Index _ | A | B | C | D | E | F | G | I | J | K | L | M | N | O | P | Q | R | S | T | U | W _ __init__() (openprotein.align.AlignAPI method) (openprotein.align.MSAFuture method) (openprotein.APISession method) (openprotein.data.AssayDataset method) (openprotein.data.DataAPI method) (openprotein.design.DesignAPI method) (openprotein.design.DesignFuture method) (openprotein.embeddings.EmbeddingsAPI method) (openprotein.embeddings.EmbeddingsGenerateFuture method) (openprotein.embeddings.EmbeddingsResultFuture method) (openprotein.embeddings.EmbeddingsScoreFuture method) (openprotein.embeddings.ESMModel method) (openprotein.embeddings.OpenProteinModel method) (openprotein.embeddings.PoET2Model method) (openprotein.embeddings.PoETModel method) (openprotein.fold.AlphaFold2Model method) (openprotein.fold.Boltz1Model method) (openprotein.fold.Boltz1xModel method) (openprotein.fold.Boltz2Model method) (openprotein.fold.ESMFoldModel method) (openprotein.fold.FoldAPI method) (openprotein.fold.FoldComplexResultFuture method) (openprotein.fold.FoldResultFuture method) (openprotein.predictor.PredictorAPI method) (openprotein.predictor.PredictorModel method) (openprotein.prompt.Prompt method) (openprotein.prompt.PromptAPI method) (openprotein.prompt.Query method) (openprotein.svd.SVDAPI method) (openprotein.svd.SVDModel method) (openprotein.umap.UMAPAPI method) (openprotein.umap.UMAPModel method) A abnumber() (openprotein.align.AlignAPI method) abnumber_file() (openprotein.align.AlignAPI method) af2 (openprotein.fold.FoldAPI attribute) affinity (openprotein.fold.FoldComplexResultFuture property) 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) APISession (class in openprotein) assay (openprotein.design.DesignFuture property) AssayDataset (class in openprotein.data) attn() (openprotein.embeddings.ESMModel method) (openprotein.embeddings.OpenProteinModel method) (openprotein.embeddings.PoET2Model method) (openprotein.embeddings.PoETModel 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) C cancelled() (openprotein.align.MSAFuture method) (openprotein.embeddings.EmbeddingsGenerateFuture method) (openprotein.embeddings.EmbeddingsResultFuture method) (openprotein.embeddings.EmbeddingsScoreFuture method) (openprotein.fold.FoldComplexResultFuture method) (openprotein.fold.FoldResultFuture method) (openprotein.prompt.Prompt method) clustalo() (openprotein.align.AlignAPI method) clustalo_file() (openprotein.align.AlignAPI method) confidence (openprotein.fold.FoldComplexResultFuture property) create() (openprotein.data.DataAPI method) (openprotein.embeddings.ESMModel class method) (openprotein.embeddings.OpenProteinModel class method) (openprotein.embeddings.PoET2Model class method) (openprotein.embeddings.PoETModel class method) (openprotein.fold.AlphaFold2Model class method) (openprotein.fold.Boltz1Model class method) (openprotein.fold.Boltz1xModel class method) (openprotein.fold.Boltz2Model class method) (openprotein.fold.ESMFoldModel 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) 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) dnas (openprotein.fold.FoldComplexResultFuture property) done() (openprotein.align.MSAFuture method) (openprotein.embeddings.EmbeddingsGenerateFuture method) (openprotein.embeddings.EmbeddingsResultFuture method) (openprotein.embeddings.EmbeddingsScoreFuture method) (openprotein.fold.FoldComplexResultFuture method) (openprotein.fold.FoldResultFuture method) (openprotein.prompt.Prompt method) E embed() (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) 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) ensemble() (openprotein.predictor.PredictorAPI method) esm1b (openprotein.embeddings.EmbeddingsAPI attribute) esm1b_t33_650M_UR50S (openprotein.embeddings.EmbeddingsAPI attribute) esm1v (openprotein.embeddings.EmbeddingsAPI attribute) esm1v_t33_650M_UR90S_1 (openprotein.embeddings.EmbeddingsAPI attribute) esm1v_t33_650M_UR90S_2 (openprotein.embeddings.EmbeddingsAPI attribute) esm1v_t33_650M_UR90S_3 (openprotein.embeddings.EmbeddingsAPI attribute) esm1v_t33_650M_UR90S_4 (openprotein.embeddings.EmbeddingsAPI attribute) esm1v_t33_650M_UR90S_5 (openprotein.embeddings.EmbeddingsAPI attribute) esm2 (openprotein.embeddings.EmbeddingsAPI attribute) esm2_t12_35M_UR50D (openprotein.embeddings.EmbeddingsAPI attribute) esm2_t30_150M_UR50D (openprotein.embeddings.EmbeddingsAPI attribute) esm2_t33_650M_UR50D (openprotein.embeddings.EmbeddingsAPI attribute) esm2_t36_3B_UR50D (openprotein.embeddings.EmbeddingsAPI attribute) esm2_t6_8M_UR50D (openprotein.embeddings.EmbeddingsAPI attribute) esmfold (openprotein.fold.FoldAPI attribute) ESMFoldModel (class in openprotein.fold) ESMModel (class in openprotein.embeddings) F fit_gp() (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.ESMModel method) (openprotein.embeddings.OpenProteinModel method) (openprotein.embeddings.PoET2Model method) (openprotein.embeddings.PoETModel method) (openprotein.svd.SVDAPI method) fit_umap() (openprotein.embeddings.ESMModel method) (openprotein.embeddings.OpenProteinModel method) (openprotein.embeddings.PoET2Model method) (openprotein.embeddings.PoETModel method) (openprotein.svd.SVDModel method) (openprotein.umap.UMAPAPI 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) FoldComplexResultFuture (class in openprotein.fold) FoldResultFuture (class in openprotein.fold) G generate() (openprotein.embeddings.PoET2Model method) (openprotein.embeddings.PoETModel method) get() (openprotein.align.MSAFuture method), [1] (openprotein.data.DataAPI method) (openprotein.design.DesignFuture method) (openprotein.embeddings.EmbeddingsGenerateFuture method) (openprotein.embeddings.EmbeddingsResultFuture method) (openprotein.embeddings.EmbeddingsScoreFuture method) (openprotein.fold.FoldComplexResultFuture method) (openprotein.fold.FoldResultFuture 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_input() (openprotein.align.MSAFuture 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.ESMModel method) (openprotein.embeddings.OpenProteinModel method) (openprotein.embeddings.PoET2Model method) (openprotein.embeddings.PoETModel method) (openprotein.fold.AlphaFold2Model method) (openprotein.fold.Boltz1Model method) (openprotein.fold.Boltz1xModel method) (openprotein.fold.Boltz2Model method) (openprotein.fold.ESMFoldModel method) get_model() (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.AlphaFold2Model class method) (openprotein.fold.Boltz1Model class method) (openprotein.fold.Boltz1xModel class method) (openprotein.fold.Boltz2Model class method) (openprotein.fold.ESMFoldModel class method) (openprotein.fold.FoldAPI method) (openprotein.predictor.PredictorModel method) (openprotein.svd.SVDModel method) (openprotein.umap.UMAPModel method) get_msa() (openprotein.align.AlignAPI 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) (openprotein.align.MSAFuture method) get_slice() (openprotein.data.AssayDataset method) get_svd() (openprotein.svd.SVDAPI method) get_umap() (openprotein.umap.UMAPAPI method) I id (openprotein.align.MSAFuture property) (openprotein.design.DesignFuture property) (openprotein.fold.FoldComplexResultFuture property) (openprotein.fold.FoldResultFuture property) (openprotein.predictor.PredictorModel property) (openprotein.svd.SVDModel property) (openprotein.umap.UMAPModel property) indel() (openprotein.embeddings.PoET2Model method) (openprotein.embeddings.PoETModel method) J job (openprotein.align.MSAFuture attribute) (openprotein.fold.FoldComplexResultFuture attribute) (openprotein.fold.FoldResultFuture attribute) (openprotein.svd.SVDModel attribute) (openprotein.umap.UMAPModel attribute) jobs (openprotein.OpenProtein property) K keys() (openprotein.fold.FoldResultFuture method) L ligands (openprotein.fold.FoldComplexResultFuture property) list() (openprotein.data.DataAPI 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) list_svd() (openprotein.svd.SVDAPI method) list_umap() (openprotein.umap.UMAPAPI method) load_assay() (openprotein.data.DataAPI method) login() (openprotein.APISession method) logits() (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.ESMModel property) (openprotein.embeddings.OpenProteinModel property) (openprotein.embeddings.PoET2Model property) (openprotein.embeddings.PoETModel