Not sure if it will help, but the python version of IsInRing checks to see
if the sssr is initialized. Here is the C++ code that is used, you may be
able to adapt it to your needs:
bool BondIsInRing(const Bond *bond) {
if (!bond->getOwningMol().getRingInfo()->isInitialized()) {
MolOps::findSSSR(bond->getOwningMol());
}
return bond->getOwningMol().getRingInfo()->numBondRings(bond->getIdx())
!= 0;
}
On Wed, Apr 13, 2016 at 11:59 AM, Yingfeng Wang <ywang...@gmail.com> wrote:
> Paolo,
>
> Thanks. As I mentioned in the end of my question, setting this flag true
> may cause other problems. In the python version, the sanitize flag is also
> false, but it works. Is it possible to figure out a workaround for checking
> whether each bond is in a ring in the C++ version?
>
> Best,
> Yingfeng
>
> On Wed, Apr 13, 2016 at 11:53 AM, Paolo Tosco <paolo.to...@unito.it>
> wrote:
>
>> Dear Yingfeng,
>>
>> the reason why RingInfo is not initialized is that you are invoking
>> SmilesToMol() with the sanitize flag set to false; setting that parameter
>> to true in the SmilesToMol() call should fix your problem.
>>
>> Kind regards,
>> Paolo
>>
>>
>> On 4/13/2016 16:48, Yingfeng Wang wrote:
>>
>> This is my C++ code.
>>
>>
>> #include <INCHI-API/inchi.h>
>> #include <GraphMol/RDKitBase.h>
>> #include <RDGeneral/types.h>
>> #include <RDGeneral/RDLog.h>
>> #include <GraphMol/SmilesParse/SmilesParse.h>
>>
>> using namespace RDKit;
>> using namespace std;
>>
>> int main(int argc, const char * argv[])
>> {
>> RWMol* pCurMol;
>> MolGraph curTopology;
>> vector<vector<int> > viiRingBonds;
>> string sSmiles = "Oc1ncnnc1-c1ccccc1";
>> list<boost::list_edge<unsigned long, boost::shared_ptr<Bond> >
>> >::const_iterator itEdge;
>>
>> pCurMol = SmilesToMol(sSmiles, 0, false);
>> curTopology = pCurMol->getTopology();
>> viiRingBonds = pCurMol->getRingInfo()->bondRings();
>> for (itEdge = curTopology.m_edges.begin(); itEdge !=
>> curTopology.m_edges.end(); ++itEdge)
>> if (queryIsBondInRing(itEdge->m_property.get()))
>> cout<<"get one ring bond"<<endl;
>>
>> return 0;
>> }
>>
>> It crashes in the following line
>>
>> queryIsBondInRing(itEdge->m_property.get())
>>
>> with the following information.
>>
>> Pre-condition Violation
>> RingInfo not initialized
>> Violation occurred on line 67 in file
>> /Users/yingfeng/software/RDKit/rdkit-Release_2015_03_1/Code/GraphMol/RingInfo.cpp
>> Failed Expression: df_init
>> ****
>>
>> libc++abi.dylib: terminating with uncaught exception of type
>> Invar::Invariant: Pre-condition Violation
>>
>>
>> Actually, the corresponding python version works.
>>
>> >>> from rdkit import Chem
>> >>> sSmiles = "Oc1ncnnc1-c1ccccc1"
>> >>> curMol =Chem.MolFromSmiles(sSmiles, False)
>> >>> iBondsNum = curMol.GetNumBonds()
>> >>> for i in range(iBondsNum):
>> ... current_bond = curMol.GetBondWithIdx(i)
>> ... if current_bond.IsInRing():
>> ... print i
>> ...
>> 1
>> 2
>> 3
>> 4
>> 5
>> 7
>> 8
>> 9
>> 10
>> 11
>> 12
>> 13
>>
>>
>> Please note that the problem cannot be solved by using
>> SmilesToMol(sSmiles, 0, true);
>>
>> because it may cause other problems, e.g.,
>> string sSmiles = "c.ccccc";
>> Therefore, I would like to stay with SmilesToMol(sSmiles, 0, false);
>>
>> Could you please give me some hints for fixing the C++ version, and
>> getting the similar results of the python version.
>>
>>
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>>
>>
>
>
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