19#include <boost/dynamic_bitset.hpp>
35 unsigned int bondStereo{
36 static_cast<unsigned int>(Bond::BondStereo::STEREONONE)};
37 unsigned int nbrSymClass{0};
38 unsigned int nbrIdx{0};
40 const canon_atom *controllingAtoms[4]{
nullptr,
nullptr,
nullptr,
nullptr};
41 const std::string *p_symbol{
43 unsigned int bondIdx{0};
47 unsigned int nsc,
unsigned int bidx)
49 bondStereo(static_cast<unsigned int>(bs)),
54 unsigned int nsc,
unsigned int bidx)
65 return compare(lhs, rhs) > 0;
69 unsigned int div = 1) {
103 unsigned int degree{0};
104 unsigned int totalNumHs{0};
105 bool hasRingNbr{
false};
106 bool isRingStereoAtom{
false};
107 unsigned int whichStereoGroup{0};
110 const std::string *p_symbol{
122 std::vector<std::pair<unsigned int, unsigned int>> &
result);
139 const boost::dynamic_bitset<> *dp_atomsInPlay{
nullptr},
140 *dp_bondsInPlay{
nullptr};
145 const boost::dynamic_bitset<> *atomsInPlay =
nullptr,
146 const boost::dynamic_bitset<> *bondsInPlay =
nullptr)
149 dp_atomsInPlay(atomsInPlay),
150 dp_bondsInPlay(bondsInPlay) {}
155 if (dp_atomsInPlay && !((*dp_atomsInPlay)[i] || (*dp_atomsInPlay)[j])) {
159 if (!dp_atomsInPlay || (*dp_atomsInPlay)[i]) {
162 if (!dp_atomsInPlay || (*dp_atomsInPlay)[j]) {
165 for (
unsigned int ii = 0;
166 ii < dp_atoms[i].bonds.size() && ii < dp_atoms[j].bonds.size(); ++ii) {
168 bondholder::compare(dp_atoms[i].bonds[ii], dp_atoms[j].bonds[ii]);
174 std::vector<std::pair<unsigned int, unsigned int>> swapsi;
175 std::vector<std::pair<unsigned int, unsigned int>> swapsj;
176 if (!dp_atomsInPlay || (*dp_atomsInPlay)[i]) {
179 if (!dp_atomsInPlay || (*dp_atomsInPlay)[j]) {
182 for (
unsigned int ii = 0; ii < swapsi.size() && ii < swapsj.size(); ++ii) {
183 int cmp = swapsi[ii].second - swapsj[ii].second;
196 const boost::dynamic_bitset<> *dp_atomsInPlay{
nullptr},
197 *dp_bondsInPlay{
nullptr};
202 const boost::dynamic_bitset<> *atomsInPlay =
nullptr,
203 const boost::dynamic_bitset<> *bondsInPlay =
nullptr)
206 dp_atomsInPlay(atomsInPlay),
207 dp_bondsInPlay(bondsInPlay) {}
212 if (dp_atomsInPlay && !((*dp_atomsInPlay)[i] || (*dp_atomsInPlay)[j])) {
216 if (dp_atoms[i].neighborNum < dp_atoms[j].neighborNum) {
218 }
else if (dp_atoms[i].neighborNum > dp_atoms[j].neighborNum) {
222 if (dp_atoms[i].revistedNeighbors < dp_atoms[j].revistedNeighbors) {
224 }
else if (dp_atoms[i].revistedNeighbors > dp_atoms[j].revistedNeighbors) {
228 if (!dp_atomsInPlay || (*dp_atomsInPlay)[i]) {
231 if (!dp_atomsInPlay || (*dp_atomsInPlay)[j]) {
234 for (
unsigned int ii = 0;
235 ii < dp_atoms[i].bonds.size() && ii < dp_atoms[j].bonds.size(); ++ii) {
237 bondholder::compare(dp_atoms[i].bonds[ii], dp_atoms[j].bonds[ii]);
243 if (dp_atoms[i].bonds.size() < dp_atoms[j].bonds.size()) {
245 }
else if (dp_atoms[i].bonds.size() > dp_atoms[j].bonds.size()) {
255 unsigned int res = 0;
256 std::vector<unsigned int>
perm;
257 perm.reserve(dp_atoms[i].atom->getDegree());
258 for (
const auto nbr : dp_mol->atomNeighbors(dp_atoms[i].atom)) {
259 auto rnk = dp_atoms[
nbr->getIdx()].index;
267 if (
perm.size() == dp_atoms[i].atom->getDegree()) {
268 auto ctag = dp_atoms[i].atom->getChiralTag();
284 unsigned int getAtomRingNbrCode(
unsigned int i)
