new_canon.h

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//
//  Copyright (C) 2014 Greg Landrum
//  Adapted from pseudo-code from Roger Sayle
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
 
#ifndef RD_NEW_CANON_H
#define RD_NEW_CANON_H
 
#include <RDGeneral/export.h>
#include <RDGeneral/hanoiSort.h>
#include <GraphMol/ROMol.h>
#include <GraphMol/RingInfo.h>
#include <GraphMol/StereoGroup.h>
#include <RDGeneral/BoostStartInclude.h>
#include <cstdint>
#include <boost/dynamic_bitset.hpp>
#include <boost/container/small_vector.hpp>
#include <RDGeneral/BoostEndInclude.h>
#include <cstring>
#include <cassert>
#include <compare>
#include <cstring>
#include <span>
#include <vector>
 
// #define VERBOSE_CANON 1
 
namespace RDKit {
namespace Canon {
struct canon_atom;
 
// Complete atom comparison key used after the current symmetry class.
struct AtomCompareCode {
  int atomMapNumber{0};
  unsigned int degree{0};
  std::uint64_t primary{0};
  std::uint64_t secondary{0};
 
  // The defaulted comparison orders atom map, degree, primary, then secondary.
  auto operator<=>(const AtomCompareCode &) const = default;
};
 
struct RDKIT_GRAPHMOL_EXPORT bondholder {
  Bond::BondType bondType{Bond::BondType::UNSPECIFIED};
  unsigned int bondStereo{
      static_cast<unsigned int>(Bond::BondStereo::STEREONONE)};
  unsigned int nbrSymClass{0};
  unsigned int nbrIdx{0};
  Bond::BondStereo stype{Bond::BondStereo::STEREONONE};
  const canon_atom *controllingAtoms[4]{nullptr, nullptr, nullptr, nullptr};
  const std::string *p_symbol{
      nullptr};  // if provided, this is used to order bonds
  unsigned int bondIdx{0};
 
  bondholder() {};
  bondholder(Bond::BondType bt, Bond::BondStereo bs, unsigned int ni,
             unsigned int nsc, unsigned int bidx)
      : bondType(bt),
        bondStereo(static_cast<unsigned int>(bs)),
        nbrSymClass(nsc),
        nbrIdx(ni),
        bondIdx(bidx) {}
  bondholder(Bond::BondType bt, unsigned int bs, unsigned int ni,
             unsigned int nsc, unsigned int bidx)
      : bondType(bt),
        bondStereo(bs),
        nbrSymClass(nsc),
        nbrIdx(ni),
        bondIdx(bidx) {}
 
  int compareStereo(const bondholder &o) const;
 
  bool operator<(const bondholder &o) const { return compare(*this, o) < 0; }
  static bool greater(const bondholder &lhs, const bondholder &rhs) {
    return compare(lhs, rhs) > 0;
  }
 
  static int compare(const bondholder &x, const bondholder &y,
                     unsigned int div = 1) {
    if (x.p_symbol && y.p_symbol) {
      auto symbolCompare = x.p_symbol->compare(*y.p_symbol);
      if (symbolCompare != 0) {
        return symbolCompare;
      }
    }
    if (x.bondType < y.bondType) {
      return -1;
    } else if (x.bondType > y.bondType) {
      return 1;
    }
    if (x.bondStereo < y.bondStereo) {
      return -1;
    } else if (x.bondStereo > y.bondStereo) {
      return 1;
    }
    auto scdiv = x.nbrSymClass / div - y.nbrSymClass / div;
    if (scdiv) {
      return scdiv;
    }
    if (x.bondStereo && y.bondStereo) {
      auto cs = x.compareStereo(y);
      if (cs) {
        return cs;
      }
    }
    return 0;
  }
};
using BondholderVector = boost::container::small_vector<bondholder, 4>;
struct RDKIT_GRAPHMOL_EXPORT canon_atom {
  const Atom *atom{nullptr};
  int index{-1};
  unsigned int degree{0};
  unsigned int totalNumHs{0};
  bool hasRingNbr{false};
  bool isRingStereoAtom{false};
  unsigned int whichStereoGroup{0};
  StereoGroupType typeOfStereoGroup{StereoGroupType::STEREO_ABSOLUTE};
  std::span<int> nbrIds;
  const std::string *p_symbol{
      nullptr};  // if provided, this is used to order atoms
  std::vector<int> neighborNum;
  std::vector<int> revistedNeighbors;
  BondholderVector bonds;
};
 
RDKIT_GRAPHMOL_EXPORT void updateAtomNeighborIndex(
    canon_atom *atoms, std::vector<bondholder> &nbrs);
RDKIT_GRAPHMOL_EXPORT void updateAtomNeighborIndex(canon_atom *atoms,
                                                   BondholderVector &nbrs);
 
