Dan,
Thank you for your reply. I copy the corresponding code segment here.
ROMol::VERTEX_ITER atBegin,atEnd;
boost::tie(atBegin,atEnd) = pCurrentROMol->getVertices();
while(atBegin!=atEnd)
{
boost::shared_ptr<Atom> atom = (*pCurrentROMol)[*atBegin];
pCurNode = new Node();
pCurNode->iNodeId = atom->getIdx();
pCurNode->sLabel = atom->getSymbol();
pCurGML->mNodeIdPos.insert(pair<int, size_t>(pCurNode->iNodeId,
pCurGML->vpNodes.size()));
pCurGML->vpNodes.push_back(pCurNode);
++atBegin;
}
The purpose here is to traverse all atoms.
Best,
Yingfeng
On Wed, Dec 12, 2018 at 12:50 AM Dan Nealschneider <
[email protected]> wrote:
> boost::shared_ptr<Atom> atom = (*pCurrentROMol)[*atBegin]
>
> should probably be:
>
> boost::shared_ptr<Atom> atom((*pCurrentROMol)[*atBegin]);
>
> Although I'm skeptical of the correctness of this code, because
> ROMol::operator[] returns a pointer to an atom owned by the ROMol. If your
> take ownership of the atom with a shared_ptr and then allow the shared_ptr
> to clean it up you're asking for trouble. Maybe you were trying to copy the
> atom, and control ownership with the shared_ptr?
>
> - dan nealschneider
>
> (né wandschneider)
>
> Senior Developer
> Schr*ö*dinger, Inc
> Portland, OR
>
>
>
>
> On Tue, Dec 11, 2018 at 3:36 PM Yingfeng Wang <[email protected]> wrote:
>
>> I am using the C++ library of RDKit on Mac. My C++ code works with
>> RDKit_2017_09_3. However, after I switch to RDKit 2018_03_4, I got the
>> following error when compiling my C++ source code.
>>
>> *Database.cpp:148:33: **error: **no viable conversion from 'const
>> RDKit::Atom *' to*
>>
>> * 'boost::shared_ptr<Atom>'*
>>
>> boost::shared_ptr<Atom> atom = (*pCurrentROMol)[*atBegin];
>>
>> * ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~*
>>
>> */usr/local/Cellar/boost/1.68.0/include/boost/smart_ptr/shared_ptr.hpp:358:21:
>> **note: *
>>
>> candidate constructor not viable: no known conversion from
>>
>> 'const RDKit::Atom *' to 'boost::detail::sp_nullptr_t' (aka
>> 'nullptr_t')
>>
>> for 1st argument
>>
>> BOOST_CONSTEXPR shared_ptr( boost::detail::sp_nullptr_t )
>> BOOST_SP_N...
>>
>> * ^*
>>
>> */usr/local/Cellar/boost/1.68.0/include/boost/smart_ptr/shared_ptr.hpp:422:5:
>> **note: *
>>
>> candidate constructor not viable: no known conversion from
>>
>> 'const RDKit::Atom *' to 'const boost::shared_ptr<RDKit::Atom> &'
>> for 1st
>>
>> argument
>>
>> shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ),
>> p...
>>
>> * ^*
>>
>> I am using Clang on Mac. The version information is given as follows.
>>
>> g++ -v
>>
>> Configured with: --prefix=/Library/Developer/CommandLineTools/usr
>> --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/c++/4.2.1
>>
>> Apple LLVM version 10.0.0 (clang-1000.10.44.4)
>>
>> Target: x86_64-apple-darwin18.2.0
>>
>> Thread model: posix
>>
>> I notice that "Starting with the 2018_03 release, the RDKit core C++
>> code is written in modern C++; for this release that means C++11. "
>>
>> Actually, I also use -std=c++11 when compiling my C++ source code. I
>> also tested RDKit 2018_09_1 and got the similar error. I am wondering how
>> to fix this problem.
>>
>> Thanks.
>>
>> Yingfeng
>>
>>
>> _______________________________________________
>> Rdkit-discuss mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>
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