fix several warnings originating from the swig wrappers (rdkit#7063)

yjmaxpayne · Jan 30, 2024 · 25b7dbf · 25b7dbf
1 parent 19aff7f
commit 25b7dbf
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Showing 10 changed files with 35 additions and 25 deletions.
diff --git a/Code/GraphMol/FilterCatalog/FilterMatcherBase.h b/Code/GraphMol/FilterCatalog/FilterMatcherBase.h
@@ -60,9 +60,6 @@ struct RDKIT_FILTERCATALOG_EXPORT FilterMatch {
               MatchVectType atomPairs)
       : filterMatch(std::move(filter)), atomPairs(std::move(atomPairs)) {}
 
-  FilterMatch(const FilterMatch &rhs)
-      : filterMatch(rhs.filterMatch), atomPairs(rhs.atomPairs) {}
-
   bool operator==(const FilterMatch &rhs) const {
     return (filterMatch.get() == rhs.filterMatch.get() &&
             atomPairs == rhs.atomPairs);

diff --git a/Code/JavaWrappers/Atom.i b/Code/JavaWrappers/Atom.i
@@ -73,7 +73,7 @@
     RDKit::markConjAtomBonds(($self));
   }
   int numBondsPlusLonePairs() {
-    RDKit::numBondsPlusLonePairs(($self));
+    return RDKit::numBondsPlusLonePairs(($self));
   }
   bool atomHasConjugatedBond() {
     return RDKit::MolOps::atomHasConjugatedBond(($self));

diff --git a/Code/JavaWrappers/Bond.i b/Code/JavaWrappers/Bond.i
@@ -60,7 +60,7 @@
   /* Methods from MolFileStereoChem.h */
   Bond::BondDir DetermineBondWedgeState(const std::map<int, std::unique_ptr<RDKit::Chirality::WedgeInfoBase>> &wedgeBonds,
                                         const RDKit::Conformer *conf) {
-    RDKit::DetermineBondWedgeState(($self), wedgeBonds, conf);
+    return RDKit::DetermineBondWedgeState(($self), wedgeBonds, conf);
   }
 
   /* Based on corresponding methods in Atom.i */

diff --git a/Code/JavaWrappers/FMCS.i b/Code/JavaWrappers/FMCS.i
@@ -58,6 +58,6 @@
 %{
 
   RDKit::MCSResult findMCS(const std::vector<RDKit::ROMOL_SPTR>& mols){
-    RDKit::findMCS(mols,static_cast<const RDKit::MCSParameters *>(NULL));
+    return RDKit::findMCS(mols,static_cast<const RDKit::MCSParameters *>(NULL));
   };
 %}
diff --git a/Code/JavaWrappers/FilterCatalog.i b/Code/JavaWrappers/FilterCatalog.i
@@ -108,7 +108,7 @@ typedef std::vector<std::string> STR_VECT;
     return new RDKit::FilterCatalog(str);
   }
 
-  bool canSerialize() const {
+  static bool canSerialize() {
     return RDKit::FilterCatalogCanSerialize();
   }
 
@@ -183,7 +183,9 @@ typedef std::vector<std::string> STR_VECT;
 #ifdef SWIGCSHARP
 %typemap(csbase) RDKit::FilterCatalogParams::FilterCatalogs "uint"
 #endif
-
+
+%immutable RDKit::DEFAULT_FILTERMATCHERBASE_NAME;
+
 %include <GraphMol/FilterCatalog/FilterMatcherBase.h>
 %include <GraphMol/FilterCatalog/FilterCatalogEntry.h>
 %include <GraphMol/FilterCatalog/FilterCatalog.h>

diff --git a/Code/JavaWrappers/ROMol.i b/Code/JavaWrappers/ROMol.i
@@ -652,7 +652,7 @@ void setAllowNontetrahedralChirality(bool);
     return RDKit::MolAlign::alignMol(*($self), refMol, prbCid, refCid, atomMap, weights, reflect, maxIters);
   }
 
-  void alignMolConformers(ROMol &mol, const std::vector<unsigned int> *atomIds=0,
+  void alignMolConformers(const std::vector<unsigned int> *atomIds=0,
                           const std::vector<unsigned int> *confIds=0,
                           const RDNumeric::DoubleVector  *weights=0,
                           bool reflect=false, unsigned int maxIters=50) {
@@ -711,13 +711,12 @@ void setAllowNontetrahedralChirality(bool);
     return std::make_pair(rmsd,score);
   }
 
-  void computeGasteigerCharges(const RDKit::ROMol *mol,int nIter=12,bool throwOnParamFailure=false){
-    RDKit::computeGasteigerCharges(*mol,nIter,throwOnParamFailure);
+  void computeGasteigerCharges(int nIter=12,bool throwOnParamFailure=false){
+    RDKit::computeGasteigerCharges(*($self),nIter,throwOnParamFailure);
   }
-  void computeGasteigerCharges(const RDKit::ROMol *mol,
-                               std::vector<double> &charges,
+  void computeGasteigerCharges(std::vector<double> &charges,
                                int nIter=12,bool throwOnParamFailure=false){
-    RDKit::computeGasteigerCharges(*mol,charges,nIter,throwOnParamFailure);
+    RDKit::computeGasteigerCharges(*($self),charges,nIter,throwOnParamFailure);
   }
 
