Index

_

_aggregate_transcripts_to_genes() (VmaxBuilder.expression.implementation.DefaultExpressionImplementation static method) _apply_global_unobserved_fill() (VmaxBuilder.protein.ptr_implementation.DefaultPTRImplementation static method) _apply_grouped_unobserved_fill() (VmaxBuilder.protein.ptr_implementation.DefaultPTRImplementation static method) _apply_identifier_mapping() (VmaxBuilder.expression.implementation.DefaultExpressionImplementation static method) _build_id_type_name() (VmaxBuilder.expression.implementation.DefaultExpressionImplementation static method) (VmaxBuilder.model.implementation.DefaultModelStageImplementation static method) _build_output_signature() (VmaxBuilder.api.orchestrator.VmaxOrchestrator static method) _build_transcript_artifacts_for_model() (VmaxBuilder.model.implementation.DefaultModelStageImplementation method) _compute_per_sample_fill_values() (VmaxBuilder.protein.ptr_implementation.DefaultPTRImplementation static method) _deduplicate_identifiers() (VmaxBuilder.database_retrieval.identifier_translation.IdentifierTranslationService static method) _ensure_runtime_ready() (VmaxBuilder.api.orchestrator.VmaxOrchestrator method) _extend_user_paths() (VmaxBuilder.config.dataclasses.LoadingPolicy method) _extract_canonical_transcript_identifier() (VmaxBuilder.database_retrieval.identifier_translation.IdentifierTranslationService static method) _extract_ensembl_gene_identifier() (VmaxBuilder.database_retrieval.identifier_translation.IdentifierTranslationService static method) _extract_output_name_component() (VmaxBuilder.config.dataclasses.LoadingPolicy static method) _extract_target_identifier() (VmaxBuilder.database_retrieval.identifier_translation.IdentifierTranslationService static method) _extract_transcript_rows_from_hit() (VmaxBuilder.database_retrieval.identifier_translation.IdentifierTranslationService method) _initialise_scaffold() (VmaxBuilder.api.orchestrator.VmaxOrchestrator static method) _load_model_from_path() (VmaxBuilder.model.implementation.DefaultModelStageImplementation method) _make_json_safe() (VmaxBuilder.api.orchestrator.VmaxOrchestrator class method) _persist_named_payloads() (VmaxBuilder.api.orchestrator.VmaxOrchestrator method)

_persist_named_value() (VmaxBuilder.api.orchestrator.VmaxOrchestrator method) _persist_runtime_state() (VmaxBuilder.api.orchestrator.VmaxOrchestrator method) _prime_output_directories() (VmaxBuilder.api.orchestrator.VmaxOrchestrator method) _query_mygene_chunk() (VmaxBuilder.database_retrieval.identifier_translation.IdentifierTranslationService static method) _resolve_grouped_fill_value() (VmaxBuilder.protein.ptr_implementation.DefaultPTRImplementation static method) _resolve_implementation() (VmaxBuilder.api.orchestrator.VmaxOrchestrator method) _resolve_model_file_path() (VmaxBuilder.model.implementation.DefaultModelStageImplementation method) _resolve_model_input() (VmaxBuilder.model.implementation.DefaultModelStageImplementation method) _resolve_unobserved_source_frame() (VmaxBuilder.protein.ptr_implementation.DefaultPTRImplementation static method) _resolve_within_sample_stat_functions() (VmaxBuilder.protein.ptr_implementation.DefaultPTRImplementation static method) _run_expression_ptr_flow() (VmaxBuilder.protein.stage_implementation.DefaultProteinStageCoordinator method) _run_proteomics_flow() (VmaxBuilder.protein.stage_implementation.DefaultProteinStageCoordinator method) _sanitise_output_name_component() (VmaxBuilder.config.dataclasses.LoadingPolicy static method) _save_json_payload() (VmaxBuilder.api.orchestrator.VmaxOrchestrator static method) _save_tabular_payload() (VmaxBuilder.api.orchestrator.VmaxOrchestrator static method) _save_text_payload() (VmaxBuilder.api.orchestrator.VmaxOrchestrator static method) _should_halt() (VmaxBuilder.diagnostics.runner.DiagnosticsRunner method) _translate_with_mygene() (VmaxBuilder.database_retrieval.identifier_translation.IdentifierTranslationService method) _validate_model_inputs() (VmaxBuilder.api.orchestrator.VmaxOrchestrator method) _validate_protein_inputs() (VmaxBuilder.api.orchestrator.VmaxOrchestrator method) _validate_within_sample_weighting() (VmaxBuilder.protein.ptr_implementation.DefaultPTRImplementation static method) _write_to_disk() (VmaxBuilder.utils.lookup_cache.LookupCache method)

