data and inst/extdata directories of the packages; the former contains the data files used to build the thermo data object, while the latter contains other data files, mostly for used by the examples. The thermo object holds the thermodynamic database of properties of species, along with operational parameters for thermo object also holds intermediate data used in calculations, in particular the definitions of basis species and species of interest input by the user, and the properties of water so that subsequent calculations at the same temperature-pressure conditions can be accelerated.
The thermo object is a list composed of data.frames or lists each representing a class of data. The object is created upon loading the package (by calling data(thermo) from within the .First.lib function) from *.csv files in the data directory of the package. thermo is globally accessible; i.e., it is present in the user's environment. After loading ls() to verify that thermo is present, or type thermo to print the entire contents of the object on the screen. The various elements of the thermo object can be accessed using R's subsetting operators; for example, typing thermo$opt at the command line displays the current list of operational parameters (some of which can be altered using functions dedicated to this purpose; see e.g. nuts).
To make persistent additions or changes to the thermodynamic database of your installation, including compositions of proteins, first locate the installation directory of the package. This will be different depending on your operating system and type of Rinstallation, but is something like /usr/lib/R/library/CHNOSZ, /Volumes/Macintosh HD/Library/Frameworks/R.framework/resources/ library/CHNOSZ, C:\Program Files\R\R-2.10.0\library\CHNOSZ, or C:\Users\[User Name]\Documents\R \win-library\2.10\CHNOSZ on Linux, Mac and Windows (XP and Vista) systems, respectively. To find the exact location of this directory on your system, use the command system.file(package="CHNOSZ"). Inside the data directory of the installation directory of the package are the .csv files that can be edited with a spreadsheet program. Edit and save the OBIGT.csv and/or protein.csv files as desired. The next time you start an R session, the new data will be available.
NOTE: As of R-2.13.0 and CHNOSZ version 0.9-5, the instructions in the above paragraph no longer apply, partly because of the R CMD build, which compresses (using gzip) the files in the data directory. If custom thermodynamic data are to be used, one can load a custom thermodynamic data file using add.obigt.
Functions are available to interactively update the thermodynamic database or definitions of buffers (mod.obigt and mod.buffer, respectively; a function named change serves as a wrapper to both of these). Changes made using these functions, as well as any interactive definitions of basis species and species of interest, are lost when the current session is closed without saving or if the thermo object is reinitialized by the command data(thermo).
data(thermo)thermo object are documented below.
thermo$optList of operational parametersTr numeric Reference temperature (K)
Pr numeric Reference pressure (bar)
Theta numeric $\Theta$in the revised HKF equations of state (K)
Psi numeric $\Psi$in the revised HKF equations of state (bar)
cutoff numeric Cutoff below which values are taken to be zero (seemakeup)
E.units character The user's units of energy (cal(default) orJ)
T.units character The user's units of temperature (C(default) orK)
P.units character The user's units of pressure (bar(default) orMPa)
state character The default physical state for searching species (aqby default)
ionize logical Shouldaffinityperform ionization calculations for proteins?
water character Computational option for properties of water (SUPCRT(default) orIAPWS)
online logical Allow online searches of protein composition? Default (NA) is to ask the user.
thermo$element
Dataframe containing the thermodynamic properties of elements taken from Cox et al., 1989 and Wagman et al., 1982. The standard molal entropy ($S$(Z)) at 25 $^{\circ}$C and 1 bar for the element of charge (Z) was calculated from $S$(H2,g) + 2$S$(Z) = 2$S$(H+), where the standard molal entropies of H2,g and H+ were taken from Cox et al., 1989. The mass of Z is taken to be zero. Accessing this dataframe using element will select the first entry found for a given element; i.e., values from Wagman et al., 1982 will only be retrieved if the properties of the element are not found from Cox et al., 1989.
