Structural API

[jaimergp]

This is now the base PR for all the structural work done in the last weeks. This contains:

• Docking pipelines by @schallerdavid (this original PR)
• Homology modelling by @glass-w (#26)
• Dunbrack featurizers by @jiayeguo (#29)

I have merged all PRs here and will work on getting them in shape for the library.

To do

• [ ] Structural object model based on MDA
• [ ] Docking
  • [ ] Librarize code that needs so
  • [ ] Ensure / add tests
  • [ ] Ensure / add docs
• [ ] Homology modeling
  • [ ] Librarize code that needs so
  • [ ] Ensure / add tests
  • [ ] Ensure / add docs
• [ ] Dunbrack featurizer
  • [ ] Librarize code that needs so
  • [ ] Ensure / add tests
  • [ ] Ensure / add docs

[schallerdavid]

Awesome, thanks @jaimergp!

[jaimergp]

Please feel free to retag me when another review is needed!

[schallerdavid]

Hey @jaimergp,

welcome back! I hope you had nice holidays. Getting a review would be great.

[schallerdavid]

Hey @jaimergp,

I think I would be ready for a review.

The protein preparation pipeline in examples/kinase_modeling.ipynp does not completely work, but thats mainly due to OESpruce bugs mentioned in the notebook. Once those are fixed, the functions might actually work out. I found it quite hard to find a good location for very KLIFS and kinase specific functions, e.g. select_structure for selecting a kinase structure for docking a small molecule, so they might be a little missplaced.

There is also a notebook analyzing the kinase domain sequences retrieved from Uniprot (examples/kinase_domain_sequence.ipynb). I think you mentioned, you were doing similar work with a student. Could you point me to that repo?

Thanks, David

[schallerdavid]

Hey @jaimergp,

ready for review. I hope it's more readable now.

David

[jaimergp]

I am taking over! Please don't add more stuff now unless we have discussed it first!