refactor: replace boost::shared_ptr with std::shared_ptr

Code/DataStructs/FPBReader.cpp

@@ -647,10 +647,10 @@ void FPBReader::destroy() {
   dp_impl = nullptr;
 };
 
-boost::shared_ptr<ExplicitBitVect> FPBReader::getFP(unsigned int idx) const {
+std::shared_ptr<ExplicitBitVect> FPBReader::getFP(unsigned int idx) const {
   PRECONDITION(df_init, "not initialized");
 
-  return boost::shared_ptr<ExplicitBitVect>(detail::extractFP(dp_impl, idx));
+  return std::shared_ptr<ExplicitBitVect>(detail::extractFP(dp_impl, idx));
 };
 boost::shared_array<boost::uint8_t> FPBReader::getBytes(
     unsigned int idx) const {

Code/DataStructs/FPBReader.h

@@ -26,7 +26,7 @@
 #include <DataStructs/ExplicitBitVect.h>
 
 #include <cstdint>
-#include <boost/shared_ptr.hpp>
+#include <memory>
 #include <boost/shared_array.hpp>
 
 namespace RDKit {
@@ -40,7 +40,7 @@ struct FPBReader_impl;
   \code
   FPBReader reader("foo.fpb");
   reader.init();
-  boost::shared_ptr<ExplicitBitVect> ebv = reader.getFP(95);
+  std::shared_ptr<ExplicitBitVect> ebv = reader.getFP(95);
   std::vector<std::pair<double, unsigned int> > nbrs =
       reader.getTanimotoNeighbors(*ebv.get(), 0.70);
   \endcode
@@ -124,14 +124,14 @@ class RDKIT_DATASTRUCTS_EXPORT FPBReader {
     df_init = false;
   }
   //! returns the requested fingerprint as an \c ExplicitBitVect
-  boost::shared_ptr<ExplicitBitVect> getFP(unsigned int idx) const;
+  std::shared_ptr<ExplicitBitVect> getFP(unsigned int idx) const;
   //! returns the requested fingerprint as an array of bytes
   boost::shared_array<std::uint8_t> getBytes(unsigned int idx) const;
 
   //! returns the id of the requested fingerprint
   std::string getId(unsigned int idx) const;
   //! returns the fingerprint and id of the requested fingerprint
-  std::pair<boost::shared_ptr<ExplicitBitVect>, std::string> operator[](
+  std::pair<std::shared_ptr<ExplicitBitVect>, std::string> operator[](
       unsigned int idx) const {
     return std::make_pair(getFP(idx), getId(idx));
   }

Code/DataStructs/MultiFPBReader.h

@@ -35,7 +35,7 @@ namespace RDKit {
   readers.append(&r2);
   MultiFPBReader fpbs(readers);
   fpbs.init();
-  boost::shared_ptr<ExplicitBitVect> ebv = fpbs.getReader(0)->getFP(95);
+  std::shared_ptr<ExplicitBitVect> ebv = fpbs.getReader(0)->getFP(95);
   std::vector<std::tuple<double,unsigned int, unsigned int> > nbrs =
       fpbs.getTanimotoNeighbors(*ebv.get(), 0.70);
   \endcode

Code/DataStructs/Wrap/SparseIntVect.cpp

@@ -133,7 +133,7 @@ struct sparseIntVec_wrapper {
   template <typename IndexType>
   static void wrapOne(const char *className) {
     python::class_<SparseIntVect<IndexType>,
-                   boost::shared_ptr<SparseIntVect<IndexType>>>(
+                   std::shared_ptr<SparseIntVect<IndexType>>>(
         className, sparseIntVectDoc.c_str(),
         python::init<IndexType>("Constructor"))
         .def(python::init<std::string>())

Code/DataStructs/Wrap/wrap_ExplicitBV.cpp

@@ -64,7 +64,7 @@ or by indexing (i.e. bv[i] = 1 or if bv[i]).\n\
 
 struct EBV_wrapper {
   static void wrap() {
-    python::class_<ExplicitBitVect, boost::shared_ptr<ExplicitBitVect>>(
+    python::class_<ExplicitBitVect, std::shared_ptr<ExplicitBitVect>>(
         "ExplicitBitVect", ebvClassDoc.c_str(), python::init<unsigned int>())
         .def(python::init<std::string>())
         .def(python::init<unsigned int, bool>(python::args("size", "bitsSet")))

