RWMOL_SPTR initProduct(const ROMOL_SPTR prodTemplateSptr) {
const ROMol *prodTemplate=prodTemplateSptr.get();
RWMol *res=new RWMol();
// --------- --------- --------- --------- --------- ---------
// Initialize by making a copy of the product template as a normal molecule.
// NOTE that we can't just use a normal copy because we do not want to end up
// with query atoms or bonds in the product.
// copy in the atoms:
ROMol::ATOM_ITER_PAIR atItP = prodTemplate->getVertices();
while(atItP.first != atItP.second ) {
Atom *oAtom=(*prodTemplate)[*(atItP.first++)].get();
Atom *newAtom=new Atom(*oAtom);
res->addAtom(newAtom,false,true);
int mapNum;
if(newAtom->getPropIfPresent(common_properties::molAtomMapNumber, mapNum)) {
// set bookmarks for the mapped atoms:
res->setAtomBookmark(newAtom,mapNum);
// now clear the molAtomMapNumber property so that it doesn't
// end up in the products (this was bug 3140490):
newAtom->clearProp(common_properties::molAtomMapNumber);
}
newAtom->setChiralTag(Atom::CHI_UNSPECIFIED);
// if the product-template atom has the inversion flag set
// to 4 (=SET), then bring its stereochem over, otherwise we'll
// ignore it:
int iFlag;
if(oAtom->getPropIfPresent(common_properties::molInversionFlag, iFlag)) {
if(iFlag==4) newAtom->setChiralTag(oAtom->getChiralTag());
}
// check for properties we need to set:
int val;
if(newAtom->getPropIfPresent(common_properties::_QueryFormalCharge, val)) {
newAtom->setFormalCharge(val);
}
if(newAtom->getPropIfPresent(common_properties::_QueryHCount, val)) {
newAtom->setNumExplicitHs(val);
}
if(newAtom->getPropIfPresent(common_properties::_QueryMass, val)) {
// FIX: technically should do something with this
//newAtom->setMass(val);
}
if(newAtom->getPropIfPresent(common_properties::_QueryIsotope, val)) {
newAtom->setIsotope(val);
}
}
// and the bonds:
ROMol::BOND_ITER_PAIR bondItP = prodTemplate->getEdges();
while(bondItP.first != bondItP.second ) {
const BOND_SPTR oldB=(*prodTemplate)[*(bondItP.first++)];
unsigned int bondIdx;
bondIdx=res->addBond(oldB->getBeginAtomIdx(),oldB->getEndAtomIdx(),oldB->getBondType())-1;
// make sure we don't lose the bond dir information:
Bond *newB=res->getBondWithIdx(bondIdx);
newB->setBondDir(oldB->getBondDir());
// Special case/hack:
// The product has been processed by the SMARTS parser.
// The SMARTS parser tags unspecified bonds as single, but then adds
// a query so that they match single or double
// This caused Issue 1748846
// http://sourceforge.net/tracker/index.php?func=detail&aid=1748846&group_id=160139&atid=814650
// We need to fix that little problem now:
if( oldB->hasQuery()) {
// remember that the product has been processed by the SMARTS parser.
