Merge pull request #2044 from e-kwsm/nullptr

Replace NULL with nullptr (C++11)

CMakeLists.txt

@@ -6,6 +6,8 @@ endif()
 project(openbabel)
 set(CMAKE_MODULE_PATH ${openbabel_SOURCE_DIR}/cmake/modules)
 
+set (CMAKE_CXX_STANDARD 11)
+
 if(COMMAND cmake_policy)
   cmake_policy(SET CMP0003 NEW)
   if(POLICY CMP0042)
@@ -15,16 +17,6 @@ endif()
 
 include (CheckCXXCompilerFlag)
 
-CHECK_CXX_COMPILER_FLAG("-std=c++11" COMPILER_SUPPORTS_CXX11)
-CHECK_CXX_COMPILER_FLAG("-std=c++0x" COMPILER_SUPPORTS_CXX0X)
-if(COMPILER_SUPPORTS_CXX11)
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-elseif(COMPILER_SUPPORTS_CXX0X)
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++0x")
-else()
-        message(STATUS "The compiler ${CMAKE_CXX_COMPILER} has no C++11 support. Multi-threaded applications may experience race conditions.")
-endif()
-
 #include (MacroEnsureVersion)
 
 # Version numbering - should be bumped for each release

include/openbabel/atom.h

@@ -165,7 +165,7 @@ namespace OpenBabel
       //! Mark an atom as belonging to at least one ring
       void SetInRing(bool value=true)         { SET_OR_UNSET_FLAG(OB_RING_ATOM); }
       //! Clear the internal coordinate pointer
-      void ClearCoordPtr()     { _c = NULL; _cidx=0; }
+      void ClearCoordPtr()     { _c = nullptr; _cidx=0; }
       //@}
 
       //! \name Methods to retrieve atomic information
@@ -241,7 +241,7 @@ namespace OpenBabel
       //! (e.g., only vector3), NULL will be returned.
       double     *GetCoordinate(){
         if (_c)          return(&(*_c)[_cidx]);
-        else             return NULL;
+        else             return nullptr;
       }
       //! \return the coordinates as a vector3 object
       vector3   &GetVector();
@@ -310,7 +310,7 @@ namespace OpenBabel
       void DeleteResidue(){
         if (_residue) {
           delete _residue;
-          _residue = NULL; // Make sure to clear that a residue existed
+          _residue = nullptr; // Make sure to clear that a residue existed
         }
       }
       //! Add a bond to the internal list. Does not update the bond.
@@ -363,11 +363,11 @@ namespace OpenBabel
        */
       std::pair<int, int> LewisAcidBaseCounts() const;
       //! \return Is there any residue information?
-      bool HasResidue()    { return(_residue != NULL);    }
+      bool HasResidue()    { return(_residue != nullptr);    }
       //! \return Is this a HETATM in a residue (returns false if not in a residue)
       //! \since version 2.4
       bool IsHetAtom() {
-        if (_residue == NULL)
+        if (_residue == nullptr)
           return false;
         else
           return _residue->IsHetAtom(this);

include/openbabel/base.h

@@ -207,7 +207,7 @@ class OBConversion; //used only as pointer
 
        A derived class may return NULL if copying is inappropriate */
     virtual OBGenericData* Clone(OBBase* /*parent*/) const
-    { return NULL; }
+    { return nullptr; }
     virtual ~OBGenericData()    {}
     //Use default copy constructor and assignment operators
     //OBGenericData& operator=(const OBGenericData &src);

include/openbabel/data.h

@@ -57,7 +57,7 @@ namespace OpenBabel
 
     public:
       //! Constructor
-      OBGlobalDataBase(): _init(false), _dataptr(NULL) { }
+      OBGlobalDataBase(): _init(false), _dataptr(nullptr) { }
       //! Destructor
       virtual ~OBGlobalDataBase()                  {}
       //! Read in the data file, falling back as needed

include/openbabel/descriptor.h

@@ -39,22 +39,22 @@ class OBAPI OBDescriptor : public OBPlugin
   const char* TypeID(){return "descriptors";};
 
   /// \return the value of a numeric descriptor
-  virtual double Predict(OBBase* /* pOb */, std::string* /* param */ =NULL)
+  virtual double Predict(OBBase* /* pOb */, std::string* /* param */ =nullptr)
   {return std::numeric_limits<double>::quiet_NaN();}
 
