From noreply at r-forge.r-project.org Thu Jan 9 13:25:41 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 9 Jan 2014 13:25:41 +0100 (CET) Subject: [CHNOSZ-commits] r60 - in pkg/CHNOSZ: . R inst man Message-ID: <20140109122541.82721186894@r-forge.r-project.org> Author: jedick Date: 2014-01-09 13:25:40 +0100 (Thu, 09 Jan 2014) New Revision: 60 Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/R/revisit.R pkg/CHNOSZ/inst/NEWS pkg/CHNOSZ/man/revisit.Rd Log: revisit() gains loga0 argument for calculating activity ratios Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2013-12-14 23:56:57 UTC (rev 59) +++ pkg/CHNOSZ/DESCRIPTION 2014-01-09 12:25:40 UTC (rev 60) @@ -1,6 +1,6 @@ Date: 2013-12-15 Package: CHNOSZ -Version: 1.0.2-1 +Version: 1.0.2-2 Title: Chemical Thermodynamics and Activity Diagrams Author: Jeffrey M. Dick Maintainer: Jeffrey Dick Modified: pkg/CHNOSZ/R/revisit.R =================================================================== --- pkg/CHNOSZ/R/revisit.R 2013-12-14 23:56:57 UTC (rev 59) +++ pkg/CHNOSZ/R/revisit.R 2014-01-09 12:25:40 UTC (rev 60) @@ -47,7 +47,7 @@ return(list(x=x, y=y)) } -revisit <- function(eout, objective = "CV", loga2 = NULL, ispecies = NULL, +revisit <- function(eout, objective = "CV", loga2 = NULL, loga0 = NULL, ispecies = NULL, col = par("fg"), yline = 2, ylim = NULL, cex = par("cex"), lwd = par("lwd"), mar = NULL, side = 1:4, xlim = NULL, labcex = 0.6, pch = 1, main = NULL, plot.it = NULL, add = FALSE, plot.optval = TRUE, @@ -100,13 +100,19 @@ if(nd==0) loga1 <- t(loga1) # convert infinite values to NA loga1[is.infinite(loga1)] <- NA + # if we have loga0, calculate the base-2 log ratio (loga1/loga0) + base <- 10 + if(!is.null(loga0)) { + loga1 <- t(t(loga1) - loga0) * log2(10) + base <- 2 + } # remove logarithms if necessary if(any(grepl("loga1", objargs))) a1 <- loga1 - else a1 <- 10^loga1 + else a1 <- base^loga1 } # these objectives also depend on reference activities (a2/loga2): - # richness, RMSD, CVRMSD, spearman, pearson, DGtr + # RMSD, CVRMSD, spearman, pearson, DGtr if(any(grepl("a2", objargs))) { # check that all needed arguments are present if(is.null(loga2)) stop(paste("loga2 must be supplied for", objective)) @@ -117,9 +123,10 @@ length(loga2), ") than list in eout (", ncol(loga1), ")", sep="")) # remove logarithms if necessary if(any(grepl("loga2", objargs))) a2 <- loga2 - else a2 <- 10^loga2 + else a2 <- base^loga2 } + # construct array of values: Astar (for DGtr) if(any(grepl("Astar", objargs))) { Astar <- eout$Astar[ispecies] Modified: pkg/CHNOSZ/inst/NEWS =================================================================== --- pkg/CHNOSZ/inst/NEWS 2013-12-14 23:56:57 UTC (rev 59) +++ pkg/CHNOSZ/inst/NEWS 2014-01-09 12:25:40 UTC (rev 60) @@ -1,4 +1,4 @@ -CHANGES IN CHNOSZ 1.0.2-1 (2013-12-15) +CHANGES IN CHNOSZ 1.0.2-2 (2013-12-17) -------------------------------------- - Updated extdata/protein/Sce.csv.xz using Saccharomyces Genome Database @@ -27,7 +27,10 @@ - In revisit(), extend ranges of axes of scatter plots. +- revisit() has new argument loga0, a single vector of base-10 logarithms of + species activities used to calculate the base-2 log ratio ( log2(a1/a0) ). + CHANGES IN CHNOSZ 1.0.1 (2013-07-04) ------------------------------------ Modified: pkg/CHNOSZ/man/revisit.Rd =================================================================== --- pkg/CHNOSZ/man/revisit.Rd 2013-12-14 23:56:57 UTC (rev 59) +++ pkg/CHNOSZ/man/revisit.Rd 2014-01-09 12:25:40 UTC (rev 60) @@ -10,11 +10,11 @@ } \usage{ - revisit(eout, objective = "CV", loga2 = NULL, ispecies = NULL, - col = par("fg"), yline = 2, ylim = NULL, cex = par("cex"), - lwd = par("lwd"), mar = NULL, side = 1:4, xlim = NULL, labcex = 0.6, - pch = 1, main = NULL, plot.it = NULL, add = FALSE, plot.optval = TRUE, - style.2D = "contour") + revisit(eout, objective = "CV", loga2 = NULL, loga0 = NULL, + ispecies = NULL, col = par("fg"), yline = 2, ylim = NULL, + cex = par("cex"), lwd = par("lwd"), mar = NULL, side = 1:4, + xlim = NULL, labcex = 0.6, pch = 1, main = NULL, plot.it = NULL, + add = FALSE, plot.optval = TRUE, style.2D = "contour") optimal.index(z, objective) extremes(z, objective) } @@ -22,7 +22,8 @@ \arguments{ \item{eout}{list, output from \code{\link{equilibrate}}, containing logarithms of activities of species} \item{objective}{character, name of \code{\link{objective}} function} - \item{loga2}{numeric array, reference values of logarithm of activities} + \item{loga2}{numeric vector, reference values of logarithm of activities} + \item{loga0}{numeric vector, logarithm of activities to calculate activity ratios} \item{ispecies}{numeric, which species to consider} \item{col}{character, color to use for points or lines} \item{yline}{numeric, margin line for y-axis label} @@ -44,13 +45,16 @@ \details{ -Most commonly, the output of \code{\link{equilibrate}} is used as the value for \code{eout}. +\code{revisit} is used to calculate the variation in the equilibrium logarithms of chemical activity (supplied in \code{eout}) or to compare the calculated values with reference (e.g. measured) values (\code{loga2}). +Usually, the output of \code{\link{equilibrate}} is used as the value for \code{eout}. The type of calculation is indicated by \code{objective}, giving the name of an \code{\link{objective}} function. -The list of logarithms of chemical activities in \code{eout$loga.equil} is passed as \code{loga1} to the objective function. -If the objective function has an argument \code{a1} instead of \code{loga1}, the activities instead of their logarithms are passed. -Reference logarithms of activities, for those objective functions that require them, are supplied in the \code{loga2} argument. +Generally, \code{loga2} is expressed in base-10 logarithms. +However, if \code{loga0} (base 10) is supplied, it is used to calculate the base-2 log ratio (log2(a1/a0)); these calculated values are then compared with values in \code{loga2} interpreted as base-2 logarithms. + +Internally, the list of logarithms of chemical activities in \code{eout$loga.equil} is passed as \code{loga1} to the objective function. +If the objective function has an argument \code{a1} instead of \code{loga1}, the activities instead of their logarithms are passed to the function. Generally, \code{loga2} must be a numeric vector with length equal to that of \code{loga1} (i.e., number of species). -If a single numeric value is supplied for \code{loga2}, it is recycled to the length of \code{loga1}. +However, if a single numeric value is supplied for \code{loga2}, it is recycled to the length of \code{loga1}. For calculations at a single condition (0-D, no variation), with the \samp{qqr} objective, a quantile-quantile plot (\code{\link{qqnorm}}) is shown. For \samp{rmsd} and other objective functions having reference values (\code{loga2}), a scatter plot is shown with a smooth line calculated using \code{\link{loess.smooth}}. @@ -162,7 +166,7 @@ w <- "ribosomal" # locate entries whose names contain w j <- grep.file(f, w) -# get the amino acid compositions of these protein +# get the amino acid compositions of these proteins aa <- read.fasta(f, j) # add these proteins to CHNOSZ's inventory ip <- add.protein(aa) From noreply at r-forge.r-project.org Sat Jan 11 05:28:51 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 11 Jan 2014 05:28:51 +0100 (CET) Subject: [CHNOSZ-commits] r61 - in pkg/CHNOSZ: . R inst inst/tests man Message-ID: <20140111042851.3120E18698E@r-forge.r-project.org> Author: jedick Date: 2014-01-11 05:28:50 +0100 (Sat, 11 Jan 2014) New Revision: 61 Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/NAMESPACE pkg/CHNOSZ/R/util.affinity.R pkg/CHNOSZ/inst/NEWS pkg/CHNOSZ/inst/tests/test-ionize.aa.R pkg/CHNOSZ/inst/tests/test-thermo.R pkg/CHNOSZ/man/CHNOSZ-package.Rd Log: update tests for development version of testthat Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2014-01-09 12:25:40 UTC (rev 60) +++ pkg/CHNOSZ/DESCRIPTION 2014-01-11 04:28:50 UTC (rev 61) @@ -1,10 +1,10 @@ -Date: 2013-12-15 +Date: 2014-01-11 Package: CHNOSZ -Version: 1.0.2-2 +Version: 1.0.2-3 Title: Chemical Thermodynamics and Activity Diagrams -Author: Jeffrey M. Dick +Author: Jeffrey Dick Maintainer: Jeffrey Dick -Depends: R (>= 2.12.0), utils +Depends: R (>= 2.12.0) Suggests: limSolve, parallel, testthat Description: This package includes functions and data sets to support chemical thermodynamic modeling in biochemistry and low-temperature geochemistry. The features include calculation Modified: pkg/CHNOSZ/NAMESPACE =================================================================== --- pkg/CHNOSZ/NAMESPACE 2014-01-09 12:25:40 UTC (rev 60) +++ pkg/CHNOSZ/NAMESPACE 2014-01-11 04:28:50 UTC (rev 61) @@ -1,13 +1,5 @@ -# modified from -# Default NAMESPACE created by R - # Export all names exportPattern(".") -# Import all packages listed as Imports or Depends -import( - utils -) - # Load shared objects useDynLib(CHNOSZ) Modified: pkg/CHNOSZ/R/util.affinity.R =================================================================== --- pkg/CHNOSZ/R/util.affinity.R 2014-01-09 12:25:40 UTC (rev 60) +++ pkg/CHNOSZ/R/util.affinity.R 2014-01-11 04:28:50 UTC (rev 61) @@ -389,7 +389,9 @@ # make a grid of all combinations # put T, P, pH in same order as they show up vars egargs <- list(T=T, P=P, pH=pH) - TPpHorder <- order(c(iT, iP, iHplus)) + # order(c(NA, NA, NA)) might segfault in some versions of R (seen in R 2.15.3 on Linux) + if(is.na(iT) & is.na(iP) & is.na(iHplus)) TPpHorder <- c(1, 2, 3) + else TPpHorder <- order(c(iT, iP, iHplus)) egargs <- c(egargs[TPpHorder], list(stringsAsFactors=FALSE)) TPpH <- do.call(expand.grid, egargs) # figure out the dimensions of T-P-pH (making sure to drop any that aren't in vars) Modified: pkg/CHNOSZ/inst/NEWS =================================================================== --- pkg/CHNOSZ/inst/NEWS 2014-01-09 12:25:40 UTC (rev 60) +++ pkg/CHNOSZ/inst/NEWS 2014-01-11 04:28:50 UTC (rev 61) @@ -1,35 +1,40 @@ -CHANGES IN CHNOSZ 1.0.2-2 (2013-12-17) +CHANGES IN CHNOSZ 1.0.2-3 (2014-01-11) -------------------------------------- -- Updated extdata/protein/Sce.csv.xz using Saccharomyces Genome Database - protein_properties.tab and SGD_features.tab dated 2013-08-24. +- Updated extdata/protein/Sce.csv.xz using Saccharomyces Genome + Database protein_properties.tab and SGD_features.tab dated + 2013-08-24. - more.aa() includes SGDID and gene name in the abbrv and ref columns. - In extdata/refseq, scripts and data files were updated for NCBI - Reference Sequence (RefSeq) release 61 (2013-09-09). Code was adapted - to deal with WP multispecies accessions. + Reference Sequence (RefSeq) release 61 (2013-09-09). Code was + adapted to deal with WP multispecies accessions. - read.fasta() gets new argument 'id'; when supplied, it skips reading the protein names from the FASTA headers. -- When reading protein names from the FASTA headers, read.fasta() stops - only at the first space, not space or underscore as before. +- When reading protein names from the FASTA headers, read.fasta() + stops only at the first space, not space or underscore as before. - info() no longer specially sets state of "O2" or "oxygen" to gas. -- In thermo$obigt, names of gases (e.g. "oxygen") are used only for the - gaseous species; names were removed from dissolved species in rows - 63-79. Both gases and aqueous species can continue to be referenced by - their chemical formula. +- In thermo$obigt, names of gases (e.g. "oxygen") are used only for + the gaseous species; names were removed from dissolved species in + rows 63-79. Both gases and aqueous species can continue to be + referenced by their chemical formulas. - In read.expr(), allow multiple filter specifications. - In revisit(), extend ranges of axes of scatter plots. -- revisit() has new argument loga0, a single vector of base-10 logarithms of - species activities used to calculate the base-2 log ratio ( log2(a1/a0) ). +- revisit() has new argument loga0, a single vector of base-10 + logarithms of activities of species used to calculate the base-2 log + ratio ( log2(a1/a0) ). +- Updated tests to be compatible with testthat version 0.8. Some tests + now check for e.g. errors *and* warnings produced by a single + function call. CHANGES IN CHNOSZ 1.0.1 (2013-07-04) ------------------------------------ Modified: pkg/CHNOSZ/inst/tests/test-ionize.aa.R =================================================================== --- pkg/CHNOSZ/inst/tests/test-ionize.aa.R 2014-01-09 12:25:40 UTC (rev 60) +++ pkg/CHNOSZ/inst/tests/test-ionize.aa.R 2014-01-11 04:28:50 UTC (rev 61) @@ -1,7 +1,8 @@ context("ionize.aa") test_that("handling of repeated T, P, pH values is correct", { - expect_message(ionize.aa(T=c(25, 25, 100, 100, 100), P=c(100, 1000, 1000, 1000, 1000)), "18 species at 3 values of T and P \\(wet\\)") + expect_message(expect_error(ionize.aa(T=c(25, 25, 100, 100, 100), P=c(100, 1000, 1000, 1000, 1000))), + "18 species at 3 values of T and P \\(wet\\)") expect_message(ia.25x10 <- ionize.aa(T=rep(25,10), ret.val="pK"), "18 species at 298.15 K and 1 bar \\(wet\\)") # we have ten rows of the same values expect_identical(ia.25x10[1, ], apply(ia.25x10, 2, unique)) Modified: pkg/CHNOSZ/inst/tests/test-thermo.R =================================================================== --- pkg/CHNOSZ/inst/tests/test-thermo.R 2014-01-09 12:25:40 UTC (rev 60) +++ pkg/CHNOSZ/inst/tests/test-thermo.R 2014-01-11 04:28:50 UTC (rev 61) @@ -26,7 +26,8 @@ # we need at least a name and some property expect_error(mod.obigt("test"), "species name and a property") # a valid formula is needed - expect_warning(mod.obigt("test", date=today()), "please supply a valid chemical formula") + expect_warning(expect_error(mod.obigt("test", date=today()), "is not a simple chemical formula"), + "please supply a valid chemical formula") # the default state is aq expect_message(itest <- mod.obigt("test", formula="Z0", date=today()), "added test\\(aq\\)") # we should get NA values of G for a species with NA properties Modified: pkg/CHNOSZ/man/CHNOSZ-package.Rd =================================================================== --- pkg/CHNOSZ/man/CHNOSZ-package.Rd 2014-01-09 12:25:40 UTC (rev 60) +++ pkg/CHNOSZ/man/CHNOSZ-package.Rd 2014-01-11 04:28:50 UTC (rev 61) @@ -56,11 +56,11 @@ \section{Compatibility}{ - The recommended version of \R is 2.14.0 or greater (to find vignettes in the \code{vignettes} directory). - The package depends on \R version 2.12.0 or greater (so useDynLib in the NAMESPACE can find the shared library on Windows). - Before version 0.9-9 of the package, the dependency was given as \R version 2.10.0 or greater (to read compressed data files). + The recommended version of \R is 2.14.0 or greater (to find vignettes in the \code{vignettes} directory, and for availability of \pkg{parallel} in the standard library). + As of version 0.9-9, the package depends on \R version 2.12.0 or greater (so useDynLib in the NAMESPACE can find the shared library on Windows). + Starting with version 0.9-6 of the package, the dependency was given as \R version 2.10.0 or greater (to read compressed data files). Before version 0.9-6 of the package, the dependency was given as \R version 2.7.0 or greater (major update of the X11 device in 2.7.0). - However, without accessing the compressed data files in \code{extdata} it should be possible to run CHNOSZ on Unix-alikes under \R versions 2.4.0 or greater (availability of the \samp{stringsAsFactors} argument of \code{\link{data.frame}}). + Without accessing the compressed data files in \code{extdata} it should be possible to run CHNOSZ on Unix-alikes under \R versions 2.4.0 or greater (availability of the \samp{stringsAsFactors} argument of \code{\link{data.frame}}). } \section{Acknowledgements}{ From noreply at r-forge.r-project.org Sun Jan 12 16:17:44 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sun, 12 Jan 2014 16:17:44 +0100 (CET) Subject: [CHNOSZ-commits] r62 - in pkg/CHNOSZ: . inst man vignettes Message-ID: <20140112151744.9AE8B18670E@r-forge.r-project.org> Author: jedick Date: 2014-01-12 16:17:43 +0100 (Sun, 12 Jan 2014) New Revision: 62 Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/inst/CHECKLIST pkg/CHNOSZ/inst/NEWS pkg/CHNOSZ/man/CHNOSZ-package.Rd pkg/CHNOSZ/vignettes/equilibrium.Rnw pkg/CHNOSZ/vignettes/equilibrium.lyx Log: prepare for release on CRAN Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2014-01-11 04:28:50 UTC (rev 61) +++ pkg/CHNOSZ/DESCRIPTION 2014-01-12 15:17:43 UTC (rev 62) @@ -1,6 +1,6 @@ -Date: 2014-01-11 +Date: 2014-01-12 Package: CHNOSZ -Version: 1.0.2-3 +Version: 1.0.3 Title: Chemical Thermodynamics and Activity Diagrams Author: Jeffrey Dick Maintainer: Jeffrey Dick Modified: pkg/CHNOSZ/inst/CHECKLIST =================================================================== --- pkg/CHNOSZ/inst/CHECKLIST 2014-01-11 04:28:50 UTC (rev 61) +++ pkg/CHNOSZ/inst/CHECKLIST 2014-01-12 15:17:43 UTC (rev 62) @@ -23,7 +23,7 @@ data files are uncompressed on installation? (from BuildResaveData: no) anim.*() produce pngs / movies (ImageMagick dependency)? -- check that dl.aa() works with current UniProt web pages +- check that uniprot.aa() works with current UniProt web pages - check for stale URLs in Rd files Modified: pkg/CHNOSZ/inst/NEWS =================================================================== --- pkg/CHNOSZ/inst/NEWS 2014-01-11 04:28:50 UTC (rev 61) +++ pkg/CHNOSZ/inst/NEWS 2014-01-12 15:17:43 UTC (rev 62) @@ -1,5 +1,5 @@ -CHANGES IN CHNOSZ 1.0.2-3 (2014-01-11) --------------------------------------- +CHANGES IN CHNOSZ 1.0.3 (2014-01-12) +------------------------------------ - Updated extdata/protein/Sce.csv.xz using Saccharomyces Genome Database protein_properties.tab and SGD_features.tab dated @@ -11,13 +11,16 @@ Reference Sequence (RefSeq) release 61 (2013-09-09). Code was adapted to deal with WP multispecies accessions. -- read.fasta() gets new argument 'id'; when supplied, it skips reading - the protein names from the FASTA headers. +- read.fasta() gets new argument 'id'; when supplied, it is used for + the protein names in the output, in place of those read from the + FASTA headers. - When reading protein names from the FASTA headers, read.fasta() stops only at the first space, not space or underscore as before. -- info() no longer specially sets state of "O2" or "oxygen" to gas. +- info() no longer specially sets state of "O2" to gas. The name + "oxygen", or the combination ("O2", "gas"), can be used to retrieve + data for the gas. - In thermo$obigt, names of gases (e.g. "oxygen") are used only for the gaseous