static bool loopVisit(const Block* b,
boost::dynamic_bitset<>& visited,
boost::dynamic_bitset<>& path) {
if (b == nullptr) return false;
auto const id = b->id();
// If we're revisiting a block in our current search, then we've
// found a backedge.
if (path.test(id)) return true;
// Otherwise if we're getting back to a block that's already been
// visited, but it hasn't been visited in this path, then we can
// prune this search.
if (visited.test(id)) return false;
visited.set(id);
path.set(id);
bool res = loopVisit(b->taken(), visited, path) ||
loopVisit(b->next(), visited, path);
path.set(id, false);
return res;
}
void DFSSortClusters::dfs(uint32_t cid) {
if (m_visited.test(cid)) return;
m_visited.set(cid);
m_list.push_back(Vlabel(cid));
// find the best successor, which is the one to which cid has the
// highest weight among the ones that haven't been visited yet
int64_t maxWgt = 0;
uint32_t bestSucc = uint32_t(-1);
for (auto& sInfo : m_clusterSuccs[cid]) {
auto succId = sInfo.first;
if (m_visited.test(succId)) continue;
auto wgt = sInfo.second;
if (wgt >= maxWgt) {
maxWgt = wgt;
bestSucc = succId;
}
}
if (bestSucc == uint32_t(-1)) return;
// visit bestSucc first
dfs(bestSucc);
// now visit the remaining ones
for (auto& sInfo : m_clusterSuccs[cid]) {
if (sInfo.first != bestSucc) {
dfs(sInfo.first);
}
}
}
void table_manager::init_migrate_done_set(boost::dynamic_bitset<> &migrate_done_set, const vector<uint64_t> ¤t_state_table)
{
int bucket_number = 0;
for (size_t i=0; i<current_state_table.size(); i+=this->copy_count) {
bucket_number = (int)current_state_table[i++]; // skip the bucket_number
bool has_migrated = false;
for (size_t j=0; j<this->copy_count; ++j) {
if (current_state_table[i+j] != server_table[bucket_number + j * this->bucket_count]) {
has_migrated = true;
break;
}
}
if (has_migrated) {
migrate_done_set.set(bucket_number, true);
log_debug("bucket[%d] has migrated");
}
}
}
bool mark (unsigned key)
{
if (flags_[key]) return false;
flags_.set(key);
return true;
}
void setChildrenOnly(const uint vertex, const bool setting) { _childrenOnly.set(vertex, setting); }
std::vector<unsigned int> generateBondHashes(const ROMol &mol, boost::dynamic_bitset<>& atomsInPath,
const std::vector<const Bond *>& bondCache,
const std::vector<short>& isQueryBond,
const PATH_TYPE &path, bool useBondOrder,
std::vector<boost::uint32_t> *atomInvariants){
PRECONDITION(!atomInvariants || atomInvariants->size() >= mol.getNumAtoms(),
"bad atomInvariants size");
std::vector<unsigned int> bondHashes;
atomsInPath.reset();
bool queryInPath=false;
std::vector<unsigned int> atomDegrees(mol.getNumAtoms(),0);
for(unsigned int i=0;i<path.size() && !queryInPath;++i){
const Bond *bi = bondCache[path[i]];
atomDegrees[bi->getBeginAtomIdx()]++;
atomDegrees[bi->getEndAtomIdx()]++;
atomsInPath.set(bi->getBeginAtomIdx());
atomsInPath.set(bi->getEndAtomIdx());
if(isQueryBond[path[i]]) queryInPath=true;
}
if(queryInPath){
return bondHashes;
}
// -----------------
// calculate the bond hashes:
std::vector<unsigned int> bondNbrs(path.size(),0);
bondHashes.reserve(path.size()+1);
for(unsigned int i=0;i<path.size();++i){
const Bond *bi = bondCache[path[i]];
#ifdef REPORT_FP_STATS
if (std::find(atomsToUse.begin(), atomsToUse.end(),
bi->getBeginAtomIdx()) == atomsToUse.end()) {
atomsToUse.push_back(bi->getBeginAtomIdx());
}
if (std::find(atomsToUse.begin(), atomsToUse.end(),
bi->getEndAtomIdx()) == atomsToUse.end()) {
atomsToUse.push_back(bi->getEndAtomIdx());
}
#endif
for(unsigned int j=i+1;j<path.size();++j){
const Bond *bj = bondCache[path[j]];
if(bi->getBeginAtomIdx()==bj->getBeginAtomIdx() ||
bi->getBeginAtomIdx()==bj->getEndAtomIdx() ||
bi->getEndAtomIdx()==bj->getBeginAtomIdx() ||
bi->getEndAtomIdx()==bj->getEndAtomIdx() ){
++bondNbrs[i];
++bondNbrs[j];
}
}
#ifdef VERBOSE_FINGERPRINTING
std::cerr << " bond(" << i << "):" << bondNbrs[i] << std::endl;
#endif
// we have the count of neighbors for bond bi, compute its hash:
unsigned int a1Hash = (*atomInvariants)[bi->getBeginAtomIdx()];
unsigned int a2Hash = (*atomInvariants)[bi->getEndAtomIdx()];
unsigned int deg1=atomDegrees[bi->getBeginAtomIdx()];
