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BioJulia / BioStructures.jl

A Julia package to read, write and manipulate macromolecular structures
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add secondary structure Information #43

Closed shuuul closed 1 year ago

shuuul commented 1 year ago

Solve the problem in https://github.com/BioJulia/BioStructures.jl/issues/33 Add ss_code field to Residue. Add run_dssp and run_stride. Add support for ProteinStructure with multiple models. Add ss_code! to assign ss_code to residue. Add ss_code to read ss_code of residue/atom. Add helixselector, sheetselector, coilselector

shuuul commented 1 year ago

Hi @jgreener64 , I made a new PR. You can check the diff easier.

codecov[bot] commented 1 year ago

Codecov Report

Patch coverage: 98.76% and project coverage change: +0.14% :tada:

Comparison is base (bc70e73) 95.51% compared to head (16d8a08) 95.66%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #43 +/- ## ========================================== + Coverage 95.51% 95.66% +0.14% ========================================== Files 6 7 +1 Lines 1695 1775 +80 ========================================== + Hits 1619 1698 +79 - Misses 76 77 +1 ``` | [Files Changed](https://app.codecov.io/gh/BioJulia/BioStructures.jl/pull/43?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia) | Coverage Δ | | |---|---|---| | [src/BioStructures.jl](https://app.codecov.io/gh/BioJulia/BioStructures.jl/pull/43?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia#diff-c3JjL0Jpb1N0cnVjdHVyZXMuamw=) | `100.00% <ø> (ø)` | | | [src/pdb.jl](https://app.codecov.io/gh/BioJulia/BioStructures.jl/pull/43?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia#diff-c3JjL3BkYi5qbA==) | `88.54% <83.33%> (-0.12%)` | :arrow_down: | | [src/mmcif.jl](https://app.codecov.io/gh/BioJulia/BioStructures.jl/pull/43?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia#diff-c3JjL21tY2lmLmps) | `98.75% <100.00%> (+0.01%)` | :arrow_up: | | [src/mmtf.jl](https://app.codecov.io/gh/BioJulia/BioStructures.jl/pull/43?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia#diff-c3JjL21tdGYuamw=) | `99.35% <100.00%> (+0.01%)` | :arrow_up: | | [src/model.jl](https://app.codecov.io/gh/BioJulia/BioStructures.jl/pull/43?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia#diff-c3JjL21vZGVsLmps) | `96.31% <100.00%> (ø)` | | | [src/secondary.jl](https://app.codecov.io/gh/BioJulia/BioStructures.jl/pull/43?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=BioJulia#diff-c3JjL3NlY29uZGFyeS5qbA==) | `100.00% <100.00%> (ø)` | |

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shuuul commented 1 year ago

Hi @jgreener64 , I just modified the PR according to your comments.

shuuul commented 1 year ago

Hi @jgreener64, I made the changes. Thanks for guiding me in making this PR. This great package saved me a lot of time.

shuuul commented 1 year ago

Hi @jgreener64 , do you plan to make a release of 2.1.0? I am building a package based on the secondary structure assignment, and I want to make the 2.1.0 my dependency.

jgreener64 commented 1 year ago

I'll try and get v2.1.0 out by the end of the week, just need to make some small updates first.

jgreener64 commented 1 year ago

v2.1.0 is out. In the end I changed the secondary structure code to be stored as a Char, so you may need to update your code as appropriate.