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MPNN Sequence Probability
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evo-design/proto-language/proto_language/constraint/sequence_scoring/mpnn_sequence_probability_constraint.py
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Constraint contributors
Score proposals by MPNN probability; lower is better.

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API Reference

ConfigMPNNSequenceProbabilityConfig Source
Configuration for structure-conditioned MPNN sequence-probability scoring.
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enum
default:"ligandmpnn"
Structure-conditioned model used to score the sequence.Options: ligandmpnn, proteinmpnn
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enum
default:"configured_structure_inputs"
Use configured structure_inputs or each proposal’s attached structure for MPNN scoring.Options: configured_structure_inputs, proposal_structure
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array
Structures for MPNN scoring; optional when using proposal structures.
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string
Structure chain corresponding to the scored input sequence.
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enum
default:"probability_loss"
Return 1-exp(avg_log_likelihood), mean NLL, or perplexity.Options: probability_loss, nll, perplexity
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enum
default:"model"
Compute MPNN probability with the model or read pmpnn from proposal generator metadata.Options: model, proposal_metadata
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string
Generator metadata namespace to read for pmpnn when score_source=‘proposal_metadata’.
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enum
default:"proteinmpnn"
ProteinMPNN weights used when model=‘proteinmpnn’.Options: proteinmpnn, v_48_002, v_48_010, v_48_030, abmpnn, soluble
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boolean
default:"False"
Whether LigandMPNN scoring conditions on fixed-residue sidechain atoms.
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number
default:"8.0"
Ligand-residue distance cutoff (Å) used by LigandMPNN scoring.
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enum
default:"ligand_mpnn"
LigandMPNN implementation used for scoring: Foundry-backed ligand_mpnn or original LigandMPNN.Options: ligand_mpnn, original
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string
Optional explicit LigandMPNN checkpoint path.
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integer
Seed for MPNN scoring. None lets proto-tools choose its default seed behavior.
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string
default:"cuda"
Device for MPNN scoring.
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boolean
default:"False"
Whether to print MPNN scoring progress.

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Usage

python

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Metadata