Fix bug in add_k_nn_edges and add minor extension

[anton-bushuiev]

Reference Issues/PRs

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What does this implement/fix? Explain your changes

This pull request fixes a bug in add_k_nn_edges. Currenly, kneighbors_graph(X=dist_mat, ...) leads to wrong results which may seem correct. According to scikit-learn docs, it does not support X to be a distance matrix.

Secondly, this PR adds filter_distmat to generalise self-loops filtering. It adds the functionality to filter inter- or intra- connections between nodes of a single or multiple chains. It may be useful to incorporate it into other functions to add edges. By running the following code you will get the visualized graphs.

for val in ['inter', 'intra']:
    edge_funcs = {
        'edge_construction_functions': [
            partial(add_k_nn_edges, k=2, long_interaction_threshold=0, exclude_edges=[val])
        ]
    }
    config = ProteinGraphConfig(**edge_funcs)
    g = construct_graph(config=config, pdb_code='10gs')
...

What testing did you do to verify the changes in this PR?

Pull Request Checklist

• Added a note about the modification or contribution to the ./CHANGELOG.md file (if applicable)
• Added appropriate unit test functions in the ./graphein/tests/* directories (if applicable)
• Modify documentation in the corresponding Jupyter Notebook under ./notebooks/ (if applicable)
• Ran python -m py.test tests/ and make sure that all unit tests pass (for small modifications, it might be sufficient to only run the specific test file, e.g., python -m py.test tests/protein/test_graphs.py)
• Checked for style issues by running black . and isort .

[a-r-j]

Thanks for this @anton-bushuiev. Good spot!

LGTM! Would you be able to add a couple tests?

[anton-bushuiev]

Yeah, I'll add them tomorrow.

[anton-bushuiev]

Hi, @a-r-j ! I've added the tests. I had to fix a new bug introduced by the distance matrix filtering (see this) 😄.

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
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No Coverage information
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[codecov-commenter]

Codecov Report

Base: 40.27% // Head: 47.86% // Increases project coverage by +7.59% 🎉

Coverage data is based on head (fd1b36b) compared to base (8123f42).
Patch coverage: 52.20% of modified lines in pull request are covered.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #229      +/-   ##
==========================================
+ Coverage   40.27%   47.86%   +7.59%     
==========================================
  Files          48       85      +37     
  Lines        2811     5398    +2587     
==========================================
+ Hits         1132     2584    +1452     
- Misses       1679     2814    +1135     

Impacted Files	Coverage Δ
graphein/ml/diffusion.py	0.00% <0.00%> (ø)
graphein/ppi/graph_metadata.py	0.00% <0.00%> (ø)
graphein/ppi/visualisation.py	0.00% <0.00%> (ø)
graphein/protein/analysis.py	0.00% <0.00%> (ø)
graphein/protein/features/sequence/utils.py	28.00% <0.00%> (+3.00%)	⬆️
graphein/protein/features/utils.py	27.77% <0.00%> (ø)
graphein/rna/utils.py	38.46% <ø> (ø)
graphein/rna/visualisation.py	28.57% <ø> (+28.57%)	⬆️
graphein/utils/config.py	100.00% <ø> (+100.00%)	⬆️
graphein/utils/config_parser.py	100.00% <ø> (ø)
... and 81 more

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[a-r-j]

Thanks for the contribution @anton-bushuiev!