RDKIT_GRAPHMOL_EXPORT void updateAtomNeighborNumSwaps(
    canon_atom *atoms, std::vector<bondholder> &nbrs, unsigned int atomIdx,
    std::vector<std::pair<unsigned int, unsigned int>> &result);
RDKIT_GRAPHMOL_EXPORT void updateAtomNeighborNumSwaps(
    canon_atom *atoms, BondholderVector &nbrs, unsigned int atomIdx,
    std::vector<std::pair<unsigned int, unsigned int>> &result);
 
/*
 * Different types of atom compare functions:
 *
 * - SpecialChiralityAtomCompareFunctor: Allows canonizing molecules exhibiting
 *dependent chirality
 * - SpecialSymmetryAtomCompareFunctor: Very specialized, allows canonizing
 *highly symmetrical graphs/molecules
 * - AtomCompareFunctor: Basic atom compare function which also allows to
 *include neighbors within the ranking
 */
 
class RDKIT_GRAPHMOL_EXPORT SpecialChiralityAtomCompareFunctor {
 public:
  Canon::canon_atom *dp_atoms{nullptr};
  const ROMol *dp_mol{nullptr};
  const boost::dynamic_bitset<> *dp_atomsInPlay{nullptr},
      *dp_bondsInPlay{nullptr};
 
  SpecialChiralityAtomCompareFunctor() {}
  SpecialChiralityAtomCompareFunctor(
      Canon::canon_atom *atoms, const ROMol &m,
      const boost::dynamic_bitset<> *atomsInPlay = nullptr,
      const boost::dynamic_bitset<> *bondsInPlay = nullptr)
      : dp_atoms(atoms),
        dp_mol(&m),
        dp_atomsInPlay(atomsInPlay),
        dp_bondsInPlay(bondsInPlay) {}
  int operator()(int i, int j) const {
    PRECONDITION(dp_atoms, "no atoms");
    PRECONDITION(dp_mol, "no molecule");
    PRECONDITION(i != j, "bad call");
    if (dp_atomsInPlay && !((*dp_atomsInPlay)[i] || (*dp_atomsInPlay)[j])) {
      return 0;
    }
 
    if (!dp_atomsInPlay || (*dp_atomsInPlay)[i]) {
      updateAtomNeighborIndex(dp_atoms, dp_atoms[i].bonds);
    }
    if (!dp_atomsInPlay || (*dp_atomsInPlay)[j]) {
      updateAtomNeighborIndex(dp_atoms, dp_atoms[j].bonds);
    }
    for (unsigned int ii = 0;
         ii < dp_atoms[i].bonds.size() && ii < dp_atoms[j].bonds.size(); ++ii) {
      int cmp =
          bondholder::compare(dp_atoms[i].bonds[ii], dp_atoms[j].bonds[ii]);
      if (cmp) {
        return cmp;
      }
    }
 
    std::vector<std::pair<unsigned int, unsigned int>> swapsi;
    std::vector<std::pair<unsigned int, unsigned int>> swapsj;
    if (!dp_atomsInPlay || (*dp_atomsInPlay)[i]) {
      updateAtomNeighborNumSwaps(dp_atoms, dp_atoms[i].bonds, i, swapsi);
    }
    if (!dp_atomsInPlay || (*dp_atomsInPlay)[j]) {
      updateAtomNeighborNumSwaps(dp_atoms, dp_atoms[j].bonds, j, swapsj);
    }
 
    for (unsigned int ii = 0; ii < swapsi.size() && ii < swapsj.size(); ++ii) {
      int cmp = swapsi[ii].second - swapsj[ii].second;
 
      if (cmp) {
        return cmp;
      }
    }
 
    return 0;
  }
};
 
class RDKIT_GRAPHMOL_EXPORT SpecialSymmetryAtomCompareFunctor {
 public:
  Canon::canon_atom *dp_atoms{nullptr};
  const ROMol *dp_mol{nullptr};
  const boost::dynamic_bitset<> *dp_atomsInPlay{nullptr},
      *dp_bondsInPlay{nullptr};
 
