Hi Jarod,
that is correct. Applying a reaction to a molecule may produce more than one
product (depending on the reaction and reactants), so the method will return a
vector of products for every reactant (i.e. a vector of vectors of molecules).
Consider adding a nested loop within your loop:
// ...
for (auto& productVector : prods) {
for (auto& mol : productVector) {
std::cout << RDKit::MolToSmiles(*mol) << std::endl;
}
}
// ...
Best,
Chris
________________________________________
From: Jarod Younker <[email protected]>
Sent: Tuesday, December 6, 2022 1:13:11 PM
To: [email protected]
Cc: [email protected]
Subject: Re: [Rdkit-discuss] std::vector<boost::shared_ptr<RDKit::ROMol> >
object (RxnSmarts)
Thank you Garth. Implement the dereference, still getting a compilation error:
test.cpp:37:37: error: no match for ‘operator*’ (operand type is
‘std::vector<boost::shared_ptr<RDKit::ROMol> >’)
37 | std::cout << RDKit::MolToSmiles(*mol) << std::endl;
It looks as if “mol” is still a “vector,” not an element of the range based
loop.
Sent from my iPhone
On Dec 5, 2022, at 9:16 AM, [email protected] wrote:
I think that you need to deference the pointer (replace mol by *mol):
for( auto & mol: prods ) {
std::cout << RDKit::MolToSmiles(*mol) << std::endl;
}
As indicated by this message:
opt/rdkit-Release_2022_09_2/Code/GraphMol/SmilesParse/SmilesWrite.h:116:45:
note: no known conversion for argument 1 from ‘std::vector<boost::shared_pt
r<RDKit::ROMol> >’ to ‘const RDKit::ROMol&’
Cheers,
Gareth
From: Jarod Younker <[email protected]>
Sent: Monday, December 5, 2022 7:32 AM
To: [email protected]
Subject: [Rdkit-discuss] std::vector<boost::shared_ptr<RDKit::ROMol> > object
(RxnSmarts)
I’m new to C++ RDKit. How do I perform functions on elements of
std::vector<boost::shared_ptr<RDKit::ROMol> > object? I’m struggle to unpack
it (see highlighted sections below).
P.S. This is simply cut and pasted from the documentation with on addition:
MolToSmiles()
Thank you, Jarod
std::string smi="[O:1]>>[N:1]";
RDKit::ChemicalReaction *rxn = RDKit::RxnSmartsToChemicalReaction(smi);
rxn->initReactantMatchers();
RDKit::MOL_SPTR_VECT reacts;
reacts.clear();
smi = "OCO";
RDKit::ROMol *mol = RDKit::SmilesToMol(smi);
reacts.push_back(RDKit::ROMOL_SPTR(mol));
std::vector<RDKit::MOL_SPTR_VECT> prods;
prods = rxn->runReactants(reacts);
// here prods has two entries, because there are two Os in the
// reactant.
for( auto & mol: prods ) {
std::cout << RDKit::MolToSmiles(mol) << std::endl;
}
reacts[0]->getAtomWithIdx(0)->setProp(RDKit::common_properties::_protected,1);
prods = rxn->runReactants(reacts);
// here prods only has one entry, the reaction at atom 0
// has been blocked by the _protected property
test.cpp: In function ‘int main()’:
test.cpp:37:36: error: no matching function for call to
‘MolToSmiles(std::vector<boost::shared_ptr<RDKit::ROMol> >&)’
37 | std::cout << RDKit::MolToSmiles(mol) << std::endl;
| ~~~~~~~~~~~~~~~~~~^~~~~
In file included from test.cpp:5:
/opt/rdkit-Release_2022_09_2/Code/GraphMol/SmilesParse/SmilesWrite.h:96:38:
note: candidate: ‘std::string RDKit::MolToSmiles(const ROMol&, const SmilesWri
teParams&)’
96 | RDKIT_SMILESPARSE_EXPORT std::string MolToSmiles(
| ^~~~~~~~~~~
/opt/rdkit-Release_2022_09_2/Code/GraphMol/SmilesParse/SmilesWrite.h:96:38:
note: candidate expects 2 arguments, 1 provided
/opt/rdkit-Release_2022_09_2/Code/GraphMol/SmilesParse/SmilesWrite.h:116:20:
note: candidate: ‘std::string RDKit::MolToSmiles(const ROMol&, bool, bool, in
t, bool, bool, bool, bool)’
116 | inline std::string MolToSmiles(const ROMol &mol, bool doIsomericSmiles
= true,
| ^~~~~~~~~~~
/opt/rdkit-Release_2022_09_2/Code/GraphMol/SmilesParse/SmilesWrite.h:116:45:
note: no known conversion for argument 1 from ‘std::vector<boost::shared_pt
r<RDKit::ROMol> >’ to ‘const RDKit::ROMol&’
116 | inline std::string MolToSmiles(const ROMol &mol, bool doIsomericSmiles
= true,
Sent from my iPhone
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