Add support for DSSP version and add rsa node features to residues with insertion codes

[biochunan]

Reference Issues/PRs

Fixes Issue #353 Fixes Issue #354

What does this implement/fix? Explain your changes

For Issue #353, this PR added a line to determine dssp version, which is passed to the function Bio.PDB.DSSP.dssp_dict_from_pdb_file otherwise, biopython will use default version number 3.9.9 and for users with dssp version >= 4.0.0, this will lead to an empty dssp DataFrame

For Issue #354, this modification fixes errors caused by missing rsa feature from nodes with insertion code. This is caused by skipping insertions when creating node_id. This modifications adds insertion codes to node_id if insertions is set to True in ProteinGraphConfiguration.

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

Added a script test_dssp.py to tests/features The example input pdb file (with cryst1 line and insertion codes) is attached here: input_pdb_cryst1.pdb.gz

File with suffix .pdb is not supported by GitHub, thus the compressed version. Need to uncompress it first before running the test.

Pull Request Checklist

• [ ] 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)
• [x] Checked for style issues by running black . and isort .

[a-r-j]

Thanks @biochunan LGTM! Only comment re: pdb files - I'm quite sure these can be uploaded uncompressed. See: https://github.com/a-r-j/graphein/tree/master/tests/protein/test_data

[a-r-j]

On second thought, it's likely the .gitignore that's preventing you from adding the .pdb file. Try: git add input_pdb_cryst1.pdb --force.

[biochunan]

Hi @a-r-j thanks for going through the PR. For the pdb file, I was trying to upload it through the PR window and GitHub doesn't support files with the suffix pdb. Will use existing pdb files in ./test_data in the future.

[biochunan]

I had a look at the three pdb files in tests/protein/test_data, and they do not have insertion code. Maybe it's a good idea to add a PDB file with insertion codes for insertions related testing.

[sonarqubecloud[bot]]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
2 Code Smells

No Coverage information
0.0% Duplication

[sonarqubecloud[bot]]

Quality Gate passed

Issues
2 New issues
0 Accepted issues

Measures
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 90.00000% with 1 lines in your changes are missing coverage. Please review.

Project coverage is 45.07%. Comparing base (8123f42) to head (26cfdbb). Report is 166 commits behind head on master.

Files	Patch %	Lines
graphein/protein/features/nodes/dssp.py	90.00%	1 Missing :warning:

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Additional details and impacted files

@@            Coverage Diff             @@
##           master     #355      +/-   ##
==========================================
+ Coverage   40.27%   45.07%   +4.80%     
==========================================
  Files          48      113      +65     
  Lines        2811     7916    +5105     
==========================================
+ Hits         1132     3568    +2436     
- Misses       1679     4348    +2669     

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