Code/DataStructs/Wrap/wrap_FPB.cpp

@@ -104,7 +104,7 @@ double getTaniHelper(const FPBReader *self, unsigned int which,
   return self->getTanimoto(which, bv);
 }
 python::tuple getItemHelper(const FPBReader *self, unsigned int which) {
-  std::pair<boost::shared_ptr<ExplicitBitVect>, std::string> v = (*self)[which];
+  std::pair<std::shared_ptr<ExplicitBitVect>, std::string> v = (*self)[which];
   return python::make_tuple(v.first, v.second);
 }
 double getTverskyHelper(const FPBReader *self, unsigned int which,

Code/DataStructs/Wrap/wrap_SparseBV.cpp

@@ -59,7 +59,7 @@ or by indexing (i.e. bv[i] = 1 or if bv[i]).\n\
 \n";
 struct SBV_wrapper {
   static void wrap() {
-    python::class_<SparseBitVect, boost::shared_ptr<SparseBitVect>>(
+    python::class_<SparseBitVect, std::shared_ptr<SparseBitVect>>(
         "SparseBitVect", sbvClassDoc.c_str(), python::init<unsigned int>())
         .def(python::init<std::string>())
         .def("SetBit", (bool(SBV::*)(unsigned int)) & SBV::setBit,

Code/DataStructs/testFPB.cpp

@@ -39,7 +39,7 @@ void _basicsTest(FPBReader &fps) {
     std::string nm = fps.getId(0);
     // std::cerr << " nm: >" << nm << "<" << std::endl;
     TEST_ASSERT(nm == "ZINC00902219");
-    boost::shared_ptr<ExplicitBitVect> fp = fps.getFP(0);
+    std::shared_ptr<ExplicitBitVect> fp = fps.getFP(0);
     TEST_ASSERT(fp);
     TEST_ASSERT(fp->getNumBits() == 2048);
     TEST_ASSERT(fp->getNumOnBits() == 17);
@@ -50,8 +50,8 @@ void _basicsTest(FPBReader &fps) {
     }
   }
   {  // operator[] version
-    std::pair<boost::shared_ptr<ExplicitBitVect>, std::string> tpl = fps[0];
-    boost::shared_ptr<ExplicitBitVect> fp = tpl.first;
+    std::pair<std::shared_ptr<ExplicitBitVect>, std::string> tpl = fps[0];
+    std::shared_ptr<ExplicitBitVect> fp = tpl.first;
     TEST_ASSERT(fp);
     TEST_ASSERT(fp->getNumBits() == 2048);
     TEST_ASSERT(fp->getNumOnBits() == 17);
@@ -63,7 +63,7 @@ void _basicsTest(FPBReader &fps) {
     TEST_ASSERT(tpl.second == "ZINC00902219");
   }
   {  // test another fp
-    boost::shared_ptr<ExplicitBitVect> fp = fps.getFP(3);
+    std::shared_ptr<ExplicitBitVect> fp = fps.getFP(3);
     TEST_ASSERT(fp);
     TEST_ASSERT(fp->getNumBits() == 2048);
     TEST_ASSERT(fp->getNumOnBits() == 20);
@@ -220,7 +220,7 @@ void test4LazyFPBReaderBasics() {
     {  // get* version
       std::string nm = fps.getId(0);
       TEST_ASSERT(nm == "ZINC00902219");
-      boost::shared_ptr<ExplicitBitVect> fp = fps.getFP(0);
+      std::shared_ptr<ExplicitBitVect> fp = fps.getFP(0);
       TEST_ASSERT(fp);
       TEST_ASSERT(fp->getNumBits() == 2048);
       TEST_ASSERT(fp->getNumOnBits() == 17);
@@ -231,8 +231,8 @@ void test4LazyFPBReaderBasics() {
       }
     }
     {  // operator[] version
-      std::pair<boost::shared_ptr<ExplicitBitVect>, std::string> tpl = fps[0];
-      boost::shared_ptr<ExplicitBitVect> fp = tpl.first;
+      std::pair<std::shared_ptr<ExplicitBitVect>, std::string> tpl = fps[0];
+      std::shared_ptr<ExplicitBitVect> fp = tpl.first;
       TEST_ASSERT(fp);
       TEST_ASSERT(fp->getNumBits() == 2048);
       TEST_ASSERT(fp->getNumOnBits() == 17);
@@ -244,7 +244,7 @@ void test4LazyFPBReaderBasics() {
       TEST_ASSERT(tpl.second == "ZINC00902219");
     }
     {  // test another fp
-      boost::shared_ptr<ExplicitBitVect> fp = fps.getFP(3);
+      std::shared_ptr<ExplicitBitVect> fp = fps.getFP(3);
       TEST_ASSERT(fp);
       TEST_ASSERT(fp->getNumBits() == 2048);
       TEST_ASSERT(fp->getNumOnBits() == 20);
@@ -279,7 +279,7 @@ void test5LazyFPBReaderTanimoto() {
       TEST_ASSERT(feq(fps.getTanimoto(1, bytes), 0.3703));
     }
     {
-      boost::shared_ptr<ExplicitBitVect> ebv = fps.getFP(0);
+      std::shared_ptr<ExplicitBitVect> ebv = fps.getFP(0);
       TEST_ASSERT(ebv);
       TEST_ASSERT(feq(fps.getTanimoto(0, *ebv.get()), 1.0));
       TEST_ASSERT(feq(fps.getTanimoto(1, *ebv.get()), 0.3703));
@@ -339,7 +339,7 @@ void test6LazyFPBReaderTanimotoNeighbors() {
       TEST_ASSERT(nbrs[1].second == 89);
     }
     {  // ebv with a threshold
-      boost::shared_ptr<ExplicitBitVect> ebv = fps.getFP(95);
+      std::shared_ptr<ExplicitBitVect> ebv = fps.getFP(95);
       TEST_ASSERT(ebv);
       std::vector<std::pair<double, unsigned int>> nbrs =
           fps.getTanimotoNeighbors(*ebv.get(), 0.30);
@@ -454,7 +454,7 @@ void test8FPBReaderContains() {
       TEST_ASSERT(nbrs[3] == 88);
     }
     {
-      boost::shared_ptr<ExplicitBitVect> ebv = fps.getFP(87);
+      std::shared_ptr<ExplicitBitVect> ebv = fps.getFP(87);
       TEST_ASSERT(ebv);
       std::vector<unsigned int> nbrs = fps.getContainingNeighbors(*ebv.get());
       TEST_ASSERT(nbrs.size() == 4);

