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__getitem__() (biotransformers.lightning_utils.data.BatchWithConstantNumberTokensDataset method) __iter__() (biotransformers.lightning_utils.data.BatchWithConstantNumberTokensSampler method) (biotransformers.lightning_utils.data.DistributedBatchWithConstantNumberTokensSampler method) __len__() (biotransformers.lightning_utils.data.BatchWithConstantNumberTokensDataset method) (biotransformers.lightning_utils.data.BatchWithConstantNumberTokensSampler method) (biotransformers.lightning_utils.data.DistributedBatchWithConstantNumberTokensSampler method) __repr__() (biotransformers.utils.compute_utils.Mutation method) __version__ (in module biotransformers) _check_batch_size() (in module biotransformers.utils.utils) _check_memory_embeddings() (in module biotransformers.utils.utils) _check_memory_logits() (in module biotransformers.utils.utils)

_check_sequence() (in module biotransformers.utils.utils) _check_tokens_list() (in module biotransformers.utils.utils) _compute_logits() (biotransformers.wrappers.transformers_wrappers.TransformersWrapper method) _gather_masked_outputs() (biotransformers.wrappers.transformers_wrappers.TransformersWrapper method) _generate_chunks() (biotransformers.wrappers.transformers_wrappers.TransformersWrapper method) (in module biotransformers.utils.utils) _get_dataloader() (biotransformers.lightning_utils.data.BatchWithConstantNumberTokensDataModule method) _get_num_batch_iter() (biotransformers.wrappers.transformers_wrappers.TransformersWrapper method) (in module biotransformers.utils.utils) _mask_inputs_tokens() (biotransformers.wrappers.transformers_wrappers.TransformersWrapper method) _model_evaluation() (biotransformers.wrappers.transformers_wrappers.TransformersWrapper method) _repeat_and_mask_inputs() (biotransformers.wrappers.transformers_wrappers.TransformersWrapper method)

A

actor() (biotransformers.utils.tqdm_utils.ProgressBar property)

AlphabetDataLoader (class in biotransformers.lightning_utils.data)

B

BACKEND_LIST (in module biotransformers.utils.constant) BatchWithConstantNumberTokensDataModule (class in biotransformers.lightning_utils.data) BatchWithConstantNumberTokensDataset (class in biotransformers.lightning_utils.data) BatchWithConstantNumberTokensSampler (class in biotransformers.lightning_utils.data) begin_token() (biotransformers.wrappers.esm_wrappers.ESMWrapper property) (biotransformers.wrappers.language_model.LanguageModel property) (biotransformers.wrappers.rostlab_wrapper.RostlabWrapper property) biotransformers module BioTransformers (class in biotransformers) (class in biotransformers.bio_transformers) biotransformers.bio_transformers module biotransformers.lightning_utils module biotransformers.lightning_utils.data module biotransformers.lightning_utils.models module biotransformers.lightning_utils.optimizer module biotransformers.tests module biotransformers.tests.conftest module biotransformers.tests.test_accuracy module biotransformers.tests.test_embeddings module biotransformers.tests.test_logits module

biotransformers.tests.test_loglikelihoods module biotransformers.tests.test_mutation_score module biotransformers.utils module biotransformers.utils.compute_utils module biotransformers.utils.constant module biotransformers.utils.deprecated module biotransformers.utils.logger module biotransformers.utils.msa_utils module biotransformers.utils.tqdm_utils module biotransformers.utils.utils module biotransformers.version module biotransformers.wrappers module biotransformers.wrappers.esm_wrappers module biotransformers.wrappers.language_model module biotransformers.wrappers.rostlab_wrapper module biotransformers.wrappers.transformers_wrappers module

