#1290 InChIGenerator endless loop


InChIGenerator running endless loop when passed the attached sdf.

my (partial) code:

while(sdfreade.hasNext()) {
...some code getting sid, etc from sdf...

InChIGenerator inchigen = InChIGeneratorFactory.getInstance().getInChIGenerator(mol);

//stuck here

inchiKey = inchigen.getInchiKey(); // generate the inchiKey based on mol structure

...some more code...


1 Attachments


  • John May

    John May - 2013-01-18
    • labels: --> InChI
  • John May

    John May - 2013-01-18

    Unfortunately, this is a problem with the actual InChI algorithm. If we run it through the the C binary it also hangs for a while then times out. CDK uses the InChI C code via JNI so I don't think there is much we could do, sorry.

    [intrepid ~/Downloads]: inchi subst_141382403.sdf 
    InChI version 1, Software version 1.03 Build of June 15, 2010
    Opened log file 'subst_141382403.sdf.log'
    Opened input file 'subst_141382403.sdf'
    Opened output file 'subst_141382403.sdf.txt'
    Opened problem file 'subst_141382403.sdf.prb'
    The command line used:
    "inchi subst_141382403.sdf"
    Generating standard InChI
    Input format: MOLfile
    Output format: Plain text
    Full Aux. info
    Timeout per structure: 60.000 sec
    Up to 1024 atoms per structure
    Error -30008 (Time limit exceeded) structure #1 component 1.
    End of file detected after structure #1.   
    Finished processing 1 structure: 1 error, processing time 0:01:00.00

    It's probably (almost definitely) getting stuck in the symmetry group calculation.

    Last edit: John May 2013-01-18
  • Egon Willighagen

    Dear CoderX,

    please contact the InChI mailing list. Of course, double check that the file content is correct, but if it is, you have indeed run into a problem with the InChI library. Their mailing list can be found at:



  • Egon Willighagen

    • labels: InChI --> InChI, upstream
    • status: open --> accepted
  • CoderX

    CoderX - 2013-01-18

    Thanks for the info... I didn't know how else to troubleshoot this.

  • John May

    John May - 2013-03-14
    • status: accepted --> closed