dbparser (version 1.2.0)

drug_exp_prop: Drug Experimental Properties parser

Description

Drug properties that have been experimentally proven

Usage

drug_exp_prop(
  save_table = FALSE,
  save_csv = FALSE,
  csv_path = ".",
  override_csv = FALSE,
  database_connection = NULL
)

Value

a tibble with the following variables:

kind

Name of the property.

value

Drug properties that have been experimentally proven.

source

Reference to the source of this experimental data.

drugbank_id

drugbank id

The following experimental properties are provided:

Water Solubility

The experimentally determined aqueous solubility of the molecule.

Molecular Formula

Protein formula of Biotech drugs

Molecular Weight

Protein weight of Biotech drugs.

Melting Point

The experimentally determined temperature at which the drug molecule changes from solid to liquid at atmospheric temperature.

Boiling Point

The experimentally determined temperature at which the drug molecule changes from liquid to gas at atmospheric temperature.

Hydrophobicity

The ability of a molecule to repel water rather than absorb or dissolve water.

Isoelectric Point

The pH value at which the net electric charge of a molecule is zero.

caco2 Permeability

A continuous line of heterogenous human epithelial colorectal adenocarcinoma cells, CAC02 cells are employed as a model of human intestinal absorption of various drugs and compounds. CAC02 cell permeability is ultimately an assay to measure drug absorption.

pKa

The experimentally determined pka value of the molecule

logP

The experimentally determined partition coefficient (LogP) based on the ratio of solubility of the molecule in 1-octanol compared to water.

logS

The intrinsic solubility of a given compound is the concentration in equilibrium with its solid phase that dissolves into solution, given as the natural logarithm (LogS) of the concentration.

Radioactivity

The property to spontaneously emit particles (alpha, beta, neutron) or radiation (gamma, K capture), or both at the same time, from the decay of certain nuclides.

Arguments

save_table

boolean, save table in database if true.

save_csv

boolean, save csv version of parsed tibble if true

csv_path

location to save csv files into it, default is current location, save_csv must be true

override_csv

override existing csv, if any, in case it is true in the new parse operation

database_connection

DBI connection object that holds a connection to user defined database. If save_table is enabled without providing value for this function an error will be thrown.

read_drugbank_xml_db

read_drugbank_xml_db function must be called first before any parser.

If read_drugbank_xml_db is called before for any reason, so no need to call it again before calling this function.

See Also

Other drugs: drug_affected_organisms(), drug_ahfs_codes(), drug_atc_codes(), drug_calc_prop(), drug_categories(), drug_classification(), drug_dosages(), drug_ex_identity(), drug_external_links(), drug_food_interactions(), drug_general_information(), drug_groups(), drug_interactions(), drug_intern_brand(), drug_manufacturers(), drug_mixtures(), drug_packagers(), drug_patents(), drug_pdb_entries(), drug_pharmacology(), drug_prices(), drug_products(), drug_reactions_enzymes(), drug_reactions(), drug_salts(), drug_sequences(), drug_snp_adverse_reactions(), drug_snp_effects(), drug_syn()

Examples

if (FALSE) {
# the same parameters and usage will be applied for any parser
# return only the parsed tibble
run_all_parsers()

# will throw an error, as database_connection is NULL
run_all_parsers(save_table = TRUE)

# save in database in SQLite in memory database and return parsed tibble
sqlite_con <- DBI::dbConnect(RSQLite::SQLite())
run_all_parsers(save_table = TRUE, database_connection = sqlite_con)

# save parsed tibble as csv if it does not exist in current location,
# and return parsed tibble.
# if the csv exist before read it and return its data.
run_all_parsers(save_csv = TRUE)

# save in database, save parsed tibble as csv,
# if it does not exist in current location and return parsed tibble.
# if the csv exist before read it and return its data.
run_all_parsers(save_table = TRUE, save_csv = TRUE,
database_connection = sqlite_con)

# save parsed tibble as csv if it does not exist in given location,
# and return parsed tibble.
# if the csv exist before read it and return its data.
run_all_parsers(save_csv = TRUE, csv_path = TRUE)

# save parsed tibble as csv if it does not exist in current location and
# return parsed tibble.
# if the csv exist override it and return it.
run_all_parsers(save_csv = TRUE, csv_path = TRUE, override = TRUE)
}