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#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);
}
};
} // 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} {}
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} {}
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(); }),
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();
target << " atoms: { ";
for (auto atom : stg.getAtoms()) {
target << atom->getIdx() << ' ';
}
if (stg.getBonds().size() > 0) {
target << " Bonds: { ";
for (auto bond : stg.getBonds()) {
target << bond->getIdx() << ' ';
}
target << '}';
}
target << '}';
return target;
}
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