Rafel,
Valgrind often reports uninitialized-variable errors and off-by-one array
index errors in system libraries. In the valgrind output you provided, the
error is in libz, the gzip-compression system library.
This has nothing to do with OpenBabel, and is probably a harmless warning.
Craig
On Thu, Sep 5, 2013 at 4:16 AM, Rafel Israels <
rafel.isra...@scai.fraunhofer.de> wrote:
> Dear all,
>
> As a new Babel-user first of all I'd like to thank you for this great
> software !!
>
> My question: what is the correct way (in c++) to generate an OBMol
> object from a smiles-code ? I know how to convert smiles e.g. to inchi
> directly using a conv->convert(), but I dont see yet how I can get
> access to the obMol object ? My below code seems to work but leads to a
> valgrind error.
>
> Related to this question: is there an API-description where I could
> have found the answer to this and similar questions ?
>
> regards,
>
> Rafel
>
>
> #include <iostream>
> #include <openbabel/obconversion.h>
> #include <openbabel/mol.h>
>
> int main() {
>
> OpenBabel::OBMol *obMol = new OpenBabel::OBMol();
>
> // conversion from smiles into inchi-key
> OpenBabel::OBConversion conv(NULL,&std::cout);
> conv.SetInAndOutFormats("SMI","inchi");
> conv.AddOption("K",OpenBabel::OBConversion::OUTOPTIONS);
>
> // following statement raises valgrind error 'conditional jump ..'
> conv.ReadString(obMol, "C");
>
> // just a test to see that obMol is assigned
> conv.Write(obMol);
> delete obMol;
>
> }
>
> valgrind error:
>
> ==13841== Conditional jump or move depends on uninitialised value(s)
> ==13841== at 0x5D154E0: inflateReset2 (in
> /lib/x86_64-linux-gnu/libz.so.1.2.3.4)
> ==13841== by 0x5D155D8: inflateInit2_ (in
> /lib/x86_64-linux-gnu/libz.so.1.2.3.4)
> ==13841== by 0x4F3CEFC: ??? (in /usr/lib/libopenbabel.so.4.0.0)
> ==13841== by 0x4F3D078: ??? (in /usr/lib/libopenbabel.so.4.0.0)
> ==13841== by 0x4F3D1A9: ??? (in /usr/lib/libopenbabel.so.4.0.0)
> ==13841== by 0x4F35398:
> OpenBabel::OBConversion::Read(OpenBabel::OBBase*, std::istream*) (in
> /usr/lib/libopenbabel.so.4.0.0)
> ==13841== by 0x4F35953:
> OpenBabel::OBConversion::ReadString(OpenBabel::OBBase*, std::string) (in
> /usr/lib/libopenbabel.so.4.0.0)
> ==13841== by 0x400F8B: main (test.cpp:20)
>
>
>
>
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