Compound class for OSP snapshot compounds — Compound • osp.snapshots

An R6 class that represents a compound in an OSP snapshot. This class provides methods to access different properties of a compound and display a summary of its information.

Compound processes are exposed via $processes, a flat named list of Process objects. The per-category tibble accessors ($protein_binding_partners, $metabolizing_enzymes, $hepatic_clearance, $transporter_proteins, $renal_clearance, $biliary_clearance, $inhibition, $induction) are lifecycle::deprecate_soft()-warned in favour of $processes and the long-form processes tibble returned by get_compounds_dfs().

Active bindings

data: The raw data of the compound (read-only). Refreshed from the embedded CalculationMethods and the cached Process objects so that mutations flow back to the export payload.
name: The name of the compound. Writable: must be a non-empty scalar string.
is_small_molecule: Whether the compound is a small molecule. Writable: a single logical value, or NULL to leave it unset (PK-Sim then defaults to TRUE).
plasma_protein_binding_partner: The plasma protein binding partner of the compound. Writable: one of "Unknown", "Albumin", "Glycoprotein", or NULL to clear.
molecular_weight: The molecular weight of the compound
molecular_weight_unit: The unit of the molecular weight
lipophilicity: The lipophilicity data of the compound. Writable: assign 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), a raw alternative list to set the array verbatim (the escape hatch for species-specific alternatives), or NULL to clear the property. A bare numeric scalar is rejected; use lipophilicity() instead.
fraction_unbound: The fraction unbound data of the compound. Writable: assign 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), a raw alternative list to set the array verbatim, or NULL to clear the property. A bare numeric scalar is rejected; use fraction_unbound() instead.
solubility: The solubility data of the compound. Writable: assign a solubility() object to express reference pH, gain per charge, or a pH/value table, 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), a raw alternative list to set the array verbatim, or NULL to clear the property. A bare numeric scalar is rejected; use solubility() instead.
intestinal_permeability: The intestinal permeability data of the compound. Writable: assign 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), a raw alternative list to set the array verbatim, or NULL to clear the property. A bare numeric scalar is rejected; use intestinal_permeability() instead.
permeability: The permeability data of the compound. Writable: assign 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), a raw alternative list to set the array verbatim, or NULL to clear the property. A bare numeric scalar is rejected; use permeability() instead.
pka_types: The pKa types of the compound. Writable: assign a list of list(type =, value =) entries (the create_compound() pKa shape, converted to list(Type =, Pka =)), a raw PkaType[] list (entries carrying Type/Pka, set verbatim), or NULL / list() to clear the pKa types.
processes: A flat named list of Process objects, one per entry in the compound's Processes array. Duplicate names are disambiguated with a numeric suffix (_1, _2, ...). The list is built once at construction so that state changes made on a Process persist across accesses. Writable: assign a list of Process objects and/or raw process lists to rebuild the processes (duplicate names are disambiguated as at construction), or NULL / list() to clear them.
calculation_methods: A CalculationMethods object holding the compound's calculation methods.
parameters: The additional parameters of the compound (excluding molecular weight)
protein_binding_partners: Deprecated. Filter get_compounds_dfs()$processes on category == "protein_binding_partners", or iterate self$processes and check process$category.
metabolizing_enzymes: Deprecated. See $protein_binding_partners.
hepatic_clearance: Deprecated. See $protein_binding_partners.
transporter_proteins: Deprecated. See $protein_binding_partners.
renal_clearance: Deprecated. See $protein_binding_partners.
biliary_clearance: Deprecated. See $protein_binding_partners.
inhibition: Deprecated. See $protein_binding_partners.
induction: Deprecated. See $protein_binding_partners.

Methods

`Compound$new()`

Create a new Compound object

Usage

Compound$new(data)

Arguments

data: Raw compound data from a snapshot

Returns

A new Compound object

`Compound$print()`

Print a summary of the compound including its properties and parameters.

Usage

Compound$print(...)

Arguments

...: Additional arguments passed to print methods

Returns

Invisibly returns the Compound object for method chaining

`Compound$to_df()`

Convert this compound's physicochemical properties and process parameters to a single long-form tibble (legacy shape).

Used by get_compounds_dfs() to assemble the compound-wide properties tibble. The process-derived rows produced here are lifecycle::deprecate_soft()-warned at the get_compounds_dfs() entry point; prefer the long-form processes tibble returned alongside.

Usage

Compound$to_df()

Returns

A tibble with columns compound, category, type, parameter, value, unit, data_source, source.

`Compound$clone()`

The objects of this class are cloneable with this method.

Usage

Compound$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.