[CHNOSZ-commits] r580 - in pkg/CHNOSZ: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Jul 25 07:47:16 CEST 2020
Author: jedick
Date: 2020-07-25 07:47:15 +0200 (Sat, 25 Jul 2020)
New Revision: 580
Removed:
pkg/CHNOSZ/man/protein.Rd
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/examples.R
pkg/CHNOSZ/man/CHNOSZ-package.Rd
pkg/CHNOSZ/man/add.protein.Rd
pkg/CHNOSZ/man/buffer.Rd
pkg/CHNOSZ/man/diagram.Rd
pkg/CHNOSZ/man/info.Rd
pkg/CHNOSZ/man/protein.info.Rd
Log:
Remove man/protein.Rd (unused examples for proteins)
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2020-07-25 05:27:55 UTC (rev 579)
+++ pkg/CHNOSZ/DESCRIPTION 2020-07-25 05:47:15 UTC (rev 580)
@@ -1,6 +1,6 @@
Date: 2020-07-25
Package: CHNOSZ
-Version: 1.3.6-53
+Version: 1.3.6-54
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/examples.R
===================================================================
--- pkg/CHNOSZ/R/examples.R 2020-07-25 05:27:55 UTC (rev 579)
+++ pkg/CHNOSZ/R/examples.R 2020-07-25 05:47:15 UTC (rev 580)
@@ -14,7 +14,7 @@
"solubility", "equilibrate",
"diagram", "mosaic", "mix",
"buffer", "nonideal", "NaCl",
- "add.protein", "protein", "ionize.aa",
+ "add.protein", "ionize.aa",
"objective", "revisit", "EOSregress", "wjd")
plot.it <- FALSE
if(is.character(save.png))
Modified: pkg/CHNOSZ/man/CHNOSZ-package.Rd
===================================================================
--- pkg/CHNOSZ/man/CHNOSZ-package.Rd 2020-07-25 05:27:55 UTC (rev 579)
+++ pkg/CHNOSZ/man/CHNOSZ-package.Rd 2020-07-25 05:47:15 UTC (rev 580)
@@ -24,7 +24,7 @@
\item Thermodynamic data: \code{\link{data}}, \code{\link{extdata}}, \code{\link{add.OBIGT}}, \code{\link{util.data}}
\item Thermodynamic calculations: \code{\link{util.formula}}, \code{\link{makeup}}, \code{\link{util.units}}, \code{\link{eos}}, \code{\link{berman}}, \code{\link{nonideal}}, \code{\link{util.misc}}
\item Water properties: \code{\link{water}}, \code{\link{util.water}}, \code{\link{DEW}}, \code{\link{IAPWS95}}
- \item Protein properties: \code{\link{protein}}, \code{\link{protein.info}}, \code{\link{add.protein}}, \code{\link{util.fasta}}, \code{\link{util.protein}}, \code{\link{util.seq}}, \code{\link{ionize.aa}}
+ \item Protein properties: \code{\link{protein.info}}, \code{\link{add.protein}}, \code{\link{util.fasta}}, \code{\link{util.protein}}, \code{\link{util.seq}}, \code{\link{ionize.aa}}
\item Other tools: \code{\link{examples}}, \code{\link{eqdata}}, \code{\link{taxonomy}}, \code{\link{util.blast}}
\item Utility functions: \code{\link{util.expression}}, \code{\link{util.plot}}, \code{\link{util.array}}, \code{\link{util.matrix}}, \code{\link{util.list}}, \code{\link{util.test}}, \code{\link{palply}}
}
Modified: pkg/CHNOSZ/man/add.protein.Rd
===================================================================
--- pkg/CHNOSZ/man/add.protein.Rd 2020-07-25 05:27:55 UTC (rev 579)
+++ pkg/CHNOSZ/man/add.protein.Rd 2020-07-25 05:47:15 UTC (rev 580)
@@ -61,8 +61,6 @@
\code{\link{read.fasta}} and \code{\link{uniprot.aa}} for other ways of getting amino acid compositions.
\code{\link{pinfo}} for protein-level functions (length, chemical formulas, reaction coefficients of basis species).
-
-\code{\link{protein}} for examples of affinity calculations and diagrams.
}
\concept{Protein properties}
Modified: pkg/CHNOSZ/man/buffer.Rd
===================================================================
--- pkg/CHNOSZ/man/buffer.Rd 2020-07-25 05:27:55 UTC (rev 579)
+++ pkg/CHNOSZ/man/buffer.Rd 2020-07-25 05:47:15 UTC (rev 580)
@@ -42,10 +42,6 @@
This function is compatible with systems of proteins, but note that for buffers \emph{made} of proteins the buffer calculations presently use whole protein formulas (instead of residue equivalents) and consider nonionized proteins only.
}
-\seealso{
-\code{\link{protein}} for an example using a buffer made of proteins.
