Unable to get INCHIKEY value for an inchi string

[Abhimanyu Sirohi]

Hi,

The following code returns a NULL pointer for inchikey:

int mol = indigoLoadMoleculeFromString("C1CCCCC1");
const char* inchi = indigoInchiGetInchi(mol); // InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2
const char* inchik = indigoInchiGetInchiKey(inchi); // NULL pointer

The problem seems to be indigoInchiGetInchiKey method of indigo_inchi_api.cpp file. The passed in inchi_string is somehow assigned to self.tmp_string which is cleared for output in IndigoInchi::InChIKeymethod of indigo_inchi_core.cpp.

Regards,

Abhi

[Savelyev Alexander]

Hi

The C interface has slightly different usage. In the current example it is not a null pointer but a error message. But the tmp buffer issue also affects the specified issue. The general usage:

int mol = indigoLoadMoleculeFromString("C1CCCCC1");

      if(mol < 0 ) {
         printf("%s\n", indigoGetLastError());
         exit(-1);

      }
      const char* inchi = indigoInchiGetInchi(mol); // InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2

      if(inchi == 0) {
         printf("%s\n", indigoGetLastError());
         exit(-1);
      }
      printf("%s\n", inchi);

      const char* inchik = indigoInchiGetInchiKey(inchi); // NULL pointer

      if (inchik == 0) {
         printf("%s\n", indigoGetLastError());
         exit(-1);
      }
      printf("%s\n", inchik);

(the returned result should be verified each time)

Output

InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2
indigo-inchi: INCHIKEY_INVALID_INCHI_PREFIX

The example above still incorrect, because inchi string is passed into the indigoInchiGetInchiKey() funciton. Each returned string should be copied! Because, it will be lost otherwise. indigoGetLastError() also uses tmp_buffer

I will use cpp code in order to decrease number of lines. But the same logic can be implemented using simple C. Also, a handler for errors (which will throw exception in our examples) can be passed as a callback, to short the code. Here is the correct usage:

static void errorHandling(const char* message, void* context) {
   throw Exception(message);
}
.......
    try {
       qword id = indigoAllocSessionId();
       indigoSetSessionId(id);
       indigoSetErrorHandler(errorHandling, 0);

       int mol = indigoLoadMoleculeFromString("C1CCCCC1");

       std::string inchi = indigoInchiGetInchi(mol); // copy inchi string
       std::cout << inchi << std::endl;;
       
       std::string inchik = indigoInchiGetInchiKey(inchi.c_str()); // pass inchi string, copy inchikey
       std::cout << inchik << std::endl;;

    catch(Exception& ex) {
         std::cout << ex.message();
    }

InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2
XDTMQSROBMDMFD-UHFFFAOYSA-N

Thanks
Alexander

[Abhimanyu Sirohi]

Thanks a lot. I got a hint after I posted this question that the inchiKey method requires a copy of the string. When I debugged the indigo code, I noticed that the passed-in string gets cleared automatically.

Thanks

Abhi