const {
285 if (!dp_atoms[i].hasRingNbr) {
289 auto nbrs = dp_atoms[i].nbrIds.get();
290 unsigned int code = 0;
291 for (
unsigned j = 0; j < dp_atoms[i].degree; ++j) {
292 if (dp_atoms[nbrs[j]].isRingStereoAtom) {
293 code += dp_atoms[nbrs[j]].index * 10000 + 1;
299 int basecomp(
int i,
int j)
const {
300 unsigned int ivi, ivj;
303 ivi = dp_atoms[i].index;
304 ivj = dp_atoms[j].index;
307 }
else if (ivi > ivj) {
315 int molAtomMapNumber_i = 0;
316 int molAtomMapNumber_j = 0;
317 dp_atoms[i].atom->getPropIfPresent(common_properties::molAtomMapNumber,
319 dp_atoms[j].atom->getPropIfPresent(common_properties::molAtomMapNumber,
321 if (molAtomMapNumber_i < molAtomMapNumber_j) {
323 }
else if (molAtomMapNumber_i > molAtomMapNumber_j) {
327 ivi = dp_atoms[i].degree;
328 ivj = dp_atoms[j].degree;
331 }
else if (ivi > ivj) {
334 if (dp_atoms[i].p_symbol && dp_atoms[j].p_symbol) {
335 if (*(dp_atoms[i].p_symbol) < *(dp_atoms[j].p_symbol)) {
337 }
else if (*(dp_atoms[i].p_symbol) > *(dp_atoms[j].p_symbol)) {
345 ivi = dp_atoms[i].atom->getAtomicNum();
346 ivj = dp_atoms[j].atom->getAtomicNum();
349 }
else if (ivi > ivj) {
353 if (df_useIsotopes) {
354 ivi = dp_atoms[i].atom->getIsotope();
355 ivj = dp_atoms[j].atom->getIsotope();
358 }
else if (ivi > ivj) {
364 ivi = dp_atoms[i].totalNumHs;
365 ivj = dp_atoms[j].totalNumHs;
368 }
else if (ivi > ivj) {
372 ivi = dp_atoms[i].atom->getFormalCharge();
373 ivj = dp_atoms[j].atom->getFormalCharge();
376 }
else if (ivi > ivj) {
380 if (df_useChirality) {
382 ivi = dp_atoms[i].whichStereoGroup;
384 ivj = dp_atoms[j].whichStereoGroup;
388 }
else if (ivj && !ivi) {
390 }
else if (ivi && ivj) {
391 ivi =
static_cast<unsigned int>(dp_atoms[i].typeOfStereoGroup);
392 ivj =
static_cast<unsigned int>(dp_atoms[j].typeOfStereoGroup);
395 }
else if (ivi > ivj) {
398 ivi = dp_atoms[i].whichStereoGroup - 1;
399 ivj = dp_atoms[j].whichStereoGroup - 1;
401 std::set<unsigned int> sgi;
403 sgi.insert(dp_atoms[sgat->getIdx()].index);
405 std::set<unsigned int> sgj;
407 sgj.insert(dp_atoms[sgat->getIdx()].index);
411 }
else if (sgi > sgj) {
421 ivi = dp_atoms[i].atom->getChiralTag() != 0;
422 ivj = dp_atoms[j].atom->getChiralTag() != 0;
425 }
else if (ivi > ivj) {
431 ivi = getChiralRank(dp_mol, dp_atoms, i);
434 ivj = getChiralRank(dp_mol, dp_atoms, j);
438 }
else if (ivi > ivj) {
445 if (df_useChiralityRings) {
447 ivi = getAtomRingNbrCode(i);
448 ivj = getAtomRingNbrCode(j);
451 }
else if (ivi > ivj) {
461 const boost::dynamic_bitset<> *dp_atomsInPlay{
nullptr},
462 *dp_bondsInPlay{
nullptr};
463 bool df_useNbrs{
false};
464 bool df_useIsotopes{
true};
465 bool df_useChirality{
true};
466 bool df_useChiralityRings{
true};
470 const boost::dynamic_bitset<> *atomsInPlay =
nullptr,
471 const boost::dynamic_bitset<> *bondsInPlay =
nullptr)
474 dp_atomsInPlay(atomsInPlay),
475 dp_bondsInPlay(bondsInPlay),
477 df_useIsotopes(true),
478 df_useChirality(true),
479 df_useChiralityRings(true) {}
481 if (dp_atomsInPlay && !((*dp_atomsInPlay)[i] || (*dp_atomsInPlay)[j])) {
484 int v = basecomp(i, j);
490 if (!dp_atomsInPlay || (*dp_atomsInPlay)[i]) {
493 if (!dp_atomsInPlay || (*dp_atomsInPlay)[j]) {
497 for (
unsigned int ii = 0;
