Make PandasTools work with pandas v2.2

Code/GraphMol/Atom.cpp

@@ -1,5 +1,5 @@
 //
-//  Copyright (C) 2001-2021 Greg Landrum and other RDKit contributors
+//  Copyright (C) 2001-2024 Greg Landrum and other RDKit contributors
 //
 //   @@ All Rights Reserved @@
 //  This file is part of the RDKit.
@@ -230,11 +230,7 @@ void Atom::initAtom() {
   d_explicitValence = -1;
 }
 
-Atom::~Atom() {
-  if (dp_monomerInfo) {
-    delete dp_monomerInfo;
-  }
-}
+Atom::~Atom() { delete dp_monomerInfo; }
 
 Atom *Atom::copy() const {
   auto *res = new Atom(*this);
@@ -317,7 +313,6 @@ unsigned int Atom::getTotalValence() const {
 namespace {
 
 int calculateExplicitValence(const Atom &atom, bool strict, bool checkIt) {
-  unsigned int res;
   // FIX: contributions of bonds to valence are being done at best
   // approximately
   double accum = 0;
@@ -349,8 +344,7 @@ int calculateExplicitValence(const Atom &atom, bool strict, bool checkIt) {
     //    nitrogen here : c1cccn1C
 
     int pval = dv + chr;
-    const INT_VECT &valens =
-        PeriodicTable::getTable()->getValenceList(atomicNum);
+    const auto &valens = PeriodicTable::getTable()->getValenceList(atomicNum);
     for (auto val : valens) {
       if (val == -1) {
         break;
@@ -386,7 +380,7 @@ int calculateExplicitValence(const Atom &atom, bool strict, bool checkIt) {
   // correctly.
   accum += 0.1;
 
-  res = static_cast<int>(std::round(accum));
+  auto res = static_cast<int>(std::round(accum));
 
   if (strict || checkIt) {
     int effectiveValence;
@@ -397,8 +391,7 @@ int calculateExplicitValence(const Atom &atom, bool strict, bool checkIt) {
       // extra valences means adding negative charge
       effectiveValence = res + atom.getFormalCharge();
     }
-    const INT_VECT &valens =
-        PeriodicTable::getTable()->getValenceList(atomicNum);
+    const auto &valens = PeriodicTable::getTable()->getValenceList(atomicNum);
 
     int maxValence = valens.back();
     // maxValence == -1 signifies that we'll take anything at the high end
@@ -437,9 +430,7 @@ int calculateImplicitValence(const Atom &atom, bool strict, bool checkIt) {
   if (atomic_num == 0) {
     return 0;
   }
-  for (const auto &nbri :
-       boost::make_iterator_range(atom.getOwningMol().getAtomBonds(&atom))) {
-    const auto bnd = atom.getOwningMol()[nbri];
+  for (const auto bnd : atom.getOwningMol().atomBonds(&atom)) {
     if (QueryOps::hasComplexBondTypeQuery(*bnd)) {
       return 0;
     }
@@ -471,7 +462,6 @@ int calculateImplicitValence(const Atom &atom, bool strict, bool checkIt) {
   // the atom and the explicit valence already specified - tells how
   // many Hs to add
   //
-  int res;
 
   // The d-block and f-block of the periodic table (i.e. transition metals,
   // lanthanoids and actinoids) have no default valence.
@@ -491,8 +481,7 @@ int calculateImplicitValence(const Atom &atom, bool strict, bool checkIt) {
   // exception
   // finally aromatic cases are dealt with differently - these atoms are allowed
   // only default valences
-  const INT_VECT &valens =
-      PeriodicTable::getTable()->getValenceList(atomic_num);
+  const auto &valens = PeriodicTable::getTable()->getValenceList(atomic_num);
 
   int explicitPlusRadV =
       atom.getExplicitValence() + atom.getNumRadicalElectrons();
@@ -535,6 +524,7 @@ int calculateImplicitValence(const Atom &atom, bool strict, bool checkIt) {
     chg = -chg;
   }
 
+  int res = 0;
   // if we have an aromatic case treat it differently
   if (isAromaticAtom(atom)) {
     if (explicitPlusRadV <= (static_cast<int>(dv) + chg)) {

Code/GraphMol/Bond.cpp

@@ -249,7 +249,7 @@ void Bond::setStereoAtoms(unsigned int bgnIdx, unsigned int endIdx) {
       getOwningMol().getBondBetweenAtoms(getEndAtomIdx(), endIdx) != nullptr,
       "endIdx not connected to end atom of bond");
 
-  INT_VECT &atoms = getStereoAtoms();
+  auto &atoms = getStereoAtoms();
   atoms.clear();
   atoms.push_back(bgnIdx);
   atoms.push_back(endIdx);