std::string queryDescription=oldB->getQuery()->getDescription();
if(queryDescription=="BondOr" &&
oldB->getBondType()==Bond::SINGLE) {
// We need to fix that little problem now:
if(newB->getBeginAtom()->getIsAromatic() && newB->getEndAtom()->getIsAromatic()) {
newB->setBondType(Bond::AROMATIC);
newB->setIsAromatic(true);
} else {
newB->setBondType(Bond::SINGLE);
newB->setIsAromatic(false);
}
} else if(queryDescription=="BondNull") {
newB->setProp(common_properties::NullBond,1);
}
}
}
return RWMOL_SPTR(res);
} // end of initProduct()
static void addResult(std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR> >&
res, // const SignatureVector& resSignature,
const ROMol& mol,
const BondVector_t& bonds_selected, size_t maxCuts) {
#ifdef _DEBUG
std::cout << res.size() + 1 << ": ";
#endif
RWMol em(mol);
// loop through the bonds to delete. == deleteBonds()
unsigned isotope = 0;
std::map<unsigned, unsigned> isotope_track;
for (size_t i = 0; i < bonds_selected.size(); i++) {
#ifdef _DEBUG
{
std::string symbol =
em.getAtomWithIdx(bonds_selected[i].first)->getSymbol();
int label = 0;
em.getAtomWithIdx(bonds_selected[i].first)
->getPropIfPresent(common_properties::molAtomMapNumber, label);
char a1[32];
if (0 == label)
sprintf(a1, "\'%s\'", symbol.c_str(), label);
else
sprintf(a1, "\'%s:%u\'", symbol.c_str(), label);
symbol = em.getAtomWithIdx(bonds_selected[i].second)->getSymbol();
label = 0;
em.getAtomWithIdx(bonds_selected[i].second)
->getPropIfPresent(common_properties::molAtomMapNumber, label);
char a2[32];
if (0 == label)
sprintf(a2, "\'%s\'", symbol.c_str(), label);
else
sprintf(a2, "\'%s:%u\'", symbol.c_str(), label);
std::cout << "(" << bonds_selected[i].first << a1 << ","
<< bonds_selected[i].second << a2 << ") ";
}
#endif
isotope += 1;
// remove the bond
em.removeBond(bonds_selected[i].first, bonds_selected[i].second);
// now add attachement points and set attachment point lables
Atom* a = new Atom(0);
a->setProp(common_properties::molAtomMapNumber, (int)isotope);
unsigned newAtomA = em.addAtom(a, true, true);
em.addBond(bonds_selected[i].first, newAtomA, Bond::SINGLE);
a = new Atom(0);
a->setProp(common_properties::molAtomMapNumber, (int)isotope);
unsigned newAtomB = em.addAtom(a, true, true);
em.addBond(bonds_selected[i].second, newAtomB, Bond::SINGLE);
// keep track of where to put isotopes
isotope_track[newAtomA] = isotope;
isotope_track[newAtomB] = isotope;
}
#ifdef _DEBUG
std::cout << "\n";
#endif
RWMOL_SPTR core, side_chains; // core & side_chains output molecules
if (isotope == 1) {
side_chains = RWMOL_SPTR(new RWMol(em)); // output = '%s,%s,,%s.%s'
// DEBUG PRINT
#ifdef _DEBUG
// OK: std::cout<<res.size()+1<<" isotope="<< isotope <<","<<
// MolToSmiles(*side_chains, true) <<"\n";
#endif
} else if (isotope >= 2) {
std::vector<std::vector<int> > frags;
unsigned int nFrags = MolOps::getMolFrags(em, frags);
//#check if its a valid triple or bigger cut. matchObj = re.search(
//'\*.*\*.*\*', f)
// check if exists a fragment with maxCut connection points (*.. *.. *)
if (isotope >= 3) {
bool valid = false;
for (size_t i = 0; i < nFrags; i++) {
unsigned nLabels = 0;
for (size_t ai = 0; ai < frags[i].size(); ai++) {
if (isotope_track.end() !=
isotope_track.find(frags[i][ai])) // new added atom
++nLabels; // found connection point
}
if (nLabels >=
maxCuts) { // looks like it should be selected as core ! ??????