element character Symbol of element
state character Stable state of element at 25 $^{\circ}$C and 1 bar
source character Source of data
mass numeric Mass of element (in natural isotopic distribution;
referenced to a mass of 12 for $^{12}$C)
s numeric Entropy of the compound of the element in its stable
state at 25 $^{\circ}$C and 1 bar (cal K$^{-1}$ mol$^{-1}$)
n numeric Number of atoms of the element in its stable
compound at 25 $^{\circ}$C and 1 bar
}
thermo$obigt
This dataframe is a thermodynamic database of standard molal thermodynamic properties and equations of state parameters of species. OBIGT is an acronym for OrganoBioGeoTherm, which refers to a software package produced by Harold C. Helgeson and coworkers at the Laboratory of Theoretical Geochemistry and Biogeochemistry at the University of California, Berkeley. (There may be an additional meaning for the acronym:
As of OBIGT.csv represent 179 minerals, 16 gases, and 294 aqueous (largely inorganic) species taken from the data file included in the SUPCRT92 distribution (Johnson et al., 1992), an additional 14 minerals, 6 gases, and 1049 aqueous organic and inorganic species from the slop98.dat file (Shock et al., 1998), and approximately 50 other minerals, 175 crystalline organic and biochemical species, 220 organic gases, 300 organic liquids, 650 aqueous inorganic, organic, and biochemical species, and 40 organic groups taken from the recent literature. Each entry is referenced to one or two literature sources listed in thermo$source. Note the following additional modifications:
Z, see above). These modifications are indicated in OBIGT.csv by having CHNOSZ as one of the sources of data. Note also that some data appearing in the slop98.dat file were corrected or modified as noted in that file, and are indicated in OBIGT.csv by having SLOP98 as one of the sources of data.
In order to represent thermodynamic data for minerals with phase transitions, the different phases of these minerals are represented as phase species that have states denoted by cr1, cr2, etc. The standard molar thermodynamic properties at 25 $^{\circ}$C and 1 bar ($T_r$ and $P_r$) of the cr2 phase species of minerals were generated by first calculating those of the cr1 phase species at the transition temperature ($T_{tr}$) and 1 bar then taking account of the volume and entropy of transition (the latter can be retrieved by combining the former with the Clausius-Clapeyron equation and values of $(dP/dT)$ of transitions taken from the SUPCRT92 data file) to calculate the standard molar entropy of the cr2 phase species at $T_{tr}$, and taking account of the enthalpy of transition (${\Delta}H^{\circ}$, taken from the SUPCRT92 data file) to calculate the standard molar enthalpy of the cr2 phase species at $T_{tr}$. The standard molar properties of the cr2 phase species at $T_{tr}$ and 1 bar calculated in this manner were combined with the equations-of-state parameters of the species to generate values of the standard molar properties at 25 $^{\circ}$C and 1 bar. This process was repeated as necessary to generate the standard molar properties of phase species represented by cr3 and cr4, referencing at each iteration the previously calculated values of the standard molar properties of the lower-temperature phase species (i.e., cr2 and cr3). A consequence of tabulating the standard molar thermodynamic properties of the phase species is that the values of $(dP/dT)$ and ${\Delta}H^{\circ}$ of phase transitions can be calculated using the equations of state and therefore do not need to be stored in the thermodynamic database. However, the transition temperatures ($T_{tr}$) generally can not be assessed by comparing the Gibbs energies of phase species and are tabulated in the database.
