Support MMTF & rename pdb_path to path throughout

a-r-j commented 1 year ago

Reference Issues/PRs

Adds support for graph construction from MMTF files. pdb_path args renamed to path throughout.

a-r-j commented 1 year ago

Temporarily blocked by https://github.com/BioPandas/biopandas/issues/120

review-notebook-app[bot] commented 1 year ago

Check out this pull request on

See visual diffs & provide feedback on Jupyter Notebooks.

Powered by ReviewNB

codecov-commenter commented 1 year ago

Codecov Report

Patch coverage: 39.89% and project coverage change: +3.63 :tada:

Comparison is base (8123f42) 40.27% compared to head (0edb0cb) 43.90%.

:mega: This organization is not using Codecov’s GitHub App Integration. We recommend you install it so Codecov can continue to function properly for your repositories. Learn more

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #293 +/- ## ========================================== + Coverage 40.27% 43.90% +3.63% ========================================== Files 48 113 +65 Lines 2811 7726 +4915 ========================================== + Hits 1132 3392 +2260 - Misses 1679 4334 +2655 ``` | [Impacted Files](https://codecov.io/gh/a-r-j/graphein/pull/293?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/293?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/293?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/293?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/293?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/293?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/293?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/293?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/293?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/293?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/293?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/293?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb) | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb)

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Do you have feedback about the report comment? Let us know in this issue.