valid = true;
break;
}
}
if (!valid) {
#ifdef _DEBUG
std::cout << "isotope>=3: invalid fragments. fragment with maxCut "
"connection points not found"
<< "\n";
#endif
return;
}
}
size_t iCore = std::numeric_limits<size_t>::max();
side_chains = RWMOL_SPTR(new RWMol);
std::map<unsigned, unsigned>
visitedBonds; // key is bond index in source molecule
unsigned maxAttachments = 0;
for (size_t i = 0; i < frags.size(); i++) {
unsigned nAttachments = 0;
for (size_t ai = 0; ai < frags[i].size(); ai++) {
if (isotope_track.end() !=
isotope_track.find(
frags[i][ai])) // == if(a->hasProp("molAtomMapNumber"))
++nAttachments;
}
if (maxAttachments < nAttachments) maxAttachments = nAttachments;
if (1 == nAttachments) { // build side-chain set of molecules from
// selected fragment
std::map<unsigned, unsigned>
newAtomMap; // key is atom index in source molecule
for (size_t ai = 0; ai < frags[i].size(); ai++) {
Atom* a = em.getAtomWithIdx(frags[i][ai]);
newAtomMap[frags[i][ai]] =
side_chains->addAtom(a->copy(), true, true);
}
// add all bonds from this fragment
for (size_t ai = 0; ai < frags[i].size(); ai++) {
Atom* a = em.getAtomWithIdx(frags[i][ai]);
ROMol::OEDGE_ITER beg, end;
for (boost::tie(beg, end) = em.getAtomBonds(a); beg != end; ++beg) {
const BOND_SPTR bond = em[*beg];
if (newAtomMap.end() == newAtomMap.find(bond->getBeginAtomIdx()) ||
newAtomMap.end() == newAtomMap.find(bond->getEndAtomIdx()) ||
visitedBonds.end() != visitedBonds.find(bond->getIdx()))
continue;
unsigned ai1 = newAtomMap[bond->getBeginAtomIdx()];
unsigned ai2 = newAtomMap[bond->getEndAtomIdx()];
unsigned bi = side_chains->addBond(ai1, ai2, bond->getBondType());
visitedBonds[bond->getIdx()] = bi;
}
}
} else { // select the core fragment
// DEBUG PRINT
#ifdef _DEBUG
if (iCore != -1)
std::cout << "Next CORE found. iCore=" << iCore << " New i=" << i
<< " nAttachments=" << nAttachments << "\n";
#endif
if (nAttachments >= maxAttachments) // Choose a fragment with maximal
// number of connection points as a
// core
iCore = i;
}
}
// build core molecule from selected fragment
if (iCore != std::numeric_limits<size_t>::max()) {
core = RWMOL_SPTR(new RWMol);
visitedBonds.clear();
std::map<unsigned, unsigned>
newAtomMap; // key is atom index in source molecule
for (size_t i = 0; i < frags[iCore].size(); i++) {
unsigned ai = frags[iCore][i];
Atom* a = em.getAtomWithIdx(ai);
newAtomMap[ai] = core->addAtom(a->copy(), true, true);
}
// add all bonds from this fragment
for (size_t ai = 0; ai < frags[iCore].size(); ai++) {
Atom* a = em.getAtomWithIdx(frags[iCore][ai]);
ROMol::OEDGE_ITER beg, end;
for (boost::tie(beg, end) = em.getAtomBonds(a); beg != end; ++beg) {
const BOND_SPTR bond = em[*beg];
if (newAtomMap.end() == newAtomMap.find(bond->getBeginAtomIdx()) ||
newAtomMap.end() == newAtomMap.find(bond->getEndAtomIdx()) ||
visitedBonds.end() != visitedBonds.find(bond->getIdx()))
continue;
unsigned ai1 = newAtomMap[bond->getBeginAtomIdx()];
unsigned ai2 = newAtomMap[bond->getEndAtomIdx()];
unsigned bi = core->addBond(ai1, ai2, bond->getBondType());
visitedBonds[bond->getIdx()] = bi;
}
}
// DEBUG PRINT
#ifdef _DEBUG
// std::cout<<res.size()+1<<" isotope="<< isotope <<" "<< MolToSmiles(*core,
