Timing out an export to InChI calculation

Hi,

In converting a large number of SMILES to InChI, I found that the InChI calculation for the complex SMILES given below never ends. I have tried leaving it running for several hours and it does not end.

Because I am regularly processing files containing a large number of SMILES to InChI, I would like to be able to either terminate each InChI calculation after a certain amount of time and move on with my main code, or alternatively provide a time limit each time I call the export function. However, I can't find any capability to do this in the documentation. I also tried spawning a separate thread for my InChI calculation, and then terminating the thread after my time has expired. However, the InChI calculation is not responding to my thread interruption; my main code proceeds, but my spawned thread will not terminate.

Is there any way that I can implement or request a time out of the InChI calculation?

 

More detail:

String preferredInchiFormat = "inchi:SAbs,AuxNone";

String smiles = "PPS(PP(S(PP)(=PP)=PP)S(=PP(S(PP)(=PP)=PP)S(PP)(=PP)=PP)(=PP(S(PP)(=PP)=PP)S(PP)(=PP)=PP)P(P(P(P=S)P(S(=PP(S(PP)(=PP)=PP)S(PP)(=PP)=PP)(=PP(S(PP)(=PP)=PP)S(PP)(=PP)=PP)P(P(S(PP)(=PP)=PP)S(PP)(=PP)=PP)S(PP)(=PP)=PP)S(=PP(S(PP)(=PP)=PP)S(PP)(=PP)=PP)(=PP(S(PP)(=PP)=PP)S(PP)(=PP)=PP)P(P(S(PP)(=PP)=PP)S(PP)(=PP)=PP)S(PP)(=PP)=PP)P(S(PP)(=PP)=PP)S(PP)(=PP)=PP)S(=PP(S(PP)(=PP)=PP)S(PP)(=PP)=PP)(=PP(S(PP)(=PP)=PP)S(PP)(=PP)=PP)P(P(S(PP)(=PP)=PP)S(PP)(=PP)=PP)S(PP)(=PP)=PP)(=PP)=PP";

Molecule mol = MolImporter.importMol(smiles, "smiles");

String inchi = MolExporter.exportToFormat(smiles, preferredInchiFormat); //never ends for the SMILES provided above

Hi,

Unfortunately there is no reliable way to stop an InChI thread because it runs native code outside the JVM.

However the InChI library provides an option to specify timeout (e.g. /W0 for none and /W60 for 60 secs), but it looks like the JNI InChI library on which we rely implements it badly. For this bug I file a report for the relevant team.

 

For the moment one much less convenient solution would be to download the InChI executables (http://www.iupac.org/home/publications/e-resources/inchi/download.html)  and call it directly from your code. This way you can use the /W... timeout option. In this case your structures have to be converted to MOL or CML format as an input to the InChI executable.

Hi,

Thank you for reporting this issue with the JNI. I look forward to hearing an update ... in the meantime we may try the executables but as you said, it's not tremendously convenient for very high-throughput processing.