A

add_reactions_slim() (in module VmaxBuilder.cobrapy_overwrites.cobrapy_model) after_stage() (VmaxBuilder.core.protocols.DiagnosticsHookProtocol method) AllocationConfig (class in VmaxBuilder.config.dataclasses)

AllocationImplementation (class in VmaxBuilder.config.registry) AllocationStageOrchestrator (class in VmaxBuilder.api.allocation) APIConfig (class in VmaxBuilder.config.dataclasses) available() (VmaxBuilder.core.protocols.RegistryProtocol method)

B

before_stage() (VmaxBuilder.core.protocols.DiagnosticsHookProtocol method) build_default_api_config() (in module VmaxBuilder.api.orchestrator) build_dynamic_results_directory_name() (VmaxBuilder.config.dataclasses.LoadingPolicy method) build_gene_to_transcripts_mapping() (in module VmaxBuilder.GPR.gpr_preprocessing), [1] build_gene_transcript_dataframe() (VmaxBuilder.database_retrieval.identifier_translation.IdentifierTranslationService method) (VmaxBuilder.model.implementation.TranscriptMetadataServiceProtocol method)

build_ifp_mapping_from_gpr_rules() (in module VmaxBuilder.GPR.gpr_preprocessing), [1] build_reaction_ifp_indexes() (in module VmaxBuilder.GPR.gpr_preprocessing), [1] build_transcript_gene_dataframe() (VmaxBuilder.database_retrieval.identifier_translation.IdentifierTranslationService method) (VmaxBuilder.expression.implementation.IdentifierTranslationServiceProtocol method)

C

calculate_ifp_expansion_count() (in module VmaxBuilder.GPR.gpr_preprocessing), [1] check_for_existing_files() (in module VmaxBuilder.utils.file_handling) check_if_string_or_integer() (in module VmaxBuilder.utils.extra_utils) clear() (VmaxBuilder.utils.lookup_cache.LookupCache method) clear_simplification_cache() (in module VmaxBuilder.GPR.gpr_preprocessing), [1] combine_expression_with_ptr() (VmaxBuilder.protein.ptr_implementation.DefaultPTRImplementation method) compare_dicts() (in module VmaxBuilder.utils.extra_utils)

config_as_plain_dict() (in module VmaxBuilder.config.validation) convert_camel_case_to_snake_case() (in module VmaxBuilder.utils.extra_utils) convert_model_to_cobra_model() (in module VmaxBuilder.utils.extra_utils) create_irreversible_model() (in module VmaxBuilder.model.preprocessing) create_task_specific_model_for_diagnostics() (in module VmaxBuilder.utils.extra_utils) CustomFormatter (class in VmaxBuilder.utils.custom_logging) CustomLogger (class in VmaxBuilder.utils.custom_logging)

