Undid some debug info.

platforms/reference/src/ReferenceKernels.cpp

@@ -1004,6 +1004,7 @@ void ReferenceCalcCustomNonbondedForceKernel::initialize(const System& system, c
     
     for (int i = 0; i < force.getNumInteractionGroups(); i++) {
         set<int> set1, set2;
+	printf("initializing interaction group %d\n", i); // DEBUG
         force.getInteractionGroupParameters(i, set1, set2);
         interactionGroups.push_back(make_pair(set1, set2));
     }

platforms/reference/src/SimTKReference/ReferenceCustomNonbondedIxn.cpp

@@ -177,7 +177,6 @@ void ReferenceCustomNonbondedIxn::calculatePairIxn( int numberOfAtoms, vector<Re
     }
     if (interactionGroups.size() > 0) {
         // The user has specified interaction groups, so compute only the requested interactions.
-        
         for (int group = 0; group < (int) interactionGroups.size(); group++) {
             const set<int>& set1 = interactionGroups[group].first;
             const set<int>& set2 = interactionGroups[group].second;

wrappers/python/src/swig_doxygen/doxygen/Doxyfile

@@ -517,7 +517,7 @@ QUIET                  = NO
 # generated by doxygen. Possible values are YES and NO. If left blank 
 # NO is used.
 
-WARNINGS               = YES
+WARNINGS               = NO
 
 # If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings 
 # for undocumented members. If EXTRACT_ALL is set to YES then this flag will 
@@ -530,7 +530,7 @@ WARN_IF_UNDOCUMENTED   = NO
 # parameters in a documented function, or documenting parameters that 
 # don't exist or using markup commands wrongly.
 
-WARN_IF_DOC_ERROR      = YES
+WARN_IF_DOC_ERROR      = NO
 
 # This WARN_NO_PARAMDOC option can be abled to get warnings for 
 # functions that are documented, but have no documentation for their parameters 
@@ -564,8 +564,14 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories 
 # with spaces.
 
-INPUT                  = "$(OPENMM_INCLUDE_PATH)/OpenMM.h" \
-                         "$(OPENMM_INCLUDE_PATH)/openmm"
+INPUT                  = "/Users/choderaj/code/openmm/openmm.jchodera/openmmapi" \
+                         "/Users/choderaj/code/openmm/openmm.jchodera/olla/include/openmm/Platform.h" \
+                         "/Users/choderaj/code/openmm/openmm.jchodera/serialization/include/openmm/serialization/SerializationNode.h" \
+                         "/Users/choderaj/code/openmm/openmm.jchodera/serialization/include/openmm/serialization/SerializationProxy.h" \
+                         "/Users/choderaj/code/openmm/openmm.jchodera/serialization/include/openmm/serialization/XmlSerializer.h" \
+                         "/Users/choderaj/code/openmm/openmm.jchodera/plugins/amoeba/openmmapi" \
+                         "/Users/choderaj/code/openmm/openmm.jchodera/plugins/rpmd/openmmapi" \
+                         "/Users/choderaj/code/openmm/openmm.jchodera/plugins/drude/openmmapi"
 
 # This tag can be used to specify the character encoding of the source files 
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is 
@@ -594,7 +600,7 @@ RECURSIVE              = YES
 # excluded from the INPUT source files. This way you can easily exclude a 
 # subdirectory from a directory tree whose root is specified with the INPUT tag.
 
-EXCLUDE                = 
+EXCLUDE                = *Impl.h
 
 # The EXCLUDE_SYMLINKS tag can be used select whether or not files or 
 # directories that are symbolic links (a Unix filesystem feature) are excluded 
@@ -608,11 +614,15 @@ EXCLUDE_SYMLINKS       = NO
 # against the file with absolute path, so to exclude all test directories 
 # for example use the pattern */test/*
 
-#EXCLUDE_PATTERNS       = */tests/* \
-#                         */src/* \
-#                         */.svn/*
 EXCLUDE_PATTERNS       = */tests/* \
-                         */.svn/*
+                         */openmmapi/src/* \
+                         */internal/* \
+                         */.svn/* \
+                         *amoebaKernels.h \
+                         *DrudeKernels.h \
+                         *RpmdKernels.h \
+                         *OpenMMFortranModule.f90 \
+                         *OpenMMCWrapper.h
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names 
 # (namespaces, classes, functions, etc.) that should be excluded from the