Index

A

AccessionManager (class in protein_information_system.operation.extraction.accessions)

B

base_module_path (protein_information_system.operation.embedding.sequence_embedding.SequenceEmbeddingManager attribute)

BaseTaskInitializer (class in protein_information_system.tasks.base) batch_size (protein_information_system.operation.embedding.sequence_embedding.SequenceEmbeddingManager attribute)

C

callback() (protein_information_system.tasks.queue.QueueTaskInitializer method) cleanup() (protein_information_system.tasks.gpu.GPUTaskInitializer method) computing_queue (protein_information_system.tasks.queue.QueueTaskInitializer property)

conf (protein_information_system.tasks.base.BaseTaskInitializer attribute) connection_params (protein_information_system.tasks.queue.QueueTaskInitializer attribute) consume_messages() (protein_information_system.tasks.queue.QueueTaskInitializer method) create_rabbitmq_connection() (protein_information_system.tasks.queue.QueueTaskInitializer method)

D

db_inserter_callback() (protein_information_system.tasks.queue.QueueTaskInitializer method)

delete_all_queues() (protein_information_system.tasks.queue.QueueTaskInitializer method)

E

encoder (protein_information_system.operation.embedding.structure_3di.Structure3DiManager attribute) enqueue() (protein_information_system.operation.embedding.sequence_embedding.SequenceEmbeddingManager method) (protein_information_system.operation.embedding.structure_3di.Structure3DiManager method) (protein_information_system.operation.extraction.protein_annotations_file.GOAnnotationsQueueProcessor method) (protein_information_system.operation.extraction.uniprot.UniProtExtractor method) (protein_information_system.tasks.gpu.GPUTaskInitializer method) (protein_information_system.tasks.queue.QueueTaskInitializer method)

F

fetch_accessions_from_api() (protein_information_system.operation.extraction.accessions.AccessionManager method)

G

get_or_create_accession() (protein_information_system.operation.extraction.protein_annotations_file.GOAnnotationsQueueProcessor method) get_or_create_association() (protein_information_system.operation.extraction.protein_annotations_file.GOAnnotationsQueueProcessor method) (protein_information_system.operation.extraction.uniprot.UniProtExtractor method) get_or_create_go_term() (protein_information_system.operation.extraction.protein_annotations_file.GOAnnotationsQueueProcessor method) (protein_information_system.operation.extraction.uniprot.UniProtExtractor method) get_or_create_protein() (protein_information_system.operation.extraction.protein_annotations_file.GOAnnotationsQueueProcessor method) (protein_information_system.operation.extraction.uniprot.UniProtExtractor method)

get_or_create_sequence() (protein_information_system.operation.extraction.protein_annotations_file.GOAnnotationsQueueProcessor method) (protein_information_system.operation.extraction.uniprot.UniProtExtractor method) get_or_create_structure() (protein_information_system.operation.extraction.uniprot.UniProtExtractor method) get_sequence_from_external_source() (protein_information_system.operation.extraction.protein_annotations_file.GOAnnotationsQueueProcessor method) GOAnnotationsQueueProcessor (class in protein_information_system.operation.extraction.protein_annotations_file) GPUTaskInitializer (class in protein_information_system.tasks.gpu)

H

handle_cross_references() (protein_information_system.operation.extraction.uniprot.UniProtExtractor method)

handle_pdb_reference() (protein_information_system.operation.extraction.uniprot.UniProtExtractor method)

I

inserting_queue (protein_information_system.tasks.queue.QueueTaskInitializer property)

L

load_accessions_from_csv() (protein_information_system.operation.extraction.accessions.AccessionManager method) load_constants() (protein_information_system.tasks.base.BaseTaskInitializer method)

load_model() (protein_information_system.tasks.gpu.GPUTaskInitializer method) load_sequences() (protein_information_system.operation.extraction.protein_annotations_file.GOAnnotationsQueueProcessor method) logger (protein_information_system.tasks.base.BaseTaskInitializer attribute)

M

model_instances (protein_information_system.operation.embedding.sequence_embedding.SequenceEmbeddingManager attribute) (protein_information_system.tasks.gpu.GPUTaskInitializer attribute) module protein_information_system.operation.embedding.sequence_embedding protein_information_system.operation.embedding.structure_3di protein_information_system.operation.extraction.accessions protein_information_system.operation.extraction.protein_annotations_file protein_information_system.operation.extraction.uniprot protein_information_system.tasks.base protein_information_system.tasks.gpu protein_information_system.tasks.queue

monitor_queues() (protein_information_system.tasks.queue.QueueTaskInitializer method)