// true)<<", "<<MolToSmiles(*side_chains, true)<<"\n";
#endif
} // iCore != -1
}
// check for duplicates:
bool resFound = false;
size_t ri = 0;
for (ri = 0; ri < res.size(); ri++) {
const std::pair<ROMOL_SPTR, ROMOL_SPTR>& r = res[ri];
if (side_chains->getNumAtoms() == r.second->getNumAtoms() &&
side_chains->getNumBonds() == r.second->getNumBonds() &&
((NULL == core.get() && NULL == r.first.get()) ||
(NULL != core.get() && NULL != r.first.get() &&
core->getNumAtoms() == r.first->getNumAtoms() &&
core->getNumBonds() == r.first->getNumBonds()))) {
// ToDo accurate check:
// 1. compare hash code
if (computeMorganCodeHash(*side_chains) ==
computeMorganCodeHash(*r.second) &&
(NULL == core ||
computeMorganCodeHash(*core) == computeMorganCodeHash(*r.first))) {
// 2. final check to exclude hash collisions
// We decided that it does not neccessary to implement
resFound = true;
break;
}
}
}
if (!resFound) {
//std::cerr << "**********************" << std::endl;
// From rfrag.py
// now change the labels on sidechains and core
// to get the new labels, cansmi the dot-disconnected side chains
// the first fragment in the side chains has attachment label 1, 2nd: 2, 3rd: 3
// then change the labels accordingly in the core
std::map<unsigned int, int> canonicalAtomMaps;
if( side_chains.get() ) {
RWMol tmp_side_chain(*(side_chains.get()));
std::vector<int> oldMaps(tmp_side_chain.getNumAtoms(), 0);
// clear atom labels (they are used in canonicalization)
// and move them to dummy storage
for (ROMol::AtomIterator at = tmp_side_chain.beginAtoms(); at != tmp_side_chain.endAtoms();
++at) {
int label = 0;
if ((*at)->getPropIfPresent(common_properties::molAtomMapNumber, label) ) {
(*at)->clearProp(common_properties::molAtomMapNumber);
oldMaps[(*at)->getIdx()] = label;
}
}
const bool doIsomericSmiles = true; // should this be false???
std::string smiles = MolToSmiles(tmp_side_chain, doIsomericSmiles);
//std::cerr << "smiles: " << smiles << std::endl;
// Get the canonical output order and use it to remap
// the atom maps int the side chains
// these will get reapplied to the core (if there is a core)
const std::vector<unsigned int> &ranks = tmp_side_chain.getProp<
std::vector<unsigned int> >(
common_properties::_smilesAtomOutputOrder);
std::vector<std::pair<unsigned int, int> > rankedAtoms;
for(size_t idx=0;idx<ranks.size();++idx) {
unsigned int atom_idx = ranks[idx];
if(oldMaps[atom_idx] >0) {
const int label = oldMaps[atom_idx];
//std::cerr << "atom_idx: " << atom_idx << " rank: " << ranks[atom_idx] <<
// " molAtomMapNumber: " << label << std::endl;
rankedAtoms.push_back(std::make_pair(idx, label));
}
}
std::sort(rankedAtoms.begin(), rankedAtoms.end());
int nextMap = 0;
for(size_t i=0;i<rankedAtoms.size();++i) {
if(canonicalAtomMaps.find(rankedAtoms[i].second) == canonicalAtomMaps.end()) {
//std::cerr << "Remapping: " << rankedAtoms[i].second << " " << " to " << (i+1) <<
// std::endl;
canonicalAtomMaps[rankedAtoms[i].second] = ++nextMap;
}
}
}
//std::cerr << "======== Remap core " << std::endl;
if( core.get() ) { // remap core if it exists
for (ROMol::AtomIterator at = core->beginAtoms(); at != core->endAtoms();