  SpecialSymmetryAtomCompareFunctor() {}
  SpecialSymmetryAtomCompareFunctor(
      Canon::canon_atom *atoms, const ROMol &m,
      const boost::dynamic_bitset<> *atomsInPlay = nullptr,
      const boost::dynamic_bitset<> *bondsInPlay = nullptr)
      : dp_atoms(atoms),
        dp_mol(&m),
        dp_atomsInPlay(atomsInPlay),
        dp_bondsInPlay(bondsInPlay) {}
  int operator()(int i, int j) const {
    PRECONDITION(dp_atoms, "no atoms");
    PRECONDITION(dp_mol, "no molecule");
    PRECONDITION(i != j, "bad call");
    if (dp_atomsInPlay && !((*dp_atomsInPlay)[i] || (*dp_atomsInPlay)[j])) {
      return 0;
    }
 
    if (dp_atoms[i].neighborNum < dp_atoms[j].neighborNum) {
      return -1;
    } else if (dp_atoms[i].neighborNum > dp_atoms[j].neighborNum) {
      return 1;
    }
 
    if (dp_atoms[i].revistedNeighbors < dp_atoms[j].revistedNeighbors) {
      return -1;
    } else if (dp_atoms[i].revistedNeighbors > dp_atoms[j].revistedNeighbors) {
      return 1;
    }
 
    if (!dp_atomsInPlay || (*dp_atomsInPlay)[i]) {
      updateAtomNeighborIndex(dp_atoms, dp_atoms[i].bonds);
    }
    if (!dp_atomsInPlay || (*dp_atomsInPlay)[j]) {
      updateAtomNeighborIndex(dp_atoms, dp_atoms[j].bonds);
    }
    for (unsigned int ii = 0;
         ii < dp_atoms[i].bonds.size() && ii < dp_atoms[j].bonds.size(); ++ii) {
      int cmp =
          bondholder::compare(dp_atoms[i].bonds[ii], dp_atoms[j].bonds[ii]);
      if (cmp) {
        return cmp;
      }
    }
 
    if (dp_atoms[i].bonds.size() < dp_atoms[j].bonds.size()) {
      return -1;
    } else if (dp_atoms[i].bonds.size() > dp_atoms[j].bonds.size()) {
      return 1;
    }
    return 0;
  }
};
 
namespace {
unsigned int getChiralRank(const ROMol *dp_mol, canon_atom *dp_atoms,
                           unsigned int i) {
  unsigned int res = 0;
  std::vector<unsigned int> perm;
  perm.reserve(dp_atoms[i].atom->getDegree());
  for (const auto nbr : dp_mol->atomNeighbors(dp_atoms[i].atom)) {
    auto rnk = dp_atoms[nbr->getIdx()].index;
    // make sure we don't have duplicate ranks
    if (std::find(perm.begin(), perm.end(), rnk) != perm.end()) {
      break;
    } else {
      perm.push_back(rnk);
    }
  }
  if (perm.size() == dp_atoms[i].atom->getDegree()) {
    auto ctag = dp_atoms[i].atom->getChiralTag();
    if (ctag == Atom::ChiralType::CHI_TETRAHEDRAL_CW ||
        ctag == Atom::ChiralType::CHI_TETRAHEDRAL_CCW) {
      auto sortedPerm = perm;
      std::sort(sortedPerm.begin(), sortedPerm.end());
      auto nswaps = countSwapsToInterconvert(perm, sortedPerm);
      res = ctag == Atom::ChiralType::CHI_TETRAHEDRAL_CW ? 2 : 1;
      if (nswaps % 2) {
        res = res == 2 ? 1 : 2;
      }
    }
  }
  return res;
}
}  // namespace
class RDKIT_GRAPHMOL_EXPORT AtomCompareFunctor {
  unsigned int getAtomRingNbrCode(unsigned int i) const {
    if (!dp_atoms[i].hasRingNbr) {
      return 0;
    }
 
    const std::span<const int> nbrs = dp_atoms[i].nbrIds;
    unsigned int code = 0;
    for (unsigned j = 0; j < dp_atoms[i].degree; ++j) {
      if (dp_atoms[nbrs[j]].isRingStereoAtom) {
        code += dp_atoms[nbrs[j]].index * 10000 + 1;  // j;
      }
    }
    return code;
  }
 
  int basecomp(int i, int j) const {
    unsigned int ivi, ivj;
 
    // always start with the current class:
    ivi = dp_atoms[i].index;
    ivj = dp_atoms[j].index;
    if (ivi < ivj) {
      return -1;
    } else if (ivi > ivj) {
      return 1;
    }
 
    if (df_useNonStereoRanks) {
      // use the non-stereo ranks if they were assigned
      int rankingNumber_i = 0;
      int rankingNumber_j = 0;
      dp_atoms[i].atom->getPropIfPresent(
          common_properties::_CanonicalRankingNumber, rankingNumber_i);
      dp_atoms[j].atom->getPropIfPresent(
          common_properties::_CanonicalRankingNumber, rankingNumber_j);
      if (rankingNumber_i < rankingNumber_j) {
        return -1;
      } else if (rankingNumber_i > rankingNumber_j) {
        return 1;
      }
    }
 
