`PDBManager` - Bug fixes, adding necessary changes to export only first PDB model, and merging-in latest updates from `master`

a-r-j commented 1 year ago

Reference Issues/PRs

@a-r-j, I noticed that our (new) default function for exporting collated groups of PDB chains does not currently export only the first model for each PDB complex file. I've added the necessary changes to make this happen, and I also added a workaround that's needed when exporting (i.e., calling to_pdb() on) PandasPdb objects that have had a model_id column added to them. In the long term, I think it'd be good to have a fix merged into the master branch of BioPandas that types the model_id column as a str -> object column, but this workaround I've proposed should work for now.

Originally posted by @amorehead in https://github.com/a-r-j/graphein/issues/309#issuecomment-1513710494

@a-r-j, note that this PR also includes a fix for dataset-splitting edge cases where you only select one splitting strategy (e.g., time-based splitting) and then try to download and export your selected PDBs. Currently, if you try to export such PDBs, the download and export functions will throw an error saying that your selected PDBs are not labeled correctly according to which split to which they are assigned. The fix for this is simple: track split names per PDB entry more thoroughly by installing them within individual splitting functions (e.g., split_df_into_time_frames). If you are good with these changes, please feel free to go ahead and merge these changes into master after testing them on your end.

Originally posted by @amorehead in https://github.com/a-r-j/graphein/issues/309#issuecomment-1513711152

What does this implement/fix? Explain your changes

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

Pull Request Checklist

[x] Added a note about the modification or contribution to the ./CHANGELOG.md file (if applicable)
[ ] Added appropriate unit test functions in the ./graphein/tests/* directories (if applicable)
[ ] Modify documentation in the corresponding Jupyter Notebook under ./notebooks/ (if applicable)
[ ] 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)
[ ] Checked for style issues by running black . and isort .

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codecov-commenter commented 1 year ago

Codecov Report

Patch coverage: 40.07% and project coverage change: +3.71 :tada:

Comparison is base (8123f42) 40.27% compared to head (628616d) 43.98%.

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Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #311 +/- ## ========================================== + Coverage 40.27% 43.98% +3.71% ========================================== Files 48 113 +65 Lines 2811 7778 +4967 ========================================== + Hits 1132 3421 +2289 - Misses 1679 4357 +2678 ``` | [Impacted Files](https://codecov.io/gh/a-r-j/graphein/pull/311?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb) | Coverage Δ | | |---|---|---| | [graphein/ml/datasets/foldcomp\_dataset.py](https://codecov.io/gh/a-r-j/graphein/pull/311?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vbWwvZGF0YXNldHMvZm9sZGNvbXBfZGF0YXNldC5weQ==) | `0.00% <0.00%> (ø)` | | | [graphein/ml/diffusion.py](https://codecov.io/gh/a-r-j/graphein/pull/311?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vbWwvZGlmZnVzaW9uLnB5) | `0.00% <0.00%> (ø)` | | | [graphein/ml/metrics/\_\_init\_\_.py](https://codecov.io/gh/a-r-j/graphein/pull/311?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vbWwvbWV0cmljcy9fX2luaXRfXy5weQ==) | `0.00% <0.00%> (ø)` | | | [graphein/ml/metrics/gdt.py](https://codecov.io/gh/a-r-j/graphein/pull/311?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vbWwvbWV0cmljcy9nZHQucHk=) | `0.00% <0.00%> (ø)` | | | [graphein/ml/metrics/tm\_score.py](https://codecov.io/gh/a-r-j/graphein/pull/311?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vbWwvbWV0cmljcy90bV9zY29yZS5weQ==) | `0.00% <0.00%> (ø)` | | | [graphein/ppi/graph\_metadata.py](https://codecov.io/gh/a-r-j/graphein/pull/311?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcHBpL2dyYXBoX21ldGFkYXRhLnB5) | `0.00% <0.00%> (ø)` | | | [graphein/ppi/visualisation.py](https://codecov.io/gh/a-r-j/graphein/pull/311?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcHBpL3Zpc3VhbGlzYXRpb24ucHk=) | `0.00% <0.00%> (ø)` | | | [graphein/protein/analysis.py](https://codecov.io/gh/a-r-j/graphein/pull/311?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcHJvdGVpbi9hbmFseXNpcy5weQ==) | `0.00% <0.00%> (ø)` | | | [graphein/protein/features/utils.py](https://codecov.io/gh/a-r-j/graphein/pull/311?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcHJvdGVpbi9mZWF0dXJlcy91dGlscy5weQ==) | `27.77% <0.00%> (ø)` | | | [graphein/protein/folding\_utils.py](https://codecov.io/gh/a-r-j/graphein/pull/311?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcHJvdGVpbi9mb2xkaW5nX3V0aWxzLnB5) | `0.00% <0.00%> (ø)` | | | ... and [95 more](https://codecov.io/gh/a-r-j/graphein/pull/311?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb) | |

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