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Project

  • OpenKinetics Predictor
    • Main use cases
    • Main users
  • Input Data
    • Required columns
    • CSV formats
      • Single-substrate CSV
      • Multi-substrate CSV
      • Full-reaction CSV
    • Method compatibility
    • Semicolon lists
    • Validation
    • Long sequences
    • Submission options
    • Templates
  • Supported Methods
    • Prediction targets
    • Supported engines
    • Model selection
  • Prediction Workflow
    • Workflow
    • Progress tracking
  • API and Limits
    • Base URL
    • Main endpoints
    • Quota
    • Good API practice

Contributor Guides

  • Contributing a New Prediction Method
    • 1. Define the Descriptor First
      • What these fields mean
    • 2. Implement Your Method’s Predictor
    • Path 1: Script + Shared Engine (default)
    • Path 2: Script + Custom Engine (only when required)
    • 3. Register Runtime Paths
    • 4. PLM Embeddings (Optional)
    • 5. Add MMseqs Similarity Dataset (Optional)
    • 6. Test Your Integration End-to-End
  • PLM Embedding Cache and Remote GPU Offload
    • 1. Purpose
    • 2. Core concepts
      • 2.1 seq_id is the cache key
      • 2.2 Planner is sparse
      • 2.3 Prediction and embedding are separate stages
    • 3. Current method-by-method behaviour
      • 3.1 KinForm-H and KinForm-L
      • 3.2 CataPro
      • 3.3 UniKP
      • 3.4 TurNup
      • 3.5 CatPred
      • 3.6 EITLEM
      • 3.7 OmniESI
      • 3.8 RealKcat
      • 3.9 IECata
      • 3.10 MMISA-KM
    • 4. Planner contract
    • 5. Backend orchestration contract
    • 6. GPU service API contract
    • 7. Step runner contract
    • 8. Progress tracking
    • 9. Contributor playbook
      • 9.1 Reuse an existing embedding family
      • 9.2 Add a new embedding family
    • 10. Full matrix policy
    • 11. Tests to add
    • 12. Operations and configuration
  • MMseqs Similarity Datasets Guide
    • 1. If Your Training Dataset Already Matches an Existing Dataset
    • 2. If You Need a New Dataset
  • Logging and Observability
    • Log Shape
    • Local Development
    • Production Observability Stack
    • Common LogQL Queries
    • Contributor Rules

