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feat: findMetSmiles and improved DLKcat I/O

Open edkerk opened this issue 1 year ago • 2 comments

Main improvements in this PR:

As suggested in #171

  • feat:
    • findMetSmiles function for querying PubChem for SMILES using metabolite names.
    • DLKcat in- and output files have reaction and gene IDs, to prevent the use of DLKcatIDs structure.

I hereby confirm that I have:

  • [x] Tested my code with all requirements for running GECKO
  • [x] Selected devel3 as a target branch (top left drop-down menu)

edkerk avatar Sep 30 '22 15:09 edkerk

Please also output the rxnID in the DLKcat input file, so it would be much easier for later mapping.

feiranl avatar Nov 10 '22 14:11 feiranl

The changes in this PR does that (see line 80 in the new writeDLKcatInput and line 47 in readDLKcatInput)! If you approve this PR it can be merged to devel3

edkerk avatar Nov 11 '22 09:11 edkerk