mfql_dessert issueshttps://git.mpi-cbg.de/mirandaa/mfql_dessert/-/issues2020-06-24T13:05:39Zhttps://git.mpi-cbg.de/mirandaa/mfql_dessert/-/issues/1minor issues2020-06-24T13:05:39Zmirandaaminor issues* [x] there are no brackets for element compositions of the fragments in
the define section
* [x] fragment ppm error should be added to the report section
* [x] ranges should also work for fragments* [x] there are no brackets for element compositions of the fragments in
the define section
* [x] fragment ppm error should be added to the report section
* [x] ranges should also work for fragmentshttps://git.mpi-cbg.de/mirandaa/mfql_dessert/-/issues/2generate the first installable2020-06-24T07:22:02Zmirandaagenerate the first installableusing setup.pyusing setup.pyhttps://git.mpi-cbg.de/mirandaa/mfql_dessert/-/issues/3potential extensions:2020-06-24T07:23:59Zmirandaapotential extensions:* [ ] scrap info (name, chemical composition) from url (either from vendor
like avanti/sigma and databases like HMDB/Chemspider etc.)
* [ ] Iterate over a list of chemical compositions/ranges
* [ ] have a clean mfql version (get rid o...* [ ] scrap info (name, chemical composition) from url (either from vendor
like avanti/sigma and databases like HMDB/Chemspider etc.)
* [ ] Iterate over a list of chemical compositions/ranges
* [ ] have a clean mfql version (get rid of the old stuff)
* [ ] extend suchthat and report section by specifying backbones (for proper
lipid annotation)https://git.mpi-cbg.de/mirandaa/mfql_dessert/-/issues/4Fragment issues2020-06-26T14:33:23ZmirandaaFragment issues* [ ] GT11: startung formula is C28H53NO3 and we assume a H adduct in pos
mode; output as mfql: C28H55N1O3 with dbe 2.
[GT11.mfql](/uploads/e57b28e1472fec02f4cc8d31b506c3a6/GT11.mfql)
It should be C28H54NO3 and a dbe of 2.5
* [ ] TGt...* [ ] GT11: startung formula is C28H53NO3 and we assume a H adduct in pos
mode; output as mfql: C28H55N1O3 with dbe 2.
[GT11.mfql](/uploads/e57b28e1472fec02f4cc8d31b506c3a6/GT11.mfql)
It should be C28H54NO3 and a dbe of 2.5
* [ ] TGtest: startung formula is C44H79D5O6 and we assume a NH4 adduct in pos
mode; output as mfql: C44H83D5O6N1 with dbe 4.[TGtest.mfql](/uploads/ebe59d3f71c0e1e69d981d52d405ebf6/TGtest.mfql)
Dbe should be 1.5.
* [ ] PCtest: startung formula is C39H71D5NO8P and we assume a HCOO adduct in
neg mode; output as mfql: C40H72D5N1O9P1 with dbe 6.
[PCtest.mfql](/uploads/efb3701e305d50242896b34b0637af86/PCtest.mfql)
It should be C40H72D5N1O10P1 and a dbe of 3.5.
* [ ] In this case I think it's just an issue to assign the adduct with HCOO,
somehow the second oxygen is missed.
For the others I think there is a problem in calculating the dbe
correctly and we have some issues with correctly combining cc and af dicts.
I checked the code, but I did not find the issues yet.
Let's iron out these small mistakes and test that LX1 and 2 are really
using the generated mfqls correctly. Then I think we can release the
first version.
Best, Oskarhttps://git.mpi-cbg.de/mirandaa/mfql_dessert/-/issues/5feature test mfqls vs alex1232020-06-29T12:37:46Zmirandaafeature test mfqls vs alex123https://git.mpi-cbg.de/mirandaa/mfql_dessert/-/issues/6link to mfql catalog2020-06-29T12:39:10Zmirandaalink to mfql catalog