Add pose IDs to mmCIF keywords via $PoseID token substitution - #82
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Reads the Fragalysis download metadata.csv (column 1 = pose code, column 3 = crystal name) to build a crystal→pose-codes mapping, then substitutes the $PoseID token wherever it appears in the mmcif-gen template output (handles both loop items and key-value pairs). Closes #81. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
The CSV uses double-quoted fields so simple split(',') left quotes in the
parsed values, preventing dict lookups from matching crystal names. Switch to
csv.reader which strips the quotes correctly.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
This was referenced Jun 10, 2026
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Summary
read_fragalysis_csv()to parse the Fragalysis downloadmetadata.csv(pose code in column 1, crystal name in column 3) into a{crystal_name: [pose_codes]}mapping--fragalysis-csv/fragalysis_csvargument (previously unused) throughrun()intoprocess_input()$PoseIDwith a comma-separated list of pose codes wherever the token appears in the mmcif-gen template output — handles loop items and key-value pair items, as well as the existing_struct.titleloopcsv.readerto correctly handle the quoted fields in the Fragalysis CSVCloses #81
Test plan
python -m pdbdepo.pdb_deposition -w <collator_dir> -m <metadata.csv> -f <fragalysis_metadata.csv>againstdata/std_test/lb32627-66_2026-04-28_struct_keywords.textin a generated_struc.cifcontains the expected pose IDs (e.g.A71EV2A-x0836a, A71EV2A-x0836bfor crystalA71EV2A-x0836)$PoseIDtokens remain in any output CIF:grep -r '\$PoseID' pdb_depo_files/🤖 Generated with Claude Code