parameterize_schmitt: Parameters for Schmitt's (2008) Tissue Partition Coefficient...

In httk: High-Throughput Toxicokinetics

Parameters for Schmitt's (2008) Tissue Partition Coefficient Method

Description

This function provides the necessary parameters to run predict_partitioning_schmitt, excluding the data in table tissue.data. The model is based on the Schmitt (2008) method for predicting tissue:plasma partition coefficients as modified by Pearce et al. (2017). The modifications include approaches adapted from Peyret et al. (2010).

Usage

parameterize_schmitt(
  chem.cas = NULL,
  chem.name = NULL,
  dtxsid = NULL,
  parameters = NULL,
  species = "Human",
  default.to.human = FALSE,
  force.human.fup = FALSE,
  adjusted.Funbound.plasma = TRUE,
  suppress.messages = FALSE,
  class.exclude = TRUE,
  minimum.Funbound.plasma = 1e-04
)

Arguments

chem.cas	Chemical Abstract Services Registry Number (CAS-RN) – if parameters is not specified then the chemical must be identified by either CAS, name, or DTXISD
chem.name	Chemical name (spaces and capitalization ignored) – if parameters is not specified then the chemical must be identified by either CAS, name, or DTXISD
dtxsid	EPA's DSSTox Structure ID (https://comptox.epa.gov/dashboard) – if parameters is not specified then the chemical must be identified by either CAS, name, or DTXSIDs
parameters	Chemcial and physiological description parameters needed to run the Schmitt et al. (2008) model
species	Species desired (either "Rat", "Rabbit", "Dog", "Mouse", or default "Human").
default.to.human	Substitutes missing fraction of unbound plasma with human values if true.
force.human.fup	Returns human fraction of unbound plasma in calculation for rats if true. When species is specified as rabbit, dog, or mouse, the human unbound fraction is substituted.
adjusted.Funbound.plasma	Uses Pearce et al. (2017) lipid binding adjustment for Funbound.plasma (which impacts partition coefficients) when set to TRUE (Default).
suppress.messages	Whether or not the output message is suppressed.
class.exclude	Exclude chemical classes identified as outside of domain of applicability by relevant modelinfo_[MODEL] file (default TRUE).
minimum.Funbound.plasma	Monte Carlo draws less than this value are set equal to this value (default is 0.0001 – half the lowest measured Fup in our dataset).

Value

Funbound.plasma	Unbound fraction in plasma, adjusted for lipid binding according to Pearce et al. (2017)
unadjusted.Funbound.plasma	measured unbound fraction in plasma (0.005 if below limit of detection)
Pow	octanol:water partition coefficient (not log transformed)
pKa_Donor	compound H dissociation equilibrium constant(s)
pKa_Accept	compound H association equilibrium constant(s)
MA	phospholipid:water distribution coefficient, membrane affinity
Fprotein.plasma	protein fraction in plasma
plasma.pH	pH of the plasma

Author(s)

Robert Pearce and John Wambaugh

References

\insertRef

pearce2017httkhttk

\insertRef

schmitt2008generalhttk

\insertRef

schmitt2008corrigendumhttk

\insertRef

pearce2017evaluationhttk

\insertRef

peyret2010unifiedhttk

See Also

predict_partitioning_schmitt

tissue.data

calc_ma

apply_fup_adjustment

Examples

parameterize_schmitt(chem.name='bisphenola')

httk documentation built on Sept. 11, 2024, 9:32 p.m.