Code/GraphMol/Conformer.cpp

@@ -1,6 +1,5 @@
-// $Id$
 //
-//  Copyright (C) 2001-2008 Greg Landrum and Rational Discovery LLC
+//  Copyright (C) 2001-2024 Greg Landrum and other RDKit contributors
 //
 //   @@ All Rights Reserved @@
 //  This file is part of the RDKit.
@@ -13,27 +12,6 @@
 
 namespace RDKit {
 
-void Conformer::initFromOther(const Conformer &conf) {
-  RDProps::operator=(conf);
-  dp_mol = conf.dp_mol;
-  auto nat = conf.getNumAtoms();
-  d_positions.resize(nat);
-  for (unsigned i = 0; i < nat; i++) {
-    d_positions[i] = conf.getAtomPos(i);
-  }
-  d_id = conf.getId();
-  df_is3D = conf.is3D();
-}
-
-Conformer::Conformer(const Conformer &conf) : RDProps() { initFromOther(conf); }
-Conformer &Conformer::operator=(const Conformer &other) {
-  if (this == &other) {
-    return *this;
-  }
-  initFromOther(other);
-  return *this;
-}
-
 void Conformer::setOwningMol(ROMol *mol) {
   PRECONDITION(mol, "");
   dp_mol = mol;
@@ -48,23 +26,21 @@ const RDGeom::POINT3D_VECT &Conformer::getPositions() const {
   return d_positions;
 }
 
-RDGeom::POINT3D_VECT &Conformer::getPositions() {
-  return d_positions;
-}
+RDGeom::POINT3D_VECT &Conformer::getPositions() { return d_positions; }
 
 const RDGeom::Point3D &Conformer::getAtomPos(unsigned int atomId) const {
   if (dp_mol) {
     PRECONDITION(dp_mol->getNumAtoms() == d_positions.size(), "");
   }
   URANGE_CHECK(atomId, d_positions.size());
-  return d_positions[atomId];
+  return d_positions.at(atomId);
 }
 
 RDGeom::Point3D &Conformer::getAtomPos(unsigned int atomId) {
   if (dp_mol) {
     PRECONDITION(dp_mol->getNumAtoms() == d_positions.size(), "");
   }
   URANGE_CHECK(atomId, d_positions.size());
-  return d_positions[atomId];
+  return d_positions.at(atomId);
 }
 }  // namespace RDKit

Code/GraphMol/Conformer.h

@@ -1,5 +1,5 @@
 //
-//  Copyright (C) 2001-2021 Greg Landrum and other RDKit contributors
+//  Copyright (C) 2001-2024 Greg Landrum and other RDKit contributors
 //
 //   @@ All Rights Reserved @@
 //  This file is part of the RDKit.
@@ -48,35 +48,29 @@ class RDKIT_GRAPHMOL_EXPORT Conformer : public RDProps {
   friend class ROMol;
 
   //! Constructor
-  Conformer() { d_positions.clear(); }
+  Conformer() = default;
 
   //! Constructor with number of atoms specified ID specification
-  Conformer(unsigned int numAtoms) {
-    if (numAtoms) {
-      d_positions.resize(numAtoms, RDGeom::Point3D(0.0, 0.0, 0.0));
-    } else {
-      d_positions.resize(0);
-      d_positions.clear();
-    }
-  }
+  Conformer(unsigned int numAtoms)
+      : d_positions(numAtoms, RDGeom::Point3D(0.0, 0.0, 0.0)) {}
 
   //! Copy Constructor: initialize from a second conformation.
-  Conformer(const Conformer &other);
-  Conformer &operator=(const Conformer &other);
+  Conformer(const Conformer &other) = default;
+  Conformer &operator=(const Conformer &other) = default;
   Conformer(Conformer &&o) noexcept
-      : RDProps(std::move(o)),
-        df_is3D(std::move(o.df_is3D)),
-        d_id(std::move(o.d_id)),
-        dp_mol(std::move(o.dp_mol)),
-        d_positions(std::move(o.d_positions)){};
+      : RDProps(o),
+        df_is3D(o.df_is3D),
+        d_id(o.d_id),
+        dp_mol(o.dp_mol),
+        d_positions(std::move(o.d_positions)) {}
   Conformer &operator=(Conformer &&o) noexcept {
     if (this == &o) {
       return *this;
     }
     RDProps::operator=(std::move(o));
-    df_is3D = std::move(o.df_is3D);
-    d_id = std::move(o.d_id);
-    dp_mol = std::move(o.dp_mol);
+    df_is3D = o.df_is3D;
+    d_id = d_id;
+    dp_mol = dp_mol;
     d_positions = std::move(o.d_positions);
     return *this;
   }
@@ -161,7 +155,6 @@ class RDKIT_GRAPHMOL_EXPORT Conformer : public RDProps {
   unsigned int d_id{0};              // id is the conformation
   ROMol *dp_mol{nullptr};            // owning molecule
   RDGeom::POINT3D_VECT d_positions;  // positions of the atoms
-  void initFromOther(const Conformer &conf);
 };
 
 typedef boost::shared_ptr<Conformer> CONFORMER_SPTR;

