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### Random Protein Sampling (`random-protein-sample`) Fills every masked position in each input sequence with a random amino acid drawn from the configured codon scheme, returning one filled sequence per input. #### API Reference

Source Protein sequence(s) to process. Can be provided as:

Source Controls which positions to mask for sampling. Position-selection method. Always `"random"` for this tier (uniform selection, no model). Exact number of positions to mask per sequence. Fraction of designable positions to mask (e.g. 0.15 for \~15%). 1-indexed positions that must NOT be masked. Applied uniformly to all sequences. Codon scheme controlling amino acid sampling probabilities. `"UNIFORM"` gives equal weight to all 20 amino acids; other schemes (NNK, NNS, NDT, etc.) weight amino acids by the number of codons encoding them. Available options: `UNIFORM`, `NNN`, `NNK`, `NNS`, `NDT`, `DBK`, `NRT` If True, the stop symbol `"*"` is included in the sampling distribution. For degenerate schemes it is weighted by its stop-codon count; for `"UNIFORM"` it is an equally weighted 21st symbol. Default: False (stops never sampled). One-letter codes of amino acids to remove from the sampling distribution after codon-scheme and stop-codon handling. An empty list is treated as `None`. Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). `True` is coerced to `1` and `False` to `0`. Device to run the tool on. Maximum execution time in seconds. `None` waits indefinitely. Random seed. When set, tools run reproducibly up to small GPU float noise (see `BaseToolOutput.approx_equal`), and the seed participates in cache keys. When None, cacheable seed-sensitive tools skip cache until seeded.

Source One sampled sequence per input, in input order. Sampled protein sequence with masked positions filled by random amino acids.

#### Applications Use this to build randomized protein libraries that mimic experimental degenerate-codon mutagenesis, for example `NNK` saturation at chosen positions for directed-evolution and combinatorial screening. It also serves as an unbiased random baseline for judging whether a model-guided designer beats chance. #### Usage Tips * **`codon_scheme` (default `UNIFORM`) sets the amino-acid distribution.** `UNIFORM` draws all twenty amino acids equally; degenerate schemes (`NNK`, `NNS`, `NDT`, `DBK`, `NRT`) weight each amino acid by how many of the scheme's codons encode it, so residues such as leucine, serine, and arginine appear more often than methionine or tryptophan. * **`NDT` gives an even 12-amino-acid library.** It encodes twelve amino acids with no codon redundancy, so each is equally likely; useful for small focused libraries. * **Stop codons are excluded by default.** Set `allow_stop_codons` to `True` to include the stop symbol `*` in the distribution: for degenerate schemes it is weighted by its stop-codon count, and for `UNIFORM` it is an equally weighted 21st symbol. * **`excluded_amino_acids` removes residues from sampling.** For example, set `["C"]` to avoid cysteine or `["C", "A"]` to remove cysteine and alanine from every masked position. An empty list is treated like `None`; excluding every residue reachable by the selected `codon_scheme` raises an error. * **`_` masks override the masking strategy.** If an input already contains `_`, exactly those positions are filled and `masking_strategy` is ignored; remove the `_` characters to let the strategy choose positions instead. * **`masking_strategy.fixed_positions` are 1-indexed.** Positions listed there are never mutated; they are specified using 1-based indexing to match biological residue selection conventions. * **Set `seed` for reproducibility.** Sampling is otherwise nondeterministic; a fixed seed makes the filled sequences reproducible across runs.