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Jhsmit / PyHDX

Derive ΔG for single residues from HDX-MS data
http://pyhdx.readthedocs.io
MIT License
28 stars 12 forks source link

yaml FD_control #303

Closed ococrook closed 1 year ago

ococrook commented 1 year ago

If I don't have a fully deuterated/ back exchange control is there a way to specifcy the yaml so that it ignores this. If I leave it blank the code complains ?

Jhsmit commented 1 year ago

You can use a flat percentage for the back exchange as well. You can do so from yaml writing:

  be_percent: 0.

instead of a "FD_control" entry.

Which will set the back exchange set zero; and then RFU will be equal to "uptake" / "ex_residues"

in this function here: https://github.com/Jhsmit/PyHDX/blob/dc82a4aeedcddad1e588c4bf2a6bda25b6c20694/pyhdx/models.py#L349

Sorry, this part isnt so well documented and the API isnt very nice. I'm planning to upgrade it in the future. I'll make an Issue on this at some point then perhaps you can give me some input on how to make it better.

ococrook commented 1 year ago

no problem about documentation, it's a little hard seeing where everything is happening but pretty much there now! Happy to help go through the documentation with you so follows from the outsiders perspective