[CHNOSZ-commits] r383 - in pkg/CHNOSZ: . R demo inst inst/extdata/OBIGT man tests/testthat vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Feb 7 02:19:56 CET 2019
Author: jedick
Date: 2019-02-07 02:19:55 +0100 (Thu, 07 Feb 2019)
New Revision: 383
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/protein.info.R
pkg/CHNOSZ/demo/Shh.R
pkg/CHNOSZ/demo/bugstab.R
pkg/CHNOSZ/demo/copper.R
pkg/CHNOSZ/demo/protein.equil.R
pkg/CHNOSZ/demo/yeastgfp.R
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/inst/extdata/OBIGT/OldAA.csv
pkg/CHNOSZ/man/protein.Rd
pkg/CHNOSZ/tests/testthat/test-add.protein.R
pkg/CHNOSZ/tests/testthat/test-affinity.R
pkg/CHNOSZ/tests/testthat/test-ionize.aa.R
pkg/CHNOSZ/tests/testthat/test-protein.info.R
pkg/CHNOSZ/vignettes/anintro.Rmd
pkg/CHNOSZ/vignettes/equilibrium.Rnw
pkg/CHNOSZ/vignettes/equilibrium.lyx
pkg/CHNOSZ/vignettes/hotspring.Rnw
pkg/CHNOSZ/vignettes/hotspring.lyx
pkg/CHNOSZ/vignettes/vig.bib
Log:
add methionine and [Met] to OBIGT/OldAA.csv
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2019-02-06 17:29:09 UTC (rev 382)
+++ pkg/CHNOSZ/DESCRIPTION 2019-02-07 01:19:55 UTC (rev 383)
@@ -1,6 +1,6 @@
-Date: 2019-02-06
+Date: 2019-02-07
Package: CHNOSZ
-Version: 1.1.3-90
+Version: 1.1.3-91
Title: Thermodynamic Calculations and Diagrams for Geochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/R/protein.info.R
===================================================================
--- pkg/CHNOSZ/R/protein.info.R 2019-02-06 17:29:09 UTC (rev 382)
+++ pkg/CHNOSZ/R/protein.info.R 2019-02-07 01:19:55 UTC (rev 383)
@@ -148,8 +148,14 @@
}
protein.equil <- function(protein, T=25, loga.protein=0, digits=4) {
+ out <- character()
+ mymessage <- function(...) {
+ message(...)
+ text <- paste(list(...), collapse = " ")
+ out <<- c(out, text)
+ }
# show the individual steps in calculating metastable equilibrium among proteins
- message("protein.equil: temperature from argument is ", T, " degrees C")
+ mymessage("protein.equil: temperature from argument is ", T, " degrees C")
TK <- convert(T, "K")
# get the amino acid compositions of the proteins
aa <- pinfo(pinfo(protein))
@@ -165,13 +171,13 @@
ionize.it <- TRUE
iword <- "ionized"
pH <- -thermo$basis$logact[match("H+", rownames(bmat))]
- message("protein.equil: pH from thermo$basis is ", pH)
+ mymessage("protein.equil: pH from thermo$basis is ", pH)
}
# tell the user whose [Met] is in thermo$obigt
info.Met <- info(info('[Met]', "aq"))
- message("protein.equil: [Met] is from reference ", info.Met$ref1)
+ mymessage("protein.equil: [Met] is from reference ", info.Met$ref1)
## first set of output: show results of calculations for a single protein
- message("protein.equil [1]: first protein is ", pname[1], " with length ", plength[1])
+ mymessage("protein.equil [1]: first protein is ", pname[1], " with length ", plength[1])
# standard Gibbs energies of basis species
G0basis <- unlist(suppressMessages(subcrt(thermo$basis$ispecies, T=T, property="G")$out))
# coefficients of basis species in formation reactions of proteins
@@ -182,71 +188,72 @@
G0prot <- unlist(suppressMessages(subcrt(pname, T=T, property="G")$out))
# standard Gibbs energy of formation reaction of nonionized protein, cal/mol
G0protform <- G0prot - G0basissum
- message("protein.equil [1]: reaction to form nonionized protein from basis species has G0(cal/mol) of ", signif(G0protform[1], digits))
+ mymessage("protein.equil [1]: reaction to form nonionized protein from basis species has G0(cal/mol) of ", signif(G0protform[1], digits))
if(ionize.it) {
# standard Gibbs energy of ionization of protein, cal/mol
G0ionization <- suppressMessages(ionize.aa(aa, property="G", T=T, pH=pH))[1, ]
