Index A | B | C | D | E | F | G | I | J | L | M | N | O | P | Q | R | S | T | U | W A abnumber() (openprotein.align.AlignAPI method) abnumber_file() (openprotein.align.AlignAPI method) af2 (openprotein.fold.FoldAPI attribute) algorithm (openprotein.design.DesignFuture property) align (openprotein.OpenProtein property) AlignAPI (class in openprotein.align) allowed_tokens (openprotein.design.DesignFuture property) alphafold2 (openprotein.fold.FoldAPI attribute) AlphaFold2Model (class in openprotein.fold) assay (openprotein.design.DesignFuture property) AssayDataset (class in openprotein.data) AssayMetadata (class in openprotein.data) attn() (openprotein.embeddings.ESMModel method) (openprotein.embeddings.OpenProteinModel method) B boltz1 (openprotein.fold.FoldAPI attribute) Boltz1Model (class in openprotein.fold) boltz1x (openprotein.fold.FoldAPI attribute) Boltz1xModel (class in openprotein.fold) boltz2 (openprotein.fold.FoldAPI attribute) Boltz2Model (class in openprotein.fold) boltz_1 (openprotein.fold.FoldAPI attribute) boltz_1x (openprotein.fold.FoldAPI attribute) boltz_2 (openprotein.fold.FoldAPI attribute) BoltzGenFuture (class in openprotein.models) C cancelled() (openprotein.embeddings.EmbeddingsGenerateFuture method) (openprotein.embeddings.EmbeddingsResultFuture method) (openprotein.embeddings.EmbeddingsScoreFuture method) (openprotein.fold.FoldResultFuture method) (openprotein.models.BoltzGenFuture method) (openprotein.models.RFdiffusionFuture method) (openprotein.prompt.Prompt method) (openprotein.svd.SVDModel method) (openprotein.umap.UMAPModel method) clustalo() (openprotein.align.AlignAPI method) clustalo_file() (openprotein.align.AlignAPI method) connect() (in module openprotein) create() (openprotein.data.DataAPI method) (openprotein.embeddings.EmbeddingModel class method) (openprotein.embeddings.ESMModel class method) (openprotein.embeddings.OpenProteinModel class method) (openprotein.embeddings.PoET2Model class method) (openprotein.embeddings.PoETModel class method) (openprotein.fold.FoldResultFuture class method) create_genetic_algorithm_design() (openprotein.design.DesignAPI method) create_msa() (openprotein.align.AlignAPI method) create_prompt() (openprotein.prompt.PromptAPI method) create_query() (openprotein.prompt.PromptAPI method) created_date (openprotein.embeddings.EmbeddingsGenerateFuture property) (openprotein.embeddings.EmbeddingsResultFuture property) (openprotein.embeddings.EmbeddingsScoreFuture property) (openprotein.fold.FoldResultFuture property) (openprotein.models.BoltzGenFuture property) (openprotein.models.RFdiffusionFuture property) (openprotein.prompt.Prompt property) (openprotein.svd.SVDModel property) (openprotein.umap.UMAPModel property) criteria (openprotein.design.DesignFuture property) crossover_prob (openprotein.design.DesignFuture property) crossover_prob_pointwise (openprotein.design.DesignFuture property) crossvalidate() (openprotein.predictor.PredictorModel method) D data (openprotein.OpenProtein property) DataAPI (class in openprotein.data) delete() (openprotein.predictor.PredictorModel method) (openprotein.svd.SVDModel method) (openprotein.umap.UMAPModel method) delete_predictor() (openprotein.predictor.PredictorAPI method) design (openprotein.OpenProtein property) DesignAPI (class in openprotein.design) DesignFuture (class in openprotein.design) done() (openprotein.embeddings.EmbeddingsGenerateFuture method) (openprotein.embeddings.EmbeddingsResultFuture method) (openprotein.embeddings.EmbeddingsScoreFuture method) (openprotein.fold.FoldResultFuture