fix disulphide bond node filtering #205 #209
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* add load local pdb_files to ProteinGraphDataset * load local pdb_files from a list * test and black and isort and add CHANGELOG.md * docstring formatting * comment jupyter; just run and ssh or vscode to interact with container * install dependency of jupyter nbextension * Fixed Dockerfile and unit tests * Update chage log Co-authored-by: xutingfeng <xutingfeng@big.ac.cn> Co-authored-by: Arian Jamasb <arjamasb@gmail.com> Co-authored-by: ryan <ryan.greenhalgh@hotmail.co.uk> Co-authored-by: Nicktf <49584439+1511878618@users.noreply.github.com> Co-authored-by: xutingfeng <xutingfeng@big.ac.cn> Co-authored-by: ryan <ryan.greenhalgh@hotmail.co.uk>
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Codecov Report
@@ Coverage Diff @@
## master #209 +/- ##
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+ Coverage 40.27% 47.89% +7.62%
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Files 48 92 +44
Lines 2811 5533 +2722
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+ Hits 1132 2650 +1518
- Misses 1679 2883 +1204
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Reference Issues/PRs
#205
What does this implement/fix? Explain your changes
Disulfide bond edges were adding nodes to the graph (e.g. if we are only looking at a graph of chain A, nodes from chain B were added). This PR adds a filtering step to ensure identified ds bonds are only added if both nodes are present in the graph.
What testing did you do to verify the changes in this PR?
Pull Request Checklist
./CHANGELOG.mdfile (if applicable)./graphein/tests/*directories (if applicable)./notebooks/(if applicable)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)black .andisort .