Improvements to Doxygen generation

Doxyfile.in

@@ -61,7 +61,10 @@ ENABLED_SECTIONS       =
 MAX_INITIALIZER_LINES  = 30
 SHOW_USED_FILES        = YES
 SHOW_DIRECTORIES       = YES
-FILE_VERSION_FILTER    = 
+FILE_VERSION_FILTER    =
+SHOW_NAMESPACES        = NO
+SHOW_FILES             = NO
+SHOW_DIRECTORIES       = NO
 #---------------------------------------------------------------------------
 # configuration options related to warning and progress messages
 #---------------------------------------------------------------------------
@@ -83,10 +86,9 @@ EXCLUDE                =
 EXCLUDE_SYMLINKS       = NO
 EXCLUDE_PATTERNS       = */tests/* \
                          */src/* \
-                         */.svn/*
-EXCLUDE_SYMBOLS        = StandardMMForceField::*Info \
-                         GBSAOBCForceField::AtomInfo \
-                         System::ConstraintInfo
+                         */.svn/* \
+                         */olla/include/openmm/kernels.h
+EXCLUDE_SYMBOLS        = 
 EXAMPLE_PATH           = 
 EXAMPLE_PATTERNS       = 
 EXAMPLE_RECURSIVE      = NO
@@ -232,4 +234,4 @@ DOT_CLEANUP            = YES
 #---------------------------------------------------------------------------
 # Configuration::additions related to the search engine   
 #---------------------------------------------------------------------------
-SEARCHENGINE           = NO
+SEARCHENGINE           = YES

olla/include/openmm/Kernel.h

@@ -47,7 +47,7 @@ namespace OpenMM {
  * 
  * The Kernel class itself does not specify any details of what calculation is to be performed or the API
  * for calling it.  Instead, subclasses of KernelImpl will define APIs which are appropriate to particular
- * calculations.  To execute a Kernel, you therefore requests its implementation object and cast it to the
+ * calculations.  To execute a Kernel, you therefore request its implementation object and cast it to the
  * correct type:
  * 
  * <pre>

openmmapi/include/openmm/CustomBondForce.h

@@ -199,6 +199,10 @@ private:
     std::vector<BondInfo> bonds;
 };
 
+/**
+ * This is an internal class used to record information about a bond.
+ * @private
+ */
 class CustomBondForce::BondInfo {
 public:
     int particle1, particle2;
@@ -210,6 +214,10 @@ public:
     }
 };
 
+/**
+ * This is an internal class used to record information about a per-bond parameter.
+ * @private
+ */
 class CustomBondForce::BondParameterInfo {
 public:
     std::string name;
@@ -219,6 +227,10 @@ public:
     }
 };
 
+/**
+ * This is an internal class used to record information about a global parameter.
+ * @private
+ */
 class CustomBondForce::GlobalParameterInfo {
 public:
     std::string name;

openmmapi/include/openmm/CustomExternalForce.h

@@ -199,6 +199,10 @@ private:
     std::vector<ParticleInfo> particles;
 };
 
+/**
+ * This is an internal class used to record information about a particle.
+ * @private
+ */
 class CustomExternalForce::ParticleInfo {
 public:
     int particle;
@@ -209,6 +213,10 @@ public:
     }
 };
 
+/**
+ * This is an internal class used to record information about a per-particle parameter.
+ * @private
+ */
 class CustomExternalForce::ParticleParameterInfo {
 public:
     std::string name;
@@ -218,6 +226,10 @@ public:
     }
 };
 
+/**
+ * This is an internal class used to record information about a global parameter.
+ * @private
+ */
 class CustomExternalForce::GlobalParameterInfo {
 public:
     std::string name;

openmmapi/include/openmm/CustomGBForce.h

@@ -506,6 +506,10 @@ private:
     std::vector<ComputationInfo> energyTerms;
 };
 
+/**
+ * This is an internal class used to record information about a particle.
+ * @private
+ */
 class CustomGBForce::ParticleInfo {
 public:
     std::vector<double> parameters;
@@ -515,6 +519,10 @@ public:
     }
 };
 