   /* From new_canon.h*/

diff --git a/Code/JavaWrappers/SubstanceGroup.i b/Code/JavaWrappers/SubstanceGroup.i
@@ -74,13 +74,13 @@ unsigned int getSubstanceGroupCount(RDKit::ROMol &mol);
     auto &attachPoints = $self->getAttachPoints();
     return &(attachPoints[idx]);
   }
-  const getBracketCount() {
+  size_t getBracketCount() {
     return $self->getBrackets().size();
   }
-  const getCStateCount() {
+  size_t getCStateCount() {
     return $self->getCStates().size();
   }
-  const getAttachPointCount() {
+  size_t getAttachPointCount() {
     return $self->getAttachPoints().size();
   }
 }

diff --git a/Code/JavaWrappers/SubstructLibrary.i b/Code/JavaWrappers/SubstructLibrary.i
@@ -77,7 +77,7 @@ using RDKit::GeneralizedSubstruct::ExtendedQueryMol;
     return new RDKit::SubstructLibrary(str);
   }
 
-  bool canSerialize() const {
+  static bool canSerialize() {
     return RDKit::SubstructLibraryCanSerialize();
   }
 }

diff --git a/Code/JavaWrappers/csharp_wrapper/GraphMolCSharp.i b/Code/JavaWrappers/csharp_wrapper/GraphMolCSharp.i
@@ -103,19 +103,19 @@
       SWIG_CSharpSetPendingException(SWIG_CSharpApplicationException, err.c_str());
       return $null;
     }
-    catch (RDKit::SmilesParseException e) {
+    catch (RDKit::SmilesParseException &e) {
       std::string err="SmilesParseException: ";
       err+=e.what();
       SWIG_CSharpSetPendingException(SWIG_CSharpApplicationException, err.c_str());
       return $null;
     }
-    catch (KeyErrorException e) {
+    catch (KeyErrorException &e) {
       std::string err="KeyError: ";
       err+=e.key();
       SWIG_CSharpSetPendingException(SWIG_CSharpApplicationException, err.c_str());
       return $null;
     }
-    catch (std::exception e) {
+    catch (std::exception &e) {
       SWIG_CSharpSetPendingException(SWIG_CSharpApplicationException, "error");
       return $null;
     }
@@ -158,6 +158,7 @@ typedef unsigned long long int	uintmax_t;
 
 %shared_ptr(std::exception)
 %shared_ptr(RDKit::RDProps)
+%shared_ptr(RDKit::Conformer)
 %shared_ptr(RDKit::ROMol)
 %shared_ptr(RDKit::RWMol)
 %shared_ptr(RDKit::Atom)
@@ -317,15 +318,15 @@ typedef unsigned long long int	uintmax_t;
   double getElement(int i) {
     return (*($self))[i];
   }
-  double setElement(int i, double value) {
+  void setElement(int i, double value) {
     (*($self))[i] = value;
   }
 }
 %extend boost::shared_array<int> {
   int getElement(int i) {
     return (*($self))[i];
   }
-  int setElement(int i, int value) {
+  void setElement(int i, int value) {
     (*($self))[i] = value;
   }
 }
@@ -344,4 +345,9 @@ typedef unsigned long long int	uintmax_t;
 %{
 #include <RDGeneral/versions.h>
 %}
+
+%immutable RDKit::rdkitVersion;
+%immutable RDKit::boostVersion;
+%immutable RDKit::rdkitBuild;
+
 %include <RDGeneral/versions.h>
diff --git a/Code/JavaWrappers/gmwrapper/GraphMolJava.i b/Code/JavaWrappers/gmwrapper/GraphMolJava.i
@@ -101,6 +101,7 @@ typedef unsigned long long int	uintmax_t;
 
 %shared_ptr(std::exception)
 %shared_ptr(RDKit::RDProps)
+%shared_ptr(RDKit::Conformer)
 %shared_ptr(RDKit::ROMol)
 %shared_ptr(RDKit::RWMol)
 %shared_ptr(RDKit::Atom)
@@ -286,15 +287,15 @@ typedef unsigned long long int	uintmax_t;
   double getElement(int i) {
     return (*($self))[i];
   }
-  double setElement(int i, double value) {
+  void setElement(int i, double value) {
     (*($self))[i] = value;
   }
 }
 %extend boost::shared_array<int> {
   int getElement(int i) {
     return (*($self))[i];
   }
-  int setElement(int i, int value) {
+  void setElement(int i, int value) {
     (*($self))[i] = value;
   }
 }
@@ -313,4 +314,9 @@ typedef unsigned long long int	uintmax_t;
 %{
 #include <RDGeneral/versions.h>
 %}
+
+%immutable RDKit::rdkitVersion;
+%immutable RDKit::boostVersion;
+%immutable RDKit::rdkitBuild;
+
 %include <RDGeneral/versions.h>