InitBrendaEntry: Create a 'brenda.entry' object.
In y1zhou/brendaDb: The BRENDA Enzyme Database

InitBrendaEntry

R Documentation

Create a `brenda.entry` object.

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

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

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 Dec. 12, 2022, 3:43 a.m.