+/**
+ * This is an internal class used to record information about a per-particle parameter.
+ * @private
+ */
 class CustomGBForce::PerParticleParameterInfo {
 public:
     std::string name;
@@ -524,6 +532,10 @@ public:
     }
 };
 
+/**
+ * This is an internal class used to record information about a global parameter.
+ * @private
+ */
 class CustomGBForce::GlobalParameterInfo {
 public:
     std::string name;
@@ -534,6 +546,10 @@ public:
     }
 };
 
+/**
+ * This is an internal class used to record information about an exclusion.
+ * @private
+ */
 class CustomGBForce::ExclusionInfo {
 public:
     int particle1, particle2;
@@ -545,6 +561,10 @@ public:
     }
 };
 
+/**
+ * This is an internal class used to record information about a tabulated function.
+ * @private
+ */
 class CustomGBForce::FunctionInfo {
 public:
     std::string name;
@@ -558,6 +578,10 @@ public:
     }
 };
 
+/**
+ * This is an internal class used to record information about a computed value or energy term.
+ * @private
+ */
 class CustomGBForce::ComputationInfo {
 public:
     std::string name;

openmmapi/include/openmm/CustomNonbondedForce.h

@@ -328,6 +328,10 @@ private:
     std::vector<FunctionInfo> functions;
 };
 
+/**
+ * This is an internal class used to record information about a particle.
+ * @private
+ */
 class CustomNonbondedForce::ParticleInfo {
 public:
     std::vector<double> parameters;
@@ -337,6 +341,10 @@ public:
     }
 };
 
+/**
+ * This is an internal class used to record information about a per-particle parameter.
+ * @private
+ */
 class CustomNonbondedForce::PerParticleParameterInfo {
 public:
     std::string name;
@@ -346,6 +354,10 @@ public:
     }
 };
 
+/**
+ * This is an internal class used to record information about a global parameter.
+ * @private
+ */
 class CustomNonbondedForce::GlobalParameterInfo {
 public:
     std::string name;
@@ -356,6 +368,10 @@ public:
     }
 };
 
+/**
+ * This is an internal class used to record information about an exclusion.
+ * @private
+ */
 class CustomNonbondedForce::ExclusionInfo {
 public:
     int particle1, particle2;
@@ -367,6 +383,10 @@ public:
     }
 };
 
+/**
+ * This is an internal class used to record information about a tabulated function.
+ * @private
+ */
 class CustomNonbondedForce::FunctionInfo {
 public:
     std::string name;

openmmapi/include/openmm/GBSAOBCForce.h

@@ -158,6 +158,10 @@ private:
     std::vector<ParticleInfo> particles;
 };
 
+/**
+ * This is an internal class used to record information about a particle.
+ * @private
+ */
 class GBSAOBCForce::ParticleInfo {
 public:
     double charge, radius, scalingFactor;

openmmapi/include/openmm/GBVIForce.h

@@ -191,24 +191,14 @@ private:
     NonbondedMethod nonbondedMethod;
     double cutoffDistance, solventDielectric, soluteDielectric;
     class BondInfo;
-
-// Retarded visual studio compiler complains about being unable to 
-// export private stl class members.
-// This stanza explains that it should temporarily shut up.
-#if defined(_MSC_VER)
-#pragma warning(push)
-#pragma warning(disable:4251)
-#endif
-
     std::vector<ParticleInfo> particles;
     std::vector<BondInfo> bonds;
-
-#if defined(_MSC_VER)
-#pragma warning(pop)
-#endif
-
 };
 
+/**
+ * This is an internal class used to record information about a particle.
+ * @private
+ */
 class GBVIForce::ParticleInfo {
 public:
     double charge, radius, gamma;
@@ -220,6 +210,10 @@ public:
     }
 };
 