method) (openprotein.jobs.Future method) (openprotein.models.BoltzGenFuture method) (openprotein.models.RFdiffusionFuture method) (openprotein.prompt.Prompt method) (openprotein.svd.SVDModel method) (openprotein.umap.UMAPModel method) E embed() (openprotein.embeddings.EmbeddingModel method) (openprotein.embeddings.ESMModel method) (openprotein.embeddings.OpenProteinModel method) (openprotein.embeddings.PoET2Model method) (openprotein.embeddings.PoETModel method) (openprotein.svd.SVDModel method) (openprotein.umap.UMAPModel method) embedding (openprotein.OpenProtein property) EmbeddingModel (class in openprotein.embeddings) embeddings (openprotein.OpenProtein property) (openprotein.umap.UMAPModel property) EmbeddingsAPI (class in openprotein.embeddings) EmbeddingsGenerateFuture (class in openprotein.embeddings) EmbeddingsResultFuture (class in openprotein.embeddings) EmbeddingsScoreFuture (class in openprotein.embeddings) end_date (openprotein.embeddings.EmbeddingsGenerateFuture property) (openprotein.embeddings.EmbeddingsResultFuture property) (openprotein.embeddings.EmbeddingsScoreFuture property) (openprotein.fold.FoldResultFuture property) (openprotein.models.BoltzGenFuture property) (openprotein.models.RFdiffusionFuture property) (openprotein.prompt.Prompt property) (openprotein.svd.SVDModel property) (openprotein.umap.UMAPModel property) ensemble() (openprotein.predictor.PredictorAPI method) esm1b (openprotein.embeddings.EmbeddingsAPI attribute) esm1v (openprotein.embeddings.EmbeddingsAPI attribute) esm2 (openprotein.embeddings.EmbeddingsAPI attribute) esmfold (openprotein.fold.FoldAPI attribute) ESMFoldModel (class in openprotein.fold) ESMModel (class in openprotein.embeddings) F fit_gp() (openprotein.embeddings.EmbeddingModel method) (openprotein.embeddings.ESMModel method) (openprotein.embeddings.OpenProteinModel method) (openprotein.embeddings.PoET2Model method) (openprotein.embeddings.PoETModel method) (openprotein.predictor.PredictorAPI method) (openprotein.svd.SVDModel method) fit_svd() (openprotein.embeddings.EmbeddingModel method) (openprotein.embeddings.ESMModel method) (openprotein.embeddings.OpenProteinModel method) (openprotein.embeddings.PoET2Model method) (openprotein.embeddings.PoETModel method) fit_umap() (openprotein.embeddings.EmbeddingModel method) (openprotein.embeddings.ESMModel method) (openprotein.embeddings.OpenProteinModel method) (openprotein.embeddings.PoET2Model method) (openprotein.embeddings.PoETModel method) (openprotein.svd.SVDModel method) fold (openprotein.OpenProtein property) fold() (openprotein.fold.AlphaFold2Model method) (openprotein.fold.Boltz1Model method) (openprotein.fold.Boltz1xModel method) (openprotein.fold.Boltz2Model method) (openprotein.fold.ESMFoldModel method) FoldAPI (class in openprotein.fold) FoldResultFuture (class in openprotein.fold) Future (class in openprotein.jobs) G generate() (openprotein.embeddings.PoET2Model method) (openprotein.embeddings.PoETModel method) (openprotein.models.ProteinMPNNModel method) get() (openprotein.align.MSAFuture method) (openprotein.data.DataAPI method) (openprotein.design.DesignFuture method) (openprotein.embeddings.EmbeddingsGenerateFuture method) (openprotein.embeddings.EmbeddingsResultFuture method) (openprotein.embeddings.EmbeddingsScoreFuture method) (openprotein.fold.FoldResultFuture method) (openprotein.jobs.Future method) (openprotein.jobs.JobsAPI method) (openprotein.models.BoltzGenFuture method) (openprotein.models.RFdiffusionFuture method) (openprotein.predictor.PredictorModel method) (openprotein.prompt.Prompt