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openkinome / kinoml

Structure-informed machine learning for kinase modeling
https://openkinome.org/kinoml/
MIT License
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Adding kinase featurizing scripts #29

Closed jiayeguo closed 4 years ago

jiayeguo commented 4 years ago

Description

Adding kinase featurizing code

Todos

Notable points that this PR has either accomplished or will accomplish.

Questions

Status

schallerdavid commented 4 years ago

Hey @jiayeguo, thanks for pushing your code and adapting it to work with MDAnalysis. Do you also have some code to assign structures to the respective Dunbrack clusters? I have the feeling you already have the code to get all necessary information and only a few lines are missing to assign the cluster.

jiayeguo commented 4 years ago

Hey @schallerdavid yes you are right. I have the code (and once put it into a jupyter notebook). Now with all the calculated dihedrals and distances, we are just a few lines of code away from Dunbrack clusters. I will have a separate script for that and add that to kinoml --- would features or analysis be a better directory?

schallerdavid commented 4 years ago

@jiayeguo,

I think features is fine. The most import for now is to get the code into the repo and to show how it works with a notebook. Later we will do the refactoring.

schallerdavid commented 4 years ago

@jiayeguo,

I will close this PR for now, since everything from here is in #31. Correct if I am wrong, than we can reopen the PR.