rdkit/Code/GraphMol/StereoGroup.cpp

#include <algorithm>
#include <utility>
#include <vector>

#include <RDGeneral/BoostStartInclude.h>
#include <boost/dynamic_bitset.hpp>
#include <RDGeneral/BoostEndInclude.h>

#include "StereoGroup.h"
#include "Atom.h"
#include "ROMol.h"

namespace RDKit {

namespace {
void storeIdsInUse(boost::dynamic_bitset<> &ids, StereoGroup &sg) {
  const auto groupId = sg.getWriteId();
  if (groupId == 0) {
    return;
  } else if (groupId >= ids.size()) {
    ids.resize(groupId + 1);
  }
  if (ids[groupId]) {
    // This id is duplicate, let's reset it so we can reassign it later
    BOOST_LOG(rdWarningLog)
        << "StereoGroup ID " << groupId
        << " is used by more than one group, and will be reassined"
        << std::endl;
    sg.setWriteId(0);
  } else {
    ids[groupId] = true;
  }
};

void assignMissingIds(const boost::dynamic_bitset<> &ids, unsigned &nextId,
                      StereoGroup &sg) {
  if (sg.getWriteId() == 0) {
    ++nextId;
    while (nextId < ids.size() && ids[nextId]) {
      ++nextId;
    }
    sg.setWriteId(nextId);
  }
};

template <typename T>
void checkForDupes(const std::vector<T *> &vec, const std::string &typeName) {
  for (auto it = vec.cbegin(); it != vec.cend(); ++it) {
    if (std::find(vec.cbegin(), it, *it) != it) {
      throw ValueErrorException("Duplicate " + typeName + " in StereoGroup");
    }
  }
}

}  // namespace

StereoGroup::StereoGroup(StereoGroupType grouptype, std::vector<Atom *> &&atoms,
                         std::vector<Bond *> &&bonds, unsigned readId)
    : d_grouptype(grouptype), d_atoms(atoms), d_bonds(bonds), d_readId{readId} {
  checkForDupes(d_atoms, "atom");
  checkForDupes(d_bonds, "bond");
}

StereoGroup::StereoGroup(StereoGroupType grouptype,
                         const std::vector<Atom *> &atoms,
                         const std::vector<Bond *> &bonds, unsigned readId)
    : d_grouptype(grouptype),
      d_atoms(std::move(atoms)),
      d_bonds(std::move(bonds)),
      d_readId{readId} {
  checkForDupes(d_atoms, "atom");
  checkForDupes(d_bonds, "bond");
}

StereoGroupType StereoGroup::getGroupType() const { return d_grouptype; }

const std::vector<Atom *> &StereoGroup::getAtoms() const { return d_atoms; }
const std::vector<Bond *> &StereoGroup::getBonds() const { return d_bonds; }

void removeGroupsWithAtom(const Atom *atom, std::vector<StereoGroup> &groups) {
  auto containsAtom = [atom](const StereoGroup &group) {
    return std::find(group.getAtoms().cbegin(), group.getAtoms().cend(),
                     atom) != group.getAtoms().cend();
  };
  groups.erase(std::remove_if(groups.begin(), groups.end(), containsAtom),
               groups.end());
}

void removeAtomFromGroups(const Atom *atom, std::vector<StereoGroup> &groups) {
  auto findAtom = [atom](StereoGroup &group) {
    return std::find(group.getAtoms().begin(), group.getAtoms().end(), atom);
  };
  for (auto &group : groups) {
    auto atomPos = findAtom(group);
    if (atomPos != group.d_atoms.end()) {
      group.d_atoms.erase(atomPos);
    }
  }
  // now remove any empty groups:
  groups.erase(std::remove_if(groups.begin(), groups.end(),
                              [](const auto &gp) {
                                return gp.getAtoms().empty() &&
                                       gp.getBonds().empty();
                              }),
               groups.end());
}