D

decorator_provide_time_information() (in module VmaxBuilder.utils.custom_logging) decorator_provide_time_information_2() (in module VmaxBuilder.utils.custom_logging) DefaultAllocationStageImplementation (class in VmaxBuilder.allocation.implementation) DefaultExpressionImplementation (class in VmaxBuilder.expression.implementation) DefaultKcatPreprocessingImplementation (class in VmaxBuilder.Kcat.kcat_preprocessing_implementation) DefaultKcatStageCoordinator (class in VmaxBuilder.Kcat.stage_orchestration) DefaultModelStageImplementation (class in VmaxBuilder.model.implementation) DefaultProteinStageCoordinator (class in VmaxBuilder.protein.stage_implementation) DefaultProteomicsImplementation (class in VmaxBuilder.protein.proteomics_implementation) DefaultPTRImplementation (class in VmaxBuilder.protein.ptr_implementation)

DefaultSmilesGettersImplementation (class in VmaxBuilder.Kcat.smiles_getters_implementation) DefaultUniKPImplementation (class in VmaxBuilder.Kcat.unikp_implementation) DefaultVmaxStageImplementation (class in VmaxBuilder.Vmax.implementation) DiagnosticRecord (class in VmaxBuilder.core.protocols) DiagnosticRecordCore (class in VmaxBuilder.core.protocols) DiagnosticSeverity (class in VmaxBuilder.config.enums) DiagnosticsHookProtocol (class in VmaxBuilder.core.protocols) DiagnosticsRunner (class in VmaxBuilder.diagnostics.runner) DiagnosticsRunnerProtocol (class in VmaxBuilder.core.protocols) dict_to_gene_result() (in module VmaxBuilder.utils.lookup_cache)

E

expand_gene_ifp_to_transcript_ifps() (in module VmaxBuilder.GPR.gpr_preprocessing), [1] ExpressionImplementation (class in VmaxBuilder.config.registry)

ExpressionInputConfig (class in VmaxBuilder.config.dataclasses) extract_compartment() (in module VmaxBuilder.utils.extra_utils)

F

filter() (VmaxBuilder.utils.custom_logging.PrintLevelFilter method) fix_non_ascii_messages_decorator() (VmaxBuilder.utils.custom_logging.CustomLogger static method)

format() (VmaxBuilder.utils.custom_logging.CustomFormatter method) from_mat_struct() (in module VmaxBuilder.cobrapy_overwrites.cobrapy_io)

G

gene_result_to_dict() (in module VmaxBuilder.utils.lookup_cache) GeneSequenceResult (class in VmaxBuilder.utils.lookup_cache) get() (VmaxBuilder.utils.lookup_cache.LookupCache method) get_allowed_values() (in module VmaxBuilder.config.options) get_available_options() (in module VmaxBuilder.config.registry) get_config_class() (in module VmaxBuilder.config.registry) get_default_cache_dir() (in module VmaxBuilder.utils.lookup_cache) get_discovery_extensions() (VmaxBuilder.config.dataclasses.LoadingPolicy method) get_discovery_prefixes() (VmaxBuilder.config.dataclasses.LoadingPolicy method) get_effective_exact_paths() (VmaxBuilder.config.dataclasses.LoadingPolicy method) get_effective_in_memory_inputs() (VmaxBuilder.config.dataclasses.LoadingPolicy method) get_implementation() (in module VmaxBuilder.config.registry)

get_info() (in module VmaxBuilder.config.registry) get_latest_preparation_diagnostics() (VmaxBuilder.protein.ptr_implementation.DefaultPTRImplementation method) get_mode_requirements() (VmaxBuilder.protein.stage_implementation.DefaultProteinStageCoordinator static method) get_output_directories() (VmaxBuilder.config.dataclasses.LoadingPolicy method) get_project_root() (in module VmaxBuilder.utils.file_handling) get_resolved_output_directory() (VmaxBuilder.config.dataclasses.LoadingPolicy method) get_scaffold_model() (in module VmaxBuilder.core.protocols) get_simplification_cache_info() (in module VmaxBuilder.GPR.gpr_preprocessing), [1] get_stage_config() (VmaxBuilder.config.dataclasses.APIConfig method) get_transport_reaction_gene_ids() (in module VmaxBuilder.utils.extra_utils) get_unique_gpr_rules() (in module VmaxBuilder.GPR.gpr_preprocessing), [1] get_weights() (VmaxBuilder.protein.ptr_implementation.DefaultPTRImplementation static method) GPRStageOrchestrator (class in VmaxBuilder.api.gpr)