The identification of species and their standard molal thermodynamic properties at 25 ${^\circ}$C and 1 bar are located in the first 12 columns of thermo$obigt:
name character Species name
abbrv character Species abbreviation
formula character Species formula
state character Physical state
source1 character Primary source
source2 character Secondary source
date character Date of data entry
G numeric Standard molal Gibbs energy of formation
from the elements (cal mol$^{-1}$)
H numeric Standard molal enthalpy of formation
from the elements (cal mol$^{-1}$)
S numeric Standard molal entropy (cal mol$^{-1}$ K$^{-1}$)
Cp numeric Standard molal isobaric heat capacity (cal mol$^{-1}$ K$^{-1}$)
V numeric Standard molal volume (cm$^3$ mol$^{-1}$)
}
The meanings of the remaining columns depend on the physical state of a particular species. If it is aqueous, the values in these columns represent parameters in the revised HKF equations of state (see hkf), otherwise they denote parameters in a general equation of state for crystalline, gas and liquid species (see cgl). The names of these columns are compounded from those of the parameters in each of the equations of state (for example, column 13 is named a1.a). Scaling of the values by orders of magnitude is adopted for some of the parameters, following common usage in the literature.
Columns 13-20 for aqueous species (parameters in the revised HKF equations of state):
a1 numeric $a_1\times10$ (cal mol$^{-1}$ bar$^{-1}$)
a2 numeric $a_2\times10^{-2}$ (cal mol$^{-1}$)
a3 numeric $a_3$ (cal K mol$^{-1}$ bar$^{-1}$)
a4 numeric $a_4\times10^{-4}$ (cal mol$^{-1}$ K)
c1 numeric $c_1$ (cal mol$^{-1}$ K$^{-1}$)
c2 numeric $c_2\times10^{-4}$ (cal mol$^{-1}$ K)
omega numeric $\omega\times10^{-5}$ (cal mol$^{-1}$)
Z numeric Charge
}
Columns 13-20 for crystalline, gas and liquid species ($Cp=a+bT+cT^{-2}+dT^{-0.5}+eT^2+fT^{\lambda}$).
a numeric $a$ (cal K$^{-1}$ mol$^{-1}$)
b numeric $b\times10^3$ (cal K$^{-2}$ mol$^{-1}$)
c numeric $c\times10^{-5}$ (cal K mol$^{-1}$)
d numeric $d$ (cal K$^{-0.5}$ mol$^{-1}$)
e numeric $e\times10^5$ (cal K$^{-3}$ mol$^{-1}$)
f numeric $f$ (cal K$^{-\lambda-1}$ mol$^{-1}$)
lambda numeric $\lambda$ (exponent on the $f$ term)
T numeric Temperature of phase transition or upper
temperature limit of validity of extrapolation (K)
}
thermo$source
Dataframe of references to sources of thermodynamic data. Source keys with a leading underscore indicate abbreviations for journals.
source character Source key
reference character Reference
}
thermo$buffer
Dataframe which contains definitions of buffers of chemical activity. Each named buffer can be composed of one or more species, which may include any species in the thermodynamic database and/or any protein. The calculations provided by buffer do not take into account phase transitions of minerals, so individual phase species of such minerals must be specified in the buffers.
name character Name of buffer
species character Name of species
state character Physical state of species
logact numeric Logarithm of activity (fugacity for gases)
}
thermo$protein
Dataframe of amino acid compositions of selected proteins. The majority of the compositions were taken from the SWISS-PROT online database (Boeckmann et al., 2003). N-terminal signal sequences were removed except for some cases where different isoforms of proteins have been identified (for example, MOD5.M and MOD5.N proteins of YEAST denote the mitochondrial and nuclear isoforms of this protein.)
protein character Identification of protein
organism character Identification of organism
source character Source of compositional data
abbrv character Abbreviation or other ID for protein
chains numeric Number of polypeptide chains in the protein
Ala...Tyr numeric Number of each amino acid in the protein
}
thermo$stress
Dataframe listing proteins identified in selected proteomic stress response experiments. The names of proteins begin at row 3, and columns are all the same length (padded as necessary at the bottom by NAs). Names correspond to ordered locus names (for SGD) or gene names (for ECO). The column names and first two rows give the following information:
colname character Name of the experiment
organism character Name of the organism (SGD or ECO)
source character Source of the data
}
thermo$groups
This is a dataframe with 22 columns for the amino acid sidechain, backbone and protein backbone groups ([Ala]..[Tyr],[AABB],[UPBB]) whose rows correspond to the elements C, H, N, O, S. It is used to quickly calculate the chemical formulas of proteins that are selected using the iprotein argument in affinity.
