Anarci API
The Anarci API runs the Antigen receptor Numbering And Receptor ClassificatIon tool for numbering amino-acid sequences of antibody and T-cell receptor variable domains with the Chothia numbering scheme or extracting variable regions from full length Fab sequences for given input FASTAs. Chothia numbering is a preprocessing required for RF-antibody and other antibody workflows.
Command Line Interface
Examples
Chothia renumber the pdb input.pdb:
lev engine submit anarci \
--pdb-file input.pdb \
--chains HL
Return a fasta file with the variable regions from input.fasta:
lev engine submit anarci --fasta-file input.fasta
Flags
--fasta-file(str) (Required)- Input FASTA file with query sequence
--pdb-file(str) (Required)- Input pdb file of antibody or TCR
--chains(str)- Chains to renumber
Python Interface
Examples
from engine import EngineClient
client = EngineClient()
client.authorize()
# Chothia renumber input.pdb
result = submit_anarci(
pdb_path="input.pdb",
chains="HL"
)
# Return a fasta file with the variable regions
result = submit_anarci(
fasta_path="input.fasta"
)
Outputs
The output is either a Chothia annotated pdb if the model has been used with a pdb input and --chains argument or a fasta file if used with a fasta input.