- message("protein.equil [1]: ionization reaction of protein has G0(cal/mol) of ", signif(G0ionization[1], digits))
+ mymessage("protein.equil [1]: ionization reaction of protein has G0(cal/mol) of ", signif(G0ionization[1], digits))
# standard Gibbs energy of formation reaction of ionized protein, cal/mol
G0protform <- G0protform + G0ionization
}
# standard Gibbs energy of formation reaction of non/ionized residue equivalents, dimensionless
R <- 1.9872 # gas constant, cal K^-1 mol^-1
G0res.RT <- G0protform/R/TK/plength
- message("protein.equil [1]: per residue, reaction to form ", iword, " protein from basis species has G0/RT of ", signif(G0res.RT[1], digits))
+ mymessage("protein.equil [1]: per residue, reaction to form ", iword, " protein from basis species has G0/RT of ", signif(G0res.RT[1], digits))
# coefficients of basis species in formation reactions of residues
resbasis <- suppressMessages(protein.basis(aa, T=T, normalize=TRUE))
# logQstar and Astar/RT
logQstar <- colSums(t(resbasis) * - thermo$basis$logact)
- message("protein.equil [1]: per residue, logQstar is ", signif(logQstar[1], digits))
+ mymessage("protein.equil [1]: per residue, logQstar is ", signif(logQstar[1], digits))
Astar.RT <- -G0res.RT - log(10)*logQstar
- message("protein.equil [1]: per residue, Astar/RT = -G0/RT - 2.303logQstar is ", signif(Astar.RT[1], digits))
- if(!is.numeric(protein)) message("protein.equil [1]: not comparing calculations with affinity() because 'protein' is not numeric")
+ mymessage("protein.equil [1]: per residue, Astar/RT = -G0/RT - 2.303logQstar is ", signif(Astar.RT[1], digits))
+ if(!is.numeric(protein)) mymessage("protein.equil [1]: not comparing calculations with affinity() because 'protein' is not numeric")
else {
# for **Astar** we have to set the activities of the proteins to zero, not loga.protein!
a <- suppressMessages(affinity(iprotein=protein, T=T, loga.protein=0))
aAstar.RT <- log(10) * as.numeric(a$values) / plength
- message("check it! per residue, Astar/RT calculated using affinity() is ", signif(aAstar.RT[1], digits))
+ mymessage("check it! per residue, Astar/RT calculated using affinity() is ", signif(aAstar.RT[1], digits))
if(!isTRUE(all.equal(Astar.RT, aAstar.RT, check.attributes=FALSE)))
stop("Bug alert! The same value for Astar/RT cannot be calculated manually as by using affinity()")
}
- if(length(pname)==1) message("protein.equil [all]: all done... give me more than one protein for equilibrium calculations")
+ if(length(pname)==1) mymessage("protein.equil [all]: all done... give me more than one protein for equilibrium calculations")
else {
## next set of output: equilibrium calculations
- message("protein.equil [all]: lengths of all proteins are ", paste(plength, collapse=" "))
- message("protein.equil [all]: Astar/RT of all residue equivalents are ", paste(signif(Astar.RT, digits), collapse=" "))
+ mymessage("protein.equil [all]: lengths of all proteins are ", paste(plength, collapse=" "))
+ mymessage("protein.equil [all]: Astar/RT of all residue equivalents are ", paste(signif(Astar.RT, digits), collapse=" "))
expAstar.RT <- exp(Astar.RT)
sumexpAstar.RT <- sum(expAstar.RT)
- message("protein.equil [all]: sum of exp(Astar/RT) of all residue equivalents is ", signif(sumexpAstar.RT, digits))
+ mymessage("protein.equil [all]: sum of exp(Astar/RT) of all residue equivalents is ", signif(sumexpAstar.RT, digits))
# boltzmann distribution
alpha <- expAstar.RT / sumexpAstar.RT
- message("protein.equil [all]: equilibrium degrees of formation (alphas) of residue equivalents are ", paste(signif(alpha, digits), collapse=" "))
+ mymessage("protein.equil [all]: equilibrium degrees of formation (alphas) of residue equivalents are ", paste(signif(alpha, digits), collapse=" "))
