Compound

Description of a compound

Public fields

ID

Id of the compound

Name

Name of the compound as used in the generic simulation

Active bindings

PartitionCoefficientMethod

Method used to calculate the partition coefficient

CellularPermeabilityMethod

Method used to calculate the cellular permeability coefficient

Protocol

Protocol used for compoud

Methods

Public methods

• Compound$new()

• Compound$getProperty()

• Compound$getAllProperty()

• Compound$setPropertyValue()

• Compound$addProperty()

• Compound$removeProperty()

• Compound$addProcessProperty()

• Compound$removeProcessProperty()

• Compound$removeProcess()

• Compound$getProcessProperty()

• Compound$getAllProcessProperty()

• Compound$setProcessPropertyValue()

• Compound$setProtocol()

• Compound$toSnapshot()

• Compound$getAllPropertyPaths()

• Compound$print()

• Compound$clone()

---

Method new()

Initialize a new instance of the class Compound

Usage

Compound$new(ID, name = "Compound", PCMethod = "PK-Sim", CPMethod = "PK-Sim")

Arguments

ID

Id of the compound

name

Name of the compound in the simulation pkmls

PCMethod

Partition coefficient method to use for the compound

CPMethod

Cellular permeability method to use for the compound

Returns

A new Compound object.

---

Method getProperty()

Get specific property of the compound

Usage

Compound$getProperty(name)

Arguments

name

Name of the property to retrieve.

Returns

The corresponding property object.

---

Method getAllProperty()

Get all defined properties of the compound

Usage

Compound$getAllProperty()

Returns

A list of all compound properties.

---

Method setPropertyValue()

Update specific property value for the compound.

Usage

Compound$setPropertyValue(name, value, unit = NULL)

Arguments

name

Name of the property to modify.

value

New value for the property.

unit

New unit to use for the property, if not given the unit is assumed to be the same as previously.

---

Method addProperty()

Add a new property for the compound.

Usage

Compound$addProperty(
  name,
  parName,
  dimension,
  value = 0,
  unit = NULL,
  enum = NULL,
  check = NULL,
  path = NULL
)

Arguments

name

Name of the property to add.

parName

Corresponding parameter name in the simulation pkml of the property to add.

dimension

Dimension of the property to add.

value

Value for the property.

unit

(Optional) Unit to use for the property. If not given, it is assumed to be the baseUnit of the dimension.

enum

(Optional) Name list mapping user friendly values to PK-Sim allowed values.

check

(Optional) Function to check the validity of the supplied value for the property, must take value, unit as argument an retrun an error if the test fails.

path

Corresponding full path of the parameter in the simulation pkml of the property to add (default to NULL to create it automatically based on parName).

---

Method removeProperty()

Remove a property from the compound.

Usage

Compound$removeProperty(name)

Arguments

name

Name of the property to remove

---

Method addProcessProperty()

Add a new process property for the compound.

Usage

Compound$addProcessProperty(
  propertyName,
  processType,
  parName,
  dimension,
  value = 0,
  unit = NULL,
  enum = NULL,
  check = NULL,
  path = NULL
)

Arguments

propertyName

Name of the property to add.

processType

Corresponding Process type. Allowed Process types are: "Liver Plasma Clearance", "Hep T1/2", "Hep Residuals", "Liver Mic T1/2", "Liver Mic Residuals", "Renal Plasma Clearance", "Tub Sec FirstOrder", "Tub Sec MM", "GFR", "Biliary Plasma Clearance".

parName

Corresponding parameter name in the simulation pkml of the property to add.

dimension

Dimension of the property to add.

value

Value for the property.

unit

(Optional) Unit to use for the property. If not given, it is assumed to be the baseUnit of the dimension.

enum

(Optional) Name list mapping user friendly values to PK-Sim allowed values.

check

(Optional) Function to check the validity of the supplied value for the property.

path

(Optional) Corresponding full path of the parameter in the simulation pkml of the property to add. Needed when using a predefined pkml for the HTPBPK simulation.

---

Method removeProcessProperty()

Remove a process property from the compound.

Usage

Compound$removeProcessProperty(propertyName, processType)

Arguments

propertyName

Name of the property to remove

processType

Type of the process to remove the property from

---

Method removeProcess()

Remove a all process propertys from the compound.

Usage

Compound$removeProcess(processType)

Arguments

processType

Type of the process to remove the property from

---

Method getProcessProperty()

Get specific process property of the compound

Usage

Compound$getProcessProperty(propertyName, processType)

Arguments

propertyName

Name of the property to get values from

processType

Type of the process to get the property from

Returns

The corresponding property object.

---

Method getAllProcessProperty()

Get all process properties defined in the compound (or from a specific process type)

Usage

Compound$getAllProcessProperty(processType = NULL)

Arguments

processType

(optional) process type for which to get all the properties defined in compound if NULL or not given all process properties for all process types are retuned

Returns

List of all process properties defined in the compound (for a specific process type if supplied).

---

Method setProcessPropertyValue()

Update specific process property value for the compound.

Usage

Compound$setProcessPropertyValue(propertyName, processType, value, unit = NULL)

Arguments

propertyName

Name of the property to set values for

processType

Type of the process to set the property from

value

New value for the property.

unit

New unit to use for the property, if not given the unit is assumed to be the same as previously.

---

Method setProtocol()

Set the administration protocol to be used for a compound

Usage

Compound$setProtocol(protocol)

Arguments

protocol

administration protocol to use for the compound. Must be an object of class SimpleProtocol or AdvancedProtocol.

---

Method toSnapshot()

Create a snapshot representation of the compound

Usage

Compound$toSnapshot()

---

Method getAllPropertyPaths()

Get the paths of all parameters defined for the compound

Usage

Compound$getAllPropertyPaths(compoundName = NULL)

Arguments

compoundName

name of the compound in the simulations

Returns

A character vector with the paths of all parameters

---

Method print()

Print the object to the console

Usage

Compound$print(...)

Arguments

...

Rest arguments.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

Compound$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.