Metadata-Version: 2.4
Name: sabr-kit
Version: 0.1.0
Summary: Structure-based Antibody Renumbering
Author: Diego del Alamo
Project-URL: Homepage, https://github.com/delalamo/SAbR
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: absl-py==2.2.2
Requires-Dist: biopython==1.85
Requires-Dist: chex==0.1.89
Requires-Dist: dm-haiku==0.0.14
Requires-Dist: etils==1.12.2
Requires-Dist: flax==0.10.6
Requires-Dist: jax==0.6.0
Requires-Dist: jaxlib==0.6.0
Requires-Dist: numpy==2.2.6
Requires-Dist: optax==0.2.4
Requires-Dist: orbax-checkpoint==0.11.13
Requires-Dist: pandas==2.2.3
Requires-Dist: protobuf==6.31.0
Requires-Dist: scipy==1.15.3
Requires-Dist: tensorstore==0.1.75
Requires-Dist: treescope==0.1.9
Provides-Extra: test
Requires-Dist: pytest>=8.0; extra == "test"
Requires-Dist: pytest-cov>=5.0; extra == "test"
Requires-Dist: numpy>=1.24; extra == "test"
Dynamic: license-file

# Structure-based Antibody Renumbering

SAbR (<u>S</U>tructure-based <u>A</u>nti<u>b</u>ody <u>R</u>enumbering) renumbers antibody PDB files using the 3D coordinate of backbone atoms. It uses custom forked versions of [SoftAlign](https://github.com/delalamo/SoftAlign) and [ANARCI](https://github.com/delalamo/ANARCI/tree/master) to align structures to SAbDaB-derived consensus embeddings and renumber to various antibody schemes, respectively.

To install:

```bash
git clone --recursive https://github.com/delalamo/SAbR.git
cd SAbR/
pip install -e .
```

Running SAbR:

```bash
usage: sabr [-h] -i INPUT_PDB -c INPUT_CHAIN -o OUTPUT_PDB [-n NUMBERING_SCHEME] [-t] [--overwrite] [-v]

Structure-based Antibody Renumbering (SAbR) renumbers antibody PDB files using the 3D coordinate of backbone atoms.

options:
  -h, --help            show this help message and exit
  -i INPUT_PDB, --input_pdb INPUT_PDB
                        Input pdb file
  -c INPUT_CHAIN, --input_chain INPUT_CHAIN
                        Input chain
  -o OUTPUT_PDB, --output_pdb OUTPUT_PDB
                        Output pdb file
  -n NUMBERING_SCHEME, --numbering_scheme NUMBERING_SCHEME
                        Numbering scheme, default is IMGT. Supports IMGT, Chothia, Kabat, Martin, AHo, and Wolfguy.
  -t, --trim            Remove regions outside aligned V-region
  --overwrite           Overwrite PDB
  -v, --verbose         Verbose output
```