H

hits_and_misses() (VmaxBuilder.utils.lookup_cache.LookupCache method)

I

IdentifierTranslationResult (class in VmaxBuilder.database_retrieval.identifier_translation) IdentifierTranslationService (class in VmaxBuilder.database_retrieval.identifier_translation) IdentifierTranslationServiceProtocol (class in VmaxBuilder.expression.implementation) ImplementationInfo (class in VmaxBuilder.config.registry) impute_proteomics() (VmaxBuilder.protein.proteomics_implementation.DefaultProteomicsImplementation method)

impute_unobserved_genes() (VmaxBuilder.protein.ptr_implementation.DefaultPTRImplementation static method) impute_within_tissue_ptrs() (VmaxBuilder.protein.ptr_implementation.DefaultPTRImplementation static method) invalidate() (VmaxBuilder.utils.lookup_cache.LookupCache method) IrreversibleModelMode (class in VmaxBuilder.model.preprocessing) is_effectively_integer() (in module VmaxBuilder.utils.extra_utils) iter_search_roots() (VmaxBuilder.config.dataclasses.LoadingPolicy method)

K

KcatLevel (class in VmaxBuilder.config.enums)

KcatStageOrchestrator (class in VmaxBuilder.Kcat.stage_orchestration) keys() (VmaxBuilder.utils.lookup_cache.LookupCache method)

L

load_existing_file_based_on_extension() (in module VmaxBuilder.utils.file_handling) load_matlab_model() (in module VmaxBuilder.cobrapy_overwrites.cobrapy_io)

LoadingPolicy (class in VmaxBuilder.config.dataclasses) LoadResolutionMode (class in VmaxBuilder.config.enums) LookupCache (class in VmaxBuilder.utils.lookup_cache)

M

memory_checker() (in module VmaxBuilder.utils.custom_logging) MinimalExpression (class in VmaxBuilder.config.registry) model_from_dict() (in module VmaxBuilder.cobrapy_overwrites.cobrapy_io) model_to_dict() (in module VmaxBuilder.cobrapy_overwrites.cobrapy_io) ModelConfig (class in VmaxBuilder.config.dataclasses) ModelPreprocessingResult (class in VmaxBuilder.model.preprocessing) ModelStageOrchestrator (class in VmaxBuilder.api.model) module VmaxBuilder.allocation VmaxBuilder.allocation.implementation VmaxBuilder.api VmaxBuilder.api.allocation VmaxBuilder.api.gpr VmaxBuilder.api.model VmaxBuilder.api.orchestrator VmaxBuilder.api.protein VmaxBuilder.api.vmax VmaxBuilder.cobrapy_overwrites VmaxBuilder.cobrapy_overwrites.cobrapy_io VmaxBuilder.cobrapy_overwrites.cobrapy_model VmaxBuilder.cobrapy_overwrites.cobrapy_reaction VmaxBuilder.config VmaxBuilder.config.dataclasses VmaxBuilder.config.enums VmaxBuilder.config.options VmaxBuilder.config.registry VmaxBuilder.config.validation VmaxBuilder.core VmaxBuilder.core.protocols VmaxBuilder.database_retrieval VmaxBuilder.database_retrieval.identifier_translation VmaxBuilder.diagnostics VmaxBuilder.diagnostics.runner VmaxBuilder.expression VmaxBuilder.expression.implementation VmaxBuilder.GPR.gpr_implementation VmaxBuilder.GPR.gpr_preprocessing VmaxBuilder.Kcat VmaxBuilder.Kcat.kcat_preprocessing_implementation VmaxBuilder.Kcat.smiles_getters_implementation VmaxBuilder.Kcat.stage_orchestration VmaxBuilder.Kcat.unikp_implementation VmaxBuilder.model VmaxBuilder.model.implementation VmaxBuilder.model.preprocessing VmaxBuilder.protein VmaxBuilder.protein.input_resolution VmaxBuilder.protein.proteomics_implementation VmaxBuilder.protein.ptr_implementation VmaxBuilder.protein.stage_implementation VmaxBuilder.registries VmaxBuilder.utils VmaxBuilder.utils.custom_exceptions VmaxBuilder.utils.custom_logging VmaxBuilder.utils.extra_utils VmaxBuilder.utils.file_handling VmaxBuilder.utils.lookup_cache VmaxBuilder.utils.transformations VmaxBuilder.utils.type_hinting VmaxBuilder.Vmax VmaxBuilder.Vmax.implementation

