integrate pdb prep into DR2#591

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509_pdbprep_dbodor

Commits on Mar 12, 2024

main function that writes new pdb files
Dani Bodor
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add pruning pdb file (steps 1-3 from pdbprep)
Dani Bodor
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style: ruff settings regarding TODOs
Dani Bodor
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copy step 4 from pdbprep (selaltloc)
Dani Bodor
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start refactoring step 4: select one of alternate locations
Dani Bodor
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identify low occupancy records
Dani Bodor
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use `_find_low_occ_records` to limit yield
Dani Bodor
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