species; names were removed from dissolved species in @@ -26,15 +29,13 @@ - In read.expr(), allow multiple filter specifications. -- In revisit(), extend ranges of axes of scatter plots. - - revisit() has new argument loga0, a single vector of base-10 logarithms of activities of species used to calculate the base-2 log ratio ( log2(a1/a0) ). -- Updated tests to be compatible with testthat version 0.8. Some tests - now check for e.g. errors *and* warnings produced by a single - function call. +- Updated tests to be compatible with testthat version 0.8 (in + development). Some tests now check for e.g. an error *and* warning + produced by a single function call. CHANGES IN CHNOSZ 1.0.1 (2013-07-04) ------------------------------------ Modified: pkg/CHNOSZ/man/CHNOSZ-package.Rd =================================================================== --- pkg/CHNOSZ/man/CHNOSZ-package.Rd 2014-01-11 04:28:50 UTC (rev 61) +++ pkg/CHNOSZ/man/CHNOSZ-package.Rd 2014-01-12 15:17:43 UTC (rev 62) @@ -77,10 +77,6 @@ \code{\link{diagram}} causes an error while plotting stability field boundaries if the x and y resolutions are not identical. } -\seealso{ - The \code{TODO} file in the package installation directory contains a list of changes anticipated or considered for future releases. -} - \examples{ ### Getting Started ## the 'thermo' object contains thermodynamic data and is also where Modified: pkg/CHNOSZ/vignettes/equilibrium.Rnw =================================================================== --- pkg/CHNOSZ/vignettes/equilibrium.Rnw 2014-01-11 04:28:50 UTC (rev 61) +++ pkg/CHNOSZ/vignettes/equilibrium.Rnw 2014-01-12 15:17:43 UTC (rev 62) @@ -1,12 +1,13 @@ -%% LyX 2.0.5 created this file. For more info, see http://www.lyx.org/. +%% LyX 2.1.0beta2 created this file. For more info, see http://www.lyx.org/. %% Do not edit unless you really know what you are doing. -\documentclass[noae]{article} +\documentclass[english,noae]{article} \usepackage{mathpazo} \usepackage[T1]{fontenc} \usepackage[latin9]{inputenc} \usepackage[letterpaper]{geometry} \geometry{verbose,tmargin=2.5cm,bmargin=2.5cm,lmargin=2.5cm,rmargin=2.5cm} \usepackage{color} +\usepackage{babel} \usepackage{amsbsy} \usepackage{amssymb} \usepackage[numbers]{natbib} @@ -130,8 +131,6 @@ - - \section{Reaction-matrix approach} @@ -159,7 +158,6 @@ species("CSG",c("METVO", "METJA")) @ - Although the basis species are defined, the temperature is not yet specified, so it is not immediately possible to calculate the ionization states of the proteins. That is why the coefficient on $\mathrm{H^{+}}$ @@ -172,7 +170,6 @@ protein.info(species()$name) @ - Note that \texttt{affinity()} is called twice by \texttt{protein.info()}; this so that both charges and standard Gibbs energies of ionization of the proteins can be calculated. The \texttt{Z} values in the table @@ -188,7 +185,6 @@ a$values @ - Since \texttt{affinity()} returns a list with a lot of information (such as the basis species and species definitions) the last command was written to only print the \texttt{values} part of that list. The @@ -267,7 +263,6 @@ e$loga.equil @ - Those are the logarithms of the equilibrium activities of the proteins. Combining these values with either Eqs. (\ref{eq:A_METVO}) or (\ref{eq:A_METJA}) gives us the same value for affinity of the formation reactions per @@ -335,7 +330,6 @@ protein.basis(species()$name, normalize=TRUE) @ - Let us denote by $\boldsymbol{A}_{12}$ and $\boldsymbol{A}_{13}$ the chemical affinities of Reactions \ref{react:CSG_METVO_residue} and \ref{react:CSG_METJA_residue}. We can write @@ -423,6 +417,8 @@ for CSG example we have been discussing. \begin{small} + +<<>>= <>= # get an error if we don't data(thermo), only in the re-building vignettes of R CMD check data(thermo) @@ -431,9 +427,9 @@ swap.basis("O2", "H2") protein.equil(protein, loga.protein=-3) @ + \end{small} - The function checks (``check it!'') against the step-by-step calculations the values of $\boldsymbol{A}^{*}$ calculated using \texttt{affinity()}, and the equilibrium activities of the proteins calculated using \texttt{equilibrate()}. @@ -469,14 +465,13 @@ title(main="Equilibrium activities of proteins, normalized formulas") @ - The reaction-matrix approach described above can also be applied to systems having conservation coefficients that differ from unity, such as many mineral and inorganic systems, where the immobile component has different molar coefficients in the formulas. For example, consider a system like that described in \citep{See96}: -\setkeys{Gin}{width=0.7\textwidth} +\setkeys{Gin}{width=0.7\textwidth}<<>>= <>= basis("CHNOS+") basis("pH",5) @@ -491,9 +486,9 @@ diagram(e, ylim=c(-30, 0), legend.x="topleft", cex.names=0.8) title(main="Aqueous sulfur speciation, normalized formulas") @ + \setkeys{Gin}{width=1.0\textwidth} - The first diagram is quantitatively very similar to the one shown by Seewald, 1997, but if we use the normalized formulas, in this case divided by $\mathrm{H_{2}S}$ in the formation reactions, the range @@ -534,10 +529,13 @@ activities (Blood plasma proteins, ``IL'' for interleukin): \begin{small} + \setkeys{Gin}{width=0.8\textwidth} + +<<>>= <>= data(thermo) # cleanup from previous plot -basis(c("CO2", "NH3", "H2S", "H2O", "O2"), c(-3, -3, -10)) +basis(c("CO2", "NH3", "H2S", "H2O", "oxygen"), c(-3, -3, -10)) f <- system.file("extdata/abundance/AA03.csv", package="CHNOSZ") pdat <- read.csv(f, as.is=TRUE) iil <- grep("^IL", pdat$name) @@ -549,17 +547,21 @@ dE <- diagram(e, main="equilibrium activities") stopifnot(identical(dA$predominant, dE$predominant)) @ + \setkeys{Gin}{width=1.0\textwidth} + \end{small} - Here is an example where the predominant species in the equilibrium assemblage are \textbf{\emph{not}} identical to those calculated the maximum affinity method, and it is not possible for the maximum affinity method to make those curved lines!! \begin{small} + \setkeys{Gin}{width=0.8\textwidth} + +<<>>= <>= basis("CHNOS+") species(aminoacids("")) @@ -569,9 +571,9 @@ e <- equilibrate(a) dE <- diagram(e, main="equilibrium activities") @ + \end{small} - Take-home: when making predominance diagrams, confidently use the maximum affinity method when \texttt{normalize=TRUE} (as done here for proteins); otherwise it is advisable to compute the equilibrium @@ -593,7 +595,6 @@ sessionInfo() @ - \bibliographystyle{plainnat} \bibliography{vig} Modified: pkg/CHNOSZ/vignettes/equilibrium.lyx =================================================================== --- pkg/CHNOSZ/vignettes/equilibrium.lyx 2014-01-11 04:28:50 UTC (rev 61) +++ pkg/CHNOSZ/vignettes/equilibrium.lyx 2014-01-12 15:17:43 UTC (rev 62) @@ -1,5 +1,5 @@ -#LyX 2.0 created this file. For more info see http://www.lyx.org/ -\lyxformat 413 +#LyX 2.1 created this file. For more info see http://www.lyx.org/ +\lyxformat 474 \begin_document \begin_header \textclass article @@ -21,13 +21,13 @@ \font_roman palatino \font_sans default \font_typewriter default +\font_math auto \font_default_family default \use_non_tex_fonts false \font_sc false \font_osf false \font_sf_scale 100 \font_tt_scale 100 - \graphics default \default_output_format default \output_sync 0 @@ -48,15 +48,24 @@ \pdf_quoted_options "citecolor=black, linkcolor=black" \papersize letterpaper \use_geometry true -\use_amsmath 1 -\use_esint 1 -\use_mhchem 1 -\use_mathdots 1 -\cite_engine natbib_numerical +\use_package amsmath 1 +\use_package amssymb 1 +\use_package cancel 0 +\use_package esint 1 +\use_package mathdots 1 +\use_package mathtools 0 +\use_package mhchem 1 +\use_package stackrel 0 +\use_package stmaryrd 0 +\use_package undertilde 0 +\cite_engine natbib +\cite_engine_type numerical +\biblio_style plainnat \use_bibtopic false \use_indices false \paperorientation portrait \suppress_date false +\justification true \use_refstyle 0 \branch scrap \selected 1 @@ -377,29 +386,37 @@ \begin_inset Branch scrap status open -\begin_layout Chunk +\begin_layout Standard +\begin_inset Flex Chunk +status open -<>= +\begin_layout Plain Layout + +\begin_inset Argument 1 +status open + +\begin_layout Plain Layout +add_obigt \end_layout -\begin_layout Chunk +\end_inset library(CHNOSZ) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout data(thermo) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout add.obigt() \end_layout -\begin_layout Chunk +\end_inset -@ + \end_layout \end_inset @@ -493,24 +510,32 @@ \begin_inset Branch scrap status open -\begin_layout Chunk +\begin_layout Standard +\begin_inset Flex Chunk +status open -<>= +\begin_layout Plain Layout + +\begin_inset Argument 1 +status open + +\begin_layout Plain Layout +ProteinFormation \end_layout -\begin_layout Chunk +\end_inset basis("CHNOS+") \end_layout -\begin_layout Chunk +\begin_layout Plain Layout species("CSG",c("METVO", "METJA")) \end_layout -\begin_layout Chunk +\end_inset -@ + \end_layout \end_inset @@ -543,19 +568,27 @@ \begin_inset Branch scrap status open -\begin_layout Chunk +\begin_layout Standard +\begin_inset Flex Chunk +status open -<>= +\begin_layout Plain Layout + +\begin_inset Argument 1 +status open + +\begin_layout Plain Layout +ProteinInfo \end_layout -\begin_layout Chunk +\end_inset protein.info(species()$name) \end_layout -\begin_layout Chunk +\end_inset -@ + \end_layout \end_inset @@ -605,24 +638,32 @@ \begin_inset Branch scrap status open -\begin_layout Chunk +\begin_layout Standard +\begin_inset Flex Chunk +status open -<>= +\begin_layout Plain Layout + +\begin_inset Argument 1 +status collapsed + +\begin_layout Plain Layout +ProteinAffinity \end_layout -\begin_layout Chunk +\end_inset a <- affinity() \end_layout -\begin_layout Chunk +\begin_layout Plain Layout a$values \end_layout -\begin_layout Chunk +\end_inset -@ + \end_layout \end_inset @@ -875,24 +916,32 @@ \begin_inset Branch scrap status open -\begin_layout Chunk +\begin_layout Standard +\begin_inset Flex Chunk +status open -<>= +\begin_layout Plain Layout + +\begin_inset Argument 1 +status open + +\begin_layout Plain Layout +ProteinActivities \end_layout -\begin_layout Chunk +\end_inset e <- equilibrate(a) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout e$loga.equil \end_layout -\begin_layout Chunk +\end_inset -@ + \end_layout \end_inset @@ -1138,19 +1187,27 @@ \begin_inset Branch scrap status open -\begin_layout Chunk +\begin_layout Standard +\begin_inset Flex Chunk +status open -<<>>= +\begin_layout Plain Layout + +\begin_inset Argument 1 +status open + +\begin_layout Plain Layout + \end_layout -\begin_layout Chunk +\end_inset protein.basis(species()$name, normalize=TRUE) \end_layout -\begin_layout Chunk +\end_inset -@ + \end_layout \end_inset @@ -1455,57 +1512,74 @@ \begin_inset Branch scrap status open -\begin_layout Chunk +\begin_layout Standard +\begin_inset ERT +status collapsed +\begin_layout Plain Layout + \backslash begin{small} \end_layout -\begin_layout Chunk +\end_inset + +\end_layout + +\begin_layout Standard +\begin_inset Flex Chunk +status open + +\begin_layout Plain Layout + <>= \end_layout -\begin_layout Chunk +\begin_layout Plain Layout # get an error if we don't data(thermo), only in the re-building vignettes of R CMD check \end_layout -\begin_layout Chunk +\begin_layout Plain Layout data(thermo) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout protein <- iprotein(c("CSG_METVO", "CSG_METJA")) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout basis("CHNOS+") \end_layout -\begin_layout Chunk +\begin_layout Plain Layout swap.basis("O2", "H2") \end_layout -\begin_layout Chunk +\begin_layout Plain Layout protein.equil(protein, loga.protein=-3) \end_layout -\begin_layout Chunk +\end_inset -@ + \end_layout \begin_layout Chunk +\begin_inset ERT +status collapsed +\begin_layout Plain Layout + \backslash end{small} \end_layout @@ -1515,6 +1589,11 @@ \end_layout +\end_inset + + +\end_layout + \begin_layout Standard The function checks ( \begin_inset Quotes eld @@ -1608,79 +1687,87 @@ \begin_inset Branch scrap status open -\begin_layout Chunk +\begin_layout Standard +\begin_inset Flex Chunk +status open -<>= +\begin_layout Plain Layout + +\begin_inset Argument 1 +status open + +\begin_layout Plain Layout +ProteinSpeciation,fig=T \end_layout -\begin_layout Chunk +\end_inset organisms <- c("METSC", "METJA", "METFE", "HALJP", \end_layout -\begin_layout Chunk +\begin_layout Plain Layout "METVO", "METBU", "ACEKI", "GEOSE", "BACLI", "AERSA") \end_layout -\begin_layout Chunk +\begin_layout Plain Layout proteins <- c(rep("CSG", 6), rep("SLAP", 4)) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout basis("CHNOS+") \end_layout -\begin_layout Chunk +\begin_layout Plain Layout species(proteins, organisms) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout a <- affinity(O2=c(-100, -65)) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout par(mfrow=c(2, 1)) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout e <- equilibrate(a) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout diagram(e, ylim=c(-5, -1), legend.x=NA) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout title(main="Equilibrium activities of proteins, whole formulas") \end_layout -\begin_layout Chunk +\begin_layout Plain Layout e <- equilibrate(a, normalize=TRUE) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout diagram(e, ylim=c(-5, -1), legend.x=NA) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout title(main="Equilibrium activities of proteins, normalized formulas") \end_layout -\begin_layout Chunk +\end_inset -@ + \end_layout \end_inset @@ -1707,88 +1794,102 @@ \begin_inset Branch scrap status open -\begin_layout Chunk +\begin_layout Standard +\begin_inset ERT +status collapsed +\begin_layout Plain Layout + \backslash setkeys{Gin}{width=0.7 \backslash textwidth} \end_layout -\begin_layout Chunk +\end_inset + +\begin_inset Flex Chunk +status open + +\begin_layout Plain Layout + <>= \end_layout -\begin_layout Chunk +\begin_layout Plain Layout basis("CHNOS+") \end_layout -\begin_layout Chunk +\begin_layout Plain Layout basis("pH",5) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout species(c("H2S", "S2-2", "S3-2", "S2O3-2", "S2O4-2", \end_layout -\begin_layout Chunk +\begin_layout Plain Layout "S3O6-2", "S5O6-2", "S2O6-2", "HSO3-", "SO2", "HSO4-")) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout a <- affinity(O2=c(-50, -15), T=325, P=350) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout par(mfrow=c(2, 1)) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout e <- equilibrate(a, loga.balance=-2) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout diagram(e, ylim=c(-30, 0), legend.x="topleft", cex.names=0.8) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout title(main="Aqueous sulfur speciation, whole formulas") \end_layout -\begin_layout Chunk +\begin_layout Plain Layout e <- equilibrate(a, loga.balance=-2, normalize=TRUE) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout diagram(e, ylim=c(-30, 0), legend.x="topleft", cex.names=0.8) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout title(main="Aqueous sulfur speciation, normalized formulas") \end_layout -\begin_layout Chunk +\end_inset -@ + \end_layout \begin_layout Chunk +\begin_inset ERT +status open +\begin_layout Plain Layout + \backslash setkeys{Gin}{width=1.0 \backslash @@ -1800,6 +1901,11 @@ \end_layout +\end_inset + + +\end_layout + \begin_layout Standard The first diagram is quantitatively very similar to the one shown by Seewald, 1997, but if we use the normalized formulas, in this case divided by @@ -1913,104 +2019,139 @@ \begin_inset Branch scrap status open -\begin_layout Chunk +\begin_layout Standard +\begin_inset ERT +status collapsed +\begin_layout Plain Layout + \backslash begin{small} \end_layout -\begin_layout Chunk +\end_inset +\end_layout + +\begin_layout Standard +\begin_inset ERT +status open + +\begin_layout Plain Layout + + \backslash setkeys{Gin}{width=0.8 \backslash textwidth} \end_layout -\begin_layout Chunk +\end_inset + +\end_layout + +\begin_layout Standard +\begin_inset Flex Chunk +status open + +\begin_layout Plain Layout + <>= \end_layout -\begin_layout Chunk +\begin_layout Plain Layout data(thermo) # cleanup from previous plot \end_layout -\begin_layout Chunk +\begin_layout Plain Layout -basis(c("CO2", "NH3", "H2S", "H2O", "O2"), c(-3, -3, -10)) +basis(c("CO2", "NH3", "H2S", "H2O", "oxygen"), c(-3, -3, -10)) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout f <- system.file("extdata/abundance/AA03.csv", package="CHNOSZ") \end_layout -\begin_layout Chunk +\begin_layout Plain Layout pdat <- read.csv(f, as.is=TRUE) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout iil <- grep("^IL", pdat$name) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout species(pdat$name[iil], "HUMAN") \end_layout -\begin_layout Chunk +\begin_layout Plain Layout a <- affinity(O2=c(-82, -78), H2O=c(-12, -2)) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout par(mfrow=c(1, 2)) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout dA <- diagram(a, normalize=TRUE, main="maximum affinity") \end_layout -\begin_layout Chunk +\begin_layout Plain Layout e <- equilibrate(a, normalize=TRUE) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout dE <- diagram(e, main="equilibrium activities") \end_layout -\begin_layout Chunk +\begin_layout Plain Layout stopifnot(identical(dA$predominant, dE$predominant)) \end_layout -\begin_layout Chunk +\end_inset -@ + \end_layout -\begin_layout Chunk +\begin_layout Standard +\begin_inset ERT +status open +\begin_layout Plain Layout + \backslash setkeys{Gin}{width=1.0 \backslash textwidth} \end_layout +\end_inset + + +\end_layout + \begin_layout Chunk +\begin_inset ERT +status open +\begin_layout Plain Layout + \backslash end{small} \end_layout @@ -2020,6 +2161,11 @@ \end_layout +\end_inset + + +\end_layout + \begin_layout Standard Here is an example where the predominant species in the equilibrium assemblage are @@ -2036,70 +2182,96 @@ \begin_inset Branch scrap status open -\begin_layout Chunk +\begin_layout Standard +\begin_inset ERT +status open +\begin_layout Plain Layout + \backslash begin{small} \end_layout -\begin_layout Chunk +\end_inset +\end_layout + +\begin_layout Standard +\begin_inset ERT +status open + +\begin_layout Plain Layout + + \backslash setkeys{Gin}{width=0.8 \backslash textwidth} \end_layout -\begin_layout Chunk +\end_inset + +\end_layout + +\begin_layout Standard +\begin_inset Flex Chunk +status open + +\begin_layout Plain Layout + <>= \end_layout -\begin_layout Chunk +\begin_layout Plain Layout basis("CHNOS+") \end_layout -\begin_layout Chunk +\begin_layout Plain Layout