unsigned int deg2=atomDegrees[bi->getEndAtomIdx()];
if(a1Hash<a2Hash){
std::swap(a1Hash,a2Hash);
std::swap(deg1,deg2);
}
else if(a1Hash==a2Hash && deg1<deg2){
std::swap(deg1,deg2);
}
unsigned int bondHash=1;
if(useBondOrder){
if(bi->getIsAromatic() || bi->getBondType()==Bond::AROMATIC){
// makes sure aromatic bonds always hash as aromatic
bondHash = Bond::AROMATIC;
}
else {
bondHash = bi->getBondType();
}
}
boost::uint32_t ourHash=bondNbrs[i];
gboost::hash_combine(ourHash,bondHash);
gboost::hash_combine(ourHash,a1Hash);
gboost::hash_combine(ourHash,deg1);
gboost::hash_combine(ourHash,a2Hash);
gboost::hash_combine(ourHash,deg2);
bondHashes.push_back(ourHash);
//std::cerr<<" "<<bi->getIdx()<<" "<<a1Hash<<"("<<deg1<<")"<<"-"<<a2Hash<<"("<<deg2<<")"<<" "<<bondHash<<" -> "<<ourHash<<std::endl;
}
return bondHashes;
}
// finds all possible chiral special cases.
// at the moment this is just candidates for ring stereochemistry
void findChiralAtomSpecialCases(ROMol &mol,
boost::dynamic_bitset<> &possibleSpecialCases) {
PRECONDITION(possibleSpecialCases.size() >= mol.getNumAtoms(),
"bit vector too small");
possibleSpecialCases.reset();
if (!mol.getRingInfo()->isInitialized()) {
VECT_INT_VECT sssrs;
MolOps::symmetrizeSSSR(mol, sssrs);
}
boost::dynamic_bitset<> atomsSeen(mol.getNumAtoms());
boost::dynamic_bitset<> atomsUsed(mol.getNumAtoms());
boost::dynamic_bitset<> bondsSeen(mol.getNumBonds());
for (ROMol::AtomIterator ait = mol.beginAtoms(); ait != mol.endAtoms();
++ait) {
const Atom *atom = *ait;
if (atomsSeen[atom->getIdx()]) continue;
if (atom->getChiralTag() == Atom::CHI_UNSPECIFIED ||
atom->hasProp(common_properties::_CIPCode) ||
!mol.getRingInfo()->numAtomRings(atom->getIdx()) ||
!atomIsCandidateForRingStereochem(mol, atom)) {
continue;
}
// do a BFS from this ring atom along ring bonds and find other
// stereochemistry candidates.
std::list<const Atom *> nextAtoms;
// start with finding viable neighbors
ROMol::OEDGE_ITER beg, end;
boost::tie(beg, end) = mol.getAtomBonds(atom);
while (beg != end) {
unsigned int bidx = mol[*beg]->getIdx();
if (!bondsSeen[bidx]) {
bondsSeen.set(bidx);
if (mol.getRingInfo()->numBondRings(bidx)) {
const Atom *oatom = mol[*beg]->getOtherAtom(atom);
if (!atomsSeen[oatom->getIdx()]) {
nextAtoms.push_back(oatom);
atomsUsed.set(oatom->getIdx());
}
}
}
++beg;
}
INT_VECT ringStereoAtoms(0);
if (!nextAtoms.empty()) {
atom->getPropIfPresent(common_properties::_ringStereoAtoms,
ringStereoAtoms);
}
while (!nextAtoms.empty()) {
const Atom *ratom = nextAtoms.front();
nextAtoms.pop_front();
atomsSeen.set(ratom->getIdx());
if (ratom->getChiralTag() != Atom::CHI_UNSPECIFIED &&
!ratom->hasProp(common_properties::_CIPCode) &&
atomIsCandidateForRingStereochem(mol, ratom)) {
int same = (ratom->getChiralTag() == atom->getChiralTag()) ? 1 : -1;
ringStereoAtoms.push_back(same * (ratom->getIdx() + 1));
INT_VECT oringatoms(0);
ratom->getPropIfPresent(common_properties::_ringStereoAtoms,
oringatoms);
oringatoms.push_back(same * (atom->getIdx() + 1));
ratom->setProp(common_properties::_ringStereoAtoms, oringatoms, true);
possibleSpecialCases.set(ratom->getIdx());
possibleSpecialCases.set(atom->getIdx());
}
// now push this atom's neighbors
boost::tie(beg, end) = mol.getAtomBonds(ratom);
while (beg != end) {
unsigned int bidx = mol[*beg]->getIdx();
if (!bondsSeen[bidx]) {
bondsSeen.set(bidx);
if (mol.getRingInfo()->numBondRings(bidx)) {
const Atom *oatom = mol[*beg]->getOtherAtom(ratom);
if (!atomsSeen[oatom->getIdx()] && !atomsUsed[oatom->getIdx()]) {
nextAtoms.push_back(oatom);
atomsUsed.set(oatom->getIdx());
}
}
}
++beg;
}
} // end of BFS
if (ringStereoAtoms.size() != 0) {
atom->setProp(common_properties::_ringStereoAtoms, ringStereoAtoms, true);
// because we're only going to hit each ring atom once, the first atom we
// encounter in a ring is going to end up with all the other atoms set as
// stereoAtoms, but each of them will only have the first atom present. We
// need to fix that. because the traverse from the first atom only
// followed ring bonds, these things are all by definition in one ring
// system. (Q: is this true if there's a spiro center in there?)