method) (openprotein.svd.SVDModel method) (openprotein.umap.UMAPModel method) get_assay() (openprotein.design.DesignFuture method) (openprotein.predictor.PredictorModel method) get_design() (openprotein.design.DesignAPI method) get_first() (openprotein.data.AssayDataset method) get_inputs() (openprotein.svd.SVDModel method) (openprotein.umap.UMAPModel method) get_item() (openprotein.embeddings.EmbeddingsResultFuture method) (openprotein.fold.FoldResultFuture method) get_metadata() (openprotein.embeddings.EmbeddingModel method) (openprotein.embeddings.ESMModel method) (openprotein.embeddings.OpenProteinModel method) (openprotein.embeddings.PoET2Model method) (openprotein.embeddings.PoETModel method) (openprotein.models.ProteinMPNNModel method) get_model() (openprotein.embeddings.EmbeddingModel class method) (openprotein.embeddings.EmbeddingsAPI method) (openprotein.embeddings.ESMModel class method) (openprotein.embeddings.OpenProteinModel class method) (openprotein.embeddings.PoET2Model class method) (openprotein.embeddings.PoETModel class method) (openprotein.fold.FoldAPI method) (openprotein.predictor.PredictorModel method) get_msa() (openprotein.align.AlignAPI method) get_pdb() (openprotein.models.BoltzGenFuture method) (openprotein.models.RFdiffusionFuture method) get_predictor() (openprotein.predictor.PredictorAPI method) get_prompt() (openprotein.align.AlignAPI method) (openprotein.prompt.PromptAPI method) get_query() (openprotein.prompt.PromptAPI method) get_results() (openprotein.fold.FoldAPI method) get_seed() (openprotein.align.AlignAPI method) get_slice() (openprotein.data.AssayDataset method) I id (openprotein.design.DesignFuture property) (openprotein.embeddings.EmbeddingsGenerateFuture property) (openprotein.embeddings.EmbeddingsResultFuture property) (openprotein.embeddings.EmbeddingsScoreFuture property) (openprotein.fold.FoldResultFuture property) (openprotein.models.BoltzGenFuture property) (openprotein.models.RFdiffusionFuture property) (openprotein.predictor.PredictorModel property) (openprotein.prompt.Prompt property) (openprotein.svd.SVDModel property) (openprotein.umap.UMAPModel property) indel() (openprotein.embeddings.PoET2Model method) (openprotein.embeddings.PoETModel method) (openprotein.models.ProteinMPNNModel method) J Job (class in openprotein.jobs) job (openprotein.fold.FoldResultFuture attribute) job_id (openprotein.embeddings.EmbeddingsGenerateFuture property) (openprotein.embeddings.EmbeddingsResultFuture property) (openprotein.embeddings.EmbeddingsScoreFuture property) (openprotein.fold.FoldResultFuture property) (openprotein.models.BoltzGenFuture property) (openprotein.models.RFdiffusionFuture property) (openprotein.prompt.Prompt property) (openprotein.svd.SVDModel property) (openprotein.umap.UMAPModel property) job_type (openprotein.embeddings.EmbeddingsGenerateFuture property) (openprotein.embeddings.EmbeddingsResultFuture property) (openprotein.embeddings.EmbeddingsScoreFuture property) (openprotein.fold.FoldResultFuture property) (openprotein.models.BoltzGenFuture property) (openprotein.models.RFdiffusionFuture property) (openprotein.prompt.Prompt property) (openprotein.svd.SVDModel property) (openprotein.umap.UMAPModel property) jobs (openprotein.OpenProtein property) JobsAPI (class in openprotein.jobs) L list() (openprotein.data.DataAPI method) (openprotein.jobs.JobsAPI method) list_designs() (openprotein.design.DesignAPI method) list_models() (openprotein.data.AssayDataset method) (openprotein.embeddings.EmbeddingsAPI method) (openprotein.fold.FoldAPI method) list_predictors() (openprotein.predictor.PredictorAPI