kamurani commented 1 year ago

Fixes #267

This ensures that atomistic level graphs have the same sequence (for each c in chain_ids) as those created with CA or residue granularity.

Tested with an assertion (comparing sequences from residue and atomistic graphs).

kamurani commented 1 year ago

@a-r-j where abouts should I put the tests that I came up with?

a-r-j commented 1 year ago

@a-r-j where abouts should I put the tests that I came up with?

https://github.com/a-r-j/graphein/blob/master/tests/protein/test_graphs.py

codecov-commenter commented 1 year ago

Codecov Report

Base: 40.27% // Head: 45.48% // Increases project coverage by +5.21% :tada:

Coverage data is based on head (5d0098e) compared to base (8123f42). Patch coverage: 49.54% of modified lines in pull request are covered.

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Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #268 +/- ## ========================================== + Coverage 40.27% 45.48% +5.21% ========================================== Files 48 111 +63 Lines 2811 7128 +4317 ========================================== + Hits 1132 3242 +2110 - Misses 1679 3886 +2207 ``` | [Impacted Files](https://codecov.io/gh/a-r-j/graphein/pull/268?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/diffusion.py](https://codecov.io/gh/a-r-j/graphein/pull/268?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/268?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/268?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/268?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/268?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/268?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/268?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/268?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/268?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)` | | | [graphein/protein/tensor/data.py](https://codecov.io/gh/a-r-j/graphein/pull/268?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Arian+Jamasb#diff-Z3JhcGhlaW4vcHJvdGVpbi90ZW5zb3IvZGF0YS5weQ==) | `30.37% <ø> (ø)` | | | ... and [107 more](https://codecov.io/gh/a-r-j/graphein/pull/268?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)

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