Merge branch 'master' of github.com:pandegroup/openmm into dpme

wrappers/python/simtk/openmm/app/gromacstopfile.py

@@ -772,7 +772,7 @@ class GromacsTopFile(object):
                                 if periodic is None:
                                     periodic = mm.PeriodicTorsionForce()
                                     sys.addForce(periodic)
-                                periodic.addTorsion(baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], baseAtomIndex+atoms[3], int(params[7]), float(params[5])*degToRad, k)
+                                periodic.addTorsion(baseAtomIndex+atoms[0], baseAtomIndex+atoms[1], baseAtomIndex+atoms[2], baseAtomIndex+atoms[3], int(float(params[7])), float(params[5])*degToRad, k)
                         elif dihedralType == '2':
                             # Harmonic torsion
                             k = float(params[6])

wrappers/python/simtk/openmm/app/modeller.py

@@ -186,8 +186,7 @@ class Modeller(object):
     def convertWater(self, model='tip3p'):
         """Convert all water molecules to a different water model.
 
-        @deprecated Use addExtraParticles() instead.  It performs the same
-        function but in a more general way.
+        @deprecated Use addExtraParticles() instead.  It performs the same function but in a more general way.
 
         Parameters
         ----------
@@ -871,7 +870,7 @@ class Modeller(object):
             # and causes hydrogens to spread out evenly.
 
             system = System()
-            nonbonded = CustomNonbondedForce('100/((r/0.1)^4+1)')
+            nonbonded = CustomNonbondedForce('100/(r/0.1)^4')
             nonbonded.setNonbondedMethod(CustomNonbondedForce.CutoffNonPeriodic);
             nonbonded.setCutoffDistance(1*nanometer)
             bonds = HarmonicBondForce()

wrappers/python/src/swig_doxygen/swigInputBuilder.py

@@ -74,6 +74,11 @@ def getNodeText(node):
             s = "%s%s\n\n" % (s, getNodeText(n))
         elif n.tag == "ref":
             s = "%s%s" % (s, getNodeText(n))
+        elif n.tag == "xrefsect":
+            title = n.find("xreftitle")
+            description = n.find("xrefdescription")
+            if title is not None and description is not None and getNodeText(title).lower() == "deprecated":
+                s = "%s\n@deprecated %s\n\n" % (s, getNodeText(description))
         else:
             if n.tag in docTags:
                 tag = docTags[n.tag]
@@ -242,6 +247,7 @@ 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 +262,8 @@ 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 +300,16 @@ 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

@@ -322,14 +322,14 @@ Parameters:
 }
 
 %extend OpenMM::XmlSerializer {
-  %feature(docstring, "This method exists only for backward compatibility. @deprecated Use serialize() instead.") serializeSystem;
+  %feature(docstring, "This method exists only for backward compatibility.\n@deprecated Use serialize() instead.") serializeSystem;
   static std::string serializeSystem(const OpenMM::System* object) {
       std::stringstream ss;
       OpenMM::XmlSerializer::serialize<OpenMM::System>(object, "System", ss);
       return ss.str();
   }
 
-  %feature(docstring, "This method exists only for backward compatibility. @deprecated Use deserialize() instead.") deserializeSystem;
+  %feature(docstring, "This method exists only for backward compatibility.\n@deprecated Use deserialize() instead.") deserializeSystem;
   %newobject deserializeSystem;
   static OpenMM::System* deserializeSystem(const char* inputString) {
       std::stringstream ss;
@@ -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);
+  }
+}