Humatch inputs and parameters
Up to 50 sequences, the chain_type that picks the heavy or light model — mislabel it and the score is meaningless; the threshold moves only the human call.
You submit sequences in one of two shapes, and the shape decides which classifiers run. Loose chains go in sequences and are scored by the per-chain heavy or light CNN. Heavy/light pairs go in chain_pairs and get both — each chain's own per-chain score and Humatch's paired classifier, which exists only for pairs and cannot be approximated from one chain alone.
The chain type is load-bearing for sequences: heavy and light use separate models, so mislabeling a chain produces a meaningless score. The threshold only affects the human / not-human classification, not the underlying score.
Loose chains
sequencesstring[]Antibody variable-region amino acid sequences, all of chain_type. One to 50 per job. Required unless you give chain_pairs — a request with neither is refused.
sequence_namesstring[]Optional names for each sequence.
Heavy/light pairs
chain_pairsobject[]Heavy/light pairs belonging to the same antibody. One to 50 per job. Each entry takes a required heavy sequence, a required light sequence (kappa or lambda), and an optional name.
Use this shape whenever you have both chains of one antibody, since the paired score is otherwise unavailable. chain_type does not apply here — each entry already says which sequence is which.
The pairing is your assertion, and nothing checks it
Humatch's paired classifier scores whatever combination it is handed. Nothing in the job can tell that two sequences came from the same antibody, so a mis-paired request returns a confident paired score for a chimera that does not exist. Pair the chains correctly before you submit; the output will not warn you.
Chain type and scheme
chain_typestringdefault: HChain type of every entry in sequences: H for heavy, L for light (kappa or lambda). Selects the matching humanness model. It does not apply to chain_pairs.
schemestringdefault: imgtNumbering scheme requested for alignment: imgt, chothia, or kabat. ⚠ Humatch always aligns to IMGT, so a chothia or kabat request is recorded and not applied — the result reports it back in requested_scheme while numbering_scheme stays imgt. Position numbers in the output are IMGT whatever you send. For Chothia or Kabat numbering, use ANARCI.
Classification threshold
score_thresholdfloatdefault: 0.5Humanness score at or above which a sequence is classified as human (0.0–1.0).
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