method) list_prompts() (openprotein.prompt.PromptAPI method) logits() (openprotein.embeddings.EmbeddingModel method) (openprotein.embeddings.ESMModel method) (openprotein.embeddings.OpenProteinModel method) (openprotein.embeddings.PoET2Model method) (openprotein.embeddings.PoETModel method) M mafft() (openprotein.align.AlignAPI method) mafft_file() (openprotein.align.AlignAPI method) metadata (openprotein.design.DesignFuture property) (openprotein.embeddings.EmbeddingModel property) (openprotein.embeddings.ESMModel property) (openprotein.embeddings.OpenProteinModel property) (openprotein.embeddings.PoET2Model property) (openprotein.embeddings.PoETModel property) (openprotein.fold.FoldResultFuture property) (openprotein.predictor.PredictorModel property) (openprotein.svd.SVDModel property) (openprotein.umap.UMAPModel property) min_dist (openprotein.umap.UMAPModel property) minifold (openprotein.fold.FoldAPI attribute) model (openprotein.predictor.PredictorModel property) (openprotein.svd.SVDModel property) (openprotein.umap.UMAPModel property) model_id (openprotein.fold.ESMFoldModel attribute) (openprotein.fold.FoldResultFuture property) models (openprotein.OpenProtein property) ModelsAPI (class in openprotein.models) msa_id (openprotein.prompt.PromptJob property) MSAFuture (class in openprotein.align) mutation_average_mutations_per_seq (openprotein.design.DesignFuture property) N n_components (openprotein.svd.SVDModel property) (openprotein.umap.UMAPModel property) n_neighbors (openprotein.umap.UMAPModel property) n_offsprings (openprotein.design.DesignFuture property) num_rows (openprotein.design.DesignFuture property) num_steps (openprotein.design.DesignFuture property) O OpenProtein (class in openprotein) OpenProteinModel (class in openprotein.embeddings) P poet (openprotein.embeddings.EmbeddingsAPI attribute) poet2 (openprotein.embeddings.EmbeddingsAPI attribute) PoET2Model (class in openprotein.embeddings) PoETModel (class in openprotein.embeddings) pop_size (openprotein.design.DesignFuture property) predict() (openprotein.predictor.PredictorModel method) predictor (openprotein.OpenProtein property) PredictorAPI (class in openprotein.predictor) PredictorModel (class in openprotein.predictor) progress_counter (openprotein.embeddings.EmbeddingsGenerateFuture property) (openprotein.embeddings.EmbeddingsResultFuture property) (openprotein.embeddings.EmbeddingsScoreFuture property) (openprotein.fold.FoldResultFuture property) (openprotein.models.BoltzGenFuture property) (openprotein.models.RFdiffusionFuture property) (openprotein.prompt.Prompt property) (openprotein.svd.SVDModel property) (openprotein.umap.UMAPModel property) Prompt (class in openprotein.prompt) prompt (openprotein.OpenProtein property) prompt_id (openprotein.prompt.PromptJob property) PromptAPI (class in openprotein.prompt) PromptJob (class in openprotein.prompt) PromptMetadata (class in openprotein.prompt) prot_seq (openprotein.embeddings.EmbeddingsAPI attribute) ProteinMPNNModel (class in openprotein.models) Q Query (class in openprotein.prompt) QueryMetadata (class in openprotein.prompt) R reduction (openprotein.predictor.PredictorModel property) (openprotein.svd.SVDModel property) (openprotein.umap.UMAPModel property) ReductionType (class in openprotein.common) refresh() (openprotein.embeddings.EmbeddingsGenerateFuture method) (openprotein.embeddings.EmbeddingsResultFuture method) (openprotein.embeddings.EmbeddingsScoreFuture method) (openprotein.fold.FoldResultFuture method) (openprotein.jobs.Future