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alphapulldown-input-parser

Reusable parser for AlphaPulldown-style fold specifications. Install it with:

pip install "alphapulldown-input-parser>=0.4.0"

or, for local development:

pip install -e /path/to/alphapulldown-input-parser

The package exposes three helpers:

  • parse_fold(...) – mirrors the historical AlphaPulldown helper and performs feature existence checks.
  • expand_fold_specification(...) – expands a single fold string without raising if features are missing.
  • parse_fold_chains(spec, protein_delimiter="+") – pure-syntactic parse of a single spec into (chain_name, copies, regions) triples, with no filesystem access or feature lookup. Useful for resource sizing or input validation before features exist on disk.

The parser is dependency-free and works across AlphaPulldown, the Snakemake pipeline, or any other tooling that consumes the same fold syntax.

As of 0.4.0, AF3 JSON feature files support the same copy/range suffixes as classic AlphaPulldown feature pickles, including discontinuous regions and copy counts. For example:

parse_fold(
    [
        "P01258_af3_input.json:1-100",
        "P01258_af3_input.json:1-100:150-200",
        "P01258_af3_input.json:2:1-100:150-200+P01579_af3_input.json",
    ],
    features_directory=["/path/to/features"],
    protein_delimiter="+",
)

AlphaPulldown and AlphaPulldownSnakemake can then preserve those AF3 JSON regions during input preparation. For the AlphaFold 3 backend, discontinuous regions are expanded into separate cropped chains rather than one continuous polymer chain.