thermo$basis
Initially NULL, reserved for a dataframe written by basis upon definition of the basis species. The number of rows of this dataframe is equal to the number of columns in ... numeric One or more columns of stoichiometric
coefficients of elements in the basis species
ispecies numeric Rownumber of basis species in thermo$obigt
logact numeric Logarithm of activity or fugacity of basis species
state character Physical state of basis species
}
thermo$species
Initially NULL, reserved for a dataframe generated by species to define the species of interest. The number of columns in thermo$basis).
... numeric One or more columns of stoichiometric
coefficients of basis species in the species of interest
ispecies numeric Rownumber of species in thermo$obigt
logact numeric Logarithm of activity or fugacity of species
state character Physical state of species
name character Name of species
}
thermo$water
The properties calculated with water at multiple T, P points (minimum of 26) are stored here so that repeated calculations at the same conditions can be done more quickly.
thermo$Psat
The values of Psat calculated with water.SUPCRT at multiple T points (minimum of 26) are stored here.
thermo$water2
The properties calculated with water.SUPCRT at multiple T, P points (minimum of 26) are stored here.
thermo$SGD
Dataframe of amino acid composition of proteins from the Saccharomyces Genome Database.
Contains twenty-two columns. Values in the first column are the rownumbers, the second column (OLN) has the ordered locus names of proteins, and the remaining twenty columns (Ala..Val) contain the numbers of the respective amino acids in each protein; the columns are arranged in alphabetical order based on the three-letter abbreviations for the amino acids. The source of data for SGD.csv is the file protein_properties.tab found on the FTP site of the SGD project on 2008-08-04. Blank entries were replaced with "NA" and column headings were added.
thermo$ECO
Contains 24 columns. Values in the first column correspond to rownumbers, the second column {AC} holds the accession numbers of the proteins, the third column (Name) has the names of the corresponding genes, and the fourth column {OLN} lists the ordered locus names of the proteins. The remaining twenty columns (A..Y) give the numbers of the respective amino acids in each protein and are ordered alphabetically by the one-letter abbreviations of the amino acids. The sources of data for ECO.csv are the files ECOLI.dat
thermo$HUM
Downloaded the file uniprot_sprot_human.dat.gz, dated 2010-08-10, from seqret tool from EMBOSS (read.fasta. Columns are as described in thermo$protein, except column protein and abbrv contain Swiss-Prot name and accession number, respectively (both taken from the header lines in the FASTA file).
thermo$yeastgfp
Has 28 columns; the names of the first five are yORF, gene name, GFP tagged?, GFP visualized?, and abundance. The remaining columns correspond to the 23 subcellular localizations considered in the YeastGFP project (Huh et al., 2003 and Ghaemmaghami et al., 2003) and hold values of either T or F for each protein. yeastgfp.csv was downloaded on 2007-02-01 from http://yeastgfp.ucsf.edu using the Advanced Search, setting options to download the entire dataset and to include localization table and abundance, sorted by orf number.
The files in the inst/extdata directory are additional data files that support the examples in the package documentation and vignettes. One of the files (inst/extdata/OBIGT-2.csv) contains supplementary thermodynamic data in the same format as data/OBIGT.csv. Some entries taken from the SUPCRT92 or slop98.dat databases have been superseded, or duplicated, by more recent data that may be present in this file; see also the help for add.obigt.
