constants.jl 1.53 KB
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"""
A named tuple that contains the magic values that are used globally for
whatever purposes.
"""
const _constants = (
    default_reaction_bound = 1e3,
    tolerance = 1e-6,
    sampling_keep_iters = 100,
    sampling_size = 1000,
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    keynames = (
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        rxns = ["reactions", "rxns", "RXNS", "REACTIONS", "Reactions", "Rxns"],
        mets = ["metabolites", "mets", "METS", "METABOLITES", "Metabolites", "Mets"],
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        genes = ["genes", "GENES", "Genes"],
        lbs = ["lbs", "lb", "lowerbounds", "lower_bounds"],
        ubs = ["ubs", "ub", "upperbounds", "upper_bounds"],
        stochiometry = ["S"],
        balance = ["b"],
        objective = ["c"],
        grrs = ["gene_reaction_rules", "grRules", "rules"],
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        ids = ["id", "description"],
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    ),
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    gene_annotation_checks = (
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        "ncbigene",
        "ncbigi",
        "refseq_locus_tag",
        "refseq_name",
        "refseq_synonym",
        "uniprot",
    ),
    reaction_annotation_checks = (
        "bigg.reaction",
        "biocyc",
        "ec-code",
        "kegg.reaction",
        "metanetx.reaction",
        "rhea",
        "sabiork",
        "seed.reaction",
    ),
    metabolite_annotation_checks = (
        "kegg.compound",
        "bigg.metabolite",
        "chebi",
        "inchi_key",
        "sabiork",
        "hmdb",
        "seed.compound",
        "metanetx.chemical",
        "reactome.compound",
        "biocyc",
    ),
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    colors = (empty = :dark_gray, payload = :default, key = :cyan),
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)
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const MAX = COBREXA.MOI.MAX_SENSE
const MIN = COBREXA.MOI.MIN_SENSE