    if (df_useAtomMaps || df_useAtomMapsOnDummies) {
      // use the atom-mapping numbers if they were assigned
      int molAtomMapNumber_i = 0;
      int molAtomMapNumber_j = 0;
      if (df_useAtomMaps ||
          (df_useAtomMapsOnDummies && dp_atoms[i].atom->getAtomicNum() == 0)) {
        dp_atoms[i].atom->getPropIfPresent(common_properties::molAtomMapNumber,
                                           molAtomMapNumber_i);
      }
      if (df_useAtomMaps ||
          (df_useAtomMapsOnDummies && dp_atoms[j].atom->getAtomicNum() == 0)) {
        dp_atoms[j].atom->getPropIfPresent(common_properties::molAtomMapNumber,
                                           molAtomMapNumber_j);
      }
      if (molAtomMapNumber_i < molAtomMapNumber_j) {
        return -1;
      } else if (molAtomMapNumber_i > molAtomMapNumber_j) {
        return 1;
      }
    }
    // start by comparing degree
    ivi = dp_atoms[i].degree;
    ivj = dp_atoms[j].degree;
    if (ivi < ivj) {
      return -1;
    } else if (ivi > ivj) {
      return 1;
    }
    if (dp_atoms[i].p_symbol && dp_atoms[j].p_symbol) {
      return dp_atoms[i].p_symbol->compare(*dp_atoms[j].p_symbol);
    }
 
    // move onto atomic number
    ivi = dp_atoms[i].atom->getAtomicNum();
    ivj = dp_atoms[j].atom->getAtomicNum();
    if (ivi < ivj) {
      return -1;
    } else if (ivi > ivj) {
      return 1;
    }
    // isotopes if we're using them
    if (df_useIsotopes) {
      ivi = dp_atoms[i].atom->getIsotope();
      ivj = dp_atoms[j].atom->getIsotope();
      if (ivi < ivj) {
        return -1;
      } else if (ivi > ivj) {
        return 1;
      }
    }
 
    // nHs
    ivi = dp_atoms[i].totalNumHs;
    ivj = dp_atoms[j].totalNumHs;
    if (ivi < ivj) {
      return -1;
    } else if (ivi > ivj) {
      return 1;
    }
    // charge
    ivi = dp_atoms[i].atom->getFormalCharge();
    ivj = dp_atoms[j].atom->getFormalCharge();
    if (ivi < ivj) {
      return -1;
    } else if (ivi > ivj) {
      return 1;
    }
    // presence of specified chirality if it's being used
    if (df_useChiralPresence) {
      ivi =
          dp_atoms[i].atom->getChiralTag() != Atom::ChiralType::CHI_UNSPECIFIED;
      ivj =
          dp_atoms[j].atom->getChiralTag() != Atom::ChiralType::CHI_UNSPECIFIED;
      if (ivi < ivj) {
        return -1;
      } else if (ivi > ivj) {
        return 1;
      }
    }
    // chirality if we're using it
    if (df_useChirality) {
      // look at enhanced stereo -  whichStereoGroup == 0 means no stereo
      ivi = dp_atoms[i].whichStereoGroup;  // can't use the index itself, but if
                                           // it's set then we're in an SG
      ivj = dp_atoms[j].whichStereoGroup;
      if (ivi || ivj) {
        if (ivi && !ivj) {
          return 1;
        } else if (ivj && !ivi) {
          return -1;
        } else if (ivi && ivj) {
          auto iType = dp_atoms[i].typeOfStereoGroup;
          auto jType = dp_atoms[j].typeOfStereoGroup;
          if (iType < jType) {
            return -1;
          } else if (iType > jType) {
            return 1;
          }
          if (ivi != ivj) {
            // now check the current classes of the other members of the SG
            std::set<unsigned int> sgi;
            for (const auto sgat :
                 dp_mol->getStereoGroups()[ivi - 1].getAtoms()) {
              sgi.insert(dp_atoms[sgat->getIdx()].index);
            }
            std::set<unsigned int> sgj;
            for (const auto sgat :
                 dp_mol->getStereoGroups()[ivj - 1].getAtoms()) {
              sgj.insert(dp_atoms[sgat->getIdx()].index);
            }
            if (sgi < sgj) {
              return -1;
            } else if (sgi > sgj) {
              return 1;
            }
          } else {  // same stereo group
            if (iType == StereoGroupType::STEREO_ABSOLUTE) {
              ivi = getChiralRank(dp_mol, dp_atoms, i);
              ivj = getChiralRank(dp_mol, dp_atoms, j);
              if (ivi < ivj) {
                return -1;
              } else if (ivi > ivj) {
                return 1;
              }
            }
          }
        }
      } else {
        // if there's no stereogroup, then use whatever atom stereochem is
        // specfied:
        ivi = 0;
        ivj = 0;
        // can't actually use values here, because they are arbitrary
        ivi = dp_atoms[i].atom->getChiralTag() != 0;
        ivj = dp_atoms[j].atom->getChiralTag() != 0;
        if (ivi < ivj) {
          return -1;
        } else if (ivi > ivj) {
          return 1;
        }
        // stereo set
        if (ivi && ivj) {
          if (ivi) {
            ivi = getChiralRank(dp_mol, dp_atoms, i);
          }
          if (ivj) {
            ivj = getChiralRank(dp_mol, dp_atoms, j);
          }
          if (ivi < ivj) {
            return -1;
          } else if (ivi > ivj) {
            return 1;
          }
        }
      }
    }
 