Other files in this directory list measurements of thermodynamic properties:
PM90.csvHeat capacities of four unfolded aqueous proteins taken from Privalov and Makhatadze, 1990. Names of proteins are in the first column, temperature in$^{\circ}$C in the second, and heat capacities in J mol$^{-1}$K$^{-1}$in the third.RH95.csvHeat capacity data for iron taken from Robie and Hemingway, 1995. Temperature in Kelvin is in the first column, heat capacity in J K$^{-1}$mol$^{-1}$in the second.RT71.csvpH titration measurements for unfolded lysozyme (LYSC_CHICK) taken from Roxby and Tanford, 1971. pH is in the first column, net charge in the second.SOJSH.csvExperimental equilibrium constants for the reaction NaCl(aq) = Na+ + Cl- as a function of temperature and pressure taken from Fig. 1 of Shock et al., 1992. Data were extracted from the figure using g3data (Some of the additional files relate to processing metagenomic data and taxonomic classification:
bisonN_vs_refseq39.blast,bisonR_vs_refseq39.blast,bisonP_vs_refseq39.blastare tabular BLAST results for proteins in the Bison Pool Environmental Genome. The BLAST files contain the first hit for each of 2500 query sequences. The target database for the searches was constructed from microbial protein sequences in National Center for Biotechnology Information (NCBI) RefSeq database version 39.extdata/gi.taxid.txtis a table that lists all of the sequence identifiers (gi numbers) that appear in the example BLAST files (for bisonN, bisonR, bisonP, see above), together with the corresponding taxon ids used in the NCBI databases.names.dmpandnodes.dmpare excerpted from the taxonomy files available on the NCBI ftp site (taxid.phylum.csvlists all of the taxon ids and the corresponding phylum and species names from the NCBI taxonomy files.The remaining files contain either protein sequences, amino acid compositions of proteins, or protein abundance data:
HTCC1062.faais a FASTA file of 1354 protein sequences in the organismPelagibacter ubiqueHTCC1062 downloaded from the NCBI RefSeq collection on 2009-04-12. The search term was Protein: txid335992[Organism:noexp] AND "refseq"[Filter].AA03.csvhas reference abundances for 71 proteins taken from Fig. 3 of Anderson and Anderson, 2002 (as corrected in Anderson and Anderson, 2003). The columns with data taken from this source are type (hemoglobin, plasma, tissue, interleukin), description (name used in the original figure), log10(pg/ml) (upper limit of abundance interval shown in figure, log10 concentration in pg/ml). The additional columns are name (nominal SWISS-PROT code for this protein) and corresponding values of protein length (number of residues), protein mass (g/mol), logm(residue) (log10 of molality of residues) and residue mass (g/mol).ISR+08.csvhas columns excerpted from Additional File 2 of Ishihama et al., 2008. The columns in this file are ID (Swiss-Prot ID), accession (Swiss-Prot accession), emPAI (exponentially modified protein abundance index), copynumber (emPAI-derived copy number/cell), GRAVY (Kyte-Doolittel), FunCat (FunCat class description), PSORT (PSORT localisation), ribosomal (yes/no).
%% \item \code{GLL+98.csv} has columns "oln" for ordered locus name and "ratio" for change in expression of yeast proteins in response to H2O2 treatment, from Godon et al., 1998. One protein, YMR108W, was listed as both induced and repressed in the original data set and is not included in this table.protein_refseq.csvcontains the average amino acid compositions of all protein sequences for each organism identified by taxonomic ID in the NCBI Reference Sequence (RefSeq) database, version 45. The file was generated using code provided in therefseqdirectory of the CHNOSZ installation directory.}
add.protein and add.obigt for adding amino acid compositions of proteins and thermodynamic data from local .csv files.
## make a table of duplicated species name <- thermo$obigt$name state <- thermo$obigt$state source <- thermo$obigt$source1 species <- paste(name,state) dups <- species[which(duplicated(species))] id <- numeric() for(i in 1:length(dups)) id <- c(id,which(species %in% dups[i])) data.frame(name=name[id],state=state[id],source=source[id])
Anderson, N. L. and Anderson, N. G., 2002. The human plasma proteome: History, character and diagnostic prospects. Molecular and Cellular Proteomics, 1, 845-867.
