abgpt 0.1.0

AbGPT: De Novo B-Cell Receptor Design via Generative Language Modeling

AbGPT

Official repository for AbGPT: De Novo B-Cell Receptor Design via Generative Language Modeling.

Setup

To use AbGPT, install via pip:

pip install abgpt

Alternatively, you can clone this repository and install the package locally:

$ git clone [e-mail]:BaratiLab/AbGPT.git 
$ pip install AbGPT

Command line usage

Full sequence generation

To generate 1000 light chain sequences starting with "QLQL":

abgpt_generate --chain_type light --starting_residue QLQL --num_seqs 1000

To generate a BCR library with 1000 sequences for a number of starting residue (e.g., "QVQL", "EVQL", "VQLV") in the heavy chain:

abgpt_generate --chain_type heavy --starting_residue QVQL,EVQL,VQLV --num_seqs_per_residue 1000

To generate a BCR library with 1000 sequences for a number of starting residue (e.g., "QVQL", "EVQL", "VQLV") in the light chain:

abgpt_generate --chain_type light --starting_residue EIVL,EIVM,DIQM --num_seqs_per_residue 1000