species(aminoacids("")) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout a <- affinity(O2=c(-71, -66), H2O=c(-8, 4)) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout par(mfrow=c(1, 2)) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout dA <- diagram(a, main="maximum affinity") \end_layout -\begin_layout Chunk +\begin_layout Plain Layout e <- equilibrate(a) \end_layout -\begin_layout Chunk +\begin_layout Plain Layout dE <- diagram(e, main="equilibrium activities") \end_layout -\begin_layout Chunk +\end_inset -@ + \end_layout \begin_layout Chunk +\begin_inset ERT +status open +\begin_layout Plain Layout + \backslash end{small} \end_layout @@ -2109,6 +2281,11 @@ \end_layout +\end_inset + + +\end_layout + \begin_layout Standard Take-home: when making predominance diagrams, confidently use the maximum affinity method when @@ -2157,19 +2334,27 @@ R session information \end_layout -\begin_layout Chunk +\begin_layout Standard +\begin_inset Flex Chunk +status open -<>= +\begin_layout Plain Layout + +\begin_inset Argument 1 +status open + +\begin_layout Plain Layout +SessionInfo \end_layout -\begin_layout Chunk +\end_inset sessionInfo() \end_layout -\begin_layout Chunk +\end_inset -@ + \end_layout \end_inset From noreply at r-forge.r-project.org Thu Jan 30 15:40:30 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 30 Jan 2014 15:40:30 +0100 (CET) Subject: [CHNOSZ-commits] r63 - in pkg/CHNOSZ: . R data inst inst/extdata/protein inst/tests man vignettes Message-ID: <20140130144030.6375D181205@r-forge.r-project.org> Author: jedick Date: 2014-01-30 15:40:30 +0100 (Thu, 30 Jan 2014) New Revision: 63 Added: pkg/CHNOSZ/inst/extdata/protein/DS11.csv pkg/CHNOSZ/inst/extdata/protein/DS13.csv Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/R/affinity.R pkg/CHNOSZ/R/iprotein.R pkg/CHNOSZ/R/util.data.R pkg/CHNOSZ/data/protein.csv pkg/CHNOSZ/inst/NEWS pkg/CHNOSZ/inst/tests/test-affinity.R pkg/CHNOSZ/man/equilibrate.Rd pkg/CHNOSZ/vignettes/hotspring.Rnw pkg/CHNOSZ/vignettes/hotspring.lyx pkg/CHNOSZ/vignettes/vig.bib Log: update hotspring.Rnw: microbial abundances, knitr Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2014-01-12 15:17:43 UTC (rev 62) +++ pkg/CHNOSZ/DESCRIPTION 2014-01-30 14:40:30 UTC (rev 63) @@ -1,11 +1,11 @@ -Date: 2014-01-12 +Date: 2014-01-30 Package: CHNOSZ -Version: 1.0.3 +Version: 1.0.3-1 Title: Chemical Thermodynamics and Activity Diagrams Author: Jeffrey Dick Maintainer: Jeffrey Dick Depends: R (>= 2.12.0) -Suggests: limSolve, parallel, testthat +Suggests: limSolve, parallel, testthat, knitr Description: This package includes functions and data sets to support chemical thermodynamic modeling in biochemistry and low-temperature geochemistry. The features include calculation of the standard molal thermodynamic properties and chemical affinities of reactions involving @@ -17,4 +17,5 @@ License: GPL (>= 2) BuildResaveData: no ZipData: no +VignetteBuilder: knitr URL: http://www.chnosz.net/, http://chnosz.r-forge.r-project.org/ Modified: pkg/CHNOSZ/R/affinity.R =================================================================== --- pkg/CHNOSZ/R/affinity.R 2014-01-12 15:17:43 UTC (rev 62) +++ pkg/CHNOSZ/R/affinity.R 2014-01-30 14:40:30 UTC (rev 63) @@ -43,6 +43,8 @@ # to ionization calculations in energy() so no explicit accounting # is needed here if(!is.null(iprotein)) { + # check all proteins are available + if(!all(iprotein %in% 1:nrow(thermo$protein))) stop("some value(s) in iprotein not in rownumbers of thermo$protein") # add protein residues to the species list resnames <- c("H2O",aminoacids(3)) # residue activities set to zero; Modified: pkg/CHNOSZ/R/iprotein.R =================================================================== --- pkg/CHNOSZ/R/iprotein.R 2014-01-12 15:17:43 UTC (rev 62) +++ pkg/CHNOSZ/R/iprotein.R 2014-01-30 14:40:30 UTC (rev 63) @@ -151,7 +151,8 @@ read.aa <- function(file="protein.csv") { # 20090428 added colClasses here - aa <- read.csv(file,colClasses=c(rep("character",4),rep("numeric",21))) + # 20140128 added as.is=TRUE (in case numeric values are stored in ref or abbrv column) + aa <- read.csv(file, colClasses=c(rep("character", 2), NA, NA, rep("numeric", 21)), as.is=TRUE) if(!identical(colnames(aa), colnames(get("thermo")$protein))) stop(paste("format of", file, "is incompatible with thermo$protein")) return(aa) Modified: pkg/CHNOSZ/R/util.data.R =================================================================== --- pkg/CHNOSZ/R/util.data.R 2014-01-12 15:17:43 UTC (rev 62) +++ pkg/CHNOSZ/R/util.data.R 2014-01-30 14:40:30 UTC (rev 63) @@ -154,9 +154,9 @@ thermo$obigt <- to1 rownames(thermo$obigt) <- 1:nrow(thermo$obigt) assign("thermo", thermo, "CHNOSZ") - msgout("add.obigt: file has ", length(does.exist), " rows; made ", + msgout("add.obigt: ", file, "\n") + msgout("add.obigt: read ", length(does.exist), " rows; made ", nexist, " replacements, ", nrow(to2), " additions, units = ", E.units, "\n") - msgout("add.obigt: file was ", file, "\n") msgout("add.obigt: use data(thermo) to restore default database\n") return(invisible(inew)) } Modified: pkg/CHNOSZ/data/protein.csv =================================================================== --- pkg/CHNOSZ/data/protein.csv 2014-01-12 15:17:43 UTC (rev 62) +++ pkg/CHNOSZ/data/protein.csv 2014-01-30 14:40:30 UTC (rev 63) @@ -368,111 +368,6 @@ P53,HUMAN,BBA+03,P04637,1,24,10,20,30,11,23,12,8,20,32,12,14,44,15,27,38,22,18,4,9 P53,MOUSE,BBA+03,P02340,1,23,12,17,32,13,24,11,9,24,35,10,8,38,14,24,35,23,20,3,12 P53,PIG,BBA+03,Q9TUB2,1,26,10,18,29,13,20,9,7,20,36,8,16,39,11,27,42,22,19,4,10 -overall,bisonN,DS11,40360,1,14.922,1.746,9.16,15.878,9.257,14.468,3.411,12.241,13.563,22.487,3.948,6.265,8.939,5.484,12.167,10.655,8.555,15.743,2.533,7.708 -overall,bisonS,DS11,50497,1,15.319,1.65,8.579,13.934,8.039,13.773,3.237,10.99,10.765,20.255,3.731,5.498,8.829,5.331,12.249,9.791,8.318,15.013,2.728,6.318 -overall,bisonR,DS11,43250,1,19.316,1.657,8.762,13.901,7.537,15.218,3.896,9.579,7.465,23.088,3.705,5.264,11.017,7.404,14.92,9.139,9.375,14.71,3.232,6.3 -overall,bisonQ,DS11,83790,1,19.892,1.985,9.262,11.632,7.118,14.472,4.135,10.287,6.095,21.305,3.849,5.547,10.512,8.425,14.349,9.991,10.214,14.059,3.13,5.544 -overall,bisonP,DS11,74082,1,19.797,1.918,9.114,11.631,6.978,14.24,4.033,10.121,5.912,21.131,3.832,5.454,10.365,8.079,14.349,9.612,10.002,14.098,3.117,5.619 -transferase,bisonN,DS11,2384,1,17.826,2.457,11.129,19.789,12.771,18.434,4.725,15.546,17.168,27.834,4.84,7.492,11.625,5.86,14.44,12.782,9.646,19.8,2.825,9.815 -transferase,bisonS,DS11,2593,1,17.772,2.041,10.087,16.539,10.112,16.445,4.142,13.171,12.829,23.834,4.344,6.18,10.771,5.235,14.137,10.99,8.821,17.86,2.766,7.589 -transferase,bisonR,DS11,2257,1,21.817,2.032,9.397,15.504,8.257,16.694,4.755,10.564,7.948,25.194,4.069,4.967,12.629,6.997,16.736,8.958,9.28,16.79,3.235,6.857 -transferase,bisonQ,DS11,4398,1,23.621,2.664,10.704,12.761,8.009,16.814,5.453,11.893,6.195,24.446,4.475,5.343,12.729,8.637,17.03,10.21,10.656,16.528,3.619,6.563 -transferase,bisonP,DS11,4136,1,23.071,2.522,10.406,12.653,7.816,16.053,5.253,11.748,6.214,23.646,4.378,5.349,12.33,8.165,16.673,9.798,10.28,16.348,3.5,6.567 -transport,bisonN,DS11,1285,1,19.84,1.037,8.664,13.107,12.286,18.088,2.977,14.872,11.693,30.72,5.205,6.607,10.183,6.345,11.893,13.233,10.914,19.511,2.919,8.018 -transport,bisonS,DS11,1731,1,20.432,1.014,8.227,12.45,10.46,17.786,2.848,14.377,9.782,28.434,5.119,5.841,9.946,6.023,12.526,12.376,10.652,19.434,2.961,6.861 -transport,bisonR,DS11,1591,1,24.206,1.109,8.411,12.995,10.58,19.485,3.503,12.388,7.338,32.636,4.95,5.469,11.757,7.957,15.659,10.889,11.277,19.404,3.561,6.641 -transport,bisonQ,DS11,3429,1,24.82,1.574,9.253,11.534,9.986,18.959,3.673,14.514,6.053,29.968,5.453,6.138,11.688,9.195,14.985,12.312,12.625,19.244,3.799,5.789 -transport,bisonP,DS11,2993,1,23.869,1.497,9.027,11.186,9.606,18.133,3.492,13.929,6.056,28.76,5.293,6.043,11.137,8.797,14.775,11.666,12.144,18.628,3.543,5.825 -dehydrogenase,bisonN,DS11,1258,1,20.49,2.546,12.002,18.991,9.459,20.089,4.488,14.651,15.539,23.797,5.347,7.723,11.894,5.762,13.851,11.467,10.343,20.96,2.909,8.579 -dehydrogenase,bisonS,DS11,1651,1,21.414,2.419,11.078,17.543,8.291,19.552,4.568,13.631,12.705,21.668,5.062,6.806,11.258,5.51,14.398,10.644,10.259,20.231,2.933,7.357 -dehydrogenase,bisonR,DS11,1604,1,25.935,2.426,10.322,17.398,7.773,20.044,5.481,12.022,8.829,24.266,5.013,5.994,13.442,7.458,16.666,9.518,11.405,19.183,3.057,7.135 -dehydrogenase,bisonQ,DS11,2626,1,26.278,2.805,10.937,14.164,7.285,19.232,5.445,12.777,7.499,22.39,5.125,6.38,12.343,8.323,15.813,10.537,11.936,18.081,2.956,6.329 -dehydrogenase,bisonP,DS11,2428,1,26.05,2.764,10.894,14.44,7.251,19.02,5.441,12.445,7.376,21.996,5.027,6.362,12.259,8.044,15.853,10.046,11.795,18.069,2.873,6.435 -synthase,bisonN,DS11,1509,1,18.371,2.543,11.486,20.482,10.113,18.758,4.72,14.913,16.131,25.031,4.993,7.036,10.965,5.895,14.054,11.603,9.995,20.034,2.43,8.892 -synthase,bisonS,DS11,1486,1,18.66,2.245,10.863,18.251,8.81,17.581,4.38,13.59,13.341,22.421,4.649,6.3,10.442,5.448,13.989,10.755,9.384,18.808,2.346,7.551 -synthase,bisonR,DS11,1206,1,23.016,2.061,10.304,17.033,7.735,18.004,5.31,11.715,8.744,24.674,4.641,5.219,12.451,7.054,16.362,9.416,10.366,17.314,2.48,6.867 -synthase,bisonQ,DS11,2323,1,24.109,2.678,11.151,14.443,7.532,17.815,5.737,12.635,7.205,23.575,4.784,5.874,12.35,9.04,16.23,10.512,11.628,16.704,2.759,6.558 -synthase,bisonP,DS11,2037,1,23.769,2.527,10.821,13.926,7.154,16.963,5.398,12.185,6.886,22.601,4.729,5.613,11.95,8.378,15.952,9.979,11.115,16.322,2.545,6.338 -ATPase,bisonN,DS11,1099,1,16.813,1.464,10.854,22.308,9.96,16.963,3.584,15.258,16.287,30.237,4.638,6.674,10.02,7.51,16.884,12.925,10.075,19.411,1.869,7.296 -ATPase,bisonS,DS11,1437,1,16.427,1.202,10.283,19.371,8.496,16.286,3.382,14.102,13.079,26.979,4.557,6.031,9.586,7.024,16.202,11.949,9.536,18.349,1.852,6.088 -ATPase,bisonR,DS11,1174,1,21.898,1.372,10.259,19.033,7.48,16.756,4.489,12.39,9.267,30.147,4.491,5.337,11.691,9.369,18.996,10.263,10.759,17.848,1.974,5.566 -ATPase,bisonQ,DS11,2235,1,22.826,1.753,11.458,16.338,7.383,16.647,4.888,13.645,7.743,28.441,5.008,6.03,11.392,11.146,18.409,11.835,12.236,17.422,2.128,5.078 -ATPase,bisonP,DS11,2038,1,22.99,1.694,11.194,16.487,7.119,16.254,4.872,13.245,7.558,28.283,4.924,5.828,11.048,10.811,18.672,11.174,11.879,17.582,2.009,5.152 -kinase,bisonN,DS11,677,1,16.511,1.818,10.617,18.4,9.625,17.768,3.872,13.498,14.539,25.739,4.168,6.26,8.846,5.529,14.093,11.572,8.861,18.31,1.852,6.882 -kinase,bisonS,DS11,836,1,18.638,1.821,10.422,16.734,8.284,17.706,3.78,12.522,11.354,23.611,4.12,5.683,9.296,5.562,14.764,11.002,9.315,17.92,2.169,5.589 -kinase,bisonR,DS11,819,1,24.486,1.764,10.426,17.683,7.592,18.879,4.972,11.294,7.768,28.418,4.343,5.125,12.371,8.369,18.432,9.884,10.906,17.79,2.773,5.543 -kinase,bisonQ,DS11,2040,1,25.404,2.379,12.046,15.717,7.421,18.296,5.591,13.392,6.95,27.756,4.741,6.24,12.689,11.192,18.016,12.251,12.713,17.947,2.768,5.503 -kinase,bisonP,DS11,1751,1,24.802,2.287,11.56,15.17,7.029,17.729,5.287,13.12,6.603,26.606,4.736,6.119,11.975,10.184,17.718,11.51,12.3,17.422,2.58,5.314 -synthetase,bisonN,DS11,1003,1,17.71,2.828,14.138,27.129,12.565,19.371,5.476,15.95,20.187,29.719,5.476,8.144,13.367,7.65,17.861,12.875,10.988,22.17,3.964,10.944 -synthetase,bisonS,DS11,1159,1,18.187,2.44,13.231,23.439,10.962,18.131,5.101,14.79,16.098,26.026,5.076,7.092,12.678,6.437,17.515,11.844,10.591,20.607,3.838,9.569 -synthetase,bisonR,DS11,891,1,22.727,2.574,12.952,22.348,10.497,18.761,5.941,13.478,12.154,28.167,5.228,6.772,15.007,9.015,19.727,10.164,11.758,18.761,3.981,9.429 -synthetase,bisonQ,DS11,1509,1,23.789,2.745,13.074,17.248,9.068,17.306,5.843,13.001,9.354,24.903,4.985,6.221,13.565,9.97,17.962,10.683,12.372,17.298,3.779,7.803 -synthetase,bisonP,DS11,1417,1,23.26,2.591,12.558,16.977,8.678,16.693,5.654,12.496,8.66,24.225,5.025,6.112,13.551,9.3,18.252,10.112,11.979,16.946,3.716,7.826 -membrane,bisonN,DS11,818,1,20.148,0.892,9.144,14.775,16.071,19.935,3.108,17.367,14.69,32.704,4.633,7.624,10.133,7.032,12.668,15.407,11.591,20.44,3.11,10.258 -membrane,bisonS,DS11,834,1,21.486,1.025,8.386,12.703,13.282,18.66,2.97,15.38,11.592,30.349,4.615,6.463,9.971,6.636,12.649,13.83,11.236,19.499,3.536,8.325 -membrane,bisonR,DS11,761,1,25.476,1.244,8.681,12.888,11.651,21.07,3.4,12.75,7.355,33.8,4.495,6.449,12.661,8.913,16.988,12.777,12.421,19.586,4.656,8.394 -membrane,bisonQ,DS11,1476,1,25.766,1.406,8.986,11.337,11.066,20.762,3.447,14.121,5.951,30.478,4.677,7.446,11.848,9.493,15.818,13.565,13.253,18.959,4.639,7.154 -membrane,bisonP,DS11,1305,1,25.992,1.349,8.741,10.794,10.684,20.141,3.458,13.569,5.726,30.691,4.731,6.804,11.668,8.904,15.9,13.017,13.036,19.05,4.746,7.251 -permease,bisonN,DS11,503,1,22.68,0.821,5.431,8.221,15.342,18.793,2.292,16.161,7.863,37.406,5.851,5.205,9.773,5.01,9.855,14.891,10.72,20.587,3.575,8.255 -permease,bisonS,DS11,748,1,23.842,0.822,5.341,7.723,13.509,19.119,2.31,15.983,6.215,34.941,5.928,4.862,9.765,5.054,10.658,13.749,11.215,20.584,3.77,7.566 -permease,bisonR,DS11,698,1,27.186,0.744,5.477,8.457,13.714,21.416,2.603,12.689,4.542,40.755,5.383,4.585,11.58,6.524,13.824,11.841,11.212,20.264,4.688,7.029 -permease,bisonQ,DS11,1568,1,26.457,1.239,6.206,7.508,12.466,20.071,2.57,16.172,3.781,35.101,5.985,5.13,11.049,7.531,13.226,12.999,12.55,20.295,5.073,5.96 -permease,bisonP,DS11,1369,1,25.953,1.272,5.938,7.226,12.197,19.419,2.506,15.758,3.751,34.306,5.959,5.154,10.633,7.143,13.053,12.316,12.066,20.11,4.627,5.995 -hydrolase,bisonN,DS11,558,1,15.842,2.172,10.697,17.595,9.084,15.803,5.828,12.461,13.468,23.165,4.296,6.272,10.061,5.242,13.043,9.975,8.669,16.918,2.618,7.763 -hydrolase,bisonS,DS11,684,1,17.148,2.124,10.975,16.136,8.883,15.718,5.7,11.997,11.254,21.924,4.3,5.844,10.224,5.291,13.674,9.838,8.782,16.635,2.983,6.798 -hydrolase,bisonR,DS11,632,1,21.331,1.962,10.419,15.812,7.782,16.6,6.272,10.253,7.551,23.709,4.149,5.245,12.642,6.91,16.212,9.114,9.418,15.426,3.435,6.845 -hydrolase,bisonQ,DS11,1271,1,22.438,2.541,11.737,13.408,7.784,16.308,6.747,11.338,6.266,22.988,4.5,5.597,12.578,8.581,16.017,10.11,11.027,15.505,3.596,6.773 -hydrolase,bisonP,DS11,1181,1,21.707,2.419,11.209,12.801,7.232,15.679,6.481,10.672,5.887,21.804,4.392,5.272,11.986,7.621,15.56,9.362,10.37,14.733,3.442,6.274 -oxidoreductase,bisonN,DS11,637,1,20.545,3.339,9.948,16.159,14.201,19.962,4.846,15.57,13.835,29.706,6.424,6.658,12.013,5.953,12.407,12.851,10.765,20.959,3.931,10.914 -oxidoreductase,bisonS,DS11,806,1,19.947,3.124,9.061,14.65,11.452,18.187,4.314,13.49,11.356,25.295,5.852,5.8,11.266,5.416,12.556,11.039,9.881,18.677,3.615,8.648 -oxidoreductase,bisonR,DS11,475,1,22.105,3.225,7.754,14.065,10.305,18.667,4.465,11.215,8.371,26.863,5.724,5.175,12.221,6.28,13.528,9.419,9.385,16.613,3.928,7.92 -oxidoreductase,bisonQ,DS11,1035,1,23.552,3.589,9.329,12.511,9.813,18.391,4.726,12.643,6.772,25.654,6.181,5.646,12.47,7.604,14.17,10.739,11.202,16.961,3.759,7.238 -oxidoreductase,bisonP,DS11,850,1,22.975,3.327,8.98,12.325,9.489,18.242,4.535,12.387,6.978,24.821,6.075,5.562,11.731,7.2,13.728,10.288,10.844,16.789,3.657,7.287 -transcription,bisonN,DS11,470,1,14.906,1.715,7.692,15.449,6.238,11.498,3.517,10.353,10.294,20.883,3.806,4.687,7.421,5.911,13.249,9.309,7.534,13.715,1.577,5.204 -transcription,bisonS,DS11,603,1,15.464,1.758,7.756,14.028,5.72,11.604,3.265,9.735,9.128,20.101,3.746,4.164,7.806,5.97,13.882,9.066,7.743,13.542,1.751,4.703 -transcription,bisonR,DS11,509,1,19.521,1.497,8.234,16.656,5.639,12.878,4.271,8.835,7.531,24.713,3.658,3.731,10.358,7.586,17.475,8.623,8.77,13.697,2.035,5.297 -transcription,bisonQ,DS11,1127,1,20.441,2.002,9.895,14.477,5.851,12.53,4.808,10.532,6.184,23.698,4.239,4.801,10.147,9.392,17.06,10.815,10.209,13.877,2.163,4.996 -transcription,bisonP,DS11,1038,1,20.12,1.922,9.512,14.456,5.677,12.502,4.765,10.48,6.075,23.203,4.24,4.793,10.063,9.13,17.133,10.284,10.011,13.978,2.158,5.06 -peptidase,bisonN,DS11,472,1,18.053,1.303,11.561,18.903,10.434,19.576,4.138,14.803,16.225,25.225,4.816,7.538,11.153,6.343,14.155,13.032,10.485,19.22,3.021,9.672 -peptidase,bisonS,DS11,497,1,20.153,1.493,12.042,17.519,9.859,19.517,4.531,14.322,13.879,24.062,4.708,7.411,11.662,6.672,15.099,12.678,10.928,19.141,3.519,8.519 -peptidase,bisonR,DS11,612,1,27.964,1.722,12.894,19.021,9.912,22.132,5.479,12.719,8.954,30.214,4.994,7.726,15.943,9.861,20.652,12.476,13.515,20.033,4.533,9.088 -peptidase,bisonQ,DS11,1064,1,26.028,1.784,12.69,15.317,9.222,20.119,5.567,12.978,7.626,26.306,4.822,7.545,14.358,10.104,17.995,12.93,13.752,17.482,3.949,8.602 -peptidase,bisonP,DS11,990,1,25.312,1.856,12.347,15.217,8.714,19.308,5.467,12.648,6.953,25.637,4.778,7.121,14.083,9.651,18.093,12.07,13.104,17.332,3.829,8.007 -ribosomal,bisonN,DS11,597,1,10.01,0.965,5.385,10.951,4.327,10.544,2.581,8.779,14.353,12.692,2.93,3.851,6.58,3.9,10.67,5.493,5.36,12.844,1.343,4.457 -ribosomal,bisonS,DS11,716,1,9.582,0.75,4.747,9.605,3.521,9.71,2.461,7.993,12.284,11.105,2.788,3.325,6.226,3.719,11.166,5.324,5.275,11.814,1.208,3.87 -ribosomal,bisonR,DS11,543,1,10.785,0.726,4.842,9.827,3.503,10.158,2.735,7.867,11.309,11.521,2.691,3.694,6.694,4.481,12.494,5.14,5.902,10.91,1.168,3.462 -ribosomal,bisonQ,DS11,882,1,11.863,0.87,5.268,9.034,3.349,9.821,2.951,7.934,9.705,11.274,2.967,3.89,6.298,5.355,12.477,5.797,6.717,10.444,1.177,3.102 -ribosomal,bisonP,DS11,860,1,11.72,0.887,5.187,9.138,3.386,10.077,2.973,7.877,9.765,11.305,2.865,3.815,6.47,5.167,12.776,5.78,6.442,10.681,1.194,3.364 -protease,bisonN,DS11,377,1,19.454,1.554,10.708,17.931,11.215,20.926,3.687,16.984,14.804,27.785,5.122,7.963,11.676,6.894,13.899,13.658,10.692,20.743,2.706,9.029 -protease,bisonS,DS11,470,1,19.645,1.515,10.268,16.328,9.5,18.498,3.385,15.411,12.409,24.492,4.428,7.33,10.977,7.015,13.434,12.296,9.755,19.128,2.717,7.4 -protease,bisonR,DS11,418,1,27.601,1.457,11.859,16.725,9.294,21.737,4.258,13.694,9.45,30.093,4.593,7.433,15.108,10.325,18.203,11.792,12.301,20.799,3.639,8.148 -protease,bisonQ,DS11,930,1,25.572,1.696,12.102,14.799,8.734,20.469,4.405,14.098,7.323,27.489,4.732,7.536,13.888,10.513,17.848,12.922,12.725,19.148,3.545,6.825 -protease,bisonP,DS11,734,1,25.296,1.471,11.764,14.461,8.307,19.868,4.256,13.463,7.315,26.264,4.681,7.356,13.522,10.012,17.403,12.008,12.164,19.114,3.456,6.674 -reductase,bisonN,DS11,536,1,18.961,4.028,11.519,20.405,10.235,19.69,4.722,15.506,17.452,24.302,5.646,8.237,11.116,6.349,13.843,12.498,10.64,19.886,3.19,9.623 -reductase,bisonS,DS11,531,1,19.207,3.522,10.251,17.416,8.889,17.94,4.377,13.343,13.638,21.166,4.949,6.799,10.339,6.213,13.348,11.205,9.917,18.337,3.055,7.332 -reductase,bisonR,DS11,378,1,20.796,2.677,9.362,15.548,7.762,17.132,4.741,11.058,8.614,21.492,4.511,5.622,11.167,6.841,15.138,9.257,9.849,16.696,2.894,7.04 -reductase,bisonQ,DS11,785,1,24.408,3.29,11.14,15.006,8.688,18.804,5.968,13.119,8.454,22.766,5.082,6.679,12.162,9.043,16.046,11.373,12.434,17.525,3.299,6.913 -reductase,bisonP,DS11,675,1,24.147,3.033,10.738,14.644,8.332,18.042,5.424,12.698,8.09,21.997,4.964,6.717,11.539,8.807,15.856,10.612,11.821,17.304,3.102,6.804 -transposase,bisonN,DS11,471,1,17.076,1.399,7.898,18.423,7.471,13.072,5.507,12.711,24.958,26.503,3.741,8.8,7.361,7.809,17.047,11.573,10.161,15.412,4.824,9.482 -transposase,bisonS,DS11,425,1,16.892,1.772,8.365,16.546,7.511,13.445,5.139,12.271,22.064,24.04,4.122,8.125,7.84,6.828,18.668,11.337,9.304,14.904,4.734,8.744 -transposase,bisonR,DS11,314,1,18.914,1.796,7.506,15.955,7.003,17.162,4.803,6.764,14.283,26.309,3.618,5.516,9.933,6.911,21.618,10.44,7.971,15.647,4.494,7.226 -transposase,bisonQ,DS11,1085,1,18.263,4.134,8.288,10.426,6.362,12.923,5.043,9.03,12.761,18.747,3.159,7.355,8.219,10.573,20.88,11.635,9.959,13.338,3.713,5.854 -transposase,bisonP,DS11,550,1,16.042,3.642,7.653,10.522,6.366,12.027,5.104,8.178,11.295,18.916,3.509,5.855,8.091,8.584,18.289,9.909,8.798,13.042,3.853,5.596 -periplasmic,bisonN,DS11,313,1,18.473,1.038,12.304,15.441,10.502,17.438,3.144,13.566,15.693,24.131,4.505,7.968,13.077,7.505,13.137,12.396,10.629,19.214,3.042,10.326 -periplasmic,bisonS,DS11,409,1,20.159,1.23,11.621,14.668,9.306,17.716,2.905,13.553,14.205,22.007,4.205,7.501,12.716,7.672,12.883,12.24,10.746,19.467,3.249,8.614 -periplasmic,bisonR,DS11,440,1,22.902,1.121,12.064,14.055,9.502,19.802,3.234,11.616,10.386,24.632,4.159,7.048,14.766,9.65,17.727,10.934,11.755,18.757,3.959,8.277 -periplasmic,bisonQ,DS11,850,1,25.292,1.418,13.372,13.453,9.034,19.272,3.292,12.875,8.955,23.404,4.208,8.377,14.853,10.484,15.908,12.673,13.488,18.094,3.978,7.245 -periplasmic,bisonP,DS11,772,1,24.144,1.339,12.953,12.882,8.589,18.782,3.276,12.034,8.744,22.184,4.133,7.948,14.29,9.956,15.784,12.2,12.912,17.553,3.965,7.153 -signal,bisonN,DS11,297,1,18.165,1.852,12.586,18.966,11.694,17.748,3.387,14.865,17.347,26.889,4.966,8.024,10.956,6.875,14.603,13.195,10.717,20.047,2.391,8.593 -signal,bisonS,DS11,408,1,18.223,1.855,10.838,15.23,8.821,16.436,3.527,12.441,12.466,22.679,4.407,6.549,10.115,6.586,14.525,10.885,10.11,18.191,2.691,5.993 -signal,bisonR,DS11,299,1,25.181,1.896,11.134,19.144,9.087,19.813,4.84,12.334,10.141,32.217,5.037,6.244,12.809,11.037,19.913,11.234,12.555,19.04,3.284,6.054 -signal,bisonQ,DS11,732,1,25.425,2.034,12.243,16.406,8.213,18.031,5.303,14.452,7.981,29.495,4.984,7.357,12.855,12.869,18.719,13.465,13.715,18.519,3.143,5.496 -signal,bisonP,DS11,641,1,23.841,1.93,11.376,15.476,7.746,16.665,5.027,13.732,7.173,28.257,4.927,6.877,11.594,11.892,18.028,12.516,12.719,17.493,2.816,4.952 -phosphatase,bisonN,DS11,364,1,15.077,1.761,11.187,16.135,9.159,15.843,4.052,11.256,12.462,22.055,3.747,5.478,9.03,4.253,11.808,10.148,8.332,16.382,2.508,7.291 -phosphatase,bisonS,DS11,372,1,15.065,1.554,9.559,14.817,8.091,14.712,3.586,10.194,10.605,19.575,3.495,4.656,7.995,4.051,11.269,9.057,7.554,15.215,2.352,5.586 -phosphatase,bisonR,DS11,324,1,19.599,1.321,9.056,13.978,7.269,16.281,4.386,9.611,7.355,22.256,3.84,4.617,9.87,5.79,12.926,8.395,8.577,13.978,2.769,5.707 -phosphatase,bisonQ,DS11,642,1,21.611,2.195,10.724,12.88,6.941,16.322,4.883,10.908,5.777,21.86,4.241,5.204,10.332,7.777,14.927,9.96,10.382,14.522,2.843,5.556 -phosphatase,bisonP,DS11,558,1,21.842,1.909,10.256,12.24,6.808,16.332,4.876,10.871,5.298,21.597,4.074,5.335,9.686,7.634,14.124,9.919,9.815,14.787,2.794,5.292 HBA,HUMAN,BBA+03,"Hemoglobin (P69905)",1,21,1,8,4,7,7,10,0,11,18,2,4,7,1,3,11,9,13,1,3 ALBU,HUMAN,BBA+03,"Albumin (P02768)",1,62,35,36,62,31,12,16,8,59,61,6,17,24,20,24,24,28,41,1,18 IGHG1,HUMAN,BBA+03,"IgG Total (P01857)",1,13,9,13,17,10,18,9,5,28,26,2,15,31,11,6,39,26,35,5,12 Modified: pkg/CHNOSZ/inst/NEWS =================================================================== --- pkg/CHNOSZ/inst/NEWS 2014-01-12 15:17:43 UTC (rev 62) +++ pkg/CHNOSZ/inst/NEWS 2014-01-30 14:40:30 UTC (rev 63) @@ -1,3 +1,13 @@ +CHANGES IN CHNOSZ 1.0.3-1 (2014-01-30) +-------------------------------------- + +- Add files with average amino acid compositions of proteins from Bison + Pool grouped according to annotation keyword (DS11.csv) (moved here + from main protein.csv) or phylum assignment (DS13.csv). + +- Convert hotspring.Rnw to use knitr, and add example calculations of + relative abundances of microbial phyla from Dick and Shock, 2013. + CHANGES IN CHNOSZ 1.0.3 (2014-01-12) ------------------------------------ Added: pkg/CHNOSZ/inst/extdata/protein/DS11.csv =================================================================== --- pkg/CHNOSZ/inst/extdata/protein/DS11.csv (rev 0) +++ pkg/CHNOSZ/inst/extdata/protein/DS11.csv 2014-01-30 14:40:30 UTC (rev 63) @@ -0,0 +1,106 @@ +"protein","organism","ref","abbrv","chains","Ala","Cys","Asp","Glu","Phe","Gly","His","Ile","Lys","Leu","Met","Asn","Pro","Gln","Arg","Ser","Thr","Val","Trp","Tyr" +"overall","bisonN","",40360,1,14.922,1.746,9.16,15.878,9.257,14.468,3.411,12.241,13.563,22.487,3.948,6.265,8.939,5.484,12.167,10.655,8.555,15.743,2.533,7.708 +"overall","bisonS","",50497,1,15.319,1.65,8.579,13.934,8.039,13.773,3.237,10.99,10.765,20.255,3.731,5.498,8.829,5.331,12.249,9.791,8.318,15.013,2.728,6.318 +"overall","bisonR","",43250,1,19.316,1.657,8.762,13.901,7.537,15.218,3.896,9.579,7.465,23.088,3.705,5.264,11.017,7.404,14.92,9.139,9.375,14.71,3.232,6.3 +"overall","bisonQ","",83790,1,19.892,1.985,9.262,11.632,7.118,14.472,4.135,10.287,6.095,21.305,3.849,5.547,10.512,8.425,14.349,9.991,10.214,14.059,3.13,5.544 +"overall","bisonP","",74082,1,19.797,1.918,9.114,11.631,6.978,14.24,4.033,10.121,5.911,21.131,3.832,5.454,10.365,8.079,14.349,9.612,10.002,14.098,3.117,5.619 +"transferase","bisonN","",2384,1,17.826,2.457,11.129,19.789,12.771,18.434,4.725,15.546,17.168,27.834,4.84,7.492,11.625,5.86,14.44,12.781,9.646,19.799,2.825,9.815 +"transferase","bisonS","",2593,1,17.772,2.041,10.087,16.539,10.111,16.445,4.142,13.171,12.829,23.834,4.344,6.18,10.771,5.235,14.137,10.99,8.821,17.86,2.766,7.589 +"transferase","bisonR","",2257,1,21.817,2.031,9.397,15.504,8.257,16.694,4.755,10.564,7.948,25.194,4.069,4.967,12.629,6.997,16.736,8.957,9.28,16.79,3.235,6.857 +"transferase","bisonQ","",4398,1,23.621,2.664,10.704,12.761,8.009,16.814,5.453,11.892,6.195,24.446,4.475,5.343,12.729,8.637,17.03,10.21,10.656,16.528,3.618,6.563 +"transferase","bisonP","",4136,1,23.071,2.522,10.406,12.653,7.816,16.052,5.253,11.748,6.214,23.646,4.378,5.349,12.33,8.165,16.673,9.798,10.279,16.348,3.5,6.567 +"transport","bisonN","",1285,1,19.84,1.037,8.664,13.107,12.286,18.088,2.977,14.872,11.693,30.72,5.205,6.607,10.183,6.345,11.893,13.233,10.914,19.511,2.919,8.018 +"transport","bisonS","",1731,1,20.432,1.014,8.227,12.449,10.46,17.786,2.848,14.377,9.782,28.434,5.119,5.841,9.946,6.023,12.526,12.376,10.652,19.434,2.961,6.861 +"transport","bisonR","",1591,1,24.206,1.109,8.411,12.995,10.58,19.485,3.503,12.388,7.338,32.636,4.95,5.469,11.757,7.957,15.659,10.889,11.277,19.404,3.561,6.64 +"transport","bisonQ","",3429,1,24.82,1.574,9.253,11.534,9.986,18.959,3.673,14.514,6.053,29.968,5.453,6.138,11.688,9.195,14.985,12.311,12.625,19.244,3.799,5.789 +"transport","bisonP","",2993,1,23.869,1.496,9.027,11.186,9.606,18.133,3.492,13.929,6.056,28.76,5.293,6.043,11.137,8.797,14.775,11.666,12.144,18.628,3.543,5.825 +"dehydrogenase","bisonN","",1258,1,20.49,2.546,12.002,18.99,9.459,20.089,4.488,14.651,15.539,23.797,5.347,7.723,11.893,5.762,13.851,11.467,10.343,20.96,2.909,8.579 +"dehydrogenase","bisonS","",1651,1,21.414,2.419,11.078,17.543,8.291,19.552,4.568,13.631,12.705,21.667,5.062,6.806,11.258,5.51,14.398,10.644,10.259,20.231,2.933,7.357 +"dehydrogenase","bisonR","",1604,1,25.935,2.426,10.322,17.398,7.773,20.044,5.481,12.022,8.829,24.266,5.012,5.994,13.442,7.458,16.666,9.518,11.405,19.183,3.057,7.135 +"dehydrogenase","bisonQ","",2626,1,26.278,2.805,10.937,14.164,7.284,19.232,5.445,12.777,7.498,22.39,5.125,6.38,12.343,8.323,15.813,10.537,11.936,18.081,2.956,6.329 +"dehydrogenase","bisonP","",2428,1,26.05,2.764,10.894,14.439,7.251,19.02,5.441,12.445,7.376,21.996,5.027,6.362,12.259,8.044,15.853,10.046,11.795,18.069,2.873,6.435 +"synthase","bisonN","",1509,1,18.371,2.543,11.486,20.482,10.113,18.758,4.72,14.913,16.131,25.031,4.993,7.036,10.965,5.895,14.054,11.603,9.995,20.034,2.43,8.892 +"synthase","bisonS","",1486,1,18.66,2.245,10.863,18.251,8.81,17.581,4.38,13.59,13.341,22.421,4.649,6.299,10.441,5.448,13.989,10.755,9.384,18.808,2.346,7.55 +"synthase","bisonR","",1206,1,23.016,2.061,10.303,17.033,7.735,18.004,5.31,11.715,8.744,24.674,4.641,5.219,12.451,7.054,16.362,9.416,10.366,17.314,2.48,6.867 +"synthase","bisonQ","",2323,1,24.109,2.678,11.151,14.443,7.532,17.814,5.737,12.635,7.205,23.575,4.784,5.874,12.35,9.04,16.23,10.512,11.628,16.704,2.759,6.558 +"synthase","bisonP","",2037,1,23.769,2.527,10.821,13.926,7.154,16.963,5.398,12.185,6.886,22.601,4.729,5.613,11.95,8.378,15.952,9.979,11.115,16.322,2.545,6.338 +"ATPase","bisonN","",1099,1,16.813,1.464,10.854,22.308,9.96,16.963,3.584,15.258,16.287,30.237,4.638,6.674,10.02,7.51,16.884,12.924,10.075,19.411,1.869,7.296 +"ATPase","bisonS","",1437,1,16.427,1.202,10.283,19.371,8.496,16.286,3.382,14.102,13.079,26.979,4.557,6.031,9.586,7.024,16.202,11.949,9.536,18.349,1.852,6.088 +"ATPase","bisonR","",1174,1,21.898,1.372,10.259,19.033,7.48,16.756,4.489,12.39,9.267,30.147,4.491,5.337,11.691,9.369,18.996,10.263,10.759,17.848,1.974,5.566 +"ATPase","bisonQ","",2235,1,22.826,1.753,11.458,16.338,7.383,16.647,4.888,13.645,7.743,28.441,5.008,6.03,11.391,11.146,18.409,11.835,12.236,17.421,2.128,5.078 +"ATPase","bisonP","",2038,1,22.99,1.694,11.194,16.487,7.119,16.254,4.872,13.245,7.558,28.283,4.924,5.828,11.048,10.811,18.672,11.174,11.879,17.581,2.009,5.152 +"kinase","bisonN","",677,1,16.511,1.818,10.617,18.4,9.625,17.768,3.871,13.498,14.539,25.739,4.168,6.26,8.846,5.529,14.093,11.572,8.861,18.31,1.852,6.882 +"kinase","bisonS","",836,1,18.638,1.821,10.422,16.734,8.283,17.706,3.78,12.522,11.354,23.611,4.12,5.683,9.295,5.562,14.764,11.002,9.315,17.92,2.169,5.589 +"kinase","bisonR","",819,1,24.486,1.764,10.426,17.683,7.592,18.879,4.972,11.294,7.768,28.418,4.343,5.125,12.371,8.369,18.432,9.884,10.906,17.79,2.773,5.543 +"kinase","bisonQ","",2040,1,25.404,2.379,12.046,15.717,7.421,18.296,5.591,13.392,6.95,27.756,4.741,6.24,12.689,11.192,18.016,12.251,12.713,17.947,2.768,5.503 +"kinase","bisonP","",1751,1,24.802,2.287,11.56,15.17,7.029,17.729,5.287,13.12,6.603,26.606,4.736,6.119,11.975,10.184,17.718,11.51,12.3,17.422,2.58,5.314 +"synthetase","bisonN","",1003,1,17.71,2.828,14.138,27.129,12.565,19.371,5.476,15.95,20.187,29.719,5.476,8.144,13.367,7.65,17.861,12.875,10.988,22.169,3.964,10.944 +"synthetase","bisonS","",1159,1,18.187,2.44,13.231,23.439,10.962,18.131,5.101,14.79,16.098,26.026,5.076,7.091,12.678,6.437,17.515,11.844,10.591,20.607,3.838,9.569 +"synthetase","bisonR","",891,1,22.727,2.574,12.952,22.348,10.497,18.761,5.941,13.478,12.154,28.167,5.228,6.772,15.007,9.015,19.727,10.164,11.758,18.761,3.981,9.429 +"synthetase","bisonQ","",1509,1,23.789,2.745,13.074,17.248,9.068,17.306,5.843,13.001,9.354,24.903,4.985,6.221,13.565,9.97,17.962,10.683,12.372,17.298,3.779,7.803 +"synthetase","bisonP","",1417,1,23.26,2.591,12.558,16.977,8.677,16.693,5.654,12.496,8.66,24.225,5.025,6.112,13.551,9.3,18.252,10.112,11.979,16.946,3.716,7.826 +"membrane","bisonN","",818,1,20.148,0.892,9.144,14.775,16.071,19.935,3.108,17.367,14.689,32.704,4.633,7.623,10.133,7.032,12.667,15.407,11.59,20.44,3.11,10.258 +"membrane","bisonS","",834,1,21.486,1.025,8.386,12.703,13.282,18.659,2.97,15.38,11.592,30.349,4.615,6.463,9.971,6.635,12.649,13.83,11.236,19.499,3.536,8.325 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+"hydrolase","bisonP","",1181,1,21.707,2.419,11.209,12.801,7.232,15.679,6.481,10.671,5.887,21.804,4.392,5.272,11.986,7.621,15.56,9.362,10.37,14.733,3.442,6.273 +"oxidoreductase","bisonN","",637,1,20.545,3.339,9.948,16.159,14.201,19.962,4.846,15.57,13.835,29.706,6.424,6.658,12.013,5.953,12.407,12.851,10.765,20.959,3.931,10.914 +"oxidoreductase","bisonS","",806,1,19.947,3.124,9.061,14.65,11.452,18.187,4.314,13.49,11.356,25.295,5.852,5.8,11.266,5.416,12.556,11.038,9.881,18.677,3.615,8.648 +"oxidoreductase","bisonR","",475,1,22.105,3.225,7.754,14.065,10.305,18.667,4.465,11.215,8.371,26.863,5.724,5.175,12.221,6.28,13.528,9.419,9.385,16.613,3.928,7.92 +"oxidoreductase","bisonQ","",1035,1,23.552,3.589,9.329,12.511,9.813,18.391,4.726,12.643,6.772,25.654,6.181,5.646,12.47,7.604,14.17,10.739,11.202,16.961,3.759,7.238 +"oxidoreductase","bisonP","",850,1,22.975,3.327,8.98,12.325,9.489,18.242,4.535,12.387,6.978,24.821,6.075,5.562,11.731,7.2,13.728,10.288,10.844,16.789,3.656,7.287 +"transcription","bisonN","",470,1,14.906,1.715,7.691,15.449,6.238,11.498,3.517,10.353,10.294,20.883,3.806,4.687,7.421,5.911,13.249,9.309,7.534,13.715,1.577,5.204 +"transcription","bisonS","",603,1,15.464,1.758,7.756,14.028,5.72,11.604,3.265,9.735,9.128,20.101,3.746,4.164,7.806,5.97,13.882,9.066,7.743,13.542,1.751,4.703 +"transcription","bisonR","",509,1,19.521,1.497,8.234,16.656,5.639,12.878,4.271,8.835,7.53,24.713,3.658,3.731,10.358,7.585,17.475,8.623,8.77,13.697,2.035,5.297 +"transcription","bisonQ","",1127,1,20.441,2.002,9.895,14.476,5.851,12.53,4.808,10.532,6.184,23.698,4.239,4.801,10.147,9.392,17.06,10.815,10.209,13.877,2.163,4.996 +"transcription","bisonP","",1038,1,20.119,1.922,9.512,14.456,5.677,12.502,4.765,10.48,6.075,23.203,4.24,4.793,10.063,9.13,17.133,10.284,10.011,13.978,2.158,5.06 +"peptidase","bisonN","",472,1,18.053,1.303,11.561,18.903,10.434,19.576,4.138,14.803,16.225,25.225,4.816,7.538,11.153,6.343,14.155,13.032,10.485,19.22,3.021,9.672 +"peptidase","bisonS","",497,1,20.153,1.493,12.042,17.519,9.859,19.517,4.531,14.322,13.879,24.062,4.708,7.41,11.662,6.672,15.099,12.678,10.928,19.141,3.519,8.519 +"peptidase","bisonR","",612,1,27.964,1.722,12.894,19.021,9.912,22.132,5.479,12.719,8.954,30.214,4.993,7.725,15.943,9.861,20.652,12.475,13.515,20.033,4.533,9.088 +"peptidase","bisonQ","",1064,1,26.028,1.784,12.69,15.317,9.222,20.119,5.567,12.978,7.626,26.305,4.822,7.545,14.358,10.104,17.995,12.93,13.752,17.482,3.949,8.602 +"peptidase","bisonP","",990,1,25.312,1.856,12.346,15.217,8.714,19.308,5.467,12.647,6.953,25.637,4.778,7.121,14.083,9.651,18.093,12.07,13.104,17.332,3.829,8.007 [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/chnosz -r 63 From noreply at r-forge.r-project.org Thu Jan 30 17:20:33 2014 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 30 Jan 2014 17:20:33 +0100 (CET) Subject: [CHNOSZ-commits] r64 - in pkg/CHNOSZ: . R inst man Message-ID: <20140130162033.2F782186CBF@r-forge.r-project.org> Author: jedick Date: 2014-01-30 17:20:32 +0100 (Thu, 30 Jan 2014) New Revision: 64 Modified: pkg/CHNOSZ/DESCRIPTION pkg/CHNOSZ/R/affinity.R pkg/CHNOSZ/R/util.affinity.R pkg/CHNOSZ/inst/NEWS pkg/CHNOSZ/man/equilibrate.Rd Log: energy(): add missing 'IS' argument in call to subcrt() Modified: pkg/CHNOSZ/DESCRIPTION =================================================================== --- pkg/CHNOSZ/DESCRIPTION 2014-01-30 14:40:30 UTC (rev 63) +++ pkg/CHNOSZ/DESCRIPTION 2014-01-30 16:20:32 UTC (rev 64) @@ -1,6 +1,6 @@ Date: 2014-01-30 Package: CHNOSZ -Version: 1.0.3-1 +Version: 1.0.3-2 Title: Chemical Thermodynamics and Activity Diagrams Author: Jeffrey Dick Maintainer: Jeffrey Dick Modified: pkg/CHNOSZ/R/affinity.R =================================================================== --- pkg/CHNOSZ/R/affinity.R 2014-01-30 14:40:30 UTC (rev 63) +++ pkg/CHNOSZ/R/affinity.R 2014-01-30 16:20:32 UTC (rev 64) @@ -213,7 +213,7 @@ else if(length(Eharg) == 2) Ehvals <- seq(Eharg[1], Eharg[2], length.out=128) vals[[iEh]] <- Ehvals } - # get pe and pH and Eh + # get pe and pH ipe <- match("pe", names(args.orig)) if(!is.na(ipe)) { ie <- match("e-", names(args$lims)) Modified: pkg/CHNOSZ/R/util.affinity.R =================================================================== --- pkg/CHNOSZ/R/util.affinity.R 2014-01-30 14:40:30 UTC (rev 63) +++ pkg/CHNOSZ/R/util.affinity.R 2014-01-30 16:20:32 UTC (rev 64) @@ -119,7 +119,7 @@ species <- c(mybasis$ispecies,myspecies$ispecies) if("T" %in% vars) T <- vals[[which(vars=="T")]] if("P" %in% vars) P <- vals[[which(vars=="P")]] - s.args <- list(species=species,property=property,T=T,P=P,grid=grid,convert=FALSE,exceed.Ttr=exceed.Ttr) + s.args <- list(species=species,property=property,T=T,P=P,IS=IS,grid=grid,convert=FALSE,exceed.Ttr=exceed.Ttr) if("IS" %in% vars) { IS <- vals[[which(vars=="IS")]] # do the calculation in parts: basis species (IS=0) Modified: pkg/CHNOSZ/inst/NEWS =================================================================== --- pkg/CHNOSZ/inst/NEWS 2014-01-30 14:40:30 UTC (rev 63) +++ pkg/CHNOSZ/inst/NEWS 2014-01-30 16:20:32 UTC (rev 64) @@ -1,4 +1,4 @@ -CHANGES IN CHNOSZ 1.0.3-1 (2014-01-30) +CHANGES IN CHNOSZ 1.0.3-2 (2014-01-30) -------------------------------------- - Add files with average amino acid compositions of proteins from Bison @@ -8,6 +8,9 @@ - Convert hotspring.Rnw to use knitr, and add example calculations of relative abundances of microbial phyla from Dick and Shock, 2013. +- In energy(), add missing 'IS' argument in call to subcrt(). Thanks to + Grayson Boyer for the bug report. + CHANGES IN CHNOSZ 1.0.3 (2014-01-12) ------------------------------------ Modified: pkg/CHNOSZ/man/equilibrate.Rd =================================================================== --- pkg/CHNOSZ/man/equilibrate.Rd 2014-01-30 14:40:30 UTC (rev 63) +++ pkg/CHNOSZ/man/equilibrate.Rd 2014-01-30 16:20:32 UTC (rev 64) @@ -85,7 +85,7 @@ } \value{ -\code{equil.reaction} and \code{equil.boltzman} each return a list with dimensions and length equal to those of \code{Astar}, giving the \code{\link{log10}} of the equilibrium activities of the species of interest. +\code{equil.reaction} and \code{equil.boltzmann} each return a list with dimensions and length equal to those of \code{Astar}, giving the \code{\link{log10}} of the equilibrium activities of the species of interest. \code{equilibrate} returns a list, containing first the values in \code{aout}, to which are appended \code{m.balance} (the balancing coefficients if \code{normalize} is TRUE, a vector of \samp{1}s otherwise), \code{n.balance} (the balancing coefficients if \code{normalize} is FALSE, a vector of \samp{1}s otherwise) and \code{loga.equil} (the calculated equilibrium activities of the species). \code{balance} returns a list containing the balancing coefficients (\code{n}) and a textual description (\code{description}). }