Different behaviour with no-structures

[fbaensch-beilstein]

Is there a reason why reactions that only contain no-structures are sometimes handled differently?

For example, an ‘empty’ RInChI with the no-struct flag is returned for this rxn file (RInChI=1.00.1S//d+/u1-1-0):

Empty_Rinchi

$RXN

  ISIS     012320160130

1 1
$MOL

-ISIS- 01231601302D

0 0 0 0 0 0 0 0 0 0999 V2000
M END
$MOL

-ISIS- 01231601302D

1 0 0 0 0 0 0 0 0 0999 V2000
8.5292 -2.7458 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0
M END

However, an error is thrown for this reaction file, which also contains two no-struct flags:

Error_reaction

$RXN

  ISIS     012320160139

1 1
$MOL

-ISIS- 01231601392D

6 6 0 0 0 0 0 0 0 0999 V2000
1.4416 -1.8375 0.0000 C 0 0 0 0 0 0 0 0 0 4 0 0
2.2666 -1.8375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.5234 -1.0534 0.0000 C 0 0 0 0 0 0 0 0 0 3 0 0
1.8541 -0.5667 0.0000 C 0 0 3 0 0 0 0 0 0 2 0 0
1.1891 -1.0534 0.0000 C 0 0 0 0 0 0 0 0 0 5 0 0
1.8529 0.2583 0.0000 R 0 0 0 0 0 0 0 0 0 1 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
5 1 1 0 0 0 0
1 2 1 0 0 0 0
4 6 1 0 0 0 0
M END
$MOL

-ISIS- 01231601392D

6 6 0 0 0 0 0 0 0 0999 V2000
6.2833 -1.8375 0.0000 C 0 0 0 0 0 0 0 0 0 4 0 0
7.1083 -1.8375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
7.3651 -1.0534 0.0000 C 0 0 0 0 0 0 0 0 0 3 0 0
6.6958 -0.5667 0.0000 C 0 0 3 0 0 0 0 0 0 2 0 0
6.0308 -1.0534 0.0000 C 0 0 0 0 0 0 0 0 0 5 0 0
6.6945 0.2583 0.0000 A 0 0 0 0 0 0 0 0 0 1 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
5 1 1 0 0 0 0
1 2 1 0 0 0 0
4 6 1 0 0 0 0
M END

In my opinion, an ‘empty’ RInChI should also be returned for the second file.

[janholstjensen]

Thanks for the report. From just eye-balling the "Error_reaction" file it doesn't look like two No-Structures (?). I would assume that the error is caused by the R-atom in the first molfile.

Can you attach the examples as text files ? Then I will try to reproduce.

[fbaensch-beilstein]

So far, I have understood a no-structure in the context of the RInChI to mean that if no InChI can be generated for a structure, a ‘no-structure’ component is generated. However, this may simply be a comprehension problem on my part.

Please find both files attached, masked with .txt extension:
empty_rinchi.rxn.txt
error_reaction.rxn.txt

[janholstjensen]

"empty_rinchi.rxn.txt"

This RXN file is perceived as two No-Structure-s since the second structure is a single 'A' atom and thus equivalent to a No-Structure from RInChI's point of view (see issue #23).

"error_reaction.rxn.txt"

The R-atom in the first input structure causes InChI generation to fail. The InChI library returns a szMessage of "Unknown element(s): R" but that message is not propagated as part of the error message of RInChI.

If the input structures are swapped, the InChI library fails with a message "Unknown element(s): A", but RInChI simply returns "Error: no InChI has been created.".

This behavior is not helpful and will be changed so the InChI error messages are propagated.

[janholstjensen]

Labelled as "documentation" issue as issue #23 covers the bug/behavior seen by these example files. The original issue name and first comment describes the documentation issue seen by example files in #24.