    if (df_useChiralityRings) {
      // ring stereochemistry
      ivi = getAtomRingNbrCode(i);
      ivj = getAtomRingNbrCode(j);
      if (ivi < ivj) {
        return -1;
      } else if (ivi > ivj) {
        return 1;
      }  // bond stereo is taken care of in the neighborhood comparison
    }
    return 0;
  }
 
 public:
  Canon::canon_atom *dp_atoms{nullptr};
  const ROMol *dp_mol{nullptr};
  const AtomCompareCode *dp_compareCodes{
      nullptr};  // optional complete atom comparison keys
  const boost::dynamic_bitset<> *dp_atomsInPlay{nullptr},
      *dp_bondsInPlay{nullptr};
  bool df_useNbrs{false};
  bool df_useIsotopes{true};
  bool df_useChirality{true};
  bool df_useChiralityRings{true};
  bool df_useAtomMaps{true};
  bool df_useNonStereoRanks{false};
  bool df_useChiralPresence{true};
  bool df_useAtomMapsOnDummies{true};
 
  AtomCompareFunctor() {}
  AtomCompareFunctor(Canon::canon_atom *atoms, const ROMol &m,
                     const boost::dynamic_bitset<> *atomsInPlay = nullptr,
                     const boost::dynamic_bitset<> *bondsInPlay = nullptr,
                     const AtomCompareCode *compareCodes = nullptr)
      : dp_atoms(atoms),
        dp_mol(&m),
        dp_compareCodes(compareCodes),
        dp_atomsInPlay(atomsInPlay),
        dp_bondsInPlay(bondsInPlay) {}
 
  int operator()(int i, int j) const {
    if (dp_atomsInPlay && !((*dp_atomsInPlay)[i] || (*dp_atomsInPlay)[j])) {
      return 0;
    }
    int v = 0;
    if (dp_compareCodes) {
      if (dp_atoms[i].index != dp_atoms[j].index) {
        v = dp_atoms[i].index < dp_atoms[j].index ? -1 : 1;
      } else {
        const auto ordering = dp_compareCodes[i] <=> dp_compareCodes[j];
        if (ordering != 0) {
          v = ordering < 0 ? -1 : 1;
        }
      }
    } else {
      v = basecomp(i, j);
    }
    if (v) {
      return v;
    }
 
    if (df_useNbrs) {
      if (!dp_atomsInPlay || (*dp_atomsInPlay)[i]) {
        updateAtomNeighborIndex(dp_atoms, dp_atoms[i].bonds);
      }
      if (!dp_atomsInPlay || (*dp_atomsInPlay)[j]) {
        updateAtomNeighborIndex(dp_atoms, dp_atoms[j].bonds);
      }
 
      for (unsigned int ii = 0;
           ii < dp_atoms[i].bonds.size() && ii < dp_atoms[j].bonds.size();
           ++ii) {
        int cmp =
            bondholder::compare(dp_atoms[i].bonds[ii], dp_atoms[j].bonds[ii]);
        if (cmp) {
          return cmp;
        }
      }
 
      if (dp_atoms[i].bonds.size() < dp_atoms[j].bonds.size()) {
        return -1;
      } else if (dp_atoms[i].bonds.size() > dp_atoms[j].bonds.size()) {
        return 1;
      }
    }
    return 0;
  }
};
 
/*
 * A compare function to discriminate chiral atoms, similar to the CIP rules.
 * This functionality is currently not used.
 */
 
const unsigned int ATNUM_CLASS_OFFSET = 10000;
class RDKIT_GRAPHMOL_EXPORT ChiralAtomCompareFunctor {
  void getAtomNeighborhood(BondholderVector &nbrs) const {
    for (unsigned j = 0; j < nbrs.size(); ++j) {
      unsigned int nbrIdx = nbrs[j].nbrIdx;
      if (nbrIdx == ATNUM_CLASS_OFFSET) {
        // Ignore the Hs
        continue;
      }
      const Atom *nbr = dp_atoms[nbrIdx].atom;
      nbrs[j].nbrSymClass =
          nbr->getAtomicNum() * ATNUM_CLASS_OFFSET + dp_atoms[nbrIdx].index + 1;
    }
    std::sort(nbrs.begin(), nbrs.end(), bondholder::greater);
    // FIX: don't want to be doing this long-term
  }
 
  int basecomp(int i, int j) const {
    PRECONDITION(dp_atoms, "no atoms");
    unsigned int ivi, ivj;
 
