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Actelion / openchemlib-hyperspace

substructure search in large combinatorial spaces using openchemlib
BSD 3-Clause "New" or "Revised" License
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Exception when importing SSS results in Datawarrior #4

Closed and-tos closed 9 months ago

and-tos commented 9 months ago

After running a SSS with the Hyperspace GUI (v 2.0.6), I export the results to CSV via Tools -> export expanded -> Save CSV . When loading the outputfile with Datawarrior (v 5.5.0), I get the following message multiple times: old idcode exception:4-Triazole_from_carboxylic_acid_000 In Datawarrior, a table is displayed that does not contain the Fragment Identifiers in FragA and FragB, but rather the values "1" and "2" in FragC and FragD respectively.

I'd really appreciate your help on this issue!

lithom commented 9 months ago

Hi, thanks for the bug report. The issue is most likely that the name of the synthon reaction contains commas that are currently not handled correctly in the csv export (i.e. the commas in the synthon reaction name go into the csv file, causing additional commas that "destroy" the csv file). I will fix this eventually (such that commas just get replaced / removed).

As a hot fix for this problem (and to make sure that this is really the issue) you can try to use the function "Tools" -> "Export expanded.." -> "copy TSV" and then in DataWarrior just use the "Edit" -> "Paste special" -> "New From Data With Header Row" to import the data. This should fix this specific problem.

and-tos commented 9 months ago

Replacing the commas in the reaction name solved the issue, thanks a lot!