Anderson, N. L. and Anderson, N. G., 2003. The human plasma proteome: History, character and diagnostic prospects (Vol. 1 (2002) 845-867). Molecular and Cellular Proteomics, 2, 50.
Cox, J. D., Wagman, D. D. and Medvedev, V. A., eds., 1989. CODATA Key Values for Thermodynamics. Hemisphere Publishing Corporation, New York, 271 p.
Dick, J. M., LaRowe, D. E. and Helgeson, H. C., 2006. Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins. Biogeosciences, 3, 311-336.
Gattiker, A., Michoud, K., Rivoire, C., Auchincloss, A. H., Coudert, E., Lima, T., Kersey, P., Pagni, M., Sigrist, C. J. A., Lachaize, C., Veuthey, A.-L., Gasteiger, E. and Bairoch, A., 2003. Automatic annotation of microbial proteomes in Swiss-Prot. Comput. Biol. Chem., 27, 49-58.
Ghaemmaghami, S., Huh, W., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K. and Weissman, J. S., 2003. Global analysis of protein expression in yeast. Nature, 425, 737-741.
HAMAP system. HAMAP FTP directory,
Huh, W. K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S. and O'Shea, E. K., 2003. Global analysis of protein localization in budding yeast. Nature, 425, 686-691.
Ishihama, Y., Schmidt, T., Rappsilber, J., Mann, M., Hartl, F. U., Kerner, M. J. and Frishman, D. Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics, 2008, 9.
Johnson, J. W., Oelkers, E. H. and Helgeson, H. C., 1992. SUPCRT92: A software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000$^{\circ}$C. Comp. Geosci., 18, 899-947.
Joint Genome Institute, 2007. Bison Pool Environmental Genome. Protein sequence files downloaded from IMG/M (
Privalov, P. L. and Makhatadze, G. I., 1990. Heat capacity of proteins. II. Partial molar heat capacity of the unfolded polypeptide chain of proteins: Protein unfolding effects. J. Mol. Biol., 213, 385-391.
Robie, R. A. and Hemingway, B. S., 1995. Thermodynamic Properties of Minerals and Related Substances at 298.15 K and 1 Bar ($10^5$ Pascals) Pressure and at Higher Temperatures. U. S. Geol. Surv., Bull. 2131, 461 p.
Roxby, R. and Tanford, C., 1971. Hydrogen ion titration curve of lysozyme in 6 M guanidine hydrochloride. Biochemistry, 10, 3348-3352.
SGD project. Saccharomyces Genome Database,
Shock, E. L. and Koretsky, C. M., 1995. Metal-organic complexes in geochemical processes: Estimation of standard partial molal thermodynamic properties of aqueous complexes between metal cations and monovalent organic acid ligands at high pressures and temperatures. Geochim. Cosmochim. Acta, 59, 1497-1532.
Shock, E. L., Oelkers, E. H., Johnson, J. W., Sverjensky, D. A. and Helgeson, H. C., 1992. Calculation of the thermodynamic properties of aqueous species at high pressures and temperatures: Effective electrostatic radii, dissociation constants and standard partial molal properties to 1000 $^{\circ}$C and 5 kbar. J. Chem. Soc. Faraday Trans., 88, 803-826.
Shock, E. L. et al., 1998. slop98.dat (computer data file).
Wagman, D. D., Evans, W. H., Parker, V. B., Schumm, R. H., Halow, I., Bailey, S. M., Churney, K. L. and Nuttall, R. L., 1982. The NBS tables of chemical thermodynamic properties. Selected values for inorganic and C$_1$ and C$_2$ organic substances in SI units. J. Phys. Chem. Ref. Data, 11 (supp. 2), 1-392.
YeastGFP project. Yeast GFP Fusion Localization Database, http://yeastgfp.ucsf.edu, accessed on 2007-02-01. Current location: