MoleculesBuildingBlock

A Molecules building block. Subclass of BuildingBlock.

Super classes

rSharp::NetObject -> ospsuite::DotNetWrapper -> ospsuite::ObjectBase -> ospsuite::BuildingBlock -> MoleculesBuildingBlock

Methods

Public methods

• MoleculesBuildingBlock$new()

• MoleculesBuildingBlock$allMoleculeNames()

• MoleculesBuildingBlock$allFloatingMoleculeNames()

• MoleculesBuildingBlock$allStationaryMoleculeNames()

• MoleculesBuildingBlock$allMoleculeNamesOfType()

• MoleculesBuildingBlock$allXenobioticFloatingMoleculeNames()

• MoleculesBuildingBlock$allEndogenousStationaryMoleculeNames()

• MoleculesBuildingBlock$moleculeTypeFor()

Inherited methods

• rSharp::NetObject$.printClass()
• rSharp::NetObject$.printLine()
• rSharp::NetObject$call()
• rSharp::NetObject$get()
• rSharp::NetObject$getFields()
• rSharp::NetObject$getMemberSignature()
• rSharp::NetObject$getMethods()
• rSharp::NetObject$getProperties()
• rSharp::NetObject$getStaticFields()
• rSharp::NetObject$getStaticMethods()
• rSharp::NetObject$getStaticProperties()
• rSharp::NetObject$set()
• ospsuite::BuildingBlock$print()

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Method new()

Initialize a new instance of the class.

Usage

MoleculesBuildingBlock$new(netObject)

Arguments

netObject

Reference to the underlying Molecules building block.

Returns

A new MoleculesBuildingBlock object.

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Method allMoleculeNames()

Returns the names of all molecules defined in the building block.

Usage

MoleculesBuildingBlock$allMoleculeNames()

Returns

Character vector of molecule names.

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Method allFloatingMoleculeNames()

Returns the names of all floating molecules in the building block (molecules with IsFloating = TRUE, e.g. drugs, metabolites).

Usage

MoleculesBuildingBlock$allFloatingMoleculeNames()

Returns

Character vector of molecule names.

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Method allStationaryMoleculeNames()

Returns the names of all stationary molecules in the building block (molecules with IsFloating = FALSE, e.g. enzymes, transporters).

Usage

MoleculesBuildingBlock$allStationaryMoleculeNames()

Returns

Character vector of molecule names.

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Method allMoleculeNamesOfType()

Returns the names of all molecules of the given type. Pass MoleculeType$Protein to obtain all proteins (the union of Enzyme, Transporter, and Binding Partner).

Usage

MoleculesBuildingBlock$allMoleculeNamesOfType(moleculeType)

Arguments

moleculeType

One of the values defined in the MoleculeType enum (e.g. Drug, Metabolite, Enzyme, Transporter, Binding Partner, Complex, Protein).

Returns

Character vector of molecule names.

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Method allXenobioticFloatingMoleculeNames()

Returns the names of all xenobiotic floating molecules in the building block (e.g. drugs, drug complexes).

Usage

MoleculesBuildingBlock$allXenobioticFloatingMoleculeNames()

Returns

Character vector of molecule names.

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Method allEndogenousStationaryMoleculeNames()

Returns the names of all endogenous stationary molecules in the building block (e.g. enzymes, transporters, other proteins).

Usage

MoleculesBuildingBlock$allEndogenousStationaryMoleculeNames()

Returns

Character vector of molecule names.

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Method moleculeTypeFor()

Returns the type of a molecule by name as it is recorded in the building block (e.g. "Drug", "Enzyme", "Transporter", "Binding Partner"). Throws an error if the molecule is not present.

Usage

MoleculesBuildingBlock$moleculeTypeFor(moleculeName)

Arguments

moleculeName

Name of the molecule to look up.

Returns

Character string with the molecule type.