CHNOSZ (version 1.1.0)

info: Search the Thermodynamic Database

Description

Search for species by name or formula, retrieve their thermodynamic properties and parameters, and add proteins to the thermodynamic database.

Usage

info(species = NULL, state = NULL, check.it=TRUE)

Arguments

species

character, names or formulas of species, or (for info only) numeric with same meaning as ispecies

state

character, physical states of the species

check.it

logical, check GHS and EOS parameters for self-consistency?

Details

info is the primary function used for querying the thermodynamic database (thermo$obigt). It is often called recursively; first with a character value (or values) for species indicating the name(s) or formula(s) of the species of interest. The result of this call is a numeric value, which can be provided as an argument in a second call to info in order to retrieve a data frame of the thermodynamic properties of the species.

The searches of the indicated species are made among the names, chemical formulas, and abbreviations (in the abbrv column) in the thermodynamic database. If the text of the species is matched the index of that species is returned. If there are multiple matches for the species, and state is NULL, the index of first match is returned. The order of entries in thermo$obigt is grouped by states in the order aq, cr, gas, liq, so for species in both aqueous and gaseous states the index of the aqueous species is returned, unless state is set to gas.

Names of species including an underscore character are indicative of proteins, e.g. LYSC_CHICK. If the name of a protein is provided to info and the composition of the protein can be found using protein, the thermodyamic properties and parameters of the nonionized protein (calculated using amino acid group additivity) are added to the thermodynamic database. Included in the return value, as for other species, is the index of the protein in the thermodynamic database or NA if the protein is not found. Names of proteins and other species can be mixed.

If no exact matches are found, info searches the database for similar names or formulas using agrep. If any of these are found, the results are summarized on the screen, but the function always returns NA in this case.

With a numeric argument, the rows of thermo$obigt indicated by ispecies are returned, after removing any order-of-magnitude scaling factors. If these species are all aqueous or are all not aqueous, the compounded column names used in thermo$obigt are replaced with names appropriate for the corresponding equations of state. A missing value of one of the standard molal Gibbs energy (G) or enthalpy (H) of formation from the elements or entropy (S) is calculated from the other two, if available. If check.it is TRUE, several checks of self consistency among the thermodynamic properties and parameters are performed using checkGHS and checkEOS.

See Also

thermo, check.obigt

Examples

# NOT RUN {
## summary of available data
info()

## species information
# search for something named (or whose formula is) "Fe"
si <- info("Fe")
# use the number to get the full record
info(si)
# it is possible to get a range of records
info(si:(si+3))

## dealing with states
# default order of preference for names: aq > gas > cr,liq
info(c("methane","ethanol","glycinate"))  # aq, aq, aq
info(c("adenosine","alanine","hydroxyapatite"))  # aq, aq, cr
# state argument overrides the default
info(c("ethanol","adenosine"),state=c("gas","cr"))
# formulas default to aqueous species, if available
info(c("CH4","CO2","CS2","MgO"))  # aq, aq, gas, cr
# state argument overrides the default
info(c("CH4","CO2","MgO"),"gas")  # gas, gas, NA
# exceptions to the aqueous default is O2
info("O2")  # gas

## partial name or formula searches
info("ATP")
info("thiol")
info("MgC")
# add an extra character to refine a search
# or to search using terms that have exact matches
info("MgC ")
info("acetate ")
info(" H2O")
# }