Sorry for the confusion,  it turns out the user reporting the problem was copy/pasting incomplete InChIs  ... I wish InChI package had  less cryptic error reporting.

Still ChemSpider searching seems to be only one to cope with incomplete InChI  - is it possible with (any) InChI library to achieve something similar - e.g. extract only a skeleton from available InChI layers ?


On 9 November 2010 10:13, Nina Jeliazkova <> wrote:
Hello All,

Attemping to parse this InChI=1S/C6H8O6/c7-1-2(8)5-3(9)4(10)6(11)12-5/h2 via org.openscience.cdk.inchi.InChIToStructure  (latest stdinchi )  fails with an error:

Aux. info suppressed
Input format: InChI (plain identifier)
Output format: Plain text
No timeout; Up to 1024 atoms per structure

Structure: 1 Syntax error (-2) in MOBILE_H (2)

Further observations:

1) OpenBabel also have troubles parsing this string.

2)   links to water (which is obviously wrong)

3) ChemSpider seems to be the only site (among I've tested ) which succeeds in finding the compound

Am I missing something? Is this a known issue ?

Best regards,