capiti 0.0.3

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 multiple bundled reference sets, selectable at invocation time. Use --set NAME (or the CAPITI_SET env var).

set	status	description
ab9	available	9 soluble enzymes (several beta-lactamases relevant to antibiotic resistance, plus other enzymes). Default.
C	planned	TBA.
E	planned	TBA.

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

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

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

Status

The 0.0.x line is research-grade. The CLI surface (flags, stdin/FASTA behaviour, exit codes) is stable; bundled models will be retrained and updated between 0.0.x releases, and should not be used for anything operational.

License

MIT.