antibody_canonical_classes
Read-only
Assign each CDR of an antibody heavy, kappa or lambda variable domain to its canonical structure class: SCALOP's length-independent clusters of known loop conformations (CDR-H1, H2, L1, L2, L3; H3 has no canonical classes).
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| scheme | No | the numbering the clusters are read in. Values: imgt (IMGT), chothia (Chothia). | imgt |
| protein | Yes | the protein sequence (one-letter amino acids); every heavy, kappa and lambda variable domain in it is classified. | |
| species | No | species whose HMMs are preferred when numbering (ANARCI's default: human and mouse). | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| definition | No | where each CDR begins and ends, by SCALOP's own tables. Values: imgt (IMGT), chothia (Chothia), north (North). | north |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| classes | Yes | one `CDR: class` string per CDR, in sequence order (`H1: H1-13-A`, `None` where no class fits) | |
| domains | Yes | per heavy, kappa or lambda domain: chain type, span, and per CDR the loop sequence, its class (cluster id), the median structure, the cluster's size, the outcome, SCALOP's threshold, every candidate cluster's score, and each residue's position, 0-based sequence index and log-odds in the assigned cluster |