├── .gitignore ├── LICENSE ├── README.md ├── environment.yml ├── setup.cfg ├── setup.py ├── src └── ab_characterisation │ ├── __init__.py │ ├── cli.py │ ├── developability_tools │ ├── __init__.py │ ├── sequence_liabilities │ │ ├── __init__.py │ │ ├── definitions.py │ │ ├── main.py │ │ ├── outputs.py │ │ ├── scanner_classes.py │ │ └── scanners.py │ ├── sequence_properties │ │ ├── calculations.py │ │ ├── main.py │ │ └── outputs.py │ ├── tap │ │ ├── __init__.py │ │ ├── definitions.py │ │ ├── main.py │ │ ├── metrics │ │ │ ├── __init__.py │ │ │ ├── base_calculator.py │ │ │ ├── hydrophobic_patches.py │ │ │ ├── negative_patches.py │ │ │ ├── positive_patches.py │ │ │ ├── sfvcsp.py │ │ │ └── total_cdr_length.py │ │ ├── outputs.py │ │ ├── psa_executables │ │ │ ├── psa │ │ │ └── psa_mac │ │ └── structure_annotation.py │ └── utils │ │ ├── input_handling.py │ │ └── outputs.py │ ├── filter_steps.py │ ├── pipeline_orchestration.py │ ├── rosetta_steps.py │ ├── sequence_steps.py │ ├── structure_steps.py │ └── utils │ ├── __init__.py │ ├── anarci_region_definition_utils.py │ ├── anarci_utils.py │ ├── chimerax_utils.py │ ├── data_classes.py │ ├── rosetta_templates │ ├── rosetta_metrics_ab_only.sh │ ├── rosetta_metrics_ab_only.xml │ ├── rosetta_metrics_complex.sh │ └── rosetta_metrics_complex.xml │ └── rosetta_utils.py └── tests ├── data ├── test_complex_reference.pdb └── test_pipeline.csv └── integration ├── chimera_test_script.py └── test_pipeline.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Exscientia/ab-characterisation/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Exscientia/ab-characterisation/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: 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