# check with equilibrate()
if(is.numeric(protein)) {
loga.equil.protein <- unlist(suppressMessages(equilibrate(a, normalize=TRUE))$loga.equil)
# here we do have to convert from logarithms of activities of proteins to degrees of formation of residue equivalents
a.equil.residue <- plength*10^loga.equil.protein
ealpha <- a.equil.residue/sum(a.equil.residue)
- message("check it! alphas of residue equivalents from equilibrate() are ", paste(signif(ealpha, digits), collapse=" "))
+ mymessage("check it! alphas of residue equivalents from equilibrate() are ", paste(signif(ealpha, digits), collapse=" "))
if(!isTRUE(all.equal(alpha, ealpha, check.attributes=FALSE)))
stop("Bug alert! The same value for alpha cannot be calculated manually as by using equilibrate()")
}
# total activity of residues
loga.residue <- log10(sum(plength * 10^loga.protein))
- message("protein.equil [all]: for activity of proteins equal to 10^", signif(loga.protein, digits), ", total activity of residues is 10^", signif(loga.residue, digits))
+ mymessage("protein.equil [all]: for activity of proteins equal to 10^", signif(loga.protein, digits), ", total activity of residues is 10^", signif(loga.residue, digits))
# equilibrium activities of residues
loga.residue.equil <- log10(alpha*10^loga.residue)
- message("protein.equil [all]: log10 equilibrium activities of residue equivalents are ", paste(signif(loga.residue.equil, digits), collapse=" "))
+ mymessage("protein.equil [all]: log10 equilibrium activities of residue equivalents are ", paste(signif(loga.residue.equil, digits), collapse=" "))
# equilibrium activities of proteins
loga.protein.equil <- log10(10^loga.residue.equil/plength)
- message("protein.equil [all]: log10 equilibrium activities of proteins are ", paste(signif(loga.protein.equil, digits), collapse=" "))
+ mymessage("protein.equil [all]: log10 equilibrium activities of proteins are ", paste(signif(loga.protein.equil, digits), collapse=" "))
# check with equilibrate()
if(is.numeric(protein)) {
eloga.protein.equil <- unlist(suppressMessages(equilibrate(a, loga.balance=loga.residue, normalize=TRUE))$loga.equil)
- message("check it! log10 eq'm activities of proteins from equilibrate() are ", paste(signif(eloga.protein.equil, digits), collapse=" "))
+ mymessage("check it! log10 eq'm activities of proteins from equilibrate() are ", paste(signif(eloga.protein.equil, digits), collapse=" "))
if(!isTRUE(all.equal(loga.protein.equil, eloga.protein.equil, check.attributes=FALSE)))
stop("Bug alert! The same value for log10 equilibrium activities of proteins cannot be calculated manually as by using equilibrate()")
}
}
+ return(out)
}
Modified: pkg/CHNOSZ/demo/Shh.R
===================================================================
--- pkg/CHNOSZ/demo/Shh.R 2019-02-06 17:29:09 UTC (rev 382)
+++ pkg/CHNOSZ/demo/Shh.R 2019-02-07 01:19:55 UTC (rev 383)
@@ -1,8 +1,8 @@
# Compare affinities of Sonic hedgehog and transcription factors involved in dorsal-ventral patterning
# (Dick, 2015. Chemical integration of proteins in signaling and development. https://doi.org/10.1101/015826)
-# to reproduce the calculations in the paper, use superseded data for [Gly] 20190206
-add.obigt("OldAA")
+# to reproduce the calculations in the paper, use superseded data for [Gly] and [UPBB] 20190206
+add.obigt("OldAA", c("[Gly]", "[UPBB]"))
# UniProt names of the proteins
pname <- c("SHH", "OLIG2", "NKX22", "FOXA2", "IRX3", "PAX6", "NKX62", "DBX1",
Modified: pkg/CHNOSZ/demo/bugstab.R
===================================================================
--- pkg/CHNOSZ/demo/bugstab.R 2019-02-06 17:29:09 UTC (rev 382)
+++ pkg/CHNOSZ/demo/bugstab.R 2019-02-07 01:19:55 UTC (rev 383)
