domain-finger-print 0.1.0a1

Build local CATH domain databases and generate structure-based domain fingerprints.

domain-finger-print

domain-finger-print is a Python package for:

• building a local CATH domain database from official domain-only structures
• generating structure-only fingerprints against that database with Foldseek

The package scope is intentionally narrow: it builds databases and writes fingerprint npz files. Visualization is not part of the package API.

What It Does

• Downloads official CATH classification files
• Downloads an official nonredundant CATH domain-only PDB archive (S20 or S40)
• Extracts one PDB file per domain into a local structures/ directory
• Excludes ...00 whole-chain entries by default, so the local DB is chopped-domain focused
• Builds a SQLite metadata index for downstream search
• Generates fixed-width fingerprints over the full CATH superfamily vocabulary
• Stores qTM and tTM separately, plus a stacked [qTM || tTM] matrix, in one compressed npz

Install

pip install -e . --no-build-isolation

Build a CATH Database

dfp build-db cath --out-dir ./cath_s20_db --redundancy 20

Useful flags:

• --redundancy 20|40
• --version latest-release
• --keep-archive
• --include-whole-chain
• --force

Generate Fingerprints

Single query:

dfp fingerprint \
  --db ./cath_s20_db \
  --query ./queries/my_protein.pdb \
  --out ./results/my_protein_fingerprint.npz

Directory of queries:

dfp fingerprint \
  --db ./cath_s20_db \
  --query-dir ./queries \
  --glob "*.pdb" \
  --out ./results/fingerprints_full.npz \
  --workers 96 \
  --prefilter-max-seqs 100

Useful flags:

• --foldseek tools/foldseek/bin/foldseek
• --foldseek-db ./foldseek_db/cath_s20
• --foldseek-gpu
• --workers 96
• --prefilter-max-seqs 100
• --foldseek-sensitivity 9.5
• --min-domain-length 0
• --min-aligned-length 60

Output Format

The package writes one compressed npz containing:

• query_labels
• q_feature_labels
• t_feature_labels
• stacked_feature_labels
• q_matrix
• t_matrix
• stacked_matrix
• metadata_json

Feature space is fixed by CATH superfamily. This means every run against the same database has the same dimensionality.

The stacked fingerprint is:

[qTM over all superfamilies || tTM over all superfamilies]

Schema details are documented in docs/fingerprint_npz_schema.md.

Output Layout

cath_s20_db/
├── db_info.json
├── downloads/
├── metadata.sqlite
└── structures/

Notes

• CATH latest-release provides nonredundant domain-only PDB archives for S20 and S40.
• By default the builder removes CATH entries whose domain number is 00, because those represent whole-chain entries without domain chopping.
• Foldseek is used directly for structure search and scoring; the package does not currently expose TM-align reranking.
• Visualization, PCA, UMAP, and heatmaps are kept out of the installable package on purpose.