P

parser (protein_information_system.operation.embedding.structure_3di.Structure3DiManager attribute) post_processing() (protein_information_system.tasks.queue.QueueTaskInitializer method) prepare_new_chain() (protein_information_system.operation.embedding.structure_3di.Structure3DiManager method) process() (protein_information_system.operation.embedding.sequence_embedding.SequenceEmbeddingManager method) (protein_information_system.operation.embedding.structure_3di.Structure3DiManager method) (protein_information_system.operation.extraction.accessions.AccessionManager method) (protein_information_system.operation.extraction.protein_annotations_file.GOAnnotationsQueueProcessor method) (protein_information_system.operation.extraction.uniprot.UniProtExtractor method) (protein_information_system.tasks.base.BaseTaskInitializer method) (protein_information_system.tasks.gpu.GPUTaskInitializer method) (protein_information_system.tasks.queue.QueueTaskInitializer method) process_chain() (protein_information_system.operation.embedding.structure_3di.Structure3DiManager method) processes (protein_information_system.tasks.queue.QueueTaskInitializer attribute) protein_information_system.operation.embedding.sequence_embedding module

protein_information_system.operation.embedding.structure_3di module protein_information_system.operation.extraction.accessions module protein_information_system.operation.extraction.protein_annotations_file module protein_information_system.operation.extraction.uniprot module protein_information_system.tasks.base module protein_information_system.tasks.gpu module protein_information_system.tasks.queue module publish_task() (protein_information_system.tasks.gpu.GPUTaskInitializer method) (protein_information_system.tasks.queue.QueueTaskInitializer method)

Q

QueueTaskInitializer (class in protein_information_system.tasks.queue)

R

reference_attribute (protein_information_system.operation.embedding.sequence_embedding.SequenceEmbeddingManager attribute) (protein_information_system.operation.embedding.structure_3di.Structure3DiManager attribute)

run_db_inserter_worker() (protein_information_system.tasks.queue.QueueTaskInitializer method) run_processor_worker() (protein_information_system.tasks.queue.QueueTaskInitializer method) run_processor_worker_sequential() (protein_information_system.tasks.gpu.GPUTaskInitializer method)

S

SequenceEmbeddingManager (class in protein_information_system.operation.embedding.sequence_embedding) session (protein_information_system.tasks.base.BaseTaskInitializer attribute) session_init() (protein_information_system.tasks.base.BaseTaskInitializer method) setup_rabbitmq() (protein_information_system.tasks.gpu.GPUTaskInitializer method) (protein_information_system.tasks.queue.QueueTaskInitializer method) start() (protein_information_system.operation.extraction.accessions.AccessionManager method) (protein_information_system.tasks.base.BaseTaskInitializer method) (protein_information_system.tasks.queue.QueueTaskInitializer method) start_workers() (protein_information_system.tasks.gpu.GPUTaskInitializer method) (protein_information_system.tasks.queue.QueueTaskInitializer method)

stop_event (protein_information_system.tasks.gpu.GPUTaskInitializer attribute) (protein_information_system.tasks.queue.QueueTaskInitializer attribute) store_entry() (protein_information_system.operation.embedding.sequence_embedding.SequenceEmbeddingManager method) (protein_information_system.operation.embedding.structure_3di.Structure3DiManager method) (protein_information_system.operation.extraction.accessions.AccessionManager method) (protein_information_system.operation.extraction.protein_annotations_file.GOAnnotationsQueueProcessor method) (protein_information_system.operation.extraction.uniprot.UniProtExtractor method) (protein_information_system.tasks.base.BaseTaskInitializer method) (protein_information_system.tasks.gpu.GPUTaskInitializer method) (protein_information_system.tasks.queue.QueueTaskInitializer method) Structure3DiManager (class in protein_information_system.operation.embedding.structure_3di)

T

threads (protein_information_system.tasks.queue.QueueTaskInitializer attribute) tokenizer_instances (protein_information_system.operation.embedding.sequence_embedding.SequenceEmbeddingManager attribute) (protein_information_system.tasks.gpu.GPUTaskInitializer attribute)

types (protein_information_system.operation.embedding.sequence_embedding.SequenceEmbeddingManager attribute)

U

UniProtExtractor (class in protein_information_system.operation.extraction.uniprot) UniProtExtractor.UniProtExtractor (class in protein_information_system.operation.extraction.uniprot)

unload_model() (protein_information_system.tasks.gpu.GPUTaskInitializer method) update_protein_details() (protein_information_system.operation.extraction.uniprot.UniProtExtractor method)