@@ -2,8 +2,8 @@
# based on "bugstab" function in Supporting Information of Dick, 2016
# (https://doi.org/10.7717/peerj.2238)
-# to reproduce the calculations in the paper, use superseded data for [Gly] 20190206
-add.obigt("OldAA")
+# to reproduce the calculations in the paper, use superseded data for [Gly] and [UPBB] 20190206
+add.obigt("OldAA", c("[Gly]", "[UPBB]"))
# set up graphics device
layout(cbind(matrix(sapply(list(c(1, 2), c(3, 4)), function(x) rep(rep(x, each=3), 3)), nrow=6, byrow=TRUE),
matrix(rep(c(0, 5, 5, 5, 5, 0), each=4), nrow=6, byrow=TRUE)))
Modified: pkg/CHNOSZ/demo/copper.R
===================================================================
--- pkg/CHNOSZ/demo/copper.R 2019-02-06 17:29:09 UTC (rev 382)
+++ pkg/CHNOSZ/demo/copper.R 2019-02-07 01:19:55 UTC (rev 383)
@@ -3,7 +3,7 @@
## (Aksu, S. and Doyle, F. M., 2001. Electrochemistry of copper in aqueous glycine
## solutions. J. Electrochem. Soc., 148, B51-B57. doi:10.1149/1.1344532)
-# we need some superseded Cu-Gly complexes 20190206
+# we need superseded data for Cu-Gly complexes 20190206
add.obigt("OldAA")
# add some new species to thermo$obigt
m1 <- makeup(info(c("Cu+", "glycinate", "glycinate")), sum=TRUE)
Modified: pkg/CHNOSZ/demo/protein.equil.R
===================================================================
--- pkg/CHNOSZ/demo/protein.equil.R 2019-02-06 17:29:09 UTC (rev 382)
+++ pkg/CHNOSZ/demo/protein.equil.R 2019-02-07 01:19:55 UTC (rev 383)
@@ -4,9 +4,7 @@
# clear out amino acid residues loaded by the example above
# ( in affinity(iprotein=ip) )
data(thermo)
-# use properties of the "old" [Met] sidechain group (Dick et al., 2006)
-mod.obigt("[Met]", G=-35245, H=-59310)
-# also use parameters for [Gly] from DLH06 20190206
+# use superseded properties of [Met], [Gly], and [UPBB] (Dick et al., 2006)
add.obigt("OldAA")
# set up the basis species to those used in DS11
basis("CHNOS+")
@@ -27,5 +25,5 @@
Aref.residue <- Astar.residue - loga.residue # 0.446, after Eq. 16
# A-star of the residue in natural log units (A/RT)
log(10) * Astar.residue # 0.4359, after Eq. 23
-# forget about the old [Met] group for whatever comes next
+# forget about the superseded group properties for whatever comes next
data(thermo)
Modified: pkg/CHNOSZ/demo/yeastgfp.R
===================================================================
--- pkg/CHNOSZ/demo/yeastgfp.R 2019-02-06 17:29:09 UTC (rev 382)
+++ pkg/CHNOSZ/demo/yeastgfp.R 2019-02-07 01:19:55 UTC (rev 383)
@@ -1,9 +1,7 @@
## Oxygen fugacity - activity of H2O predominance
## diagrams for proteologs for 23 YeastGFP localizations
-# use old properties of [Met] (Dick et al., 2006) to reproduce this example
+# use superseded properties of [Met], [Gly], and [UPBB] (Dick et al., 2006)
data(thermo)
-mod.obigt("[Met]", G=-35245, H=-59310)
-# also use parameters for [Gly] from DLH06 20190206
add.obigt("OldAA")
# arranged by decreasing metastability:
# order of this list of locations is based on the
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2019-02-06 17:29:09 UTC (rev 382)
+++ pkg/CHNOSZ/inst/NEWS 2019-02-07 01:19:55 UTC (rev 383)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.3-90 (2019-02-06)
+CHANGES IN CHNOSZ 1.1.3-91 (2019-02-07)
---------------------------------------
BUG FIXES
@@ -168,8 +168,12 @@
- Add or update glycine, diglycine, and triglycine (zwitterions and
ions), and diketopiperazine, [Gly] and [UPBB] groups from Kitadai,
- 2014. Superseded data have been moved to OBIGT/OldAA.csv.
+ 2014.
+- For reproducing previous calculations, superseded data for [Gly] and
+ [UPBB], as well as [Met] (earlier superseded by LaRowe and Dick,
+ 2012), have been moved to OBIGT/OldAA.csv.