C

clean_model_id() (biotransformers.wrappers.esm_wrappers.ESMWrapper property) (biotransformers.wrappers.language_model.LanguageModel property) (biotransformers.wrappers.rostlab_wrapper.RostlabWrapper property) collate_fn() (in module biotransformers.lightning_utils.data) compute_accuracy() (biotransformers.wrappers.transformers_wrappers.TransformersWrapper method) compute_embeddings() (biotransformers.wrappers.transformers_wrappers.TransformersWrapper method) compute_logits() (biotransformers.wrappers.transformers_wrappers.TransformersWrapper method) compute_loglikelihood() (biotransformers.wrappers.transformers_wrappers.TransformersWrapper method)

compute_mutation_score() (biotransformers.wrappers.transformers_wrappers.TransformersWrapper method) compute_probabilities() (biotransformers.wrappers.transformers_wrappers.TransformersWrapper method) configure_optimizers() (biotransformers.lightning_utils.models.LightningModule method) convert_bytes_size() (in module biotransformers.utils.utils) convert_ckpt_to_statedict() (in module biotransformers.lightning_utils.data) counter (biotransformers.utils.tqdm_utils.ProgressBarActor attribute) crop_sequence() (in module biotransformers.lightning_utils.data) cross_entropy_loss() (biotransformers.lightning_utils.models.LightningModule method)

D

DEFAULT_ESM_MODEL (in module biotransformers.utils.constant) DEFAULT_ROSTLAB_MODEL (in module biotransformers.utils.constant) delete_ray_workers() (biotransformers.wrappers.transformers_wrappers.TransformersWrapper method) delta (biotransformers.utils.tqdm_utils.ProgressBarActor attribute) deprecated_alias() (in module biotransformers.utils.deprecated)

description (biotransformers.utils.tqdm_utils.ProgressBar attribute) DistributedBatchWithConstantNumberTokensSampler (class in biotransformers.lightning_utils.data) does_end_token_exist() (biotransformers.wrappers.esm_wrappers.ESMWrapper property) (biotransformers.wrappers.language_model.LanguageModel property) (biotransformers.wrappers.rostlab_wrapper.RostlabWrapper property)

E

embeddings_size() (biotransformers.wrappers.esm_wrappers.ESMWrapper property) (biotransformers.wrappers.language_model.LanguageModel property) (biotransformers.wrappers.rostlab_wrapper.RostlabWrapper property) end_token() (biotransformers.wrappers.esm_wrappers.ESMWrapper property) (biotransformers.wrappers.language_model.LanguageModel property) (biotransformers.wrappers.rostlab_wrapper.RostlabWrapper property)

ESM_LIST (in module biotransformers.utils.constant) ESMWrapper (class in biotransformers.wrappers.esm_wrappers) event (biotransformers.utils.tqdm_utils.ProgressBarActor attribute)

F

fasta_path() (in module biotransformers.tests.conftest) finetune() (biotransformers.wrappers.transformers_wrappers.TransformersWrapper method)

format_backend() (in module biotransformers.utils.utils) forward() (biotransformers.lightning_utils.models.LightningModule method)

G

get_alphabet_dataloader() (biotransformers.wrappers.esm_wrappers.ESMWrapper method) (biotransformers.wrappers.language_model.LanguageModel method) (biotransformers.wrappers.rostlab_wrapper.RostlabWrapper method) get_batch_indices() (in module biotransformers.lightning_utils.data) get_counter() (biotransformers.utils.tqdm_utils.ProgressBarActor method) get_list_probs() (in module biotransformers.utils.compute_utils)

get_logs_version() (in module biotransformers.utils.utils) get_msa_lengths() (in module biotransformers.utils.msa_utils) get_msa_list() (in module biotransformers.utils.msa_utils) get_tensor_accuracy() (biotransformers.lightning_utils.models.LightningModule method) get_translation() (in module biotransformers.utils.msa_utils) get_vocabulary_mask() (biotransformers.wrappers.transformers_wrappers.TransformersWrapper method)

I

init_model() (in module biotransformers.tests.conftest) init_model_sequences() (in module biotransformers.utils.utils)

init_ray_workers() (biotransformers.wrappers.transformers_wrappers.TransformersWrapper method) InvalidPositionStringError is_valid_mutation() (biotransformers.utils.compute_utils.Mutation method)

