fix disulphide bond node filtering #205

[a-r-j]

Reference Issues/PRs

205

What does this implement/fix? Explain your changes

Disulfide bond edges were adding nodes to the graph (e.g. if we are only looking at a graph of chain A, nodes from chain B were added). This PR adds a filtering step to ensure identified ds bonds are only added if both nodes are present in the graph.

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

Pull Request Checklist

• [x] Added a note about the modification or contribution to the ./CHANGELOG.md file (if applicable)
• [x] Added appropriate unit test functions in the ./graphein/tests/* directories (if applicable)
• [x] 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)
• [x] Checked for style issues by running black . and isort .

[review-notebook-app[bot]]

Check out this pull request on 

See visual diffs & provide feedback on Jupyter Notebooks.

---

Powered by ReviewNB

[sonarcloud[bot]]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[codecov-commenter]

Codecov Report

Merging #209 (8abdb2a) into master (8123f42) will increase coverage by 7.62%. The diff coverage is 51.22%.

@@            Coverage Diff             @@
##           master     #209      +/-   ##
==========================================
+ Coverage   40.27%   47.89%   +7.62%     
==========================================
  Files          48       92      +44     
  Lines        2811     5533    +2722     
==========================================
+ Hits         1132     2650    +1518     
- Misses       1679     2883    +1204     

Impacted Files	Coverage Δ
graphein/grn/parse_trrust.py	37.77% <ø> (ø)
graphein/ml/diffusion.py	0.00% <0.00%> (ø)
graphein/ppi/edges.py	100.00% <ø> (ø)
graphein/ppi/graph_metadata.py	0.00% <ø> (ø)
graphein/ppi/graphs.py	54.34% <ø> (ø)
graphein/ppi/parse_biogrid.py	75.00% <ø> (ø)
graphein/ppi/visualisation.py	0.00% <0.00%> (ø)
graphein/protein/analysis.py	0.00% <0.00%> (ø)
graphein/protein/edges/intramolecular.py	22.68% <0.00%> (ø)
graphein/protein/features/sequence/utils.py	28.00% <0.00%> (+3.00%)	:arrow_up:
... and 80 more

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.