+
DIAGRAMS
- Lines in 1-D diagram()s can optionally be drawn as splines using the
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/OldAA.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/OldAA.csv 2019-02-06 17:29:09 UTC (rev 382)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/OldAA.csv 2019-02-07 01:19:55 UTC (rev 383)
@@ -5,7 +5,9 @@
diketopiperazine,NA,C4H6N2O2,aq,Sho92,CHNOSZ.6,28.Feb.92,-57440,-99300,53.5,17,76.73,12.1058,16.0764,11.6608,-3.4435,19.5904,-3.4064,-0.4702,0
glycine,Gly,C2H5NO2,aq,"AH97b.2 [S07]","DLH06.1 [S07]",25.Aug.06,-90950,-124780,39.29,9.3,43.2,11.3,0.71,3.99,-3.04,28.5,-8.4,0.23,0
glycinium,Gly+,C2H6NO2+,aq,"AH97b.2 [S07]","DLH06.1 [S07]",25.Aug.06,-94160,-125720,46.91,40,56.4,19.57,-7.58,-40.35,5.41,49,-1.8,0.59,0
+methionine,Met,C5H11NO2S,aq,AH97b,DLH06,25.Aug.06,-120120,-178520,62.36,70.7,105.4,24.95,6.9,13.59,-7.77,85.3,-6.6,0.13,0
[Gly],NA,H,aq,"DLH06 [S15]",NA,25.Aug.06,-6075,-5570,17.31,11.371,9.606,1.83,2.57,1.22,-1.27,6.9,2.2,0,0
+[Met],NA,C3H7S,aq,DLH06,NA,25.Aug.06,-35245,-59310,40.38,72.739,71.832,15.48,8.76,10.82,-6,63.7,4,-0.1,0
[UPBB],NA,C2H2NO,aq,"DLH06 [S15]",NA,25.Aug.06,-21436,-45220,1.62,-4.496,26.296,8.1,-3.75,-6.73,1.13,11.2,-7.5,0.05,0
alanate,NA,C3H6NO2-,aq,"SK95.1 [S98]",AH97b.1,3.Sep.06,-75360,-121470,30.71,17.8,61.88,10.6281,17.3648,0.6505,-3.4968,12.685,-4.1859,1.17,-1
glycinate,NA,C2H4NO2-,aq,"SK95.1 [S98]",AH97b.1,3.Sep.06,-77610,-114190,30.07,-6.6,43.77,8.1592,11.7696,1.921,-3.2655,12.9389,-4.1859,1.1975,-1
Modified: pkg/CHNOSZ/man/protein.Rd
===================================================================
--- pkg/CHNOSZ/man/protein.Rd 2019-02-06 17:29:09 UTC (rev 382)
+++ pkg/CHNOSZ/man/protein.Rd 2019-02-07 01:19:55 UTC (rev 383)
@@ -29,9 +29,10 @@
## surface-layer proteins from Methanococcus and others
## as a function of oxygen fugacity, after Dick, 2008, Fig. 5b
-# use old properties of [Met] (Dick et al., 2006) to reproduce this example
+# to reproduce the calculations in the paper,
+# use superseded data for [Met], [Gly] and [UPBB]
data(thermo)
-mod.obigt("[Met]", G=-35245, H=-59310)
+add.obigt("OldAA")
# make our protein list
organisms <- c("METSC", "METJA", "METFE", "HALJP", "METVO",
"METBU", "ACEKI", "GEOSE", "BACLI", "AERSA")
Modified: pkg/CHNOSZ/tests/testthat/test-add.protein.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-add.protein.R 2019-02-06 17:29:09 UTC (rev 382)
+++ pkg/CHNOSZ/tests/testthat/test-add.protein.R 2019-02-07 01:19:55 UTC (rev 383)
@@ -27,10 +27,7 @@
Cp <- 6415.5
V <- 10421
formula <- "C613H959N193O185S10"
- # use parameters for [Met] sidechain group from DLH06
- # (OBIGT.csv uses updated values from LaRowe and Dick, 2012 (Geochim Cosmochim Acta 80, 70-91))
- mod.obigt("[Met]", G=-35245, H=-59310)
- # also use parameters for [Gly] from DLH06 20190206
+ # to reproduce, use superseded properties of [Met], [Gly], and [UPBB] (Dick et al., 2006)
add.obigt("OldAA")
lprop <- info(info("LYSC_CHICK"))
expect_equal(G, lprop$G)
Modified: pkg/CHNOSZ/tests/testthat/test-affinity.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-affinity.R 2019-02-06 17:29:09 UTC (rev 382)
+++ pkg/CHNOSZ/tests/testthat/test-affinity.R 2019-02-07 01:19:55 UTC (rev 383)
@@ -111,9 +111,7 @@
file <- system.file("extdata/protein/DS11.csv", package="CHNOSZ")
aa <- read.csv(file, as.is=TRUE)
ip <- add.protein(aa[1:5, ])
- # to reproduce, we need use the "old" parameters for [Met] from Dick et al., 2006
- mod.obigt("[Met]", G=-35245, H=-59310)
- # also use parameters for [Gly] from DLH06 20190206