Code/GraphMol/MonomerInfo.h

@@ -1,5 +1,5 @@
 //
-//  Copyright (C) 2013-2021 Greg Landrum and other RDKit contributors
+//  Copyright (C) 2013-2024 Greg Landrum and other RDKit contributors
 //
 //   @@ All Rights Reserved @@
 //  This file is part of the RDKit.
@@ -29,11 +29,10 @@ class RDKIT_GRAPHMOL_EXPORT AtomMonomerInfo {
 
   virtual ~AtomMonomerInfo() {}
 
-  AtomMonomerInfo() : d_name("") {}
+  AtomMonomerInfo() = default;
   AtomMonomerInfo(AtomMonomerType typ, std::string nm = "")
       : d_monomerType(typ), d_name(std::move(nm)) {}
-  AtomMonomerInfo(const AtomMonomerInfo &other)
-      : d_monomerType(other.d_monomerType), d_name(other.d_name) {}
+  AtomMonomerInfo(const AtomMonomerInfo &other) = default;
 
   const std::string &getName() const { return d_name; }
   void setName(const std::string &nm) { d_name = nm; }
@@ -44,26 +43,14 @@ class RDKIT_GRAPHMOL_EXPORT AtomMonomerInfo {
 
  private:
   AtomMonomerType d_monomerType{UNKNOWN};
-  std::string d_name;
+  std::string d_name{""};
 };
 
 //! Captures atom-level information about peptide residues
 class RDKIT_GRAPHMOL_EXPORT AtomPDBResidueInfo : public AtomMonomerInfo {
  public:
   AtomPDBResidueInfo() : AtomMonomerInfo(PDBRESIDUE) {}
-  AtomPDBResidueInfo(const AtomPDBResidueInfo &other)
-      : AtomMonomerInfo(other),
-        d_serialNumber(other.d_serialNumber),
-        d_altLoc(other.d_altLoc),
-        d_residueName(other.d_residueName),
-        d_residueNumber(other.d_residueNumber),
-        d_chainId(other.d_chainId),
-        d_insertionCode(other.d_insertionCode),
-        d_occupancy(other.d_occupancy),
-        d_tempFactor(other.d_tempFactor),
-        df_heteroAtom(other.df_heteroAtom),
-        d_secondaryStructure(other.d_secondaryStructure),
-        d_segmentNumber(other.d_segmentNumber) {}
+  AtomPDBResidueInfo(const AtomPDBResidueInfo &other) = default;
 
   AtomPDBResidueInfo(const std::string &atomName, int serialNumber = 0,
                      std::string altLoc = "", std::string residueName = "",

Code/GraphMol/QueryAtom.h

@@ -132,16 +132,16 @@ class RDKIT_GRAPHMOL_EXPORT QueryAtom : public Atom {
 };  // end o' class
 
 namespace detail {
-inline std::string qhelper(Atom::QUERYATOM_QUERY *q, unsigned int depth) {
+inline std::string qhelper(const Atom::QUERYATOM_QUERY *q, unsigned int depth) {
   std::string res = "";
   if (q) {
     for (unsigned int i = 0; i < depth; ++i) {
       res += "  ";
     }
     res += q->getFullDescription() + "\n";
-    for (Atom::QUERYATOM_QUERY::CHILD_VECT_CI ci = q->beginChildren();
-         ci != q->endChildren(); ++ci) {
-      res += qhelper((*ci).get(), depth + 1);
+    for (const auto &child :
+         boost::make_iterator_range(q->beginChildren(), q->endChildren())) {
+      res += qhelper(child.get(), depth + 1);
     }
   }
   return res;

Code/GraphMol/QueryBond.h

@@ -118,16 +118,16 @@ class RDKIT_GRAPHMOL_EXPORT QueryBond : public Bond {
 };
 
 namespace detail {
-inline std::string qhelper(Bond::QUERYBOND_QUERY *q, unsigned int depth) {
+inline std::string qhelper(const Bond::QUERYBOND_QUERY *q, unsigned int depth) {
   std::string res;
   if (q) {
     for (unsigned int i = 0; i < depth; ++i) {
       res += "  ";
     }
     res += q->getFullDescription() + "\n";
-    for (Bond::QUERYBOND_QUERY::CHILD_VECT_CI ci = q->beginChildren();
-         ci != q->endChildren(); ++ci) {
-      res += qhelper((*ci).get(), depth + 1);
+    for (const auto &child :
+         boost::make_iterator_range(q->beginChildren(), q->endChildren())) {
+      res += qhelper(child.get(), depth + 1);
     }
   }
   return res;