Evcomplex2 #225
Evcomplex2 #225
Conversation
…nt all ECs used for scoring
…nto feature/avoid_self
There was a problem hiding this comment.
Almost complete review, still missing are:
- evcouplings/couplings/protocol.py
- evcouplings/couplings/pairs.py
All small-ish stuff except for evcouplings/compare/protocol.py - I think most of the additions there regarding the machine learning models do not belong into the comparison stage which should really just compare results to experiments. I think this stuff belongs more into the complex submodule, and maybe means another stage for the complex pipeline is needed?
| uniprot_to_embl_table: /n/groups/marks/databases/complexes/idmapping/idmapping_uniprot_embl_2017_02.txt | ||
| ena_genome_location_table: /n/groups/marks/databases/complexes/ena/2017_02/cds_pro.txt | ||
| structurefree_model_file: /n/groups/marks/users/agreen/dev/EVcouplings/evcouplings/compare/aux/residue_strucfree.saved |
There was a problem hiding this comment.
We should have these somewhere publicly accessible
| temp_dataframe = id_dataframe.copy() | ||
|
|
||
| id_strings = [_split_annotation_string(x) for x in temp_dataframe.id_1] | ||
| temp_dataframe["id_string_1"], temp_dataframe["r_s_1"], temp_dataframe["r_e_1"] = \ |
There was a problem hiding this comment.
not a big fan of new lines with backslash - nicer to wrap first part of assignment in (...)
There was a problem hiding this comment.
I can't picture what you mean here, sorry, was only using the slash because the assignment doesn't seem to nicely support wrapping with ()
|
Plan for getting this into develop:
|
There was a problem hiding this comment.
Here is review of second bit - major comments:
-
Please refactor complex_mean_field() and mean_field() like done for plm-based protocols (See detailed comments above)
-
the _postprocess_inference() method should stay as it is (may need making the pymol creation functions more generic to handle segments as well)
|
Reminder: check that Issue #252 is resolved |
Conflicts: evcouplings/couplings/protocol.py test/TestComplex.py
This pull request includes all the functions used for calculations in Green & Elhabashy, et al. https://www.biorxiv.org/content/10.1101/791293v1