+ # to reproduce, use superseded properties of [Met], [Gly], and [UPBB] (Dick et al., 2006)
add.obigt("OldAA")
a <- affinity(T=T, pH=pH, H2=H2, iprotein=ip)
# divide A/2.303RT by protein length
Modified: pkg/CHNOSZ/tests/testthat/test-ionize.aa.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-ionize.aa.R 2019-02-06 17:29:09 UTC (rev 382)
+++ pkg/CHNOSZ/tests/testthat/test-ionize.aa.R 2019-02-07 01:19:55 UTC (rev 383)
@@ -64,9 +64,7 @@
# digitized from Fig. 12 of Dick et al., 2006
G.AMY_BACSU.25 <- c(-24.9, -24.9, -24.7, -24.5, -24.4, -23.9, -23.5, -23.2)
G.AMY_BACSU.100 <- c(-26.7, -26.7, -26.4, -26.1, -25.7, -25.1, -24.9, -24.9)
- # calculate the Gibbs energies of the nonionized proteins using the same [Met] parameters as in the paper
- mod.obigt("[Met]", G=-35245, H=-59310)
- # also use parameters for [Gly] from DLH06 20190206
+ # to reproduce the calculations in the paper, use superseded properties of [Met], [Gly], and [UPBB]
add.obigt("OldAA")
G.nonionized <- subcrt("AMY_BACSU", T=c(25, 100))$out[[1]]$G
aa <- pinfo(pinfo("AMY_BACSU"))
Modified: pkg/CHNOSZ/tests/testthat/test-protein.info.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-protein.info.R 2019-02-06 17:29:09 UTC (rev 382)
+++ pkg/CHNOSZ/tests/testthat/test-protein.info.R 2019-02-07 01:19:55 UTC (rev 383)
@@ -13,22 +13,18 @@
expect_equal(pinfo(c("LYSC_CHICK", "MYGPHYCA")), c(6, NA))
})
-# 20170430 comment this section becuase `pequil` somehow is just empty
-# using the current development version of testthat (on Github)
-## test_that somehow affects capture.output so we set up the problem here
-#protein <- pinfo(c("CSG_METVO", "CSG_METJA"))
-#suppressMessages(mod.obigt("[Met]", G=-35245, H=-59310))
-#basis("CHNOS+")
-#suppressMessages(swap.basis("O2", "H2"))
-#pequil <- capture.output(protein.equil(protein, loga.protein=-3), type="message")
-#
-#test_that("protein.equil() reports values consistent with Dick and Shock (2011)", {
-# # the Astar/RT in the paragraph following Eq. 23, p. 6 of DS11
-# # (truncated because of rounding)
-# expect_true(any(grepl(c("0\\.435.*1\\.36"), pequil)))
-# # the log10 activities of the proteins in the left-hand column of the same page
-# expect_true(any(grepl(c("-3\\.256.*-2\\.834"), pequil)))
-#})
+test_that("protein.equil() reports values consistent with Dick and Shock (2011)", {
+ protein <- pinfo(c("CSG_METVO", "CSG_METJA"))
+ suppressMessages(add.obigt("OldAA"))
+ basis("CHNOS+")
+ suppressMessages(swap.basis("O2", "H2"))
+ pequil <- protein.equil(protein, loga.protein=-3)
+ # the Astar/RT in the paragraph following Eq. 23, p. 6 of DS11
+ # (truncated because of rounding)
+ expect_true(any(grepl(c("0\\.435.*1\\.36"), pequil)))
+ # the log10 activities of the proteins in the left-hand column of the same page
+ expect_true(any(grepl(c("-3\\.256.*-2\\.834"), pequil)))
+})
# references
# Dick, J. M. and Shock, E. L. (2011) Calculation of the relative chemical stabilities of proteins
Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd 2019-02-06 17:29:09 UTC (rev 382)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd 2019-02-07 01:19:55 UTC (rev 383)
@@ -1522,15 +1522,13 @@
logabundance <- unitize(log10(y$abundance[!ina]), pl)
```
-Now we can load the proteins and calculate their activities in metastable equilibrium as a function of `r logfO2`:
-```{marginfigure}
-The commented line uses <span style="color:red">`mod.obigt()`</span> and <span style="color:red">`add.obigt()`</span> to revert the parameters of the methionine and glycine sidechain groups to those present in older versions of CHNOSZ (Dick et al., 2006).
-The current database, with parameters set by <span style="color:red">`data(thermo)`</span> and used here, contains updated group additivity parameters for methionine (LaRowe and Dick, 2012).
-```
+Now we can load the proteins and calculate their activities in metastable equilibrium as a function of `r logfO2`.
+The commented line uses <span style="color:red">`add.obigt()`</span> to revert the group additivity parameters to those present in older versions of CHNOSZ (Dick et al., 2006).
+The current database, with parameters set by <span style="color:red">`data(thermo)`</span> and used here, contains updated group additivity parameters for the sidechain groups of methionine (LaRowe and Dick, 2012) and glycine and the protein backbone [@Kit14].
+
```{r yeastplot, eval=FALSE, echo=1:6}
par(mfrow = c(1, 3))
basis("CHNOS+")
-#mod.obigt("[Met]", G = -35245, H = -59310)
#add.obigt("OldAA")
a <- affinity(O2 = c(-80, -73), iprotein = ip, loga.protein = logact)
e <- equilibrate(a)
@@ -1559,7 +1557,7 @@
```
The minimum free energy difference occurs near `r logfO2` = -78.
-This agrees with the assessment shown in Figure 4 of @Dic09 (note that the old parameters for the methionine sidechain group were used in that study).
+This agrees with the assessment shown in Figure 4 of @Dic09 (but the updated group additivity parameters make the results slightly different).
## An affinity baseline
Modified: pkg/CHNOSZ/vignettes/equilibrium.Rnw
===================================================================
--- pkg/CHNOSZ/vignettes/equilibrium.Rnw 2019-02-06 17:29:09 UTC (rev 382)
+++ pkg/CHNOSZ/vignettes/equilibrium.Rnw 2019-02-07 01:19:55 UTC (rev 383)
@@ -714,13 +714,12 @@
For the CSG examples below, we would like to reproduce exactly the
values appearing in publications. Because recent versions of CHNOSZ
-incorporate data updates for the methionine and glycine sidechain
-groups, we should therefore revert to the previous values \citep{DLH06}
-before proceeding.
+incorporate data updates for the protein backbone and methionine and
+glycine sidechain groups, we should therefore revert to the previous
+values \citep{DLH06} before proceeding.
<<AddObigt>>=
data(thermo)
-mod.obigt("[Met]", G=-35245, H=-59310)
add.obigt("OldAA")
@
Modified: pkg/CHNOSZ/vignettes/equilibrium.lyx
===================================================================
--- pkg/CHNOSZ/vignettes/equilibrium.lyx 2019-02-06 17:29:09 UTC (rev 382)
+++ pkg/CHNOSZ/vignettes/equilibrium.lyx 2019-02-07 01:19:55 UTC (rev 383)
@@ -3112,9 +3112,9 @@
\begin_layout Standard
For the CSG examples below, we would like to reproduce exactly the values
appearing in publications.
- Because recent versions of CHNOSZ incorporate data updates for the methionine
- and glycine sidechain groups, we should therefore revert to the previous
- values
+ Because recent versions of CHNOSZ incorporate data updates for the protein
+ backbone and methionine and glycine sidechain groups, we should therefore
+ revert to the previous values
\begin_inset CommandInset citation
LatexCommand citep
key "DLH06"
@@ -3141,11 +3141,6 @@
\begin_layout Plain Layout
-mod.obigt("[Met]", G=-35245, H=-59310)
-\end_layout
-
-\begin_layout Plain Layout
-
add.obigt(
\begin_inset Quotes eld
\end_inset
Modified: pkg/CHNOSZ/vignettes/hotspring.Rnw
===================================================================
--- pkg/CHNOSZ/vignettes/hotspring.Rnw 2019-02-06 17:29:09 UTC (rev 382)
+++ pkg/CHNOSZ/vignettes/hotspring.Rnw 2019-02-07 01:19:55 UTC (rev 383)
@@ -73,17 +73,16 @@
the code.