   /// \return the value of the descriptor and adds it to the object's OBPairData
-  double PredictAndSave(OBBase* pOb, std::string* param=NULL);
+  double PredictAndSave(OBBase* pOb, std::string* param=nullptr);
 
   ///Provides a string value for non-numeric descriptors and returns NaN, or a string representation and returns a numeric value
-  virtual double GetStringValue(OBBase* pOb, std::string& svalue, std::string* param=NULL);
+  virtual double GetStringValue(OBBase* pOb, std::string& svalue, std::string* param=nullptr);
 
   ///Parses the filter stream for a relational expression and returns its result when applied to the chemical object
-  virtual bool Compare(OBBase* pOb, std::istream& ss, bool noEval, std::string* param=NULL);
+  virtual bool Compare(OBBase* pOb, std::istream& ss, bool noEval, std::string* param=nullptr);
 
   ///Write information on a plugin class to the string txt.
   ///If the parameter is a descriptor ID, displays the verbose description for that descriptor only
   /// e.g. babel -L descriptors HBA1
-  virtual bool Display(std::string& txt, const char* param, const char* ID=NULL);
+  virtual bool Display(std::string& txt, const char* param, const char* ID=nullptr);
 
   /// Comparison of the values of the descriptor. Used in sorting.
   /// Descriptors may use more complicated ordering than this default (e.g.InChIFilter)

include/openbabel/forcefield.h

@@ -246,7 +246,7 @@ const double GAS_CONSTANT = 8.31446261815324e-3 / KCAL_TO_KJ;  //!< kcal mol^-1
     //! Constructor
     OBFFConstraint()
       {
-        a = b = c = d = NULL;
+        a = b = c = d = nullptr;
         ia = ib = ic = id = 0;
         constraint_value = 0.0;
         factor = 0.0;
@@ -573,13 +573,13 @@ const double GAS_CONSTANT = 8.31446261815324e-3 / KCAL_TO_KJ;  //!< kcal mol^-1
     //! Destructor
     virtual ~OBForceField()
     {
-      if (_grad1 != NULL) {
+      if (_grad1 != nullptr) {
         delete [] _grad1;
-        _grad1 = NULL;
+        _grad1 = nullptr;
       }
-      if (_gradientPtr != NULL) {
+      if (_gradientPtr != nullptr) {
         delete [] _gradientPtr;
-	_gradientPtr = NULL;
+	_gradientPtr = nullptr;
       }
     }
 

include/openbabel/format.h

@@ -133,18 +133,18 @@ std::cerr << "Not a valid input format"; return false;}
     /// in the program.
     virtual OBFormat* MakeNewInstance()
       {
-        return NULL; //shows not implemented in the format class
+        return nullptr; //shows not implemented in the format class
       }
 
     //New functions since OBFormat is derived from OBPlugin
     //\brief Called from, and an alternative to, OBConversion::RegisterFormat();
-    int RegisterFormat(const char* ID, const char* MIME = NULL);
+    int RegisterFormat(const char* ID, const char* MIME = nullptr);
 
     ///\brief Provides a description in txt of the format specified by itr.
     ///If param starts with "in", "read", "out" or "write" only the
     ///appropriate formats are output. The others return false.
     ///If param contains "verbose", the whole description is output.
-    virtual bool Display(std::string& txt, const char* param, const char* ID=NULL);
+    virtual bool Display(std::string& txt, const char* param, const char* ID=nullptr);
 
     static OBFormat* FormatFromMIME(const char* MIME);
 

include/openbabel/generic.h

@@ -72,7 +72,7 @@ namespace OpenBabel
     OBAtom *_atom;
     OBBond *_bond;
   public:
-  OBExternalBond(): _idx(0), _atom(NULL), _bond(NULL) {}
+  OBExternalBond(): _idx(0), _atom(nullptr), _bond(nullptr) {}
     OBExternalBond(OBAtom *,OBBond *,int);
     OBExternalBond(const OBExternalBond &);
     ~OBExternalBond()   {}
@@ -95,7 +95,7 @@ namespace OpenBabel
     OBExternalBondData();
 
     //Copying is not used and too much work to set up
-    virtual OBGenericData* Clone(OBBase* /*parent*/) const{return NULL;}
+    virtual OBGenericData* Clone(OBBase* /*parent*/) const{return nullptr;}
 
     void SetData(OBAtom*,OBBond*,int);
     std::vector<OBExternalBond> *GetData()
@@ -182,7 +182,7 @@ namespace OpenBabel
         if ((*i)->GetAttribute() == s)
           return(*i);
 