L

LanguageModel (class in biotransformers.wrappers.language_model) lengths_sequence_fasta() (in module biotransformers.tests.conftest) LightningModule (class in biotransformers.lightning_utils.models) list_backend() (biotransformers.bio_transformers.BioTransformers static method) (biotransformers.BioTransformers static method) (in module biotransformers.utils.utils) load_fasta() (in module biotransformers.utils.utils) load_model() (biotransformers.wrappers.transformers_wrappers.TransformersWrapper method) log (in module biotransformers) (in module biotransformers.utils.utils) (in module biotransformers.wrappers.esm_wrappers) (in module biotransformers.wrappers.rostlab_wrapper) (in module biotransformers.wrappers.transformers_wrappers)

logger() (in module biotransformers) (in module biotransformers.utils.logger) loglikelihoods_fasta_results() (in module biotransformers.tests.conftest) loglikelihoods_results() (in module biotransformers.tests.conftest) lr_update() (in module biotransformers.lightning_utils.optimizer)

M

MAPPING_PROTBERT (in module biotransformers.utils.constant) mask_seq() (in module biotransformers.lightning_utils.data) mask_token() (biotransformers.wrappers.esm_wrappers.ESMWrapper property) (biotransformers.wrappers.language_model.LanguageModel property) (biotransformers.wrappers.rostlab_wrapper.RostlabWrapper property) model() (biotransformers.wrappers.esm_wrappers.ESMWrapper property) (biotransformers.wrappers.language_model.LanguageModel property) (biotransformers.wrappers.rostlab_wrapper.RostlabWrapper property) model_id() (biotransformers.wrappers.language_model.LanguageModel property) model_pass() (biotransformers.wrappers.esm_wrappers.ESMWrapper method) (biotransformers.wrappers.language_model.LanguageModel method) (biotransformers.wrappers.rostlab_wrapper.RostlabWrapper method) model_vocabulary() (biotransformers.wrappers.esm_wrappers.ESMWrapper property) (biotransformers.wrappers.language_model.LanguageModel property) (biotransformers.wrappers.rostlab_wrapper.RostlabWrapper property) module biotransformers biotransformers.bio_transformers biotransformers.lightning_utils biotransformers.lightning_utils.data biotransformers.lightning_utils.models biotransformers.lightning_utils.optimizer biotransformers.tests biotransformers.tests.conftest biotransformers.tests.test_accuracy biotransformers.tests.test_embeddings biotransformers.tests.test_logits biotransformers.tests.test_loglikelihoods biotransformers.tests.test_mutation_score biotransformers.utils biotransformers.utils.compute_utils biotransformers.utils.constant biotransformers.utils.deprecated biotransformers.utils.logger biotransformers.utils.msa_utils biotransformers.utils.tqdm_utils biotransformers.utils.utils biotransformers.version biotransformers.wrappers biotransformers.wrappers.esm_wrappers biotransformers.wrappers.language_model biotransformers.wrappers.rostlab_wrapper biotransformers.wrappers.transformers_wrappers

msa_to_remove() (in module biotransformers.utils.msa_utils) Mutation (class in biotransformers.utils.compute_utils) mutation_score() (in module biotransformers.utils.compute_utils) mutations_score_results() (in module biotransformers.tests.conftest)

N

NATURAL_AAS_LIST (in module biotransformers.utils.constant)

P

pad_token() (biotransformers.wrappers.esm_wrappers.ESMWrapper property) (biotransformers.wrappers.language_model.LanguageModel property) (biotransformers.wrappers.rostlab_wrapper.RostlabWrapper property) path_msa_folder (in module biotransformers.wrappers.esm_wrappers) PathMsaFolder (in module biotransformers.wrappers.transformers_wrappers) pbar (biotransformers.utils.tqdm_utils.ProgressBar attribute) print_until_done() (biotransformers.utils.tqdm_utils.ProgressBar method)

ProbTuple (in module biotransformers.utils.compute_utils) process_sequences_and_tokens() (biotransformers.wrappers.esm_wrappers.ESMWrapper method) (biotransformers.wrappers.language_model.LanguageModel method) (biotransformers.wrappers.rostlab_wrapper.RostlabWrapper method) progress_actor (biotransformers.utils.tqdm_utils.ProgressBar attribute) ProgressBar (class in biotransformers.utils.tqdm_utils) ProgressBarActor (class in biotransformers.utils.tqdm_utils)