MValueTrimmingConfig (class in VmaxBuilder.config.dataclasses)

N

normalize_loaded_dataframe() (in module VmaxBuilder.protein.input_resolution)

O

OptionSpec (class in VmaxBuilder.config.options)

P

parse_log_file() (in module VmaxBuilder.utils.custom_logging) parse_type_hint() (in module VmaxBuilder.utils.type_hinting) path (VmaxBuilder.utils.lookup_cache.LookupCache property) populate_solver_from_model() (in module VmaxBuilder.cobrapy_overwrites.cobrapy_model) prepare_expression_frame() (VmaxBuilder.expression.implementation.DefaultExpressionImplementation method) prepare_ptr_frame() (VmaxBuilder.protein.ptr_implementation.DefaultPTRImplementation method) preprocess_model() (in module VmaxBuilder.model.preprocessing) PrimaryOutputFormat (class in VmaxBuilder.config.enums) PrintLevelFilter (class in VmaxBuilder.utils.custom_logging) process_stack() (VmaxBuilder.utils.custom_logging.CustomLogger method)

profile_memory_full() (in module VmaxBuilder.utils.custom_logging) profile_time() (in module VmaxBuilder.utils.custom_logging) progressBar() (in module VmaxBuilder.utils.custom_logging) ProteinConfig (class in VmaxBuilder.config.dataclasses) ProteinSourceMode (class in VmaxBuilder.config.enums) ProteinStageOrchestrator (class in VmaxBuilder.api.protein) ProteomicsImplementation (class in VmaxBuilder.config.registry) ProteomicsInputConfig (class in VmaxBuilder.config.dataclasses) PTRImplementation (class in VmaxBuilder.config.registry) PTRInputConfig (class in VmaxBuilder.config.dataclasses)

