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Swagger doc - tools/remove-sugar endpoint gives an error as "Error generating SMILES" for the first example. #386

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Tracked by #379
CS76 opened this issue Sep 9, 2023 · 4 comments · Fixed by #395 or #397
Closed
Tracked by #379

Swagger doc - tools/remove-sugar endpoint gives an error as "Error generating SMILES" for the first example. #386

CS76 opened this issue Sep 9, 2023 · 4 comments · Fixed by #395 or #397
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@JonasSchaub

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CS76 commented Sep 9, 2023

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@CS76 CS76 mentioned this issue Sep 9, 2023
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@CS76 CS76 changed the title Swagger doc - tools/remove-sugar endpoint gives an error as "Error generating SMILES" for the first parameter. Swagger doc - tools/remove-sugar endpoint gives an error as "Error generating SMILES" for the first example. Sep 9, 2023
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My guess is that this is a general problem. The error seems to occur whenever you give it a molecule that consists of sugars completely (e.g. Glucose "C(C1C(C(C(C(O1)O)O)O)O)O"). The SRU returns an empty IAtomContainer object in this case which seems to cause troubles down the line. You could check and treat this using IAtomContainer.isEmpty().

If you would like me to take care of this, it would be nice if someone could guide me on how to set the project up locally and how to push changes correctly.

CS76 added a commit that referenced this issue Sep 11, 2023
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fix: added empty molecule checks for sugar removal routines - resolves …
0b8414d 
…#386
@CS76 CS76 mentioned this issue Sep 11, 2023
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CS76 commented Sep 11, 2023

Thanks @JonasSchaub. This is resolved now - #393

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We have the same problem with the other two sugar removal routines.

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CS76 commented Sep 11, 2023 •
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Fixed here #395

@NishaSharma14 NishaSharma14 linked a pull request Sep 11, 2023 that will close this issue
fix: removed exception for empty IAtomContainer - returning empty string for now #395
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@CS76 CS76 closed this as completed Sep 11, 2023
@NishaSharma14 NishaSharma14 mentioned this issue Sep 11, 2023
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