property) (openprotein.fold.AlphaFold2Model property) (openprotein.fold.Boltz1Model property) (openprotein.fold.Boltz1xModel property) (openprotein.fold.Boltz2Model property) (openprotein.fold.ESMFoldModel property) (openprotein.predictor.PredictorModel property) (openprotein.svd.SVDModel property) (openprotein.umap.UMAPModel property) min_dist (openprotein.umap.UMAPModel property) model (openprotein.predictor.PredictorModel property) (openprotein.svd.SVDModel property) (openprotein.umap.UMAPModel property) model_id (openprotein.embeddings.OpenProteinModel attribute) (openprotein.fold.ESMFoldModel attribute) (openprotein.fold.FoldComplexResultFuture property) (openprotein.fold.FoldResultFuture property) msa_id (openprotein.align.MSAFuture attribute) 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 pae (openprotein.fold.FoldComplexResultFuture property) page_size (openprotein.align.MSAFuture attribute) pde (openprotein.fold.FoldComplexResultFuture property) plddt (openprotein.fold.FoldComplexResultFuture property) poet (openprotein.embeddings.EmbeddingsAPI attribute) poet2 (openprotein.embeddings.EmbeddingsAPI attribute) PoET2Model (class in openprotein.embeddings) poet_2 (openprotein.embeddings.EmbeddingsAPI attribute) PoETModel (class in openprotein.embeddings) pop_size (openprotein.design.DesignFuture property) post() (openprotein.APISession method) predict() (openprotein.predictor.PredictorModel method) predictor (openprotein.OpenProtein property) PredictorAPI (class in openprotein.predictor) PredictorModel (class in openprotein.predictor) Prompt (class in openprotein.prompt) prompt (openprotein.OpenProtein property) PromptAPI (class in openprotein.prompt) prot_seq (openprotein.embeddings.EmbeddingsAPI attribute) proteins (openprotein.fold.FoldComplexResultFuture property) Q Query (class in openprotein.prompt) R reduction (openprotein.predictor.PredictorModel property) (openprotein.svd.SVDModel property) (openprotein.umap.UMAPModel property) refresh() (openprotein.align.MSAFuture method) (openprotein.embeddings.EmbeddingsGenerateFuture method) (openprotein.embeddings.EmbeddingsResultFuture method) (openprotein.embeddings.EmbeddingsScoreFuture method) (openprotein.fold.FoldComplexResultFuture method) (openprotein.fold.FoldResultFuture method) (openprotein.prompt.Prompt method) rnas (openprotein.fold.FoldComplexResultFuture property) rotaprot_large_uniref50w (openprotein.embeddings.EmbeddingsAPI attribute) rotaprot_large_uniref90_ft (openprotein.embeddings.EmbeddingsAPI attribute) S sample_prompt() (openprotein.align.MSAFuture method), [1] score() (openprotein.embeddings.PoET2Model method) (openprotein.embeddings.PoETModel method) sequence_length (openprotein.predictor.PredictorModel property) (openprotein.svd.SVDModel property) (openprotein.umap.UMAPModel property) sequences (openprotein.fold.FoldResultFuture property) (openprotein.umap.UMAPModel property) session (openprotein.align.MSAFuture attribute) single_site() (openprotein.embeddings.PoET2Model method) (openprotein.embeddings.PoETModel method) (openprotein.predictor.PredictorModel method) 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) SVDAPI (class in openprotein.svd) SVDModel (class in openprotein.svd) T training_assay (openprotein.predictor.PredictorModel property) training_properties (openprotein.predictor.PredictorModel property) U umap (openprotein.OpenProtein property) UMAPAPI (class in openprotein.umap) 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.align.MSAFuture method) (openprotein.embeddings.EmbeddingsGenerateFuture method) (openprotein.embeddings.EmbeddingsResultFuture method) (openprotein.embeddings.EmbeddingsScoreFuture method) (openprotein.fold.FoldComplexResultFuture method) (openprotein.fold.FoldResultFuture method) (openprotein.prompt.Prompt method) wait_until_done() (openprotein.align.MSAFuture method) (openprotein.embeddings.EmbeddingsGenerateFuture method) (openprotein.embeddings.EmbeddingsResultFuture method) (openprotein.embeddings.EmbeddingsScoreFuture method) (openprotein.fold.FoldComplexResultFuture method) (openprotein.fold.FoldResultFuture method) (openprotein.prompt.Prompt method)