sabr-kit 0.1.0__tar.gz

sabr_kit-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 Diego del Alamo
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

sabr_kit-0.1.0/MANIFEST.in

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+include LICENSE
+include README.md
+
+recursive-include src/sabr/assets *.npz
+recursive-include external/SoftAlign/softalign/models *
+recursive-include external/SoftAlign/softalign *
+recursive-include external/ANARCI/src/ANARCI *
+
+prune dist
+prune build
+prune sabr.egg-info
+prune src/sabr.egg-info

sabr_kit-0.1.0/PKG-INFO

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+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
+```

sabr_kit-0.1.0/README.md

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+# 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
+```