-      return(NULL);
+      return(nullptr);
     }
 
     //! \return the OBGenericData associate with the attribute name parameter.
@@ -194,7 +194,7 @@ namespace OpenBabel
         if ((*i)->GetAttribute() == s)
           return(*i);
 
-      return(NULL);
+      return(nullptr);
     }
 
     //! Gets the entire set.
@@ -264,7 +264,7 @@ namespace OpenBabel
     // exist due to Kekulize() in EndModify() in operator= in OBMol. Having
     // more than one RingData causes problems as one of them can become invalid
     // and cause segfaults.
-    virtual OBGenericData* Clone(OBBase* /*parent*/) const{return NULL;}
+    virtual OBGenericData* Clone(OBBase* /*parent*/) const{return nullptr;}
     ~OBRingData();
 
     OBRingData &operator=(const OBRingData &);
@@ -607,7 +607,7 @@ namespace OpenBabel
     //! double is angle in radians
     std::vector<triple<OBAtom*,OBAtom*,double> > _ads;
 
-    OBTorsion(): _bc((OBAtom *)NULL, (OBAtom *)NULL)      {      }
+    OBTorsion(): _bc((OBAtom *)nullptr, (OBAtom *)nullptr)      {      }
     //protected for use only by friend classes
     OBTorsion(OBAtom *, OBAtom *, OBAtom *, OBAtom *);
 
@@ -720,7 +720,7 @@ namespace OpenBabel
     OBAngle(const OBAngle &);
     ~OBAngle()
       {
-        _vertex = NULL;
+        _vertex = nullptr;
       }
 
     OBAngle &operator = (const OBAngle &);
@@ -1140,13 +1140,13 @@ namespace OpenBabel
     OBFreeGridPoint *BeginPoint(OBFreeGridPointIterator &i)
     {
       i = _points.begin();
-      return((i == _points.end()) ? (OBFreeGridPoint*)NULL : (OBFreeGridPoint*)*i);
+      return((i == _points.end()) ? (OBFreeGridPoint*)nullptr : (OBFreeGridPoint*)*i);
     }
 
     OBFreeGridPoint *NextPoint(OBFreeGridPointIterator &i)
     {
       ++i;
-      return((i == _points.end()) ? (OBFreeGridPoint*)NULL : (OBFreeGridPoint*)*i);
+      return((i == _points.end()) ? (OBFreeGridPoint*)nullptr : (OBFreeGridPoint*)*i);
     }
 
     void Clear();

include/openbabel/graphsym.h

@@ -47,7 +47,7 @@ namespace OpenBabel {
 
     public:
       //! Constructor
-      OBGraphSym(OBMol* pmol, const OBBitVec* frag_atoms = NULL);
+      OBGraphSym(OBMol* pmol, const OBBitVec* frag_atoms = nullptr);
       //! Destructor
       virtual ~OBGraphSym();
 

include/openbabel/grid.h

@@ -112,7 +112,7 @@ namespace OpenBabel
 
   public:
 
-    OBFloatGrid() : _ival(NULL), _halfSpace(0.0) {}
+    OBFloatGrid() : _ival(nullptr), _halfSpace(0.0) {}
     ~OBFloatGrid()
     {
       if (_ival) delete [] _ival;

include/openbabel/groupcontrib.h

@@ -62,7 +62,7 @@ class OBDESC OBGroupContrib : public OBDescriptor
   }
 
 
-  virtual double Predict(OBBase* pOb, std::string* param=NULL);
+  virtual double Predict(OBBase* pOb, std::string* param=nullptr);
 
  private:
   bool ParseFile();

include/openbabel/internalcoord.h

@@ -70,7 +70,7 @@ namespace OpenBabel
     double  _tor; //!< Torsional/dihedral angle between this, _a, _b, and _c
 
     //! Constructor
-  OBInternalCoord(OBAtom *a= NULL, OBAtom *b= NULL, OBAtom *c= NULL,
+  OBInternalCoord(OBAtom *a= nullptr, OBAtom *b= nullptr, OBAtom *c= nullptr,
                   double dst = 0.0, double ang = 0.0, double tor = 0.0) :
     _a(a), _b(b), _c(c), _dst(dst), _ang(ang), _tor(tor)
       {}

