Add new helper functions to PDBManager
#322
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…with the PDBManager
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| assert ( | ||
| len(filtered_pdb) > 0 | ||
| ), "Filtered DataFrame must contain atoms." | ||
| if "ATOM" in key and len(filtered_pdb) == 0: |
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I may be being a little pedantic here but I see two possible edge cases with this:
- Sometimes protein atoms are stored as HETATMs (typically modified residues but this kind of bad practice does happen as an abuse of the PDB format to suit some niche way to store structure data)
- Similarly, what if the desired selection is actually the HETATM data? Protein-nucleic acid complexes or protein-peptide complexes may store the ligand as a HETATM
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No problem. Points 1 and 2 didn't come to my mind when I originally implemented this, and I kept expanding on it until now. In light of these points, I think it makes more sense to avoid skipping such DataFrames altogether. It will then be the user's responsibility to "vet" the exported PDB files for these kinds of edge cases in their selected PDBs. Better yet, we can simply issue a warning to users that no "standard" atoms were found post-filtering. However, we would then still export the PDB complex as requested.
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I've modified this logic to only issue a warning in such an edge case now.
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## master #322 +/- ##
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+ Coverage 40.27% 43.74% +3.47%
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Files 48 113 +65
Lines 2811 7829 +5018
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+ Hits 1132 3425 +2293
- Misses 1679 4404 +2725
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Feel free to merge this PR if and when you are ready to. |
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What does this implement/fix? Explain your changes
Adds some new helper functions to the
PDBManagerto allow one to work more easily with heterogeneous protein complexes.What testing did you do to verify the changes in this PR?
I evaluated these functions in a local copy of this repository.
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 .