INT_VECT same(mol.getNumAtoms(), 0);
BOOST_FOREACH (int ringAtomEntry, ringStereoAtoms) {
int ringAtomIdx =
ringAtomEntry < 0 ? -ringAtomEntry - 1 : ringAtomEntry - 1;
same[ringAtomIdx] = ringAtomEntry;
}
for (INT_VECT_CI rae = ringStereoAtoms.begin();
rae != ringStereoAtoms.end(); ++rae) {
int ringAtomEntry = *rae;
int ringAtomIdx =
ringAtomEntry < 0 ? -ringAtomEntry - 1 : ringAtomEntry - 1;
INT_VECT lringatoms(0);
mol.getAtomWithIdx(ringAtomIdx)
->getPropIfPresent(common_properties::_ringStereoAtoms, lringatoms);
CHECK_INVARIANT(lringatoms.size() > 0, "no other ring atoms found.");
for (INT_VECT_CI orae = rae + 1; orae != ringStereoAtoms.end();
++orae) {
int oringAtomEntry = *orae;
int oringAtomIdx =
oringAtomEntry < 0 ? -oringAtomEntry - 1 : oringAtomEntry - 1;
int theseDifferent = (ringAtomEntry < 0) ^ (oringAtomEntry < 0);
lringatoms.push_back(theseDifferent ? -(oringAtomIdx + 1)
: (oringAtomIdx + 1));
INT_VECT olringatoms(0);
mol.getAtomWithIdx(oringAtomIdx)
->getPropIfPresent(common_properties::_ringStereoAtoms,
olringatoms);
CHECK_INVARIANT(olringatoms.size() > 0, "no other ring atoms found.");
olringatoms.push_back(theseDifferent ? -(ringAtomIdx + 1)
: (ringAtomIdx + 1));
mol.getAtomWithIdx(oringAtomIdx)
->setProp(common_properties::_ringStereoAtoms, olringatoms);
}
mol.getAtomWithIdx(ringAtomIdx)
->setProp(common_properties::_ringStereoAtoms, lringatoms);
}
} else {
/******************************************************************************
* Performs the actual rejection of particles.
******************************************************************************/
size_t SliceModifier::filterParticles(boost::dynamic_bitset<>& mask, TimePoint time, TimeInterval& validityInterval)
{
// Get the required input properties.
ParticlePropertyObject* const posProperty = expectStandardProperty(ParticleProperty::PositionProperty);
ParticlePropertyObject* const selProperty = applyToSelection() ? inputStandardProperty(ParticleProperty::SelectionProperty) : nullptr;
OVITO_ASSERT(posProperty->size() == mask.size());
OVITO_ASSERT(!selProperty || selProperty->size() == mask.size());
FloatType sliceWidth = 0;
if(_widthCtrl) sliceWidth = _widthCtrl->getFloatValue(time, validityInterval);
sliceWidth *= 0.5;
Plane3 plane = slicingPlane(time, validityInterval);
size_t na = 0;
boost::dynamic_bitset<>::size_type i = 0;
const Point3* p = posProperty->constDataPoint3();
const Point3* p_end = p + posProperty->size();
if(sliceWidth <= 0) {
if(selProperty) {
const int* s = selProperty->constDataInt();
for(; p != p_end; ++p, ++s, ++i) {
if(*s && plane.pointDistance(*p) > 0) {
mask.set(i);
na++;
}
else mask.reset(i);
}
}
else {
for(; p != p_end; ++p, ++i) {
if(plane.pointDistance(*p) > 0) {
mask.set(i);
na++;
}
else mask.reset(i);
}
}
}
else {
bool invert = inverse();
if(selProperty) {
const int* s = selProperty->constDataInt();
for(; p != p_end; ++p, ++s, ++i) {
if(*s && invert == (plane.classifyPoint(*p, sliceWidth) == 0)) {
mask.set(i);
na++;
}
else mask.reset(i);
}
}
else {
for(; p != p_end; ++p, ++i) {
if(invert == (plane.classifyPoint(*p, sliceWidth) == 0)) {
mask.set(i);
na++;
}
else mask.reset(i);
}
}
}
return na;
}