Correct the coordinates computation for small residue graohs, and when granularity: centroids

[manonreau]

Reference Issues/PRs

Fixes #219

What does this implement/fix? Explain your changes

• Add conditions to graphein/protein/edges/distance.py not to compute distances and angles on empty dataframes
• Ensure the good calculation of centroids coordinates by correcting the selection (atoms.groupby("residue_number") -> atoms.groupby(["residue_number","chain_id","residue_name"]))

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

from graphein.protein.graphs import construct_graph
from graphein.protein.config import ProteinGraphConfig
from graphein.protein.edges.distance import (add_peptide_bonds,
                                             add_hydrogen_bond_interactions,
                                             add_disulfide_interactions,
                                             add_ionic_interactions,
                                             add_aromatic_interactions,
                                             add_aromatic_sulphur_interactions,
                                             add_cation_pi_interactions,
                                             add_distance_threshold
                                            )


new_edge_funcs = {"edge_construction_functions": [add_peptide_bonds,
                                                  add_aromatic_interactions,
                                                  add_hydrogen_bond_interactions,
                                                  add_disulfide_interactions,
                                                  add_ionic_interactions,
                                                  add_aromatic_sulphur_interactions,
                                                  add_cation_pi_interactions,
                                                  partial(add_distance_threshold, long_interaction_threshold=2, threshold=20.)]}

params_to_change = {"granularity": "centroids"}
config = ProteinGraphConfig(**new_edge_funcs, **params_to_change)

pdb_name = 'xxxx.pdb'
g = construct_graph(config=config, pdb_path=pdb_name)
g.coords

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 .

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
2 Code Smells

No Coverage information
12.5% Duplication

[codecov-commenter]

Codecov Report

Base: 40.27% // Head: 47.76% // Increases project coverage by +7.49% 🎉

Coverage data is based on head (3eb36cf) compared to base (8123f42).
Patch coverage: 51.86% of modified lines in pull request are covered.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #220      +/-   ##
==========================================
+ Coverage   40.27%   47.76%   +7.49%     
==========================================
  Files          48       85      +37     
  Lines        2811     5435    +2624     
==========================================
+ Hits         1132     2596    +1464     
- Misses       1679     2839    +1160     

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%)	⬆️
... and 77 more

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

☔ View full report at Codecov.
📢 Do you have feedback about the report comment? Let us know in this issue.

[helder-ribeiro]

Hi all! Just a comment regarding the updates in the atoms.groupby called inside the centroid calculations. It seems the input list starts with residue_number which makes the centroid data.frame being ordered by the residue_number. In the case we are working with two protein chains, the rows of this data.frame will be different from the G.graph["pdb_df"] called, for instance, inside the add_distance_threshold. Thus, the edges are created between wrong nodes. It seems that just changing the order of the input list for atoms.groupby (starting for instance by chaid_id) could correct this issue, but not sure about downstream impacts of this modification.