[WIP] Implementing gemmi-based mmcif reader (with easy extension to PDB/PDBx and mmJSON)
#4712
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Hello @marinegor! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:
Comment last updated at 2024-09-20 22:02:54 UTC |
Linter Bot Results:Hi @marinegor! Thanks for making this PR. We linted your code and found the following: Some issues were found with the formatting of your code.
Please have a look at the Please note: The |
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| class MMCIFWriter(base.WriterBase): |
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I wouldn't include this at this stage, Writer is optional
| from .base import TopologyReaderBase | ||
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| def _into_idx(arr: list[int]) -> list[int]: |
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Document what this does, ideally with an example
| record_types, # res.het_flag | ||
| tempfactors, # at.b_iso | ||
| residx, # _into_idx(res.seqid.num) | ||
| ) = map( # this is probably not pretty, but it's efficient -- one loop over the mmcif |
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Are all the fields here guaranteed in a valid pdbx? One benefit to working column by column is that you can do optional columns
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Do you have an example of a PDBx in mind, or like a test set for them? I've never actually worked with the format, since in RCSB afaik we have only pdb or mmcif
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I'm struggling to follow the logic here, a comment breaking down what this double nested loop iteration into a zip is doing would be nice
| @@ -78,6 +78,7 @@ extra_formats = [ | |||
| "pytng>=0.2.3", | |||
| "gsd>3.0.0", | |||
| "rdkit>=2020.03.1", | |||
| "gemmi", # for mmcif format | |||
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This will probably be optional, so other imports will have to respect that too
Fixes #2367 and also extends #4303
Changes made in this Pull Request:
gemmilibrary (link) to parse mmcif filesclass MMCIFReader(base.SingleFrameReaderBase)andclass MMCIFParser(TopologyReaderBase)classes for thatAs a bonus, this implementation would potentially allow to read any of the gemmi-supported formats (source):
Also, this (with slight modifications) also would allow reading mmcif with multiple models sharing the same topology, as well as more feature-rich parsing of PDBs (the same code without changes can be used for parsing altlocs, charges, etc, from all of these formats).
However, I'm slightly lost on what's to be done next for this PR to be merged, so I'm asking if someone could help me navigate here (tagging @richardjgowers here as author of original PDBx implementation 4303).
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📚 Documentation preview 📚: https://mdanalysis--4712.org.readthedocs.build/en/4712/