Greg,
Thanks. The first way does not work. I got the following error message.
*Database.cpp:148:15: **error: **cannot initialize a variable of type
'RDKit::Atom *'*
* with an rvalue of type 'const RDKit::Atom *'*
Atom *atom = (*pCurrentROMol)[*atBegin];
The second way, which uses "auto", works. I also updated the code for bond
and got a new error with the following error message.
*Database.cpp:164:49: **error: **no member named 'get' in 'RDKit::Bond'*
sEdgeLabel += ((queryIsBondInRing(bond->get())) ? "ring|" :
"linear|" );
* ~~~~ ^*
1 error generated.
Could you please confirm that the updated class Bond removes method get()?
If this is the case, which method should I use?
Again, thank you very much for your help!
Yingfeng
On Wed, Dec 12, 2018 at 12:58 AM Greg Landrum <[email protected]>
wrote:
> Hi Yingfeng,
>
> As part of the move over to Modern C++ we also changed the way atoms and
> bonds are stored in molecules: you now get raw pointers back instead of
> smart pointers.
> If you change your code from:
> boost::shared_ptr<Atom> atom = (*pCurrentROMol)[*atBegin];
> to:
> Atom *atom = (*pCurrentROMol)[*atBegin];
> or, even simpler:
> auto atom = (*pCurrentROMol)[*atBegin];
>
> things should work.
> -greg
>
>
> On Wed, Dec 12, 2018 at 12:36 AM 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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