Code/Demos/boost/smartPtrsAndIters/module.cpp

@@ -6,7 +6,7 @@
 #include <boost/python.hpp>
 #include <boost/python/suite/indexing/vector_indexing_suite.hpp>
 #include <boost/python/detail/api_placeholder.hpp>
-#include <boost/shared_ptr.hpp>
+#include <memory>
 
 #include <vector>
 
@@ -20,7 +20,7 @@ class DemoKlass {
  private:
   int val_;
 };
-typedef boost::shared_ptr<DemoKlass> DemoKlassSPtr;
+typedef std::shared_ptr<DemoKlass> DemoKlassSPtr;
 typedef std::vector<DemoKlass *> DemoKlassPtrVect;
 typedef std::vector<DemoKlassSPtr> DemoKlassSPtrVect;
 

Code/DistGeom/BoundsMatrix.h

@@ -115,7 +115,7 @@ class RDKIT_DISTGEOMETRY_EXPORT BoundsMatrix
   }
 };
 
-typedef boost::shared_ptr<BoundsMatrix> BoundsMatPtr;
+typedef std::shared_ptr<BoundsMatrix> BoundsMatPtr;
 }  // namespace DistGeom
 
 #endif

Code/DistGeom/ChiralSet.h

@@ -51,7 +51,7 @@ class RDKIT_DISTGEOMETRY_EXPORT ChiralSet {
   inline double getLowerVolumeBound() const { return d_volumeLowerBound; }
 };
 
-typedef boost::shared_ptr<ChiralSet> ChiralSetPtr;
+typedef std::shared_ptr<ChiralSet> ChiralSetPtr;
 typedef std::vector<ChiralSetPtr> VECT_CHIRALSET;
 }  // namespace DistGeom
 

