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VmaxBuilder 1.0.0 documentation
VmaxBuilder 1.0.0 documentation

Contents

  • Getting Started
  • Installation
  • Examples
  • Use Cases
  • Usage
  • VmaxBuilder (API)
    • api
      • allocation
        • AllocationStageOrchestrator
      • gpr
        • GPRStageOrchestrator
      • model
        • ModelStageOrchestrator
      • orchestrator
        • VmaxOrchestrator
        • build_default_api_config()
        • some_function()
      • protein
        • ProteinStageOrchestrator
      • vmax
        • VmaxStageOrchestrator
    • config
      • dataclasses
        • APIConfig
        • AllocationConfig
        • ExpressionInputConfig
        • LoadingPolicy
        • MValueTrimmingConfig
        • ModelConfig
        • PTRInputConfig
        • ProteinConfig
        • ProteomicsInputConfig
        • StageConfig
        • TranscriptProcessingConfig
        • ValidationPolicy
        • VmaxConfig
      • enums
        • DiagnosticSeverity
        • KcatLevel
        • LoadResolutionMode
        • PrimaryOutputFormat
        • ProteinSourceMode
        • ReactionNotation
        • StageName
        • ValidationMode
      • options
        • OptionSpec
        • get_allowed_values()
      • registry
        • AllocationImplementation
        • ExpressionImplementation
        • ImplementationInfo
        • MinimalExpression
        • PTRImplementation
        • ProteomicsImplementation
        • TPMExpression
        • TrimmingImplementation
        • get_available_options()
        • get_config_class()
        • get_implementation()
        • get_info()
        • register_implementation()
      • validation
        • config_as_plain_dict()
        • resolve_validation_mode()
        • validate_allowed_value()
        • validate_loading_policy()
        • validate_model_config()
        • validate_option_map()
    • core
      • protocols
        • DiagnosticRecord
        • DiagnosticRecordCore
        • DiagnosticsHookProtocol
        • DiagnosticsRunnerProtocol
        • RegistryProtocol
        • Scaffold
        • StageProtocol
        • StrategyProtocol
        • get_scaffold_model()
    • expression
      • implementation
        • DefaultExpressionImplementation
        • IdentifierTranslationServiceProtocol
    • model
      • implementation
        • DefaultModelStageImplementation
        • TranscriptMetadataServiceProtocol
      • preprocessing
        • IrreversibleModelMode
        • ModelPreprocessingResult
        • create_irreversible_model()
        • preprocess_model()
    • protein
      • input_resolution
        • normalize_loaded_dataframe()
        • resolve_dataframe_input()
        • resolve_input_file_path()
      • proteomics_implementation
        • DefaultProteomicsImplementation
      • ptr_implementation
        • DefaultPTRImplementation
      • stage_implementation
        • DefaultProteinStageCoordinator
    • Kcat
      • kcat_preprocessing_implementation
        • DefaultKcatPreprocessingImplementation
      • smiles_getters_implementation
        • DefaultSmilesGettersImplementation
      • stage_orchestration
        • DefaultKcatStageCoordinator
        • KcatStageOrchestrator
      • unikp_implementation
        • DefaultUniKPImplementation
    • allocation
      • implementation
        • DefaultAllocationStageImplementation
    • Vmax
      • implementation
        • DefaultVmaxStageImplementation
    • diagnostics
      • runner
        • DiagnosticsRunner
    • registries
    • database_retrieval
      • identifier_translation
        • IdentifierTranslationResult
        • IdentifierTranslationService
    • cobrapy_overwrites
      • cobrapy_io
        • from_mat_struct()
        • load_matlab_model()
        • model_from_dict()
        • model_to_dict()
        • save_json_model()
      • cobrapy_model
        • add_reactions_slim()
        • populate_solver_from_model()
      • cobrapy_reaction
        • update_variable_bounds_slim()
    • utils
      • custom_exceptions
      • custom_logging
        • CustomFormatter
        • CustomLogger
        • PrintLevelFilter
        • decorator_provide_time_information()
        • decorator_provide_time_information_2()
        • memory_checker()
        • parse_log_file()
        • profile_memory_full()
        • profile_time()
        • progressBar()
        • time_checker()
      • extra_utils
        • check_if_string_or_integer()
        • compare_dicts()
        • convert_camel_case_to_snake_case()
        • convert_model_to_cobra_model()
        • create_task_specific_model_for_diagnostics()
        • extract_compartment()
        • get_transport_reaction_gene_ids()
        • is_effectively_integer()
        • remove_compartment()
        • resolve_gene_or_reaction_group_members()
      • file_handling
        • check_for_existing_files()
        • get_project_root()
        • load_existing_file_based_on_extension()
        • save_with_tries()
      • lookup_cache
        • GeneSequenceResult
        • LookupCache
        • SequenceRecord
        • dict_to_gene_result()
        • gene_result_to_dict()
        • get_default_cache_dir()
        • sequence_cache_key()
        • smiles_cache_key()
      • transformations
        • transform_dataframe()
      • type_hinting
        • TypeNode
        • UnionNode
        • parse_type_hint()
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gpr

Classes

GPRStageOrchestrator([implementation])

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Copyright © 2026, Jelle Bonthuis, Marian Breuer, Michiel Adriaens
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Last updated on Jun 18, 2026