Search the Thermodynamic Database
Search for species by name or formula, retrieve their thermodynamic properties and parameters, and add proteins to the thermodynamic database.
1 2 3 4 5
character, names or formulas of species, or (for
character, physical states of the species
logical, check GHS and EOS parameters for self-consistency?
logical, check if a matching protein can be found?
numeric, index of species in the thermodynamic database
info is the primary function used for querying the thermodynamic database (
thermo$obigt). In common usage, it is called recursively; first with a character value (or values) for
species indicating the name(s) or formula(s) of the species of interest. The result of this call is a numeric value, which can be provided as an argument in a second call to
info in order to retrieve a data frame of the thermodynamic properties of the species. For its work,
info calls on the other functions that are described below, which unlike
info all expect arguments with length=1.
info.character searches for matches of the indicated
species to names, chemical formulas, and abbreviations (in the abbrv column) in the thermodynamic database. If the text of the
species is matched the index of that species is returned. If there are multiple matches for the
state is NULL, the index of first match is returned. The order of entries in
thermo$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. The two exceptions are species identified by O2 or oxygen (which without any indicated
state matches the gaseous species) and H2O (which matches the liquid species even if the indicated state is aq). Normally, if a species match can not be located, the function then looks for proteins with the name of
iprotein), computes its properties if found (
ip2aa) and adds this to the thermodynamic database (
check.protein prevents the processing of proteins and is provided to avoid an infinite loop in the interaction with
info.character has additional logic for dealing with proteins and with multiple matches for the cr state. If the
state is cr, matches will be counted for states entered as cr1, cr2 etc in the database, and all of the species indices will be returned. Note, however, that
info only ever returns a single species index, which becomes NA in the case of multiple matches to cr. This functionality of
info.character is used in
subcrt to handle minerals with phase transitions.
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.character 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.
info.approx searches the database for similar names or formulas using
agrep. If one or more of these is found, the results are summarized on the screen, and the indices of the approximately matching species are returned. Species that have no approximate matches are indicated by
NA in the return value. When invoked by
info, the latter function accepts the species index only for a single approximate match; multiple matches are translated to NA.
info.numeric returns the rows of
thermo$obigt indicated by
ispeices, after removing any order-of-magnitude scaling factors. If these species are all aqueous or are all not aqueous, the compounded column names used in
thermo$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
checkEOS (this depends on the completeness of the data entry).
thermo for the thermodynamic database (specifically,
check.obigt for checking self-consistency of individual entries in the database.
protein for gathering compositions and thermodynamic properties of proteins.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38
## summary of available data info() ## Not run: ## run a consistency check on each species in the database # (marked dontrun because it takes a while) info(check=TRUE) ## End(Not run) ## 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")