Load CHNOSZ and the thermodynamic database. In order to reproduce
-the calculations from the 2011 paper, we modify the methionine sidechain
-group using old values of standard Gibbs energy and enthalpy from
-\citep{DLH06}; these are inaccurate values that were updated by \citep{LD12}
-and are available starting in CHNOSZ\_0.9-9 (the current values are
-used further below). In addition, we load values for the glycine group
-that were superseded in 2019.
+the calculations from the 2011 paper, we load old values of standard
+Gibbs energy and enthalpy of the methionine sidechain group from \citep{DLH06};
+these are inaccurate values that were updated by \citep{LD12} and
+are available starting in CHNOSZ\_0.9-9 (the current values are used
+further below). This step also loads values for the glycine group
+and the protein backone {[}UPBB{]} that were superseded in 2019.
<<libraryCHNOSZ>>=
library(CHNOSZ)
data(thermo)
-mod.obigt("[Met]", G=-35245, H=-59310)
add.obigt("OldAA")
@
@@ -414,7 +413,7 @@
# use old [Met] for first row and new [Met] for second row
if(j==2) {
data(thermo)
- add.obigt("OldAA")
+ add.obigt("OldAA", c("[Gly]", "[UPBB]"))
ip.annot <- add.protein(aa.annot)
}
# setup basis species and proteins
Modified: pkg/CHNOSZ/vignettes/hotspring.lyx
===================================================================
--- pkg/CHNOSZ/vignettes/hotspring.lyx 2019-02-06 17:29:09 UTC (rev 382)
+++ pkg/CHNOSZ/vignettes/hotspring.lyx 2019-02-07 01:19:55 UTC (rev 383)
@@ -245,9 +245,9 @@
\begin_layout Standard
Load CHNOSZ and the thermodynamic database.
- In order to reproduce the calculations from the 2011 paper, we modify the
- methionine sidechain group using old values of standard Gibbs energy and
- enthalpy from
+ In order to reproduce the calculations from the 2011 paper, we load old
+ values of standard Gibbs energy and enthalpy of the methionine sidechain
+ group from
\begin_inset CommandInset citation
LatexCommand citep
key "DLH06"
@@ -265,8 +265,8 @@
and are available starting in CHNOSZ_0.9-9 (the current values are used
further below).
- In addition, we load values for the glycine group that were superseded
- in 2019.
+ This step also loads values for the glycine group and the protein backone
+ [UPBB] that were superseded in 2019.
\end_layout
\begin_layout Standard
@@ -290,11 +290,6 @@
\begin_layout Plain Layout
-mod.obigt("[Met]", G=-35245, H=-59310)
-\end_layout
-
-\begin_layout Plain Layout
-
add.obigt(
\begin_inset Quotes eld
\end_inset
@@ -1820,7 +1815,23 @@
\begin_inset Quotes erd
\end_inset
-)
+, c(
+\begin_inset Quotes eld
+\end_inset
+
+[Gly]
+\begin_inset Quotes erd
+\end_inset
+
+,
+\begin_inset Quotes eld
+\end_inset
+
+[UPBB]
+\begin_inset Quotes erd
+\end_inset
+
+))
\end_layout
\begin_layout Plain Layout
Modified: pkg/CHNOSZ/vignettes/vig.bib
===================================================================
--- pkg/CHNOSZ/vignettes/vig.bib 2019-02-06 17:29:09 UTC (rev 382)
+++ pkg/CHNOSZ/vignettes/vig.bib 2019-02-07 01:19:55 UTC (rev 383)
@@ -223,6 +223,19 @@
doi = {10.1016/0098-3004(92)90029-Q},
}
+ at Article{Kit14,
+ author = {Kitadai, Norio},
+ journal = {Journal of Molecular Evolution},
+ title = {{T}hermodynamic prediction of glycine polymerization as a function of temperature and p{H} consistent with experimentally obtained results},
+ year = {2014},
+ volume = {78},
+ number = {3-4},
+ pages = {171--187},
+ doi = {10.1007/s00239-014-9616-1},
+ issn = {0022-2844},
+ language = {English},
+}
+
@Article{LD12,
author = {LaRowe, Douglas E. and Dick, Jeffrey M.},
journal = {Geochimica et Cosmochimica Acta},
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