InitBrendaEntry: Create a 'brenda.entry' object.

Description Usage Arguments Details Value Examples

View source: R/brendaEntry.R

Description

The list should contain 6 sublists: nomenclature, interactions, parameters, molecular, stability, and bibliography. All sublists should be empty by default apart from EC under nomenclature.

Usage

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InitBrendaEntry(
  EC,
  protein = NA,
  systematic.name = NA,
  recommended.name = NA,
  synonyms = NA,
  reaction = NA,
  reaction.type = NA,
  substrate.product = NA,
  natural.substrate.product = NA,
  cofactor = NA,
  metals.ions = NA,
  inhibitors = NA,
  activating.compound = NA,
  km.value = NA,
  turnover.number = NA,
  ki.value = NA,
  pi.value = NA,
  ph.optimum = NA,
  ph.range = NA,
  temperature.optimum = NA,
  temperature.range = NA,
  specific.activity = NA,
  ic50 = NA,
  source.tissue = NA,
  localization = NA,
  general.stability = NA,
  storage.stability = NA,
  ph.stability = NA,
  organic.solvent.stability = NA,
  oxidation.stability = NA,
  temperature.stability = NA,
  purification = NA,
  cloned = NA,
  engineering = NA,
  renatured = NA,
  application = NA,
  molecular.weight = NA,
  subunits = NA,
  posttranslational.modification = NA,
  crystallization = NA,
  bibliography = NA
)

is.brenda.entry(x, verbose = FALSE)

Arguments

EC

A string indicating EC number of the enzyme.

protein

The description string of a PR field.

systematic.name

The description string of a SN field.

recommended.name

The description string of a RN field.

synonyms

The description string of a SY field.

reaction

The description string of a RE field.

reaction.type

The description string of a RT field.

substrate.product

The description string of a SP field.

natural.substrate.product

The description string of a NSP field.

cofactor

The description string of a CF field.

metals.ions

The description string of a ME field.

inhibitors

The description string of a IN field.

activating.compound

The description string of a AC field.

km.value

The description string of a KM field.

turnover.number

The description string of a TN field.

ki.value

The description string of a KI field.

pi.value

The description string of a PI field.

ph.optimum

The description string of a PHO field.

ph.range

The description string of a PHR field.

temperature.optimum

The description string of a TO field.

temperature.range

The description string of a TR field.

specific.activity

The description string of a SA field.

ic50

The description string of a IC50 field.

source.tissue

The description string of a ST field.

localization

The description string of a LO field.

general.stability

The description string of a GS field.

storage.stability

The description string of a SS field.

ph.stability

The description string of a PHS field.

organic.solvent.stability

The description string of a OSS field.

oxidation.stability

The description string of a OS field.

temperature.stability

The description string of a TS field.

purification

The description string of a PU field.

cloned

The description string of a CL field.

engineering

The description string of a EN field.

renatured

The description string of a REN field.

application

The description string of a AP field.

molecular.weight

The description string of a MW field.

subunits

The description string of a SU field.

posttranslational.modification

The description string of a PM field.

crystallization

The description string of a CR field.

bibliography

The description string of a RF field.

x

Any object.

verbose

Boolean value default to FALSE. If TRUE, prints message when all elements are brenda.entries.

Details

is.brenda.entry checks if an object is a brenda.entry object. If the input is a brenda.entries object, check all items in the list to see if they are brenda.entry objects and return a boolean vector of the same length.

Value

A brenda.entry object with all fields other than nomenclature$ec being NA.

A boolean vector of the same length as x.

Examples

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brendaDb:::InitBrendaEntry("1.1.1.100")
df <- ReadBrenda(system.file("extdata", "brenda_download_test.txt",
                          package = "brendaDb"))
is.brenda.entry(QueryBrenda(df, "6.3.5.8"))

y1zhou/brendaDb documentation built on July 24, 2021, 7:14 p.m.