++at) {
int label = 0;
if ((*at)->getPropIfPresent(common_properties::molAtomMapNumber, label) ) {
//std::cerr << "remapping core: " << label << " :" << canonicalAtomMaps[label] <<
// std::endl;
(*at)->setProp(common_properties::molAtomMapNumber, canonicalAtomMaps[label]);
}
}
}
//std::cerr << "======== Remap side-chain " << std::endl;
for (ROMol::AtomIterator at = side_chains->beginAtoms(); at != side_chains->endAtoms();
++at) {
int label = 0;
if ((*at)->getPropIfPresent(common_properties::molAtomMapNumber, label) ) {
//std::cerr << "remapping side chain: " << label << " :" <<
// canonicalAtomMaps[label] << std::endl;
(*at)->setProp(common_properties::molAtomMapNumber, canonicalAtomMaps[label]);
}
}
res.push_back(std::pair<ROMOL_SPTR, ROMOL_SPTR>(core, side_chains)); //
}
#ifdef _DEBUG
else
std::cout << res.size() + 1 << " --- DUPLICATE Result FOUND --- ri=" << ri
<< "\n";
#endif
}
double *getDistanceMat(const ROMol &mol,bool useBO,
bool useAtomWts,
bool force,
const char *propNamePrefix){
std::string propName;
boost::shared_array<double> sptr;
if(propNamePrefix){
propName = propNamePrefix;
} else {
propName = "";
}
propName+="DistanceMatrix";
// make sure we don't use the nonBO cache for the BO matrix and vice versa:
if(useBO) propName+="BO";
if(!force && mol.hasProp(propName)){
mol.getProp(propName,sptr);
return sptr.get();
}
int nAts=mol.getNumAtoms();
double *dMat = new double[nAts*nAts];
int i,j;
// initialize off diagonals to LOCAL_INF and diagonals to 0
for(i=0;i<nAts*nAts;i++) dMat[i] = LOCAL_INF;
for(i=0;i<nAts;i++) dMat[i*nAts+i]=0.0;
ROMol::EDGE_ITER firstB,lastB;
boost::tie(firstB,lastB) = mol.getEdges();
while(firstB!=lastB){
const BOND_SPTR bond = mol[*firstB];
i = bond->getBeginAtomIdx();
j = bond->getEndAtomIdx();
double contrib;
if(useBO){
if(!bond->getIsAromatic()){
contrib = 1./bond->getBondTypeAsDouble();
} else {
contrib = 2. / 3.;
}
} else {
contrib = 1.0;
}
dMat[i*nAts+j]=contrib;
dMat[j*nAts+i]=contrib;
++firstB;
}
int *pathMat = new int[nAts*nAts];
memset(static_cast<void *>(pathMat),0,nAts*nAts*sizeof(int));
FloydWarshall(nAts,dMat,pathMat);
if(useAtomWts){
for (i = 0; i < nAts; i++) {
int anum = mol.getAtomWithIdx(i)->getAtomicNum();
dMat[i*nAts+i] = 6.0/anum;
}
}
sptr.reset(dMat);
mol.setProp(propName,sptr,true);
boost::shared_array<int> iSptr(pathMat);
mol.setProp(propName+"_Paths",iSptr,true);
return dMat;
};
static void addResult(std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR> >&
res, // const SignatureVector& resSignature,
const ROMol& mol,
const BondVector_t& bonds_selected, size_t maxCuts) {
#ifdef _DEBUG
std::cout << res.size() + 1 << ": ";
#endif
RWMol em(mol);
// loop through the bonds to delete. == deleteBonds()
unsigned isotope = 0;
std::map<unsigned, unsigned> isotope_track;
for (size_t i = 0; i < bonds_selected.size(); i++) {
#ifdef _DEBUG
{
std::string symbol =
em.getAtomWithIdx(bonds_selected[i].first)->getSymbol();
int label = 0;
em.getAtomWithIdx(bonds_selected[i].first)
->getPropIfPresent(common_properties::molAtomMapNumber, label);
char a1[32];
if (0 == label)
sprintf(a1, "\'%s\'", symbol.c_str(), label);
else
sprintf(a1, "\'%s:%u\'", symbol.c_str(), label);
