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Haddox / score_monomeric_designs

Computational pipeline for scoring protein designs using a variety of biophysical metrics
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make everything self contained, with no external dependencies on the Baker lab server #6

Open Haddox opened 5 years ago

Haddox commented 5 years ago

@grocklin: I just wanted to give you a heads up that I am going to try to make a list of all external dependencies in the scoring pipeline and try to move them into the repo, or at least make a list of what they are and try to make it clear how to change the scripts so that they can be used by others not in the Baker lab. I imagine this might be useful to you in your new lab. The fragment-picking step is probably the biggest thing to take care of. Just wanted to let you know in case you've already though about how to set up fragment picking in your lab. Maybe there's an easy way where we could make the path to fragment-picking scripts an easily definable input variable to the scoring pipeline.

To do:

grocklin commented 5 years ago

Pretty sure np_aa_burial is no longer necessarily, replaced by a filter

On Thu, Feb 14, 2019 at 9:46 AM Hugh Haddox notifications@github.com wrote:

@grocklin https://github.com/grocklin: I just wanted to give you a heads up that I am going to try to make a list of all external dependencies in the scoring pipeline and try to move them into the repo, or at least make a list of what they are and try to make it clear how to change the scripts so that they can be used by others not on the Baker-lab. I imagine this might be useful to you in your new lab. The fragment-picking step is probably the biggest thing to take care of. Just wanted to let you know in case you've already though about how to set up fragment picking in your lab. Maybe there's an easy way where we could make the path to fragment-picking scripts an easily definable input variable to the scoring pipeline.

To do:

-

np_aa_burial.py: line 14 calls rosetta_scripts

make_fragments.py: relies on the Baker lab's fragment picker

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Haddox commented 5 years ago

Added a bunch of auxiliary scripts in commit 33ec237

Haddox commented 5 years ago

@grocklin: is it a filter that is already in the pipeline? Or do we need to add it? All the XMLs are in the directory scripts/xmls/ named according to the filter name.

grocklin commented 5 years ago

I think it's identical to buried_npsa_FAMILYVW

On Thu, Feb 14, 2019 at 9:53 AM Hugh Haddox notifications@github.com wrote:

@grocklin https://github.com/grocklin: is it a filter that is already in the pipeline? Or do we need to add it? All the XMLs are in the directory scripts/xmls/ named according to the filter name.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Haddox/score_monomeric_designs/issues/6#issuecomment-463725194, or mute the thread https://github.com/notifications/unsubscribe-auth/AErvpyR8DLm_asUj6XtZwHH7UsjhtKYoks5vNaK0gaJpZM4a8HQ4 .