Create a new compound

Create a Compound building block from named arguments. This is a thin factory around Compound$new() that builds the raw list shape for you, including the physicochemical properties, pKa, and processes.

Each of lipophilicity, fraction unbound, solubility (including reference pH, gain per charge, and table solubility), intestinal permeability, permeability, and pKa must be set through its dedicated argument (or by mutating the matching writable Compound field). The parameters argument is for additional/loose compound parameters only; it cannot set these physicochemical properties, because each lives in its own top-level alternative array or typed list rather than in Parameters.

Usage

create_compound(
  name,
  description = NULL,
  is_small_molecule = NULL,
  plasma_protein_binding_partner = NULL,
  molecular_weight = NULL,
  molecular_weight_unit = "g/mol",
  calculation_methods = NULL,
  parameters = NULL,
  lipophilicity = NULL,
  fraction_unbound = NULL,
  solubility = NULL,
  intestinal_permeability = NULL,
  permeability = NULL,
  pKa = NULL,
  processes = NULL
)

Arguments

name: Character. Name of the compound (required).
description: Character. Free-text description of the compound.
is_small_molecule: Logical. Whether the compound is a small molecule. Defaults to TRUE in PK-Sim when omitted.
plasma_protein_binding_partner: Character. Name of the plasma protein binding partner: one of "Unknown", "Albumin", "Glycoprotein".
molecular_weight: Numeric. Molecular weight value.
molecular_weight_unit: Character. Unit for molecular weight. Defaults to "g/mol".
calculation_methods: Character vector. Calculation method names that PK-Sim uses to derive compound quantities.
parameters: List of Parameter objects (created with create_parameter()) or raw parameter lists to attach as additional compound parameters. This does not set physicochemical properties; use the dedicated arguments below for those.
lipophilicity: A lipophilicity() object, a list of such objects to define several named alternatives (mark exactly one with default = TRUE to designate the group default; when none is marked, the first element is the default), or NULL. When supplied, one Lipophilicity alternative is created per element.
fraction_unbound: A fraction_unbound() object, a list of such objects to define several named alternatives (mark exactly one with default = TRUE to designate the group default; when none is marked, the first element is the default), or NULL. When supplied, one FractionUnbound alternative is created per element.
solubility: A solubility() object, a list of such objects to define several named alternatives (mark exactly one with default = TRUE to designate the group default; when none is marked, the first element is the default), or NULL. Each object expresses either the scalar form (value at a reference pH, with optional gain per charge) or the table form (a pH/value table); a list may mix both forms. When supplied, one Solubility alternative is created per element. See solubility() for the scalar vs table forms and the mutual-exclusivity rule.
intestinal_permeability: An intestinal_permeability() object, a list of such objects to define several named alternatives (mark exactly one with default = TRUE to designate the group default; when none is marked, the first element is the default), or NULL. When supplied, one IntestinalPermeability alternative is created per element.
permeability: A permeability() object, a list of such objects to define several named alternatives (mark exactly one with default = TRUE to designate the group default; when none is marked, the first element is the default), or NULL. When supplied, one Permeability alternative is created per element.
pKa: List of typed pKa entries, each a list with a type (one of "Acid", "Base", "Neutral") and a numeric value, for example list(list(type = "Base", value = 10.02)). Order is preserved. Both NULL (the default) and an empty list() leave the created compound with no pKa types set. (The clearing semantics, where an empty list() removes existing values, apply to the writable Compound$pka_types field, not to construction.)
processes: List of Process objects (created with create_process()) or raw process lists to attach to the compound.

Value

A Compound object.

Examples

# Create a minimal compound
compound <- create_compound(name = "Drug X")

# Create a small molecule with molecular weight and binding partner
compound <- create_compound(
  name = "Drug X",
  is_small_molecule = TRUE,
  molecular_weight = 250.3,
  plasma_protein_binding_partner = "Albumin"
)

# Set the single-parameter physicochemical properties
compound <- create_compound(
  name = "Drug X",
  lipophilicity = lipophilicity(2.5),
  fraction_unbound = fraction_unbound(0.1),
  intestinal_permeability = intestinal_permeability(1.14e-05),
  permeability = permeability(0.0069)
)

# Solubility with reference pH and gain per charge
compound <- create_compound(
  name = "Drug X",
  solubility = solubility(9999, reference_pH = 7, gain_per_charge = 1000)
)

# Table-based solubility (first column pH, second column value)
compound <- create_compound(
  name = "Drug X",
  solubility = solubility(
    table = data.frame(
      pH = c(3, 6, 6.8),
      value = c(5000, 3000, 90)
    )
  )
)

# Several named solubility alternatives (the first is the default)
compound <- create_compound(
  name = "Drug X",
  solubility = list(
    solubility(9999, name = "Aqueous"),
    solubility(200, name = "FaSSIF")
  )
)

# Several named solubility alternatives, explicitly marking the default
compound <- create_compound(
  name = "Drug X",
  solubility = list(
    solubility(9999, name = "Aqueous"),
    solubility(200, name = "FaSSIF", default = TRUE)
  )
)

# Multiple pKa entries
compound <- create_compound(
  name = "Drug X",
  pKa = list(
    list(type = "Base", value = 10.02),
    list(type = "Acid", value = 1.7)
  )
)

# Attach a process
compound <- create_compound(
  name = "Drug X",
  processes = list(
    create_process(
      internal_name = "GlomerularFiltration",
      data_source = "Publication X"
    )
  )
)

# Additional/loose parameters (not physicochemical properties)
compound <- create_compound(
  name = "Drug X",
  parameters = list(
    create_parameter(name = "Cl_spec", value = 5, unit = "ml/min/kg")
  )
)

Usage

Arguments

Value

See also

Examples