R

read_msa() (in module biotransformers.utils.msa_utils) read_sequence() (in module biotransformers.utils.msa_utils) remove_insertions() (in module biotransformers.utils.msa_utils)

rename_kwargs() (in module biotransformers.utils.deprecated) ROSTLAB_LIST (in module biotransformers.utils.constant) RostlabWrapper (class in biotransformers.wrappers.rostlab_wrapper)

S

SequenceProbsList (in module biotransformers.utils.compute_utils) (in module biotransformers.wrappers.transformers_wrappers) sequences() (in module biotransformers.tests.conftest) set_epoch() (biotransformers.lightning_utils.data.DistributedBatchWithConstantNumberTokensSampler method)

set_model() (biotransformers.wrappers.esm_wrappers.ESMWrapper method) (biotransformers.wrappers.language_model.LanguageModel method) (biotransformers.wrappers.rostlab_wrapper.RostlabWrapper method) split_list() (in module biotransformers.utils.compute_utils)

T

test_accuracy_type_and_range() (in module biotransformers.tests.test_accuracy) test_accuracy_type_and_range_fasta() (in module biotransformers.tests.test_accuracy) test_embeddings_type_and_shape() (in module biotransformers.tests.test_embeddings) test_embeddings_type_and_shape_fasta() (in module biotransformers.tests.test_embeddings) test_logits_type() (in module biotransformers.tests.test_logits) test_logits_type_fasta() (in module biotransformers.tests.test_logits) test_loglikelihoods_type_shape_and_range() (in module biotransformers.tests.test_loglikelihoods) test_loglikelihoods_type_shape_and_range_fasta() (in module biotransformers.tests.test_loglikelihoods) test_models (in module biotransformers.tests.conftest) test_mutation_score_type_shape_and_range() (in module biotransformers.tests.test_mutation_score) test_params (in module biotransformers.tests.test_accuracy) (in module biotransformers.tests.test_embeddings) (in module biotransformers.tests.test_logits) (in module biotransformers.tests.test_loglikelihoods) (in module biotransformers.tests.test_mutation_score)

test_params_fasta (in module biotransformers.tests.test_accuracy) (in module biotransformers.tests.test_logits) (in module biotransformers.tests.test_loglikelihoods) tok_to_idx() (biotransformers.lightning_utils.data.AlphabetDataLoader method) token_to_id() (biotransformers.wrappers.esm_wrappers.ESMWrapper property) (biotransformers.wrappers.language_model.LanguageModel property) (biotransformers.wrappers.rostlab_wrapper.RostlabWrapper property) tokenizer() (biotransformers.lightning_utils.data.AlphabetDataLoader method) TokenProbsDict (in module biotransformers.utils.compute_utils) (in module biotransformers.wrappers.transformers_wrappers) total (biotransformers.utils.tqdm_utils.ProgressBar attribute) train_dataloader() (biotransformers.lightning_utils.data.BatchWithConstantNumberTokensDataModule method) training_step() (biotransformers.lightning_utils.models.LightningModule method) TransformersWrapper (class in biotransformers.wrappers.transformers_wrappers)

U

update() (biotransformers.utils.tqdm_utils.ProgressBarActor method)

V

val_dataloader() (biotransformers.lightning_utils.data.BatchWithConstantNumberTokensDataModule method) validate_position_str() (in module biotransformers.utils.compute_utils) validation_step() (biotransformers.lightning_utils.models.LightningModule method) VERSION (in module biotransformers) (in module biotransformers.version)

vocab_size() (biotransformers.wrappers.esm_wrappers.ESMWrapper property) (biotransformers.wrappers.language_model.LanguageModel property) (biotransformers.wrappers.rostlab_wrapper.RostlabWrapper property)

W

wait_for_update() (biotransformers.utils.tqdm_utils.ProgressBarActor method)

worker_init_fn() (in module biotransformers.lightning_utils.data)