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Add a converter from PDB to Zarr to the DatasetFactory#171

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zhu0619 merged 38 commits into
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feat/pdb
Aug 19, 2024
Merged

Add a converter from PDB to Zarr to the DatasetFactory#171
zhu0619 merged 38 commits into
mainfrom
feat/pdb

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@zhu0619

@zhu0619 zhu0619 commented Aug 9, 2024

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Changelogs

  • Added PDBConverter which is able to convert pdb files to zarr file
  • Added ARRAY_TO_PDB which is able to load pdb from zarr file
  • Allow add_from_file to handle multiple files.
  • Added simple tutorial for creating dataset from pdb file.

Checklist:

  • Was this PR discussed in an issue? It is recommended to first discuss a new feature into a GitHub issue before opening a PR.
  • Add tests to cover the fixed bug(s) or the newly introduced feature(s) (if appropriate).
  • Update the API documentation if a new function is added, or an existing one is deleted.
  • Write concise and explanatory changelogs above.
  • If possible, assign one of the following labels to the PR: feature, fix, chore, documentation or test (or ask a maintainer to do it for you).

Issue #172

During the conversion, only the most essential structural information is retained, including 3D coordinates, chain ID, residue ID, insertion code, residue name, heteroatom indicator, atom name, element, atom ID, B-factor, occupancy, and charge.

@zhu0619 zhu0619 requested a review from cwognum as a code owner August 9, 2024 17:40
@zhu0619 zhu0619 marked this pull request as draft August 9, 2024 17:40
@zhu0619 zhu0619 changed the title PDB converter feature/PDB converter Aug 9, 2024
@zhu0619 zhu0619 added the feature Annotates any PR that adds new features; Used in the release process label Aug 9, 2024
@zhu0619 zhu0619 linked an issue Aug 9, 2024 that may be closed by this pull request
@zhu0619 zhu0619 marked this pull request as ready for review August 9, 2024 18:56
@zhu0619

zhu0619 commented Aug 9, 2024

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Currently, fastpdb can only be installed via pip. I created an issue in their repository to request support for conda installation.

@zhu0619 zhu0619 requested a review from Andrewq11 August 9, 2024 19:12

@cwognum cwognum left a comment

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Thanks @zhu0619 !

I know it took some searching, but I think the solution you came up using fastpdb with is very polished! 💅

I did have some comments. In addition to these comments, would you also mind adding test cases?

Comment thread env.yml
Comment thread polaris/dataset/_adapters.py Outdated
Comment thread polaris/dataset/_adapter_utils.py Outdated
Comment thread polaris/dataset/_factory.py Outdated
Comment thread polaris/dataset/_adapter_utils.py Outdated
Comment thread polaris/dataset/converters/_pdb.py
Comment thread polaris/dataset/converters/_pdb.py Outdated
Comment thread polaris/dataset/converters/_pdb.py
Comment thread polaris/dataset/converters/_pdb.py
Comment thread polaris/dataset/converters/_pdb.py Outdated
@zhu0619 zhu0619 requested a review from cwognum August 15, 2024 13:57
@cwognum cwognum changed the title feature/PDB converter Add a converter from PDB to Zarr to the DatasetFactory Aug 15, 2024
@cwognum

cwognum commented Aug 16, 2024

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FYI - We'll hold of on merging this to give #121 priority!

@zhu0619 zhu0619 merged commit e23c4a1 into main Aug 19, 2024
@zhu0619 zhu0619 deleted the feat/pdb branch August 27, 2024 16:06
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Adding a pdbConverter

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