198 #199 #200

What does this implement/fix? Explain your changes

Adds missing MSE residue to constants
Fixes chain id check in atomic edge construction
Fixes incorrect deprotonation proceduce in protein graph construction

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)
[x] 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 .

codecov-commenter commented 2 years ago

Codecov Report

Merging #201 (4d3684f) into master (8123f42) will increase coverage by 7.62%. The diff coverage is 51.35%.

@@            Coverage Diff             @@
##           master     #201      +/-   ##
==========================================
+ Coverage   40.27%   47.89%   +7.62%     
==========================================
  Files          48       92      +44     
  Lines        2811     5502    +2691     
==========================================
+ Hits         1132     2635    +1503     
- Misses       1679     2867    +1188

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 79 more