symbol = em.getAtomWithIdx(bonds_selected[i].second)->getSymbol();
label = 0;
em.getAtomWithIdx(bonds_selected[i].second)
->getPropIfPresent(common_properties::molAtomMapNumber, label);
char a2[32];
if (0 == label)
sprintf(a2, "\'%s\'", symbol.c_str(), label);
else
sprintf(a2, "\'%s:%u\'", symbol.c_str(), label);
std::cout << "(" << bonds_selected[i].first << a1 << ","
<< bonds_selected[i].second << a2 << ") ";
}
#endif
isotope += 1;
// remove the bond
em.removeBond(bonds_selected[i].first, bonds_selected[i].second);
// now add attachement points and set attachment point lables
Atom* a = new Atom(0);
a->setProp(common_properties::molAtomMapNumber, (int)isotope);
unsigned newAtomA = em.addAtom(a, true, true);
em.addBond(bonds_selected[i].first, newAtomA, Bond::SINGLE);
a = new Atom(0);
a->setProp(common_properties::molAtomMapNumber, (int)isotope);
unsigned newAtomB = em.addAtom(a, true, true);
em.addBond(bonds_selected[i].second, newAtomB, Bond::SINGLE);
// keep track of where to put isotopes
isotope_track[newAtomA] = isotope;
isotope_track[newAtomB] = isotope;
}
#ifdef _DEBUG
std::cout << "\n";
#endif
RWMOL_SPTR core, side_chains; // core & side_chains output molecules
if (isotope == 1) {
side_chains = RWMOL_SPTR(new RWMol(em)); // output = '%s,%s,,%s.%s'
// DEBUG PRINT
#ifdef _DEBUG
// OK: std::cout<<res.size()+1<<" isotope="<< isotope <<","<<
// MolToSmiles(*side_chains, true) <<"\n";
#endif
} else if (isotope >= 2) {
std::vector<std::vector<int> > frags;
unsigned int nFrags = MolOps::getMolFrags(em, frags);
//#check if its a valid triple or bigger cut. matchObj = re.search(
//'\*.*\*.*\*', f)
// check if exists a fragment with maxCut connection points (*.. *.. *)
if (isotope >= 3) {
bool valid = false;
for (size_t i = 0; i < nFrags; i++) {
unsigned nLabels = 0;
for (size_t ai = 0; ai < frags[i].size(); ai++) {
if (isotope_track.end() !=
isotope_track.find(frags[i][ai])) // new added atom
++nLabels; // found connection point
}
if (nLabels >=
maxCuts) { // looks like it should be selected as core ! ??????
valid = true;
break;
}
}
if (!valid) {
#ifdef _DEBUG
std::cout << "isotope>=3: invalid fragments. fragment with maxCut "
"connection points not found"
<< "\n";
#endif
return;
}
}
size_t iCore = std::numeric_limits<size_t>::max();
side_chains = RWMOL_SPTR(new RWMol);
std::map<unsigned, unsigned>
visitedBonds; // key is bond index in source molecule
unsigned maxAttachments = 0;
for (size_t i = 0; i < frags.size(); i++) {
unsigned nAttachments = 0;
for (size_t ai = 0; ai < frags[i].size(); ai++) {
if (isotope_track.end() !=
isotope_track.find(
frags[i][ai])) // == if(a->hasProp("molAtomMapNumber"))
++nAttachments;
}
if (maxAttachments < nAttachments) maxAttachments = nAttachments;
if (1 == nAttachments) { // build side-chain set of molecules from
// selected fragment
std::map<unsigned, unsigned>
newAtomMap; // key is atom index in source molecule
for (size_t ai = 0; ai < frags[i].size(); ai++) {
Atom* a = em.getAtomWithIdx(frags[i][ai]);
newAtomMap[frags[i][ai]] =
side_chains->addAtom(a->copy(), true, true);
}
// add all bonds from this fragment
for (size_t ai = 0; ai < frags[i].size(); ai++) {
