Support copy() and deepcopy() for TabulatedFunctions

openmmapi/include/openmm/TabulatedFunction.h

@@ -59,6 +59,9 @@ class OPENMM_EXPORT TabulatedFunction {
 public:
     virtual ~TabulatedFunction() {
     }
+    /**
+     * @deprecated This will be removed in a future release.
+     */
     virtual TabulatedFunction* Copy() const = 0;
 };
 
@@ -99,6 +102,8 @@ public:
     void setFunctionParameters(const std::vector<double>& values, double min, double max);
     /**
      * Create a deep copy of the tabulated function.
+     * 
+     * @deprecated This will be removed in a future release.
      */
     Continuous1DFunction* Copy() const;
 private:
@@ -158,6 +163,8 @@ public:
     void setFunctionParameters(int xsize, int ysize, const std::vector<double>& values, double xmin, double xmax, double ymin, double ymax);
     /**
      * Create a deep copy of the tabulated function
+     * 
+     * @deprecated This will be removed in a future release.
      */
     Continuous2DFunction* Copy() const;
 private:
@@ -233,6 +240,8 @@ public:
     void setFunctionParameters(int xsize, int ysize, int zsize, const std::vector<double>& values, double xmin, double xmax, double ymin, double ymax, double zmin, double zmax);
     /**
      * Create a deep copy of the tabulated function
+     * 
+     * @deprecated This will be removed in a future release.
      */
     Continuous3DFunction* Copy() const;
 private:
@@ -268,6 +277,8 @@ public:
     void setFunctionParameters(const std::vector<double>& values);
     /**
      * Create a deep copy of the tabulated function
+     * 
+     * @deprecated This will be removed in a future release.
      */
     Discrete1DFunction* Copy() const;
 private:
@@ -310,6 +321,8 @@ public:
     void setFunctionParameters(int xsize, int ysize, const std::vector<double>& values);
     /**
      * Create a deep copy of the tabulated function
+     * 
+     * @deprecated This will be removed in a future release.
      */
     Discrete2DFunction* Copy() const;
 private:
@@ -356,6 +369,8 @@ public:
     void setFunctionParameters(int xsize, int ysize, int zsize, const std::vector<double>& values);
     /**
      * Create a deep copy of the tabulated function
+     * 
+     * @deprecated This will be removed in a future release.
      */
     Discrete3DFunction* Copy() const;
 private:

wrappers/python/src/swig_doxygen/swigInputBuilder.py

@@ -242,6 +242,7 @@ class SwigInputBuilder:
         self.fOut.write("\n/* Declare factories */\n\n")
         forceSubclassList = []
         integratorSubclassList = []
+        tabulatedFunctionSubclassList = []
         for classNode in findNodes(self.doc.getroot(), "compounddef", kind="class", prot="public"):
             className = getText("compoundname", classNode)
             shortClassName=stripOpenmmPrefix(className)
@@ -256,6 +257,8 @@ class SwigInputBuilder:
                         forceSubclassList.append(shortClassName)
                     elif baseName == 'OpenMM::Integrator':
                         integratorSubclassList.append(shortClassName)
+                    elif baseName == 'OpenMM::TabulatedFunction':
+                        tabulatedFunctionSubclassList.append(shortClassName)
 
         self.fOut.write("%factory(OpenMM::Force& OpenMM::System::getForce")
         for name in sorted(forceSubclassList):
@@ -292,6 +295,16 @@ class SwigInputBuilder:
             self.fOut.write(",\n         OpenMM::%s" % name)
         self.fOut.write(");\n\n")
 
+        self.fOut.write("%factory(OpenMM::TabulatedFunction* OpenMM::TabulatedFunction::__copy__")
+        for name in sorted(tabulatedFunctionSubclassList):
+            self.fOut.write(",\n         OpenMM::%s" % name)
+        self.fOut.write(");\n\n")
+
+        self.fOut.write("%factory(OpenMM::TabulatedFunction* OpenMM_XmlSerializer__deserializeTabulatedFunction")
+        for name in sorted(tabulatedFunctionSubclassList):
+            self.fOut.write(",\n         OpenMM::%s" % name)
+        self.fOut.write(");\n\n")
+
         self.fOut.write("%factory(OpenMM::VirtualSite& OpenMM::System::getVirtualSite, OpenMM::TwoParticleAverageSite, OpenMM::ThreeParticleAverageSite, OpenMM::OutOfPlaneSite, OpenMM::LocalCoordinatesSite);\n\n")
         self.fOut.write("\n")
 

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

@@ -363,6 +363,19 @@ Parameters:
       return OpenMM::XmlSerializer::deserialize<OpenMM::Integrator>(ss);
   }
 
+  static std::string _serializeTabulatedFunction(const OpenMM::TabulatedFunction* object) {
+      std::stringstream ss;
+      OpenMM::XmlSerializer::serialize<OpenMM::TabulatedFunction>(object, "TabulatedFunction", ss);
+      return ss.str();
+  }
+
+  %newobject _deserializeTabulatedFunction;
+  static OpenMM::TabulatedFunction* _deserializeTabulatedFunction(const char* inputString) {
+      std::stringstream ss;
+      ss << inputString;
+      return OpenMM::XmlSerializer::deserialize<OpenMM::TabulatedFunction>(ss);
+  }
+
   static std::string _serializeStateAsLists(
                                 const std::vector<Vec3>& pos,
                                 const std::vector<Vec3>& vel,
@@ -463,6 +476,8 @@ Parameters:
         return XmlSerializer._serializeIntegrator(object)
       elif isinstance(object, State):
         return XmlSerializer._serializeState(object)
+      elif isinstance(object, TabulatedFunction):
+        return XmlSerializer._serializeTabulatedFunction(object)
       raise ValueError("Unsupported object type")
 
     @staticmethod
@@ -481,6 +496,8 @@ Parameters:
         return XmlSerializer._deserializeIntegrator(inputString)
       if type == "State":
         return XmlSerializer._deserializeState(inputString)
+      if type == "TabulatedFunction":
+        return XmlSerializer._deserializeTabulatedFunction(inputString)
       raise ValueError("Unsupported object type")
   %}
 }
@@ -530,3 +547,22 @@ Parameters:
       return OpenMM::XmlSerializer::clone<OpenMM::Integrator>(*self);
   }
 }
+
+%extend OpenMM::TabulatedFunction {
+  %pythoncode %{
+    def __getstate__(self):
+        serializationString = XmlSerializer.serialize(self)
+        return serializationString
+
+    def __setstate__(self, serializationString):
+        system = XmlSerializer.deserialize(serializationString)
+        self.this = system.this
+
+    def __deepcopy__(self, memo):
+        return self.__copy__()
+  %}
+  %newobject __copy__;
+  OpenMM::TabulatedFunction* __copy__() {
+      return OpenMM::XmlSerializer::clone<OpenMM::TabulatedFunction>(*self);
+  }
+}