    // always start with the current class:
    ivi = dp_atoms[i].index;
    ivj = dp_atoms[j].index;
    if (ivi < ivj) {
      return -1;
    } else if (ivi > ivj) {
      return 1;
    }
 
    // move onto atomic number
    ivi = dp_atoms[i].atom->getAtomicNum();
    ivj = dp_atoms[j].atom->getAtomicNum();
    if (ivi < ivj) {
      return -1;
    } else if (ivi > ivj) {
      return 1;
    }
 
    // isotopes:
    ivi = dp_atoms[i].atom->getIsotope();
    ivj = dp_atoms[j].atom->getIsotope();
    if (ivi < ivj) {
      return -1;
    } else if (ivi > ivj) {
      return 1;
    }
 
    // atom stereochem:
    ivi = 0;
    ivj = 0;
    std::string cipCode;
    if (dp_atoms[i].atom->getPropIfPresent(common_properties::_CIPCode,
                                           cipCode)) {
      ivi = cipCode == "R" ? 2 : 1;
    }
    if (dp_atoms[j].atom->getPropIfPresent(common_properties::_CIPCode,
                                           cipCode)) {
      ivj = cipCode == "R" ? 2 : 1;
    }
    if (ivi < ivj) {
      return -1;
    } else if (ivi > ivj) {
      return 1;
    }
 
    // bond stereo is taken care of in the neighborhood comparison
    return 0;
  }
 
 public:
  Canon::canon_atom *dp_atoms{nullptr};
  const ROMol *dp_mol{nullptr};
  bool df_useNbrs{false};
  ChiralAtomCompareFunctor() {}
  ChiralAtomCompareFunctor(Canon::canon_atom *atoms, const ROMol &m)
      : dp_atoms(atoms), dp_mol(&m), df_useNbrs(false) {}
  int operator()(int i, int j) const {
    PRECONDITION(dp_atoms, "no atoms");
    PRECONDITION(dp_mol, "no molecule");
    PRECONDITION(i != j, "bad call");
    int v = basecomp(i, j);
    if (v) {
      return v;
    }
 
    if (df_useNbrs) {
      getAtomNeighborhood(dp_atoms[i].bonds);
      getAtomNeighborhood(dp_atoms[j].bonds);
 
      // we do two passes through the neighbor lists. The first just uses the
      // atomic numbers (by passing the optional 10000 to bondholder::compare),
      // the second takes the already-computed index into account
      for (unsigned int ii = 0;
           ii < dp_atoms[i].bonds.size() && ii < dp_atoms[j].bonds.size();
           ++ii) {
        int cmp = bondholder::compare(
            dp_atoms[i].bonds[ii], dp_atoms[j].bonds[ii], ATNUM_CLASS_OFFSET);
        if (cmp) {
          return cmp;
        }
      }
      for (unsigned int ii = 0;
           ii < dp_atoms[i].bonds.size() && ii < dp_atoms[j].bonds.size();
           ++ii) {
        int cmp =
            bondholder::compare(dp_atoms[i].bonds[ii], dp_atoms[j].bonds[ii]);
        if (cmp) {
          return cmp;
        }
      }
      if (dp_atoms[i].bonds.size() < dp_atoms[j].bonds.size()) {
        return -1;
      } else if (dp_atoms[i].bonds.size() > dp_atoms[j].bonds.size()) {
        return 1;
      }
    }
    return 0;
  }
};
 
/*
 * Basic canonicalization function to organize the partitions which will be
 * sorted next.
 * */
 
template <typename CompareFunc>
void RefinePartitions(const ROMol &mol, canon_atom *atoms, CompareFunc compar,
                      int mode, std::vector<int> &order,
                      std::vector<int> &count, int &activeset,
                      std::vector<int> &next, std::vector<int> &changed,
                      std::vector<char> &touchedPartitions,
                      std::vector<int> *hanoiTemp = nullptr) {
  unsigned int nAtoms = mol.getNumAtoms();
  std::vector<int> localHanoiTemp;
  if (!hanoiTemp) {
    localHanoiTemp.resize(nAtoms);
    hanoiTemp = &localHanoiTemp;
  }
  int partition;
  int symclass = 0;
  int offset;
  int index;
  int len;
  int i;
  PRECONDITION(hanoiTemp->size() >= nAtoms, "hanoi scratch is too small");
  // std::vector<char> touchedPartitions(mol.getNumAtoms(),0);
 
