capiti 0.1.0

Tiny protein-function classifier distilled from ProteinMPNN, for edge deployment.

capiti

Tiny protein-function classifier for edge deployment. Given a nucleotide sequence encoding a protein, capiti flags whether the encoded protein is expected to retain the enzymatic function of one of a small reference set.

Weighs ~1 MB on disk, runs inference in tens of milliseconds on a Raspberry Pi. Trained by distilling ProteinMPNN's function-preserving design prior into a small 1D CNN.

Overview (each ResidualDilatedBlock collapsed to one box):

Inside one ResidualDilatedBlock:

See docs/capiti.summary.txt for the full per-layer size / FLOP table.

Install

pip install capiti

Use

capiti ATGCGTAAAGTGGCC...           # prints TRUE or FALSE (default set ab9)
capiti ATGCGT...  --cutoff 0.8 -v   # TRUE  p_inset=0.995
capiti --fasta seqs.fa              # batch over a FASTA
echo ATGCGT... | capiti --stdin

Reference sets

capiti ships three bundled reference sets, selectable at invocation time via --set NAME (or CAPITI_SET).

set	targets	description
ab9	9	Beta-lactamases relevant to antibiotic resistance plus other soluble enzymes. Default.
E	59	Larger enzyme panel (54 PDB + 5 AlphaFold-only entries).
C	235	Broad enzyme panel sourced from PDB.

capiti ATGCGT... --set ab9
capiti --fasta seqs.fa --set C
CAPITI_SET=E capiti --stdin

Inference-time gate

Capiti pairs the CNN with a SIFTS-backed fixed-position gate by default: if the model picks a target Ti and the query has a mutated residue at any of Ti's catalytic / active-site positions, the in-set score is forced to 0. This catches single-residue active-site knockouts the masked-mean CNN under-weights. Disable with --no-gate.

Exit code is 0 on TRUE, 1 on FALSE, suitable for shell pipelines:

capiti ATGCGT... && echo "in set" || echo "not in set"

Benchmarks

On the held-out test split for each set (gate on, natural threshold):

set	targets	AUC	mpnn_pos	ala_scan
ab9	9	1.000	0.999	1.000
E	59	0.984	0.983	0.966
C	235	0.970	0.964	0.953

Side-by-side comparison with BLAST and k-mer baselines at docs/benchmark/CE_summary.md. Per-set ROC, PR, per-class plots at docs/benchmark/v3/, docs/benchmark/E_v1/, docs/benchmark/C_v1/.

Status

Research-grade. The CLI surface (flags, stdin/FASTA behaviour, exit codes) is stable; bundled models may be retrained and updated between 0.x releases. Not for operational use.

License

MIT.