API Reference#
This section contains the complete API reference for PrxteinMPNN.
API Reference:
JacobianSpecificationJacobianSpecification.apc_batch_sizeJacobianSpecification.apc_residue_batch_sizeJacobianSpecification.average_encodingsJacobianSpecification.average_logitsJacobianSpecification.combineJacobianSpecification.combine_batch_sizeJacobianSpecification.combine_fnJacobianSpecification.combine_fn_kwargsJacobianSpecification.combine_noise_batch_sizeJacobianSpecification.combine_weightsJacobianSpecification.compute_apcJacobianSpecification.jacobian_batch_sizeJacobianSpecification.noise_batch_sizeJacobianSpecification.output_h5_path
RunSpecificationRunSpecification.inputsRunSpecification.model_weightsRunSpecification.model_versionRunSpecification.batch_sizeRunSpecification.backbone_noiseRunSpecification.foldcomp_databaseRunSpecification.ar_maskRunSpecification.random_seedRunSpecification.chain_idRunSpecification.modelRunSpecification.altlocRunSpecification.decoding_order_fnRunSpecification.conformational_statesRunSpecification.altlocRunSpecification.ar_maskRunSpecification.backbone_noiseRunSpecification.batch_sizeRunSpecification.cache_pathRunSpecification.chain_idRunSpecification.conformational_statesRunSpecification.decoding_order_fnRunSpecification.foldcomp_databaseRunSpecification.modelRunSpecification.model_versionRunSpecification.model_weightsRunSpecification.output_pathRunSpecification.overwrite_cacheRunSpecification.pass_modeRunSpecification.random_seedRunSpecification.tied_positionsRunSpecification.topologyRunSpecification.inputs
SamplingSpecificationSamplingSpecification.average_encodingsSamplingSpecification.average_logitsSamplingSpecification.biasSamplingSpecification.fixed_positionsSamplingSpecification.iterationsSamplingSpecification.learning_rateSamplingSpecification.multi_state_alphaSamplingSpecification.multi_state_strategySamplingSpecification.noise_batch_sizeSamplingSpecification.num_samplesSamplingSpecification.output_h5_pathSamplingSpecification.samples_batch_sizeSamplingSpecification.sampling_strategySamplingSpecification.temperature
ScoringSpecificationScoringSpecification.sequences_to_scoreScoringSpecification.temperatureScoringSpecification.return_logitsScoringSpecification.return_decoding_ordersScoringSpecification.return_all_scoresScoringSpecification.score_batch_sizeScoringSpecification.output_h5_pathScoringSpecification.output_h5_pathScoringSpecification.return_all_scoresScoringSpecification.return_decoding_ordersScoringSpecification.return_logitsScoringSpecification.score_batch_sizeScoringSpecification.sequences_to_scoreScoringSpecification.temperature
sample()score()- io: Input/Output for Structure and Trajectories
- mpnn: Fetch model parameters
- model: MPNN model architecture
- sampling: Sampling methods for MPNN
- scoring: Scoring functions for MPNN
- utils: Utility functions for MPNN