Fix for issue 72, only one parent molecule for each fragment after pipeline

[JonasSchaub]

@FelixBaensch the cause of the issue (after pipeline fragmentation, every fragment has only one parent molecule assigned to it) seems to be in the pipeline routine of the FragmentationService. I kind of fixed it but this routine is complex (props to you who wrote it), so I am unsure whether this is correct. Also, I feel like there is one parent molecule missing in the overview in some cases. Could you kindly check this?

[FelixBaensch]

@FelixBaensch the cause of the issue (after pipeline fragmentation, every fragment has only one parent molecule assigned to it) seems to be in the pipeline routine of the FragmentationService. I kind of fixed it but this routine is complex (props to you who wrote it), so I am unsure whether this is correct. Also, I feel like there is one parent molecule missing in the overview in some cases. Could you kindly check this?

Could you provide me your test set please

[JonasSchaub]

Could you provide me your test set please

It is our Caffeine Derivatives https://drive.google.com/file/d/1G8E8dsFJMyDwgxsf4wPAeoP6DjLpXE9z/view?usp=drive_link which I fragmented with a pipeline of SRU (return only aglycone) and Ertl (return only functional groups).

[FelixBaensch]

First, let's clarify what should be included in the parent overview after a pipeline run. Should it contain the original structures, the intermediate structures that emerge after each step, or just the final intermediate structures or ...? The same applies to the frequencies.

[JonasSchaub]

I'd say the original structures, i.e. structures from the imported molecule set. All intermediates are so far not defined in out logic and the "parents" are the imported molecules in every other place. The "molecule frequencies" should also relate to them. And the fragment frequencies to the final result, i.e. the last pipeline step result, whose fragments are displayed.

[FelixBaensch]

I'd say the original structures, i.e. structures from the imported molecule set. All intermediates are so far not defined in out logic and the "parents" are the imported molecules in every other place. The "molecule frequencies" should also relate to them. And the fragment frequencies to the final result, i.e. the last pipeline step result, whose fragments are displayed.

So we agree on that. I'll take care of it, because that seems to be the problem, disagreement on the situation.

[JonasSchaub]

Thank you so much.

[sonarcloud[bot]]

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[FelixBaensch]

Thank you so much.

Could you please test it, and check if the fragment frequencies are correct

[JonasSchaub]

From what I see, everything looks alright! Shall I merge?

[FelixBaensch]

If the fragment frequencies after the pipeline are also correct, please.