method) (openprotein.models.BoltzGenFuture method) (openprotein.models.RFdiffusionFuture method) (openprotein.prompt.Prompt method) (openprotein.svd.SVDModel method) (openprotein.umap.UMAPModel method) rf3 (openprotein.fold.FoldAPI attribute) RFdiffusionFuture (class in openprotein.models) rosettafold_3 (openprotein.fold.FoldAPI attribute) rotaprot_large_uniref50w (openprotein.embeddings.EmbeddingsAPI attribute) rotaprot_large_uniref90_ft (openprotein.embeddings.EmbeddingsAPI attribute) S sample_prompt() (openprotein.align.MSAFuture method) score() (openprotein.embeddings.PoET2Model method) (openprotein.embeddings.PoETModel method) (openprotein.models.ProteinMPNNModel method) sequence_length (openprotein.predictor.PredictorModel property) (openprotein.svd.SVDModel property) (openprotein.umap.UMAPModel property) sequences (openprotein.fold.FoldResultFuture property) (openprotein.umap.UMAPModel property) single_site() (openprotein.embeddings.PoET2Model method) (openprotein.embeddings.PoETModel method) (openprotein.models.ProteinMPNNModel method) (openprotein.predictor.PredictorModel method) start_date (openprotein.embeddings.EmbeddingsGenerateFuture property) (openprotein.embeddings.EmbeddingsResultFuture property) (openprotein.embeddings.EmbeddingsScoreFuture property) (openprotein.fold.FoldResultFuture property) (openprotein.models.BoltzGenFuture property) (openprotein.models.RFdiffusionFuture property) (openprotein.prompt.Prompt property) (openprotein.svd.SVDModel property) (openprotein.umap.UMAPModel property) status (openprotein.embeddings.EmbeddingsGenerateFuture property) (openprotein.embeddings.EmbeddingsResultFuture property) (openprotein.embeddings.EmbeddingsScoreFuture property) (openprotein.fold.FoldResultFuture property) (openprotein.models.BoltzGenFuture property) (openprotein.models.RFdiffusionFuture property) (openprotein.prompt.Prompt property) (openprotein.svd.SVDModel property) (openprotein.umap.UMAPModel property) stream() (openprotein.design.DesignFuture method) (openprotein.embeddings.EmbeddingsGenerateFuture method) (openprotein.embeddings.EmbeddingsResultFuture method) (openprotein.embeddings.EmbeddingsScoreFuture method) (openprotein.fold.FoldResultFuture method) svd (openprotein.OpenProtein property) SVDModel (class in openprotein.svd) T training_assay (openprotein.predictor.PredictorModel property) training_properties (openprotein.predictor.PredictorModel property) U umap (openprotein.OpenProtein property) UMAPModel (class in openprotein.umap) update() (openprotein.data.AssayDataset method) upload_msa() (openprotein.align.AlignAPI method) upload_prompt() (openprotein.align.AlignAPI method) W wait() (openprotein.embeddings.EmbeddingsGenerateFuture method) (openprotein.embeddings.EmbeddingsResultFuture method) (openprotein.embeddings.EmbeddingsScoreFuture method) (openprotein.fold.FoldResultFuture method) (openprotein.jobs.Future method) (openprotein.jobs.JobsAPI method) (openprotein.models.BoltzGenFuture method) (openprotein.models.RFdiffusionFuture method) (openprotein.prompt.Prompt method) (openprotein.svd.SVDModel method) (openprotein.umap.UMAPModel method) wait_until_done() (openprotein.embeddings.EmbeddingsGenerateFuture method) (openprotein.embeddings.EmbeddingsResultFuture method) (openprotein.embeddings.EmbeddingsScoreFuture method) (openprotein.fold.FoldResultFuture method) (openprotein.jobs.Future method) (openprotein.models.BoltzGenFuture method) (openprotein.models.RFdiffusionFuture method) (openprotein.prompt.Prompt method) (openprotein.svd.SVDModel method) (openprotein.umap.UMAPModel method)