Atom* a = em.getAtomWithIdx(frags[i][ai]);
ROMol::OEDGE_ITER beg, end;
for (boost::tie(beg, end) = em.getAtomBonds(a); beg != end; ++beg) {
const BOND_SPTR bond = em[*beg];
if (newAtomMap.end() == newAtomMap.find(bond->getBeginAtomIdx()) ||
newAtomMap.end() == newAtomMap.find(bond->getEndAtomIdx()) ||
visitedBonds.end() != visitedBonds.find(bond->getIdx()))
continue;
unsigned ai1 = newAtomMap[bond->getBeginAtomIdx()];
unsigned ai2 = newAtomMap[bond->getEndAtomIdx()];
unsigned bi = side_chains->addBond(ai1, ai2, bond->getBondType());
visitedBonds[bond->getIdx()] = bi;
}
}
} else { // select the core fragment
// DEBUG PRINT
#ifdef _DEBUG
if (iCore != -1)
std::cout << "Next CORE found. iCore=" << iCore << " New i=" << i
<< " nAttachments=" << nAttachments << "\n";
#endif
if (nAttachments >= maxAttachments) // Choose a fragment with maximal
// number of connection points as a
// core
iCore = i;
}
}
// build core molecule from selected fragment
if (iCore != std::numeric_limits<size_t>::max()) {
core = RWMOL_SPTR(new RWMol);
visitedBonds.clear();
std::map<unsigned, unsigned>
newAtomMap; // key is atom index in source molecule
for (size_t i = 0; i < frags[iCore].size(); i++) {
unsigned ai = frags[iCore][i];
Atom* a = em.getAtomWithIdx(ai);
newAtomMap[ai] = core->addAtom(a->copy(), true, true);
}
// add all bonds from this fragment
for (size_t ai = 0; ai < frags[iCore].size(); ai++) {
Atom* a = em.getAtomWithIdx(frags[iCore][ai]);
ROMol::OEDGE_ITER beg, end;
for (boost::tie(beg, end) = em.getAtomBonds(a); beg != end; ++beg) {
const BOND_SPTR bond = em[*beg];
if (newAtomMap.end() == newAtomMap.find(bond->getBeginAtomIdx()) ||
newAtomMap.end() == newAtomMap.find(bond->getEndAtomIdx()) ||
visitedBonds.end() != visitedBonds.find(bond->getIdx()))
continue;
unsigned ai1 = newAtomMap[bond->getBeginAtomIdx()];
unsigned ai2 = newAtomMap[bond->getEndAtomIdx()];
unsigned bi = core->addBond(ai1, ai2, bond->getBondType());
visitedBonds[bond->getIdx()] = bi;
}
}
// DEBUG PRINT
#ifdef _DEBUG
// std::cout<<res.size()+1<<" isotope="<< isotope <<" "<< MolToSmiles(*core,
// true)<<", "<<MolToSmiles(*side_chains, true)<<"\n";
#endif
} // iCore != -1
}
// check for dublicates:
bool resFound = false;
size_t ri = 0;
for (ri = 0; ri < res.size(); ri++) {
const std::pair<ROMOL_SPTR, ROMOL_SPTR>& r = res[ri];
if (side_chains->getNumAtoms() == r.second->getNumAtoms() &&
side_chains->getNumBonds() == r.second->getNumBonds() &&
((NULL == core.get() && NULL == r.first.get()) ||
(NULL != core.get() && NULL != r.first.get() &&
core->getNumAtoms() == r.first->getNumAtoms() &&
core->getNumBonds() == r.first->getNumBonds()))) {
// ToDo accurate check:
// 1. compare hash code
if (computeMorganCodeHash(*side_chains) ==
computeMorganCodeHash(*r.second) &&
(NULL == core ||
computeMorganCodeHash(*core) == computeMorganCodeHash(*r.first))) {
// 2. final check to exclude hash collisions
// We decided that it does not neccessary to implement
resFound = true;
break;
}
}
}
if (!resFound)
res.push_back(std::pair<ROMOL_SPTR, ROMOL_SPTR>(core, side_chains)); //
#ifdef _DEBUG
else
std::cout << res.size() + 1 << " --- DUPLICATE Result FOUND --- ri=" << ri
<< "\n";
#endif
}