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database format #2

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bernt-matthias opened this issue Mar 29, 2019 · 0 comments
Open

database format #2

bernt-matthias opened this issue Mar 29, 2019 · 0 comments

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@bernt-matthias
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The local database in cfm-id and metfrag seems very similar. But its csv in one and tsv in the other. Maybe it would be good to have this consistent. I would prefer tsv since InChI contains commas (question would be if this works anyway with csv if there are additional commas). Then the same input can easily be used in both files (ie the metfrag input can be used in cfm-id - since the first columns are the same)

Maybe we should allow omitting InChI or SMILES (in the python sources there is a TODO anyway). Due to the use of the python wrapper we are free to define the format as we wish. Possibilities:

  • Allow to keep one column empty (maybe this is possible anyway)
  • Make column 3 inchi/smiles .. let the python check for startswith("InChi")?
  • Detect by column header
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