R

ReactionNotation (class in VmaxBuilder.config.enums) register() (VmaxBuilder.core.protocols.RegistryProtocol method) register_implementation() (in module VmaxBuilder.config.registry) RegistryProtocol (class in VmaxBuilder.core.protocols) remove_compartment() (in module VmaxBuilder.utils.extra_utils) remove_ptr_duplicates() (VmaxBuilder.protein.ptr_implementation.DefaultPTRImplementation static method) requires_sample_type_map() (VmaxBuilder.protein.ptr_implementation.DefaultPTRImplementation class method) resolve() (VmaxBuilder.core.protocols.RegistryProtocol method) resolve_dataframe_input() (in module VmaxBuilder.protein.input_resolution) resolve_expression_frame() (VmaxBuilder.expression.implementation.DefaultExpressionImplementation method) resolve_gene_or_reaction_group_members() (in module VmaxBuilder.utils.extra_utils) resolve_input_file_path() (in module VmaxBuilder.protein.input_resolution) resolve_mode() (VmaxBuilder.config.dataclasses.ValidationPolicy method) resolve_proteomics_frame() (VmaxBuilder.protein.proteomics_implementation.DefaultProteomicsImplementation method) resolve_ptr_frame() (VmaxBuilder.protein.ptr_implementation.DefaultPTRImplementation method) resolve_sample_type_map() (VmaxBuilder.protein.ptr_implementation.DefaultPTRImplementation static method) resolve_special_gene_groups() (VmaxBuilder.protein.ptr_implementation.DefaultPTRImplementation static method) resolve_trimming_implementation() (VmaxBuilder.config.dataclasses.APIConfig method) resolve_validation_mode() (in module VmaxBuilder.config.validation) run() (VmaxBuilder.allocation.implementation.DefaultAllocationStageImplementation method) (VmaxBuilder.api.allocation.AllocationStageOrchestrator method) (VmaxBuilder.api.gpr.GPRStageOrchestrator method) (VmaxBuilder.api.model.ModelStageOrchestrator method) (VmaxBuilder.api.orchestrator.VmaxOrchestrator method) (VmaxBuilder.api.protein.ProteinStageOrchestrator method) (VmaxBuilder.api.vmax.VmaxStageOrchestrator method) (VmaxBuilder.core.protocols.StageProtocol method) (VmaxBuilder.core.protocols.StrategyProtocol method) (VmaxBuilder.Kcat.kcat_preprocessing_implementation.DefaultKcatPreprocessingImplementation method) (VmaxBuilder.Kcat.smiles_getters_implementation.DefaultSmilesGettersImplementation method) (VmaxBuilder.Kcat.stage_orchestration.DefaultKcatStageCoordinator method) (VmaxBuilder.Kcat.stage_orchestration.KcatStageOrchestrator method) (VmaxBuilder.Kcat.unikp_implementation.DefaultUniKPImplementation method) (VmaxBuilder.model.implementation.DefaultModelStageImplementation method) (VmaxBuilder.protein.stage_implementation.DefaultProteinStageCoordinator method) (VmaxBuilder.Vmax.implementation.DefaultVmaxStageImplementation method)

run_all() (VmaxBuilder.api.orchestrator.VmaxOrchestrator method) run_allocation() (VmaxBuilder.api.orchestrator.VmaxOrchestrator method) run_gpr() (VmaxBuilder.api.orchestrator.VmaxOrchestrator method) run_hooks() (VmaxBuilder.core.protocols.DiagnosticsRunnerProtocol method) (VmaxBuilder.diagnostics.runner.DiagnosticsRunner method) run_model() (VmaxBuilder.api.orchestrator.VmaxOrchestrator method) run_protein() (VmaxBuilder.api.orchestrator.VmaxOrchestrator method) run_vmax() (VmaxBuilder.api.orchestrator.VmaxOrchestrator method)

S

save() (VmaxBuilder.utils.lookup_cache.LookupCache method) save_json_model() (in module VmaxBuilder.cobrapy_overwrites.cobrapy_io) save_with_tries() (in module VmaxBuilder.utils.file_handling) Scaffold (class in VmaxBuilder.core.protocols) sequence_cache_key() (in module VmaxBuilder.utils.lookup_cache) SequenceRecord (class in VmaxBuilder.utils.lookup_cache) set() (VmaxBuilder.utils.lookup_cache.LookupCache method) set_log_files_location() (VmaxBuilder.utils.custom_logging.CustomLogger method) set_many() (VmaxBuilder.utils.lookup_cache.LookupCache method)

set_print_level() (VmaxBuilder.utils.custom_logging.CustomLogger method) simplify_gpr_rule() (in module VmaxBuilder.GPR.gpr_preprocessing), [1] simplify_gpr_rule_cached() (in module VmaxBuilder.GPR.gpr_preprocessing), [1] smiles_cache_key() (in module VmaxBuilder.utils.lookup_cache) some_function() (in module VmaxBuilder.api.orchestrator) StageConfig (class in VmaxBuilder.config.dataclasses) StageName (class in VmaxBuilder.config.enums) StageProtocol (class in VmaxBuilder.core.protocols) standardize_ptr_frame() (VmaxBuilder.protein.ptr_implementation.DefaultPTRImplementation static method) StrategyProtocol (class in VmaxBuilder.core.protocols)