Reference

  • API Reference
  • Documentation Notes
    • Application setup
    • Build these docs locally
    • Where to start
  • API Reference
    • api_auth
      • Module Contents
        • require_api_key()
    • v1_views
      • Authentication
      • Quota
      • Module Contents
        • api_health()
        • api_gpu_status()
        • api_list_methods()
        • api_quota()
        • api_submit_job()
        • api_job_status()
        • api_download_result()
        • api_validate()
    • job_utils
      • Module Contents
        • coerce_bool_param()
        • canonicalise_targets()
        • canonical_prediction_type()
        • validate_prediction_parameters()
        • validate_sequence_handling_option()
        • determine_required_columns()
        • validate_required_columns_for_methods()
        • create_job_directory()
        • save_job_input_file()
        • get_experimental_results()
        • extract_job_parameters_from_request()
        • create_rate_limit_headers()
        • get_queue_position()
        • create_job_status_response_data()
    • recon_xkg
      • Module Contents
        • coerce_recon_xkg()
        • is_recon_xkg_allowed()
        • resolve_recon_xkg()
        • log_recon_xkg_outcome()
    • extra_info
      • Module Contents
        • build_extra_info()
    • http_utils
      • Module Contents
        • validate_post_request()
        • validate_post_request_similarity()
        • extract_file_from_request()
        • extract_csv_file_from_request()
        • extract_session_id_from_request()
        • extract_validation_session_id()
        • validate_post_with_file_request()
        • extract_csv_file_with_validation()
    • job_service
      • Module Contents
        • process_job_submission()
        • process_job_submission_from_params()
        • handle_quota_validation()
        • create_job_record()
        • dispatch_prediction_task()
        • dispatch_recon_xkg_cache_task()
        • get_job_status_data()
    • restart_job
    • api_key_views
      • Module Contents
        • api_key_status()
        • api_key_generate()
        • api_key_revoke()
    • result_service
      • Module Contents
        • serialize_result_csv()
    • create_api_key
    • recon_xkg_admin
    • prediction_store
      • Design notes
      • Module Contents
        • CachedFailure
        • sha256_text()
        • canonical_unit()
        • params_fingerprint()
        • make_lookup_key()
        • build_unit_keys()
        • coerce_value()
        • cached_outcome_is_valid()
        • is_cacheable_failure_reason()
        • get_many()
        • upsert_many()
        • get_similarity_many()
        • upsert_similarity_many()
    • similarity_utils
      • Module Contents
        • extract_protein_sequences_from_csv()
        • create_unique_sequence_mapping()
        • create_fasta_file()
        • create_mmseqs_database()
        • run_mmseqs_search()
        • parse_mmseqs_results()
        • parse_mmseqs_results_raw()
        • map_results_to_original_sequences()
        • calculate_identity_histogram()
        • calculate_average_similarity()
        • cleanup_temporary_files()
    • validation_utils
      • Module Contents
        • safe_convert_to_mol()
        • split_single_substrate_components()
        • validate_csv_structure()
        • validate_single_substrate_schema()
        • validate_substrate_list_schema()
        • validate_products_column()
        • validate_substrates()
        • validate_protein_sequence_characters()
        • calculate_sequence_length_violations()
        • validate_protein_sequences()
        • clean_data_for_json()
        • parse_csv_file()
        • validate_file_format()
        • validate_required_columns()
        • validate_column_emptiness()
    • benchmark_methods
    • similarity_config
    • similarity_service
      • Module Contents
        • SimilarityCacheOnlyMiss
        • analyze_sequence_similarity()
        • analyze_similarity_for_method()
        • similarity_cache_label_for_method()
        • append_kcat_similarity_columns_to_output_csv()
        • kcat_similarity_sequences_for_output_rows()
    • validation_service
      • Module Contents
        • validate_input_file()
    • sequence_expansion
      • Module Contents
        • ExpandedSequence
        • SequenceExpansionPlan
        • TargetPredictionUnit
        • TargetExpansionPlan
        • split_sequence_list()
        • count_multi_sequence_rows()
        • reduce_sequence_predictions()
    • about_stats_service
      • Module Contents
        • mark_about_stats_cache_stale()
        • refresh_about_stats_cache()
        • get_about_stats()
    • substrate_expansion
      • Module Contents
        • ExpandedSubstrate
        • SubstrateExpansionPlan
        • split_substrate_list()
        • reduce_substrate_predictions()
    • job_progress_service
      • Module Contents
        • initialise_job_progress_stages()
    • resubmit_pending_jobs
      • Strategy
    • migrate_json_to_sqlite
    • prediction_batch_service
      • Module Contents
        • SequenceBatchPlan
        • TargetBatchPlan
        • build_target_batch_plan()
    • embedding_progress_service
      • Module Contents
        • start_embedding_tracking()
    • recon_xkg_preflight_service
      • Module Contents
        • ReconXkgCacheSnapshot
        • preflight_recon_xkg_cache()
    • gpu_precompute_status_service
Open Kinetics Predictor
  • API Reference
  • View page source

API Reference

This page contains auto-generated API reference documentation [1].

  • api_auth
  • v1_views
  • job_utils
  • recon_xkg
  • extra_info
  • http_utils
  • job_service
  • restart_job
  • api_key_views
  • result_service
  • create_api_key
  • recon_xkg_admin
  • prediction_store
  • similarity_utils
  • validation_utils
  • benchmark_methods
  • similarity_config
  • similarity_service
  • validation_service
  • sequence_expansion
  • about_stats_service
  • substrate_expansion
  • job_progress_service
  • resubmit_pending_jobs
  • migrate_json_to_sqlite
  • prediction_batch_service
  • embedding_progress_service
  • recon_xkg_preflight_service
  • gpu_precompute_status_service
[1]

Created with sphinx-autoapi

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