get_physchem_param: Get physico-chemical parameters from...

In httk: High-Throughput Toxicokinetics

Get physico-chemical parameters from chem.physical_and_invitro.data table

Description

This function retrieves physico-chemical properties ("param") for the chemical specified by chem.name or chem.cas from the table chem.physical_and_invitro.data. This function is distinguished from get_invitroPK_param in that there are no species-specific values. Physically meaningful values for ionization equilibria are NA/none (that is, no ionization), a single value, or a series of values separated by commas. If logMA (log10 membrane affinity) is NA, we use calc_ma() to predict it later on in the model parameterization functions.

Usage

get_physchem_param(param, chem.name = NULL, chem.cas = NULL, dtxsid = NULL)

Arguments

param	The desired parameters, a vector or single value.
chem.name	The chemical names that you want parameters for, a vector or single value
chem.cas	The chemical CAS numbers that you want parameters for, a vector or single value
dtxsid	EPA's 'DSSTox Structure ID (https://comptox.epa.gov/dashboard) the chemical must be identified by either CAS, name, or DTXSIDs

Details

Note that this function works with a local version of the chem.physical_and_invitro.data table to allow users to add/modify chemical data (for example, adding new data via add_chemtable or loading in silico predictions distributed with httk via load_sipes2017, load_pradeep2020, load_dawson2021, or load_honda2023).

User can request the following via argument param (case-insensitive):

Parameter	Description	Units
MW	Molecular weight	g/mole
pKa_Donor	Hydrogen donor ionization equilibria (acidic pKa)	pH
pKa_Accept	Hyrdogen acceptor ionization equilibria (basic pKa	pH
logMA	log10 Membrane Affinity	unitless
logP	log10 Octanol:Water Partition Coefficient (hydrophobicity)	unitless
logPwa	log10 Water:Air Partition Coefficient	unitless
logHenry	log10 Henry's Law Constant	atm-m3/mole
logWSol	log10 Water Solubility	moles/L: Water solubility at 25C
MP	Melting point	deg C

Value

The parameters, either a single value, a named list for a single chemical, or a list of lists

Author(s)

John Wambaugh and Robert Pearce

See Also

chem.physical_and_invitro.data

get_invitroPK_param

add_chemtable

Examples

get_physchem_param(param = 'logP', chem.cas = '80-05-7')
get_physchem_param(param = c('logP','MW'), chem.cas = c('80-05-7','81-81-2'))
# This function should be case-insensitive:
try(get_physchem_param(chem.cas="80-05-7","LogP"))
# Asking for a parameter we "don't" have produces an error:
try(get_physchem_param(chem.cas="80-05-7","MA"))
get_physchem_param(chem.cas="80-05-7","logMA")
# Ionization equilibria can be NA/none, a single value, or a series of values
# separated by commas:
get_physchem_param(chem.cas="80-05-7","pKa_Donor")
get_physchem_param(chem.cas="80-05-7","pKa_Accept")
get_physchem_param(chem.cas="71751-41-2","pKa_Donor")
get_physchem_param(chem.cas="71751-41-2","pKa_Accept")
# If logMA (log10 membrane affinity) is NA, we use calc_ma() to predict it
# in the parameterization functions:
get_physchem_param(chem.cas="71751-41-2","logMA")
parameterize_steadystate(chem.cas="71751-41-2")

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