T

time_checker() (in module VmaxBuilder.utils.custom_logging) TPMExpression (class in VmaxBuilder.config.registry) TranscriptIfpExpansionOutcome (class in VmaxBuilder.GPR.gpr_preprocessing), [1] TranscriptMetadataServiceProtocol (class in VmaxBuilder.model.implementation) TranscriptProcessingConfig (class in VmaxBuilder.config.dataclasses)

transform_dataframe() (in module VmaxBuilder.utils.transformations) transform_ptr_to_linear() (VmaxBuilder.protein.ptr_implementation.DefaultPTRImplementation static method) translate_identifiers() (VmaxBuilder.database_retrieval.identifier_translation.IdentifierTranslationService method) (VmaxBuilder.expression.implementation.IdentifierTranslationServiceProtocol method) TrimmingImplementation (class in VmaxBuilder.config.registry) TypeNode (class in VmaxBuilder.utils.type_hinting)

U

UnionNode (class in VmaxBuilder.utils.type_hinting)

update_variable_bounds_slim() (in module VmaxBuilder.cobrapy_overwrites.cobrapy_reaction)

V

validate_allowed_value() (in module VmaxBuilder.config.validation) validate_loading_policy() (in module VmaxBuilder.config.validation) validate_model_config() (in module VmaxBuilder.config.validation) validate_option_map() (in module VmaxBuilder.config.validation) ValidationMode (class in VmaxBuilder.config.enums) ValidationPolicy (class in VmaxBuilder.config.dataclasses) VmaxBuilder.allocation module VmaxBuilder.allocation.implementation module VmaxBuilder.api module VmaxBuilder.api.allocation module VmaxBuilder.api.gpr module VmaxBuilder.api.model module VmaxBuilder.api.orchestrator module VmaxBuilder.api.protein module VmaxBuilder.api.vmax module VmaxBuilder.cobrapy_overwrites module VmaxBuilder.cobrapy_overwrites.cobrapy_io module VmaxBuilder.cobrapy_overwrites.cobrapy_model module VmaxBuilder.cobrapy_overwrites.cobrapy_reaction module VmaxBuilder.config module VmaxBuilder.config.dataclasses module VmaxBuilder.config.enums module VmaxBuilder.config.options module VmaxBuilder.config.registry module VmaxBuilder.config.validation module VmaxBuilder.core module VmaxBuilder.core.protocols module VmaxBuilder.database_retrieval module VmaxBuilder.database_retrieval.identifier_translation module VmaxBuilder.diagnostics module VmaxBuilder.diagnostics.runner module VmaxBuilder.expression module

VmaxBuilder.expression.implementation module VmaxBuilder.GPR.gpr_implementation module VmaxBuilder.GPR.gpr_preprocessing module VmaxBuilder.Kcat module VmaxBuilder.Kcat.kcat_preprocessing_implementation module VmaxBuilder.Kcat.smiles_getters_implementation module VmaxBuilder.Kcat.stage_orchestration module VmaxBuilder.Kcat.unikp_implementation module VmaxBuilder.model module VmaxBuilder.model.implementation module VmaxBuilder.model.preprocessing module VmaxBuilder.protein module VmaxBuilder.protein.input_resolution module VmaxBuilder.protein.proteomics_implementation module VmaxBuilder.protein.ptr_implementation module VmaxBuilder.protein.stage_implementation module VmaxBuilder.registries module VmaxBuilder.utils module VmaxBuilder.utils.custom_exceptions module VmaxBuilder.utils.custom_logging module VmaxBuilder.utils.extra_utils module VmaxBuilder.utils.file_handling module VmaxBuilder.utils.lookup_cache module VmaxBuilder.utils.transformations module VmaxBuilder.utils.type_hinting module VmaxBuilder.Vmax module VmaxBuilder.Vmax.implementation module VmaxConfig (class in VmaxBuilder.config.dataclasses) VmaxOrchestrator (class in VmaxBuilder.api.orchestrator) VmaxStageOrchestrator (class in VmaxBuilder.api.vmax)