Code/ForceField/ForceField.h

@@ -41,7 +41,7 @@ computeDihedral(const RDGeom::Point3D *p1, const RDGeom::Point3D *p2,
 namespace ForceFields {
 class ForceFieldContrib;
 typedef std::vector<int> INT_VECT;
-typedef boost::shared_ptr<const ForceFieldContrib> ContribPtr;
+typedef std::shared_ptr<const ForceFieldContrib> ContribPtr;
 typedef std::vector<ContribPtr> ContribPtrVect;
 
 //-------------------------------------------------------

Code/ForceField/Wrap/PyForceField.h

@@ -14,7 +14,7 @@
 #include <ForceField/MMFF/Params.h>
 #include <GraphMol/Trajectory/Snapshot.h>
 #include <boost/python/tuple.hpp>
-#include <boost/shared_ptr.hpp>
+#include <memory>
 #include <vector>
 #include <algorithm>
 #include <Geometry/point.h>
@@ -36,7 +36,7 @@ class PyForceField {
   int addExtraPoint(double x, double y, double z, bool fixed = true) {
     PRECONDITION(this->field, "no force field");
     RDGeom::Point3D *pt = new RDGeom::Point3D(x, y, z);
-    this->extraPoints.push_back(boost::shared_ptr<RDGeom::Point3D>(pt));
+    this->extraPoints.push_back(std::shared_ptr<RDGeom::Point3D>(pt));
     unsigned int ptIdx = this->extraPoints.size() - 1;
     RDGeom::Point3D *ptr = this->extraPoints[ptIdx].get();
     this->field->positions().push_back(ptr);
@@ -79,8 +79,8 @@ class PyForceField {
   }
 
   // private:
-  std::vector<boost::shared_ptr<RDGeom::Point3D>> extraPoints;
-  boost::shared_ptr<ForceField> field;
+  std::vector<std::shared_ptr<RDGeom::Point3D>> extraPoints;
+  std::shared_ptr<ForceField> field;
 };
 
 class PyMMFFMolProperties {
@@ -153,7 +153,7 @@ class PyMMFFMolProperties {
   void setMMFFVerbosity(unsigned int verbosity) {
     mmffMolProperties->setMMFFVerbosity(verbosity);
   }
-  boost::shared_ptr<RDKit::MMFF::MMFFMolProperties> mmffMolProperties;
+  std::shared_ptr<RDKit::MMFF::MMFFMolProperties> mmffMolProperties;
 };
 PyObject *getUFFBondStretchParams(const RDKit::ROMol &mol,
                                   const unsigned int idx1,

Code/Geometry/point.h

@@ -406,7 +406,7 @@ class RDKIT_RDGEOMETRYLIB_EXPORT Point2D : public Point {
 
 class RDKIT_RDGEOMETRYLIB_EXPORT PointND : public Point {
  public:
-  typedef boost::shared_ptr<RDNumeric::Vector<double>> VECT_SH_PTR;
+  typedef std::shared_ptr<RDNumeric::Vector<double>> VECT_SH_PTR;
 
   PointND(unsigned int dim) {
     RDNumeric::Vector<double> *nvec = new RDNumeric::Vector<double>(dim, 0.0);

Code/GraphMol/Basement/FeatTrees/FeatTree.h

@@ -14,7 +14,7 @@
 
 #include <boost/graph/adjacency_list.hpp>
 #include <boost/property_map.hpp>
-#include <boost/shared_ptr.hpp>
+#include <memory>
 #include <set>
 
 namespace RDKit {
@@ -44,7 +44,7 @@ typedef boost::property<FeatTreeEdge_t, unsigned int> FeatTreeEdge;
 typedef boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS,
                               FeatTreeNode, FeatTreeEdge>
     FeatTreeGraph;
-typedef boost::shared_ptr<FeatTreeGraph> FeatTreeGraphSPtr;
+typedef std::shared_ptr<FeatTreeGraph> FeatTreeGraphSPtr;
 
 typedef boost::property_map<FeatTreeGraph, FeatTreeEdge_t>::type
     FeatTreeEdgePMap;