  // std::cerr<<"&&&&&&&&&&&&&&&& RP"<<std::endl;
  while (activeset != -1) {
    // std::cerr<<"ITER: "<<activeset<<" next: "<<next[activeset]<<std::endl;
    // std::cerr<<" next: ";
    // for(unsigned int ii=0;ii<nAtoms;++ii){
    //   std::cerr<<ii<<":"<<next[ii]<<" ";
    // }
    // std::cerr<<std::endl;
    // for(unsigned int ii=0;ii<nAtoms;++ii){
    //   std::cerr<<order[ii]<<" count: "<<count[order[ii]]<<" index:
    //   "<<atoms[order[ii]].index<<std::endl;
    // }
 
    partition = activeset;
    activeset = next[partition];
    next[partition] = -2;
 
    len = count[partition];
    offset = atoms[partition].index;
    auto start = std::span<int>(&order[offset], len);
    // std::cerr<<"\n\n**************************************************************"<<std::endl;
    // std::cerr<<"  sort - class:"<<atoms[partition].index<<" len:
    // "<<len<<":"; for(unsigned int ii=0;ii<len;++ii){
    //   std::cerr<<" "<<order[offset+ii]+1;
    // }
    // std::cerr<<std::endl;
    // for(unsigned int ii=0;ii<nAtoms;++ii){
    //   std::cerr<<order[ii]+1<<" count: "<<count[order[ii]]<<" index:
    //   "<<atoms[order[ii]].index<<std::endl;
    // }
    if (RDKit::detail::hanoi(start.data(), len, hanoiTemp->data(), count.data(),
                             changed.data(), compar)) {
      std::copy_n(hanoiTemp->begin(), len, start.begin());
    }
    // std::cerr<<"*_*_*_*_*_*_*_*_*_*_*_*_*_*_*_*"<<std::endl;
    // std::cerr<<"  result:";
    // for(unsigned int ii=0;ii<nAtoms;++ii){
    //    std::cerr<<order[ii]+1<<" count: "<<count[order[ii]]<<" index:
    //    "<<atoms[order[ii]].index<<std::endl;
    //  }
    for (int k = 0; k < len; ++k) {
      changed[start[k]] = 0;
    }
 
    index = start[0];
    // std::cerr<<"  len:"<<len<<" index:"<<index<<"
    // count:"<<count[index]<<std::endl;
    for (i = count[index]; i < len; i++) {
      index = start[i];
      if (count[index]) {
        symclass = offset + i;
      }
      atoms[index].index = symclass;
      // std::cerr<<" "<<index+1<<"("<<symclass<<")";
      // if(mode && (activeset<0 || count[index]>count[activeset]) ){
      //  activeset=index;
      //}
      for (unsigned j = 0; j < atoms[index].degree; ++j) {
        changed[atoms[index].nbrIds[j]] = 1;
      }
    }
    // std::cerr<<std::endl;
 
    if (mode) {
      index = start[0];
      for (i = count[index]; i < len; i++) {
        index = start[i];
        for (unsigned j = 0; j < atoms[index].degree; ++j) {
          unsigned int nbor = atoms[index].nbrIds[j];
          touchedPartitions[atoms[nbor].index] = 1;
        }
      }
      for (unsigned int ii = 0; ii < nAtoms; ++ii) {
        if (touchedPartitions[ii]) {
          partition = order[ii];
          if ((count[partition] > 1) && (next[partition] == -2)) {
            next[partition] = activeset;
            activeset = partition;
          }
          touchedPartitions[ii] = 0;
        }
      }
    }
  }
}  // end of RefinePartitions()
 
template <typename CompareFunc>
void BreakTies(const ROMol &mol, canon_atom *atoms, CompareFunc compar,
               int mode, std::vector<int> &order, std::vector<int> &count,
               int &activeset, std::vector<int> &next,
               std::vector<int> &changed, std::vector<char> &touchedPartitions,
               std::vector<int> *hanoiTemp = nullptr) {
  unsigned int nAtoms = mol.getNumAtoms();
  int partition;
  int offset;
  int index;
  int len;
  int oldPart = 0;
 
  for (unsigned int i = 0; i < nAtoms; i++) {
    partition = order[i];
    oldPart = atoms[partition].index;
    while (count[partition] > 1) {
      len = count[partition];
      offset = atoms[partition].index + len - 1;
      index = order[offset];
      atoms[index].index = offset;
      count[partition] = len - 1;
      count[index] = 1;
 