void removeBondFromGroups(const Bond *bond, std::vector<StereoGroup> &groups) {
  auto findBond = [bond](StereoGroup &group) {
    return std::find(group.getBonds().begin(), group.getBonds().end(), bond);
  };
  for (auto &group : groups) {
    auto bondPos = findBond(group);
    if (bondPos != group.d_bonds.end()) {
      group.d_bonds.erase(bondPos);
    }
  }
  // now remove any empty groups:
  groups.erase(std::remove_if(groups.begin(), groups.end(),
                              [](const auto &gp) {
                                return gp.getAtoms().empty() &&
                                       gp.getBonds().empty();
                              }),
               groups.end());
}

void removeGroupsWithBond(const Bond *bond, std::vector<StereoGroup> &groups) {
  auto containsBond = [bond](const StereoGroup &group) {
    return std::find(group.getBonds().cbegin(), group.getBonds().cend(),
                     bond) != group.getBonds().cend();
  };
  groups.erase(std::remove_if(groups.begin(), groups.end(), containsBond),
               groups.end());
}

void removeGroupsWithAtoms(const std::vector<Atom *> &atoms,
                           std::vector<StereoGroup> &groups) {
  auto containsAnyAtom = [&atoms](const StereoGroup &group) {
    for (auto atom : atoms) {
      if (std::find(group.getAtoms().cbegin(), group.getAtoms().cend(), atom) !=
          group.getAtoms().cend()) {
        return true;
      }
    }
    return false;
  };
  groups.erase(std::remove_if(groups.begin(), groups.end(), containsAnyAtom),
               groups.end());
}

void removeGroupsWithBonds(const std::vector<Bond *> &bonds,
                           std::vector<StereoGroup> &groups) {
  auto containsAnyBond = [&bonds](const StereoGroup &group) {
    for (auto bond : bonds) {
      if (std::find(group.getBonds().cbegin(), group.getBonds().cend(), bond) !=
          group.getBonds().cend()) {
        return true;
      }
    }
    return false;
  };
  groups.erase(std::remove_if(groups.begin(), groups.end(), containsAnyBond),
               groups.end());
}

void assignStereoGroupIds(std::vector<StereoGroup> &groups) {
  if (groups.empty()) {
    return;
  }

  boost::dynamic_bitset<> andIds;
  boost::dynamic_bitset<> orIds;

  for (auto &sg : groups) {
    if (sg.getGroupType() == StereoGroupType::STEREO_AND) {
      storeIdsInUse(andIds, sg);
    } else if (sg.getGroupType() == StereoGroupType::STEREO_OR) {
      storeIdsInUse(orIds, sg);
    }
  }

  unsigned andId = 0;
  unsigned orId = 0;
  for (auto &sg : groups) {
    if (sg.getGroupType() == StereoGroupType::STEREO_AND) {
      assignMissingIds(andIds, andId, sg);
    } else if (sg.getGroupType() == StereoGroupType::STEREO_OR) {
      assignMissingIds(orIds, orId, sg);
    }
  }
}

void forwardStereoGroupIds(ROMol &mol) {
  auto stgs = mol.getStereoGroups();
  for (auto &stg : stgs) {
    stg.setWriteId(stg.getReadId());
  }
  mol.setStereoGroups(stgs);
}

}  // namespace RDKit

std::ostream &operator<<(std::ostream &target, const RDKit::StereoGroup &stg) {
  switch (stg.getGroupType()) {
    case RDKit::StereoGroupType::STEREO_ABSOLUTE:
      target << "ABS";
      break;
    case RDKit::StereoGroupType::STEREO_OR:
      target << "OR ";
      break;
    case RDKit::StereoGroupType::STEREO_AND:
      target << "AND";
      break;
  }
  target << " rId: " << stg.getReadId();
  target << " wId: " << stg.getWriteId();
  if (!stg.getAtoms().empty()) {
    target << " atoms: { ";
    for (auto atom : stg.getAtoms()) {
      target << atom->getIdx() << ' ';
    }
    target << '}';
  }
  if (!stg.getBonds().empty()) {
    target << " bonds: { ";
    for (auto bond : stg.getBonds()) {
      target << bond->getIdx() << ' ';
    }
    target << '}';
  }

  return target;
}