static inline void processCuts(
size_t i, size_t maxCuts, BondVector_t& bonds_selected,
const std::vector<BondVector_t>& matching_bonds, const ROMol& mol,
std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR> >& res) {
for (size_t x = i; x < matching_bonds.size(); x++) {
appendBonds(bonds_selected, matching_bonds[x]);
addResult(res, mol, bonds_selected, maxCuts);
if (bonds_selected.size() < maxCuts)
processCuts(x + 1, maxCuts, bonds_selected, matching_bonds, mol, res);
bonds_selected.pop_back();
}
}
bool fragmentMol(const ROMol& mol,
std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR> >& res,
const std::vector<unsigned int>& bondsToCut,
unsigned int minCuts,
unsigned int maxCuts) {
std::vector<BondVector_t> matching_bonds; // List of matched query's bonds
BOOST_FOREACH(unsigned int i, bondsToCut) {
const Bond *bond = mol.getBondWithIdx(i);
BondVector_t bonds;
unsigned int a1 = bond->getBeginAtomIdx();
unsigned int a2 = bond->getEndAtomIdx();
bonds.push_back( std::make_pair(a1, a2) );
matching_bonds.push_back(bonds);
}
// loop to generate every cut in the molecule
BondVector_t bonds_selected;
processCuts(0, minCuts, maxCuts, bonds_selected, matching_bonds, mol, res);
return true;
}
static inline void processCuts(
size_t i, size_t minCuts, size_t maxCuts, BondVector_t& bonds_selected,
const std::vector<BondVector_t>& matching_bonds, const ROMol& mol,
std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR> >& res) {
if(maxCuts < minCuts)
throw ValueErrorException("supplied maxCuts is less than minCuts");
if(minCuts==0)
throw ValueErrorException("minCuts must be greater than 0");
for (size_t x = i; x < matching_bonds.size(); x++) {
appendBonds(bonds_selected, matching_bonds[x]);
if(bonds_selected.size() >= minCuts) {
addResult(res, mol, bonds_selected, maxCuts);
}
if (bonds_selected.size() < maxCuts) {
processCuts(x + 1, minCuts, maxCuts, bonds_selected, matching_bonds, mol, res);
}
bonds_selected.pop_back();
}
}
bool fragmentMol(const ROMol& mol,
std::vector<std::pair<ROMOL_SPTR, ROMOL_SPTR> >& res,
unsigned int minCuts,
unsigned int maxCuts,
unsigned int maxCutBonds,
const std::string& pattern) {
#ifdef _DEBUG
for (size_t i = 0; i < mol.getNumAtoms(); i++) {
std::string symbol = mol.getAtomWithIdx(i)->getSymbol();
int label = 0;
mol.getAtomWithIdx(i)->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);
std::cout << "Atom " << i << ": " << a1; //<<" Bonds:";
std::cout << "\n";
}
#endif
res.clear();
std::auto_ptr<const ROMol> smarts((const ROMol*)SmartsToMol(pattern));
std::vector<MatchVectType>
matching_atoms; // one bond per match ! with default pattern
unsigned int total = SubstructMatch(mol, *smarts, matching_atoms);
#ifdef _DEBUG
std::cout << "total substructs =" << total
<< "\nmatching bonds (atom1, atom2):\n";
#endif
if (0 == total) // Not found. Return empty set of molecules
return false;
#ifdef _DEBUG
for (size_t i = 0; i < matching_atoms.size(); i++) {
std::string symbol =
mol.getAtomWithIdx(matching_atoms[i][0].second)->getSymbol();
int label = 0;
mol.getAtomWithIdx(matching_atoms[i][0].second)
->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 = mol.getAtomWithIdx(matching_atoms[i][1].second)->getSymbol();
label = 0;
mol.getAtomWithIdx(matching_atoms[i][1].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 << i << ": (" << matching_atoms[i][0].second << a1 << ","
<< matching_atoms[i][1].second << a2 << ") \n";
}
#endif
std::vector<BondVector_t> matching_bonds; // List of matched query's bonds
convertMatchingToBondVect(matching_bonds, matching_atoms, mol);
if (matching_bonds.size() > maxCutBonds) return false;
#ifdef _DEBUG
std::cout << "total matching_bonds = " << matching_bonds.size() << "\n";
#endif
// loop to generate every cut in the molecule
BondVector_t bonds_selected;
processCuts(0, minCuts, maxCuts, bonds_selected, matching_bonds, mol, res);
return true;
}