called, and are now unneeded by the user code, and only pollute the
+  # namespace
+  __all__ = [k for k in locals().keys() if not k.endswith('_swigregister')]
+%}
+
 /*
 %extend OpenMM::XmlSerializer {
     %template(XmlSerializer_serialize_AndersenThermostat) XmlSerializer::serialize<AndersenThermostat>;

wrappers/python/src/swig_doxygen/swig_lib/python/pythoncode.i

@@ -5,6 +5,7 @@ try:
 except:
     pass
 
+import sys
 import math
 RMIN_PER_SIGMA=math.pow(2, 1/6.0)
 RVDW_PER_SIGMA=math.pow(2, 1/6.0)/2.0
@@ -273,14 +274,15 @@ def stripUnits(args):
     """
     newArgList=[]
     for arg in args:
-        if unit.is_quantity(arg):
+        if 'numpy' in sys.modules and isinstance(arg, numpy.ndarray):
+           arg = arg.tolist()
+        elif unit.is_quantity(arg):
             # JDC: Ugly workaround for OpenMM using 'bar' for fundamental pressure unit.
             if arg.unit.is_compatible(unit.bar):
                 arg = arg / unit.bar
             else:
                 arg=arg.value_in_unit_system(unit.md_unit_system)                
             # JDC: End workaround.
-            #arg=arg.value_in_unit_system(unit.md_unit_system)
         elif isinstance(arg, dict):
             newKeys = stripUnits(arg.keys())
             newValues = stripUnits(arg.values())