biolabcalc 0.2.0__py3-none-any.whl

biolabcalc/__init__.py

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+"""BioLabCalc: A multifaceted Python library and Excel extension for daily molecular biology research."""
+
+__version__ = "0.2.0"
+
+from .seq_utils import (
+    clean_sequence,
+    validate_sequence,
+    reverse_complement,
+    calculate_gc_content,
+    count_bases,
+    translate_dna,
+)
+
+from .molecular_weight import (
+    calculate_dna_mw,
+    calculate_rna_mw,
+    calculate_protein_mw,
+    mass_to_moles,
+    moles_to_mass,
+    mass_to_copy_number,
+    copy_number_to_mass,
+    concentration_to_molarity,
+    MolecularWeightResult,
+)
+
+from .transcription import (
+    calculate_ivt_yield,
+    optimize_transcription_time,
+    detect_and_trim_promoter,
+    evaluate_initiation_efficiency,
+    PROMOTER_SEQUENCES,
+    InitiationAnalysis,
+    IVTResult,
+    TranscriptionTimeOptimizationResult,
+)
+
+from .pcr import (
+    calculate_pcr_kinetics,
+    calculate_qpcr_efficiency,
+    build_master_mix,
+    optimize_pcr_protocol,
+    PCRResult,
+    MasterMixItem,
+    PCROptimizationResult,
+)
+
+from .protein import (
+    calculate_extinction_coefficient,
+    quantify_protein_a280,
+    fit_standard_curve,
+    ExtinctionCoefficientResult,
+    ProteinYieldResult,
+    StandardCurveResult,
+)
+
+from .primers import (
+    calculate_tm_santaluicia,
+    analyze_primer,
+    design_primers,
+    check_heterodimer,
+    PrimerAnalysis,
+    PrimerPair,
+)
+
+from .fluorescence import (
+    get_fluorophore,
+    apply_fluorophore_modification,
+    calculate_degree_of_labeling,
+    Fluorophore,
+    LabeledMoleculeResult,
+    DegreeOfLabelingResult,
+    FLUOROPHORE_DATABASE,
+)
+
+from .spectroscopy import (
+    prepare_standard_solution,
+    assess_nanodrop_purity,
+    SolutionRecipeResult,
+    NanoDropPurityResult,
+)
+
+from .gels import (
+    simulate_gel,
+    calculate_rf,
+    GelLaneSimulation,
+    GelBand,
+    LADDER_CATALOG,
+)
+
+from .ecoli_growth import (
+    calculate_ecoli_growth,
+    calculate_inoculation_volume,
+    estimate_plasmid_yield,
+    optimize_protein_induction,
+    EcoliGrowthResult,
+    PlasmidYieldResult,
+    ProteinInductionResult,
+)
+
+from .cloning import (
+    get_restriction_enzyme,
+    plan_restriction_digest,
+    calculate_ligation,
+    calculate_gibson_assembly,
+    calculate_golden_gate_assembly,
+    are_overhangs_compatible,
+    register_custom_enzyme,
+    ENZYME_DATABASE,
+    DigestSetupResult,
+    LigationSetupResult,
+    GibsonAssemblyResult,
+    GoldenGateResult,
+)
+
+from .buffers import (
+    calculate_buffer_recipe,
+    calculate_hepes_ivt_buffer,
+    calculate_tris_temperature_shift,
+    register_custom_buffer,
+    create_custom_buffer,
+    save_custom_buffer_to_disk,
+    load_custom_buffers_from_disk,
+    list_custom_buffers,
+    delete_custom_buffer,
+    CustomBufferBuilder,
+    CustomBufferComponent,
+    BUFFER_CATALOG,
+    BufferRecipeResult,
+    BufferComponent,
+    calculate_ntp_ph_adjustment,
+    NTPNeutralizationResult,
+    HepesIVTBufferResult,
+)
+
+from .lab_report import (
+    LabReport,
+    MeasurementRecord,
+    ParameterStatistics,
+    new_lab_report,
+    get_active_report,
+    record_measurement,
+)
+
+from .western_blot import (
+    plan_western_blot,
+    calculate_transfer_conditions,
+    calculate_lysate_loading,
+    calculate_antibody_dilution,