498 ii < dp_atoms[i].bonds.size() && ii < dp_atoms[j].bonds.size();
501 bondholder::compare(dp_atoms[i].bonds[ii], dp_atoms[j].bonds[ii]);
507 if (dp_atoms[i].bonds.size() < dp_atoms[j].bonds.size()) {
509 }
else if (dp_atoms[i].bonds.size() > dp_atoms[j].bonds.size()) {
524 void getAtomNeighborhood(std::vector<bondholder> &nbrs)
const {
525 for (
unsigned j = 0; j < nbrs.size(); ++j) {
526 unsigned int nbrIdx = nbrs[j].nbrIdx;
531 const Atom *nbr = dp_atoms[nbrIdx].atom;
532 nbrs[j].nbrSymClass =
535 std::sort(nbrs.begin(), nbrs.end(), bondholder::greater);
539 int basecomp(
int i,
int j)
const {
541 unsigned int ivi, ivj;
544 ivi = dp_atoms[i].index;
545 ivj = dp_atoms[j].index;
548 }
else if (ivi > ivj) {
553 ivi = dp_atoms[i].atom->getAtomicNum();
554 ivj = dp_atoms[j].atom->getAtomicNum();
557 }
else if (ivi > ivj) {
562 ivi = dp_atoms[i].atom->getIsotope();
563 ivj = dp_atoms[j].atom->getIsotope();
566 }
else if (ivi > ivj) {
574 if (dp_atoms[i].atom->getPropIfPresent(common_properties::_CIPCode,
576 ivi = cipCode ==
"R" ? 2 : 1;
578 if (dp_atoms[j].atom->getPropIfPresent(common_properties::_CIPCode,
580 ivj = cipCode ==
"R" ? 2 : 1;
584 }
else if (ivi > ivj) {
595 bool df_useNbrs{
false};
598 : dp_atoms(atoms), dp_mol(&m), df_useNbrs(false) {}
603 int v = basecomp(i, j);
609 getAtomNeighborhood(dp_atoms[i].bonds);
610 getAtomNeighborhood(dp_atoms[j].bonds);
615 for (
unsigned int ii = 0;
616 ii < dp_atoms[i].bonds.size() && ii < dp_atoms[j].bonds.size();
618 int cmp = bondholder::compare(
624 for (
unsigned int ii = 0;
625 ii < dp_atoms[i].bonds.size() && ii < dp_atoms[j].bonds.size();
628 bondholder::compare(dp_atoms[i].bonds[ii], dp_atoms[j].bonds[ii]);
633 if (dp_atoms[i].bonds.size() < dp_atoms[j].bonds.size()) {
635 }
else if (dp_atoms[i].bonds.size() > dp_atoms[j].bonds.size()) {
648template <
typename CompareFunc>
681 start = order + offset;
699 for (
int k = 0;
k <
len; ++
k) {
706 for (i =
count[index]; i <
len; i++) {
716 for (
unsigned j = 0;
j < atoms[index].
degree; ++
j) {
724 for (i =
count[index]; i <
len; i++) {
726 for (
unsigned j = 0;
j < atoms[index].
degree; ++
j) {
745template <
typename CompareFunc>
756 for (
unsigned int i = 0; i <
nAtoms; i++) {
762 index = order[offset];
763 atoms[index].
index = offset;
768 if (atoms[index].degree < 1) {
771 for (
unsigned j = 0;
j < atoms[index].
degree; ++
j) {
798 int *order,
int *
count,
806 std::vector<unsigned int> &
res,
807 bool breakTies =
true,
812 const ROMol &mol, std::vector<unsigned int> &
res,
815 const std::vector<std::string> *atomSymbols,
816 const std::vector<std::string> *
bondSymbols,
bool breakTies,
820 const ROMol &mol, std::vector<unsigned int> &
res,
823 const std::vector<std::string> *atomSymbols =
nullptr,
831 std::vector<unsigned int> &
res);
834 std::vector<Canon::canon_atom> &atoms,
839 std::vector<Canon::canon_atom> &atoms,
841 const std::vector<std::string> *atomSymbols,
848 bool useSpecial =
false,
bool useChirality =
false,
849 const boost::dynamic_bitset<> *
atomsInPlay =
nullptr,
850 const boost::dynamic_bitset<> *
bondsInPlay =
nullptr);
#define PRECONDITION(expr, mess)
Defines the primary molecule class ROMol as well as associated typedefs.