Code/GraphMol/ChemReactions/Enumerate/EnumerateBase.h

@@ -63,8 +63,8 @@ namespace RDKit {
 class RDKIT_CHEMREACTIONS_EXPORT EnumerateLibraryBase {
  protected:
   ChemicalReaction m_rxn;
-  boost::shared_ptr<EnumerationStrategyBase> m_enumerator;
-  boost::shared_ptr<EnumerationStrategyBase> m_initialEnumerator;
+  std::shared_ptr<EnumerationStrategyBase> m_enumerator;
+  std::shared_ptr<EnumerationStrategyBase> m_initialEnumerator;
 
  public:
   //! default constructor

Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp

@@ -60,7 +60,7 @@ std::string GetClass(const EnumerationStrategyBase *en) {
 
 namespace EnumerationStrategyPickler {
 
-void pickle(const boost::shared_ptr<EnumerationStrategyBase> &enumerator,
+void pickle(const std::shared_ptr<EnumerationStrategyBase> &enumerator,
             std::ostream &ss) {
 #ifdef RDK_USE_BOOST_SERIALIZATION
   boost::archive::text_oarchive ar(ss);
@@ -72,7 +72,7 @@ void pickle(const boost::shared_ptr<EnumerationStrategyBase> &enumerator,
 #endif
 }
 
-void pickle(const boost::shared_ptr<EnumerationStrategyBase> &enumerator,
+void pickle(const std::shared_ptr<EnumerationStrategyBase> &enumerator,
             std::string &s) {
 #ifdef RDK_USE_BOOST_SERIALIZATION
   std::stringstream ss;
@@ -85,8 +85,8 @@ void pickle(const boost::shared_ptr<EnumerationStrategyBase> &enumerator,
 #endif
 }
 
-boost::shared_ptr<EnumerationStrategyBase> fromPickle(std::istream &pickle) {
-  boost::shared_ptr<EnumerationStrategyBase> enumerator;
+std::shared_ptr<EnumerationStrategyBase> fromPickle(std::istream &pickle) {
+  std::shared_ptr<EnumerationStrategyBase> enumerator;
 #ifdef RDK_USE_BOOST_SERIALIZATION
   boost::archive::text_iarchive ar(pickle);
   ar &enumerator;
@@ -97,15 +97,14 @@ boost::shared_ptr<EnumerationStrategyBase> fromPickle(std::istream &pickle) {
 #endif
 }
 
-boost::shared_ptr<EnumerationStrategyBase> fromPickle(
-    const std::string &pickle) {
+std::shared_ptr<EnumerationStrategyBase> fromPickle(const std::string &pickle) {
 #ifdef RDK_USE_BOOST_SERIALIZATION
   std::stringstream ss(pickle);
   return fromPickle(ss);
 #else
   RDUNUSED_PARAM(pickle);
   PRECONDITION(0, "BOOST SERIALIZATION NOT INSTALLED");
-  return boost::shared_ptr<EnumerationStrategyBase>();
+  return std::shared_ptr<EnumerationStrategyBase>();
 #endif
 }
 }  // namespace EnumerationStrategyPickler

Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.h

@@ -39,21 +39,20 @@ namespace RDKit {
 namespace EnumerationStrategyPickler {
 //! pickles a EnumerationStrategy and adds the results to a stream \c ss
 RDKIT_CHEMREACTIONS_EXPORT void pickle(
-    const boost::shared_ptr<EnumerationStrategyBase> &enumerator,
+    const std::shared_ptr<EnumerationStrategyBase> &enumerator,
     std::ostream &ss);
 RDKIT_CHEMREACTIONS_EXPORT void pickle(
-    const boost::shared_ptr<EnumerationStrategyBase> &enumerator,
-    std::string &s);
+    const std::shared_ptr<EnumerationStrategyBase> &enumerator, std::string &s);
 
 //! constructs a EnumerationStrategy from a pickle stored in a string
 //!  Since an EnumerationStrategyBase is polymorphic, this must return
 //!  a shared pointer to the EnumerationStrategyBase
-RDKIT_CHEMREACTIONS_EXPORT boost::shared_ptr<EnumerationStrategyBase>
-fromPickle(std::istream &pickle);
+RDKIT_CHEMREACTIONS_EXPORT std::shared_ptr<EnumerationStrategyBase> fromPickle(
+    std::istream &pickle);
 
 //!  a pointer to the EnumerationStrategyBase
-RDKIT_CHEMREACTIONS_EXPORT boost::shared_ptr<EnumerationStrategyBase>
-fromPickle(const std::string &pickle);
+RDKIT_CHEMREACTIONS_EXPORT std::shared_ptr<EnumerationStrategyBase> fromPickle(
+    const std::string &pickle);
 }  // namespace EnumerationStrategyPickler
 }  // namespace RDKit