Solubility value object

Build a solubility value object for create_compound()'s solubility argument (or the writable Compound$solubility field). Expresses either the scalar form (a single solubility value at a reference pH, optionally with a solubility gain per charge) or the mutually exclusive table form (a pH/value table).

The scalar-form arguments (value, reference_pH, gain_per_charge) and table are mutually exclusive: supplying table together with any of them is an error. Unlike the previous create_compound() behaviour, where reference_pH / gain_per_charge were silently ignored on the table path, this helper rejects the combination so the intent is unambiguous.

Usage

solubility(
  value = NULL,
  unit = "mg/l",
  reference_pH = NULL,
  gain_per_charge = NULL,
  table = NULL,
  name = "User defined",
  default = FALSE
)

Arguments

value

Numeric scalar. Solubility-at-reference-pH value for the scalar form. Leave NULL for the table form.

unit

Character. Unit for the solubility value (scalar form) and for the table Y values, validated against dimension "Concentration (mass)". Defaults to "mg/l".

reference_pH

Numeric scalar. Reference pH added to the scalar Solubility alternative. Scalar form only.

gain_per_charge

Numeric scalar. Optional Solubility gain per charge parameter added to the scalar Solubility alternative. Scalar form only.

table

Two-column data frame giving table-based solubility: the first column is pH and the second is the solubility value. When supplied, the table form is built and the scalar-form arguments must be left unset.

name

Character. Name of the created alternative (scalar or table). Defaults to "User defined".

default

Logical. Whether this alternative is the group's default when it appears in a list of alternatives passed to the matching create_compound() argument or Compound field. Defaults to FALSE. Ignored for a single (non-list) value object, which is always the default. When a list has no element marked default = TRUE, the first element is the default (unchanged behaviour); marking two or more elements default = TRUE in the same list is an error.

Value

A solubility_spec object to pass to create_compound().

See also

create_compound()

Other value-object helpers: age(), error(), fraction_unbound(), gestational_age(), height(), intestinal_permeability(), lipophilicity(), permeability(), time(), values(), weight()

Examples

# Scalar form with reference pH and gain per charge
solubility(9999, reference_pH = 7, gain_per_charge = 1000)
#> $value
#> [1] 9999
#> 
#> $unit
#> [1] "mg/l"
#> 
#> $reference_pH
#> [1] 7
#> 
#> $gain_per_charge
#> [1] 1000
#> 
#> $table
#> NULL
#> 
#> $name
#> [1] "User defined"
#> 
#> $form
#> [1] "scalar"
#> 
#> $default
#> [1] FALSE
#> 
#> attr(,"class")
#> [1] "solubility_spec" "osp_value_spec" 

# Table form (first column pH, second column value)
solubility(table = data.frame(pH = c(3, 6, 6.8), value = c(5000, 3000, 90)))
#> $value
#> NULL
#> 
#> $unit
#> [1] "mg/l"
#> 
#> $reference_pH
#> NULL
#> 
#> $gain_per_charge
#> NULL
#> 
#> $table
#>    pH value
#> 1 3.0  5000
#> 2 6.0  3000
#> 3 6.8    90
#> 
#> $name
#> [1] "User defined"
#> 
#> $form
#> [1] "table"
#> 
#> $default
#> [1] FALSE
#> 
#> attr(,"class")
#> [1] "solubility_spec" "osp_value_spec" 

# Several alternatives, the second marked as the default
create_compound(
  name = "Drug X",
  solubility = list(
    solubility(9999, name = "Aqueous"),
    solubility(200, name = "FaSSIF", default = TRUE)
  )
)
#> 
#> ── Compound: Drug X ────────────────────────────────────────────────────────────
#> 
#> ── Basic Properties ──
#> 
#> ── Physicochemical Properties ──
#> 
#> • Solubility:
#>   • Aqueous: 9999 mg/l [Unknown]
#>   • FaSSIF (Default): 200 mg/l [Unknown]