Main

Code/GraphMol/AddHs.cpp

@@ -1095,7 +1095,7 @@ void mergeQueryHs(RWMol &mol, bool mergeUnmappedOnly) {
       // recurse if needed (was github isusue 544)
       if (atom->hasQuery()) {
         // std::cerr<<"  q: "<<atom->getQuery()->getDescription()<<std::endl;
-        if (atom->getQuery()->getDescription() == "RecursiveStructure") {
+        if (atom->getQuery()->getDescription() == "RS") {
           auto *rqm = static_cast<RWMol *>(const_cast<ROMol *>(
               static_cast<RecursiveStructureQuery *>(atom->getQuery())
                   ->getQueryMol()));
@@ -1109,7 +1109,7 @@ void mergeQueryHs(RWMol &mol, bool mergeUnmappedOnly) {
           QueryAtom::QUERYATOM_QUERY::CHILD_TYPE qry = childStack.front();
           childStack.pop_front();
           // std::cerr<<"      child: "<<qry->getDescription()<<std::endl;
-          if (qry->getDescription() == "RecursiveStructure") {
+          if (qry->getDescription() == "RS") {
             // std::cerr<<"    recurse"<<std::endl;
             auto *rqm = static_cast<RWMol *>(const_cast<ROMol *>(
                 static_cast<RecursiveStructureQuery *>(qry.get())

Code/GraphMol/Atom.cpp

@@ -586,6 +586,21 @@ int Atom::getPerturbationOrder(const INT_LIST &probe) const {
   int nSwaps = static_cast<int>(countSwapsToInterconvert(probe, ref));
   return nSwaps;
 }
+int Atom::getPerturbationOrder(const INT_VECT &probe) const {
+  PRECONDITION(
+      dp_mol,
+      "perturbation order not defined for atoms not associated with molecules")
+  INT_VECT ref;
+  ref.reserve(getOwningMol().getAtomDegree(this));
+  ROMol::OEDGE_ITER beg, end;
+  boost::tie(beg, end) = getOwningMol().getAtomBonds(this);
+  while (beg != end) {
+    ref.push_back(getOwningMol()[*beg]->getIdx());
+    ++beg;
+  }
+  int nSwaps = static_cast<int>(countSwapsToInterconvert(probe, ref));
+  return nSwaps;
+}
 
 void Atom::invertChirality() {
   switch (getChiralTag()) {

Code/GraphMol/Atom.h

@@ -332,6 +332,7 @@ class RDKIT_GRAPHMOL_EXPORT Atom : public RDProps {
 
   */
   int getPerturbationOrder(const INT_LIST &probe) const;
+  int getPerturbationOrder(const INT_VECT &probe) const;
 
   //! calculates any of our lazy \c properties
   /*!

Code/GraphMol/Bond.cpp

@@ -177,6 +177,60 @@ double Bond::getBondTypeAsDouble() const {
   }
 }
 
+uint8_t Bond::getTwiceBondType() const {
+  switch (getBondType()) {
+    case UNSPECIFIED:
+    case IONIC:
+    case ZERO:
+      return 0;
+      break;
+    case SINGLE:
+      return 2;
+      break;
+    case DOUBLE:
+      return 4;
+      break;
+    case TRIPLE:
+      return 6;
+      break;
+    case QUADRUPLE:
+      return 8;
+      break;
+    case QUINTUPLE:
+      return 10;
+      break;
+    case HEXTUPLE:
+      return 12;
+      break;
+    case ONEANDAHALF:
+      return 3;
+      break;
+    case TWOANDAHALF:
+      return 5;
+      break;
+    case THREEANDAHALF:
+      return 7;
+      break;
+    case FOURANDAHALF:
+      return 9;
+      break;
+    case FIVEANDAHALF:
+      return 11;
+      break;
+    case AROMATIC:
+      return 3;
+      break;
+    case DATIVEONE:
+      return 2;
+      break;  // FIX: this should probably be different
+    case DATIVE:
+      return 2;
+      break;  // FIX: again probably wrong
+    default:
+      UNDER_CONSTRUCTION("Bad bond type");
+  }
+}
+
 double Bond::getValenceContrib(const Atom *atom) const {
   switch (getBondType()) {
     case UNSPECIFIED:

Code/GraphMol/Bond.h

@@ -124,6 +124,9 @@ class RDKIT_GRAPHMOL_EXPORT Bond : public RDProps {
   //! \brief returns our \c bondType as a double
   //!   (e.g. SINGLE->1.0, AROMATIC->1.5, etc.)
   double getBondTypeAsDouble() const;
+  //! \brief returns twice our \c bondType
+  //!   (e.g. SINGLE->2, AROMATIC->3, etc.)
+  uint8_t getTwiceBondType() const;
 
   //! returns our contribution to the explicit valence of an Atom
   /*!
@@ -335,8 +338,8 @@ class RDKIT_GRAPHMOL_EXPORT Bond : public RDProps {
   std::uint8_t d_bondType;
   std::uint8_t d_dirTag;
   std::uint8_t d_stereo;
-  atomindex_t d_index;
-  atomindex_t d_beginAtomIdx, d_endAtomIdx;
+  std::uint16_t d_index;
+  std::uint16_t d_beginAtomIdx, d_endAtomIdx;
   ROMol *dp_mol;
   INT_VECT *dp_stereoAtoms;