Defines the class StereoGroup which stores relationships between the absolute configurations of atoms...
The class for representing atoms.
int getAtomicNum() const
returns our atomic number
@ CHI_TETRAHEDRAL_CW
tetrahedral: clockwise rotation (SMILES @@)
@ CHI_TETRAHEDRAL_CCW
tetrahedral: counter-clockwise rotation (SMILES
BondStereo
the nature of the bond's stereochem (for cis/trans)
AtomCompareFunctor(Canon::canon_atom *atoms, const ROMol &m, const boost::dynamic_bitset<> *atomsInPlay=nullptr, const boost::dynamic_bitset<> *bondsInPlay=nullptr)
int operator()(int i, int j) const
ChiralAtomCompareFunctor(Canon::canon_atom *atoms, const ROMol &m)
int operator()(int i, int j) const
ChiralAtomCompareFunctor()
int operator()(int i, int j) const
SpecialChiralityAtomCompareFunctor(Canon::canon_atom *atoms, const ROMol &m, const boost::dynamic_bitset<> *atomsInPlay=nullptr, const boost::dynamic_bitset<> *bondsInPlay=nullptr)
SpecialChiralityAtomCompareFunctor()
SpecialSymmetryAtomCompareFunctor()
SpecialSymmetryAtomCompareFunctor(Canon::canon_atom *atoms, const ROMol &m, const boost::dynamic_bitset<> *atomsInPlay=nullptr, const boost::dynamic_bitset<> *bondsInPlay=nullptr)
int operator()(int i, int j) const
const std::vector< StereoGroup > & getStereoGroups() const
Gets a reference to the groups of atoms with relative stereochemistry.
unsigned int getNumAtoms() const
returns our number of atoms
#define RDKIT_GRAPHMOL_EXPORT
void rankWithFunctor(T &ftor, bool breakTies, int *order, bool useSpecial=false, bool useChirality=false, const boost::dynamic_bitset<> *atomsInPlay=nullptr, const boost::dynamic_bitset<> *bondsInPlay=nullptr)
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, bool needsInit)
RDKIT_GRAPHMOL_EXPORT void CreateSinglePartition(unsigned int nAtoms, int *order, int *count, canon_atom *atoms)
RDKIT_GRAPHMOL_EXPORT void initCanonAtoms(const ROMol &mol, std::vector< Canon::canon_atom > &atoms, bool includeChirality=true)
RDKIT_GRAPHMOL_EXPORT void ActivatePartitions(unsigned int nAtoms, int *order, int *count, int &activeset, int *next, int *changed)
const unsigned int ATNUM_CLASS_OFFSET
RDKIT_GRAPHMOL_EXPORT void updateAtomNeighborNumSwaps(canon_atom *atoms, std::vector< bondholder > &nbrs, unsigned int atomIdx, std::vector< std::pair< unsigned int, unsigned int > > &result)
void BreakTies(const ROMol &mol, canon_atom *atoms, CompareFunc compar, int mode, int *order, int *count, int &activeset, int *next, int *changed, char *touchedPartitions)
void RefinePartitions(const ROMol &mol, canon_atom *atoms, CompareFunc compar, int mode, int *order, int *count, int &activeset, int *next, int *changed, char *touchedPartitions)
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)
RDKIT_GRAPHMOL_EXPORT void chiralRankMolAtoms(const ROMol &mol, std::vector< unsigned int > &res)
RDKIT_GRAPHMOL_EXPORT void updateAtomNeighborIndex(canon_atom *atoms, std::vector< bondholder > &nbrs)
RDKIT_GRAPHMOL_EXPORT void rankMolAtoms(const ROMol &mol, std::vector< unsigned int > &res, bool breakTies=true, bool includeChirality=true, bool includeIsotopes=true)
bool rdvalue_is(const RDValue_cast_t)
void hanoisort(int *base, int nel, int *count, int *changed, CompareFunc compar)
unsigned int countSwapsToInterconvert(const T &ref, T probe)
const std::string * p_symbol
static bool greater(const bondholder &lhs, const bondholder &rhs)
bool operator<(const bondholder &o) const
int compareStereo(const bondholder &o) const
bondholder(Bond::BondType bt, unsigned int bs, unsigned int ni, unsigned int nsc, unsigned int bidx)
bondholder(Bond::BondType bt, Bond::BondStereo bs, unsigned int ni, unsigned int nsc, unsigned int bidx)
static int compare(const bondholder &x, const bondholder &y, unsigned int div=1)
std::vector< bondholder > bonds
std::unique_ptr< int[]> nbrIds
std::vector< int > revistedNeighbors
std::vector< int > neighborNum