      // test for ions, water molecules with no
      if (atoms[index].degree < 1) {
        continue;
      }
      for (unsigned j = 0; j < atoms[index].degree; ++j) {
        unsigned int nbor = atoms[index].nbrIds[j];
        touchedPartitions[atoms[nbor].index] = 1;
        changed[nbor] = 1;
      }
 
      for (unsigned int ii = 0; ii < nAtoms; ++ii) {
        if (touchedPartitions[ii]) {
          int npart = order[ii];
          if ((count[npart] > 1) && (next[npart] == -2)) {
            next[npart] = activeset;
            activeset = npart;
          }
          touchedPartitions[ii] = 0;
        }
      }
      RefinePartitions(mol, atoms, compar, mode, order, count, activeset, next,
                       changed, touchedPartitions, hanoiTemp);
    }
    // not sure if this works each time
    if (atoms[partition].index != oldPart) {
      i -= 1;
    }
  }
}  // end of BreakTies()
 
RDKIT_GRAPHMOL_EXPORT void CreateSinglePartition(unsigned int nAtoms,
                                                 std::vector<int> &order,
                                                 std::vector<int> &count,
                                                 canon_atom *atoms);
 
RDKIT_GRAPHMOL_EXPORT void ActivatePartitions(
    unsigned int nAtoms, std::vector<int> &order, std::vector<int> &count,
    int &activeset, std::vector<int> &next, std::vector<int> &changed);
 
//! Note that atom maps on dummy atoms will always be used
RDKIT_GRAPHMOL_EXPORT void rankMolAtoms(
    const ROMol &mol, std::vector<unsigned int> &res, bool breakTies = true,
    bool includeChirality = true, bool includeIsotopes = true,
    bool includeAtomMaps = true, bool includeChiralPresence = false,
    bool includeStereoGroups = true, bool useNonStereoRanks = false,
    bool includeRingStereo = true);
 
//! Note that atom maps on dummy atoms will always be used
RDKIT_GRAPHMOL_EXPORT void rankFragmentAtoms(
    const ROMol &mol, std::vector<unsigned int> &res,
    const boost::dynamic_bitset<> &atomsInPlay,
    const boost::dynamic_bitset<> &bondsInPlay,
    const std::vector<std::string> *atomSymbols,
    const std::vector<std::string> *bondSymbols, bool breakTies,
    bool includeChirality, bool includeIsotope, bool includeAtomMaps,
    bool includeChiralPresence, bool includeRingStereo = true);
 
//! Note that atom maps on dummy atoms will always be used
inline void rankFragmentAtoms(
    const ROMol &mol, std::vector<unsigned int> &res,
    const boost::dynamic_bitset<> &atomsInPlay,
    const boost::dynamic_bitset<> &bondsInPlay,
    const std::vector<std::string> *atomSymbols = nullptr,
    bool breakTies = true, bool includeChirality = true,
    bool includeIsotopes = true, bool includeAtomMaps = true,
    bool includeChiralPresence = false, bool includeRingStereo = true) {
  rankFragmentAtoms(mol, res, atomsInPlay, bondsInPlay, atomSymbols, nullptr,
                    breakTies, includeChirality, includeIsotopes,
                    includeAtomMaps, includeChiralPresence, includeRingStereo);
};
 
RDKIT_GRAPHMOL_EXPORT void chiralRankMolAtoms(const ROMol &mol,
                                              std::vector<unsigned int> &res);
 
RDKIT_GRAPHMOL_EXPORT void initCanonAtoms(const ROMol &mol,
                                          std::vector<Canon::canon_atom> &atoms,
                                          std::span<int> neighborIds,
                                          bool includeChirality = true,
                                          bool includeStereoGroups = true);
 
namespace detail {
void initFragmentCanonAtoms(const ROMol &mol,
                            std::vector<Canon::canon_atom> &atoms,
                            bool includeChirality,
                            const std::vector<std::string> *atomSymbols,
                            const std::vector<std::string> *bondSymbols,
                            const boost::dynamic_bitset<> &atomsInPlay,
                            const boost::dynamic_bitset<> &bondsInPlay,
                            std::span<int> neighborIds, bool needsInit);
template <typename T>
void rankWithFunctor(T &ftor, bool breakTies, std::vector<int> &order,
                     bool useSpecial = false, bool useChirality = false,
                     bool includeRingStereo = true,
                     const boost::dynamic_bitset<> *atomsInPlay = nullptr,
                     const boost::dynamic_bitset<> *bondsInPlay = nullptr);
 
}  // namespace detail
 
}  // namespace Canon
}  // namespace RDKit
 
#endif  // RD_NEW_CANON_H