include/openbabel/lineend.h

@@ -60,7 +60,7 @@ namespace OpenBabel
   {
   public:
     FilteringInputStreambuf(
-      std::istream*        source = NULL) ;
+      std::istream*        source = nullptr) ;
     virtual                 ~FilteringInputStreambuf()
     {
       //sync(); comment out so can be deleted in OBConversion destructor
@@ -131,7 +131,7 @@ namespace OpenBabel
     int result( EOF ) ;
     if( gptr() < egptr() )
       result = *gptr() ;
-    else if ( mySource != NULL )
+    else if ( mySource != nullptr )
     {
       result = myExtractor( *mySource ) ;
       if ( result != EOF )
@@ -151,7 +151,7 @@ namespace OpenBabel
   FilteringInputStreambuf< Extractor >::sync()
   {
     int result( 0 ) ;
-    if ( mySource != NULL )
+    if ( mySource != nullptr )
     {
       if ( gptr() < egptr() )
       { //have read something but not provided it

include/openbabel/mol.h

@@ -480,10 +480,10 @@ enum HydrogenType { AllHydrogen, PolarHydrogen, NonPolarHydrogen };
     //! Iterative component of Separate to copy one fragment at a time
     bool GetNextFragment( OpenBabel::OBMolAtomDFSIter& iter, OBMol& newMol );
     // docs in mol.cpp
-    bool CopySubstructure(OBMol& newmol, OBBitVec *includeatoms, OBBitVec *excludebonds = (OBBitVec*)0,
+    bool CopySubstructure(OBMol& newmol, OBBitVec *includeatoms, OBBitVec *excludebonds = (OBBitVec*)nullptr,
       unsigned int correctvalence=1,
-      std::vector<unsigned int> *atomorder=(std::vector<unsigned int>*)0,
-      std::vector<unsigned int> *bondorder=(std::vector<unsigned int>*)0);
+      std::vector<unsigned int> *atomorder=(std::vector<unsigned int>*)nullptr,
+      std::vector<unsigned int> *bondorder=(std::vector<unsigned int>*)nullptr);
     //! Converts the charged form of coordinate bonds, e.g.[N+]([O-])=O to N(=O)=O
     bool ConvertDativeBonds();
     //! Converts 5-valent N and P only. Return true if conversion occurred.
@@ -630,12 +630,12 @@ enum HydrogenType { AllHydrogen, PolarHydrogen, NonPolarHydrogen };
     //! \return the array of coordinates for the first conformer
     double  *BeginConformer(std::vector<double*>::iterator&i)
     { i = _vconf.begin();
-      return((i == _vconf.end()) ? NULL:*i); }
+      return((i == _vconf.end()) ? nullptr:*i); }
     //! Advance the iterator to the next confomer, if possible
     //! \return The array of coordinates for the next conformer, or NULL if none exist
     double  *NextConformer(std::vector<double*>::iterator&i)
     { ++i;
-      return((i == _vconf.end()) ? NULL:*i); }
+      return((i == _vconf.end()) ? nullptr:*i); }
     //! \return the entire set of conformers for this molecule as a vector of floating point arrays
     std::vector<double*> &GetConformers() {   return(_vconf);     }
     //@}
@@ -672,30 +672,30 @@ enum HydrogenType { AllHydrogen, PolarHydrogen, NonPolarHydrogen };
     OBResidue *BeginResidue(OBResidueIterator &i)
     {
       i = _residue.begin();
-      return((i == _residue.end()) ? NULL:*i);
+      return((i == _residue.end()) ? nullptr:*i);
     }
     //! Advance the iterator @p i to the next residue in the molecule
     //! \return the next residue (if any, or NULL if not possible)
     OBResidue *NextResidue(OBResidueIterator &i)
     {
       ++i;
-      return((i == _residue.end()) ? NULL:*i);
+      return((i == _residue.end()) ? nullptr:*i);
     }
     //! Set the iterator to the beginning of the internal coordinate list
     //! \return the first internal coordinate record, or NULL if none exist
     //! \see SetInternalCoord
     OBInternalCoord *BeginInternalCoord(std::vector<OBInternalCoord*>::iterator &i)
     {
       i = _internals.begin();
-      return((i == _internals.end()) ? NULL:*i);
+      return((i == _internals.end()) ? nullptr:*i);
     }
     //! Advance the iterator to the next internal coordinate record
     //! \return the next first internal coordinate record, or NULL if none exist
     //! \see SetInternalCoord
     OBInternalCoord *NextInternalCoord(std::vector<OBInternalCoord*>::iterator &i)
     {
       ++i;
-      return((i == _internals.end()) ? NULL:*i);
+      return((i == _internals.end()) ? nullptr:*i);
     }
     //@}