avivko commented 2 years ago

Reference Issues/PRs

Fixes #171 (was not properly fixed by #172 )

What does this implement/fix? Explain your changes

Includes refactoring of g.graph to always include the parameters "name", "pdb_code", and "pdb_path".
adds hover titles to the correlation graphs, so that we know which residue we are looking at.

Rational for refactoring: Before this PR, after we read a pdb and make a DataFrame out of it, as far as I know, we didn't save the original path to the pdb in the graph metadata. This is why previously, once we wanted to get the dssp features of a local pdb, we ran into problems as long as the structure was not in the pdb_dir. I wanted to make G.graph always contain the following three separate parameters from here on out: name, pdb_code, pdb_path. This way, when pdb_code is not None, we know we have a pdb from the protein database (and can also use download_pdb(pdb_code) etc.); Otherwise, we know are dealing with a local pdb and we keep the path to where it was originally stored. It is important to note that the pdb file might be moved after a graph was generated, therefore yielding a dead pdb_path. For getting dssp features, this PR also provides the option to provide a new pdb_path in such a case.

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

I ran the Jupyter notebooks from the protein tutorials as well as my own local pdb + dssp graph conversion workflow and it all works.

codecov-commenter commented 2 years ago

Codecov Report

Merging #176 (fd7f92f) into master (8123f42) will increase coverage by 8.76%. The diff coverage is 56.38%.

@@            Coverage Diff             @@
##           master     #176      +/-   ##
==========================================
+ Coverage   40.27%   49.03%   +8.76%     
==========================================
  Files          48       74      +26     
  Lines        2811     4264    +1453     
==========================================
+ Hits         1132     2091     +959     
- Misses       1679     2173     +494

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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avivko commented 2 years ago

Would you like me to me to also add a test for dssp with both a pdb code a local pdb structure? I could also add the show_edges visualization from #167 to the corresponding notebook while I'm already on it.