+    troubleshoot_western_blot,
+    WesternBlotPlanResult,
+    TransferConditionsResult,
+    LysateLoadingResult,
+    AntibodyDilutionResult,
+    WesternTroubleshootingResult,
+    TROUBLESHOOTING_DATABASE,
+)
+
+from .protocols import (
+    PROTOCOL_CATALOG,
+    LabProtocol,
+    ProtocolStep,
+    ProtocolReagent,
+    TroubleshootingItem,
+    get_protocol,
+    list_protocols,
+    format_protocol_markdown,
+    export_all_protocols_markdown,
+)
+
+from .precipitation import (
+    calculate_precipitation,
+    calculate_phenol_chloroform_extraction,
+    PrecipitationProtocol,
+    PhenolChloroformProtocol,
+)
+
+from .interactive_gel import (
+    get_interactive_html,
+    save_interactive_app,
+    calculate_ladder_standard_curve,
+    estimate_band_mw,
+    launch_interactive_annotator,
+)
+
+from .gel_annotator import (
+    GelAnnotator,
+)
+
+from .excel_extension import (
+    batch_process_excel,
+    generate_lab_notebook_template,
+    export_analysis_to_excel,
+)
+
+__all__ = [
+    "clean_sequence",
+    "validate_sequence",
+    "reverse_complement",
+    "calculate_gc_content",
+    "count_bases",
+    "translate_dna",
+    "calculate_dna_mw",
+    "calculate_rna_mw",
+    "calculate_protein_mw",
+    "mass_to_moles",
+    "moles_to_mass",
+    "mass_to_copy_number",
+    "copy_number_to_mass",
+    "concentration_to_molarity",
+    "MolecularWeightResult",
+    "calculate_ivt_yield",
+    "IVTResult",
+    "calculate_pcr_kinetics",
+    "calculate_qpcr_efficiency",
+    "build_master_mix",
+    "optimize_pcr_protocol",
+    "PCRResult",
+    "MasterMixItem",
+    "PCROptimizationResult",
+    "calculate_extinction_coefficient",
+    "quantify_protein_a280",
+    "fit_standard_curve",
+    "ExtinctionCoefficientResult",
+    "ProteinYieldResult",
+    "StandardCurveResult",
+    "calculate_tm_santaluicia",
+    "analyze_primer",
+    "design_primers",
+    "PrimerAnalysis",
+    "PrimerPair",
+    "get_fluorophore",
+    "apply_fluorophore_modification",
+    "calculate_degree_of_labeling",
+    "Fluorophore",
+    "LabeledMoleculeResult",
+    "DegreeOfLabelingResult",
+    "FLUOROPHORE_DATABASE",
+    "prepare_standard_solution",
+    "SolutionRecipeResult",
+    "simulate_gel",
+    "calculate_rf",
+    "GelLaneSimulation",
+    "GelBand",
+    "LADDER_CATALOG",
+    "calculate_ecoli_growth",
+    "estimate_plasmid_yield",
+    "optimize_protein_induction",
+    "EcoliGrowthResult",
+    "PlasmidYieldResult",
+    "ProteinInductionResult",
+    "generate_lab_notebook_template",
+    "batch_process_excel",
+    "get_restriction_enzyme",
+    "plan_restriction_digest",
+    "calculate_ligation",
+    "calculate_gibson_assembly",
+    "ENZYME_DATABASE",
+    "DigestSetupResult",
+    "LigationSetupResult",
+    "GibsonAssemblyResult",
+    "calculate_buffer_recipe",
+    "calculate_ntp_ph_adjustment",
+    "NTPNeutralizationResult",
+    "BUFFER_CATALOG",
+    "PROTOCOL_CATALOG",
+    "LabProtocol",
+    "ProtocolStep",
+    "ProtocolReagent",
+    "TroubleshootingItem",
+    "get_protocol",
+    "list_protocols",
+    "format_protocol_markdown",
+    "export_all_protocols_markdown",
+    "BufferRecipeResult",
+    "BufferComponent",
+    "calculate_precipitation",
+    "PrecipitationProtocol",
+    "export_analysis_to_excel",
+    "GelAnnotator",
+    "get_interactive_html",
+    "save_interactive_app",
+    "calculate_ladder_standard_curve",
+    "estimate_band_mw",
+    "launch_interactive_annotator",
+]