+/**
+ * This is an internal class used to record information about a bond.
+ * @private
+ */
 class GBVIForce::BondInfo {
 public:
     int particle1, particle2;

openmmapi/include/openmm/HarmonicAngleForce.h

@@ -95,21 +95,13 @@ protected:
     ForceImpl* createImpl();
 private:
     class AngleInfo;
-
-// Retarded visual studio compiler complains about being unable to 
-// export private stl class members.
-// This stanza explains that it should temporarily shut up.
-#if defined(_MSC_VER)
-#pragma warning(push)
-#pragma warning(disable:4251)
-#endif
     std::vector<AngleInfo> angles;
-#if defined(_MSC_VER)
-#pragma warning(pop)
-#endif
-
 };
 
+/**
+ * This is an internal class used to record information about an angle.
+ * @private
+ */
 class HarmonicAngleForce::AngleInfo {
 public:
     int particle1, particle2, particle3;

openmmapi/include/openmm/HarmonicBondForce.h

@@ -92,21 +92,13 @@ protected:
     ForceImpl* createImpl();
 private:
     class BondInfo;
-
-// Retarded visual studio compiler complains about being unable to 
-// export private stl class members.
-// This stanza explains that it should temporarily shut up.
-#if defined(_MSC_VER)
-#pragma warning(push)
-#pragma warning(disable:4251)
-#endif
     std::vector<BondInfo> bonds;
-#if defined(_MSC_VER)
-#pragma warning(pop)
-#endif
-
 };
 
+/**
+ * This is an internal class used to record information about a bond.
+ * @private
+ */
 class HarmonicBondForce::BondInfo {
 public:
     int particle1, particle2;

openmmapi/include/openmm/NonbondedForce.h

@@ -254,6 +254,10 @@ private:
     std::map<std::pair<int, int>, int> exceptionMap;
 };
 
+/**
+ * This is an internal class used to record information about a particle.
+ * @private
+ */
 class NonbondedForce::ParticleInfo {
 public:
     double charge, sigma, epsilon;
@@ -265,6 +269,10 @@ public:
     }
 };
 
+/**
+ * This is an internal class used to record information about an exception.
+ * @private
+ */
 class NonbondedForce::ExceptionInfo {
 public:
     int particle1, particle2;

openmmapi/include/openmm/PeriodicTorsionForce.h

@@ -101,21 +101,13 @@ protected:
     ForceImpl* createImpl();
 private:
     class PeriodicTorsionInfo;
-
-// Retarded visual studio compiler complains about being unable to 
-// export private stl class members.
-// This stanza explains that it should temporarily shut up.
-#if defined(_MSC_VER)
-#pragma warning(push)
-#pragma warning(disable:4251)
-#endif
     std::vector<PeriodicTorsionInfo> periodicTorsions;
-#if defined(_MSC_VER)
-#pragma warning(pop)
-#endif
-
 };
 
+/**
+ * This is an internal class used to record information about a torsion.
+ * @private
+ */
 class PeriodicTorsionForce::PeriodicTorsionInfo {
 public:
     int particle1, particle2, particle3, particle4, periodicity;

openmmapi/include/openmm/RBTorsionForce.h

@@ -110,21 +110,13 @@ protected:
     ForceImpl* createImpl();
 private:
     class RBTorsionInfo;
-
-// Retarded visual studio compiler complains about being unable to 
-// export private stl class members.
-// This stanza explains that it should temporarily shut up.
-#if defined(_MSC_VER)
-#pragma warning(push)
-#pragma warning(disable:4251)
-#endif
     std::vector<RBTorsionInfo> rbTorsions;
-#if defined(_MSC_VER)
-#pragma warning(pop)
-#endif
-
 };
 
+/**
+ * This is an internal class used to record information about a torsion.
+ * @private
+ */
 class RBTorsionForce::RBTorsionInfo {
 public:
     int particle1, particle2, particle3, particle4;

openmmapi/include/openmm/System.h

@@ -196,6 +196,10 @@ private:
     std::vector<Force*> forces;
 };
 
+/**
+ * This is an internal class used to record information about a constraint.
+ * @private
+ */
 class System::ConstraintInfo {
 public:
     int particle1, particle2;