yuanqidu commented 2 years ago

PRs

Fixes #155. Add support for small molecules. Support reading molecules from SMILES strings, .mol2, .sdf, .pdb files Support one-hot node features Support fully-connected, knn, bond, distance threshold edges

Test

See tests/molecule/test_data and tests/molecule/test_graphs.py

test basic functions to read either long or short molecules in the aforementioned ways

codecov-commenter commented 2 years ago

Codecov Report

Merging #157 (7a0d1a5) into master (8123f42) will increase coverage by 8.98%. The diff coverage is 58.00%.

@@            Coverage Diff             @@
##           master     #157      +/-   ##
==========================================
+ Coverage   40.27%   49.25%   +8.98%     
==========================================
  Files          48       74      +26     
  Lines        2811     4172    +1361     
==========================================
+ Hits         1132     2055     +923     
- Misses       1679     2117     +438

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/features/sequence/sequence.py	`71.42% <0.00%> (+2.67%)`	:arrow_up:
graphein/protein/features/sequence/utils.py	`28.00% <0.00%> (+3.00%)`	:arrow_up:
... and 59 more

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