-}
-
\examples{
\dontshow{reset()}
## list the buffers
Modified: pkg/CHNOSZ/man/diagram.Rd
===================================================================
--- pkg/CHNOSZ/man/diagram.Rd 2020-07-25 05:27:55 UTC (rev 579)
+++ pkg/CHNOSZ/man/diagram.Rd 2020-07-25 05:47:15 UTC (rev 580)
@@ -180,7 +180,7 @@
}
\seealso{
-Other examples are present in the help for \code{\link{protein}} and \code{\link{buffer}}, and even more can be found in \code{\link{demos}}.
+Other examples are present in the help for \code{\link{buffer}}, and even more can be found in \code{\link{demos}}.
}
\examples{
Modified: pkg/CHNOSZ/man/info.Rd
===================================================================
--- pkg/CHNOSZ/man/info.Rd 2020-07-25 05:27:55 UTC (rev 579)
+++ pkg/CHNOSZ/man/info.Rd 2020-07-25 05:47:15 UTC (rev 580)
@@ -29,7 +29,7 @@
Note that names (not formulas) of inorganic species, such as \samp{oxygen} and \samp{methane}, are used only for the gas.
Names of species including an underscore character are indicative of proteins, e.g. \samp{LYSC_CHICK}.
-If the name of a protein is provided to \code{info} and the composition of the protein can be found using \code{\link{protein}}, the thermodyamic properties and parameters of the nonionized protein (calculated using amino acid group additivity) are added to the thermodynamic database.
+If the name of a protein is provided to \code{info} and the composition of the protein can be found using \code{\link{pinfo}}, the thermodyamic properties and parameters of the nonionized protein (calculated using amino acid group additivity) are added to the thermodynamic database.
Included in the return value, as for other species, is the index of the protein in the thermodynamic database or \code{NA} if the protein is not found. Names of proteins and other species can be mixed.
If no exact matches are found, \code{info} searches the database for similar names or formulas using \code{\link{agrep}}.
Deleted: pkg/CHNOSZ/man/protein.Rd
===================================================================
--- pkg/CHNOSZ/man/protein.Rd 2020-07-25 05:27:55 UTC (rev 579)
+++ pkg/CHNOSZ/man/protein.Rd 2020-07-25 05:47:15 UTC (rev 580)
@@ -1,80 +0,0 @@
-\encoding{UTF-8}
-\name{protein}
-\alias{protein}
-\title{Examples of Calculations for Proteins}
-\description{
-This page contains some examples of using the functions in CHNOSZ to calculate thermodynamic properties of and make diagrams for proteins.
-}
-
-\examples{\dontshow{reset()}
-## Standard molal entropy of a protein reaction
-basis("CHNOS")
-# here we provide the reaction coefficients of the
-# proteins (per protein backbone); subcrt() calculates
-# the coefficients of the basis species in the reaction
-s <- subcrt(c("CSG_METTL", "CSG_METJA"), c(-1/530, 1/530),
- T=seq(0, 350, length.out=50))
-# note: this uses the properties of the nonionized proteins
-
-## logfO2-pH potential diagram
-# with a charged basis, we calculate properties of ionized proteins
-basis("CHNOS+")
-file <- system.file("extdata/protein/POLG.csv", package = "CHNOSZ")
-aa <- read.csv(file, as.is = TRUE)
-ip <- add.protein(aa)
-a <- affinity(pH = c(6, 12), O2 = c(-64, -61), T = 75, iprotein = ip)
-diagram(a)
-title(main = "Poliovirus proteins")
-
-## surface-layer proteins from Methanococcus and others
-## as a function of oxygen fugacity, after Dick, 2008, Fig. 5b
-# to reproduce the calculations in the paper,
-# use superseded data for [Met], [Gly] and [UPBB]
-reset()
-add.OBIGT("OldAA")
-# make our protein list
-organisms <- c("METSC", "METJA", "METFE", "HALJP", "METVO",
- "METBU", "ACEKI", "GEOSE", "BACLI", "AERSA")
-proteins <- c(rep("CSG", 6), rep("SLAP", 4))
-proteins <- paste(proteins, organisms, sep="_")
-# load the basis species and proteins
-basis("CHNOS+")
-species(proteins)
-# calculate affinities; we go to lower logfO2 than Dick, 2008
-# and find an interesting convergence of stabilities there
-a <- affinity(O2=c(-100, -65))
-# try normalize=FALSE to make Fig. 5a in the paper
-e <- equilibrate(a, normalize=TRUE)
-d <- diagram(e, ylim=c(-5, -1), names=organisms, format.names=FALSE)
-# add water stability line
-abline(v=-83.1, lty=2)
-title(main="Surface-layer proteins, after Dick, 2008")
-# checking the geometry of the diagram
-# most preominant along the x-axis
-stopifnot(organisms[unique(which.pmax(e$loga.equil))] ==
- c("METFE", "METJA", "METVO", "HALJP"))
-# stability order close to logfO2=-83.1
-stopifnot(order(as.data.frame(e$loga.equil)[124,],
- decreasing=TRUE)==c(2, 6, 7, 5, 3, 1, 9, 8, 10, 4))
-# reset thermodynamic database
-reset()
-
-## relative stabilities of bovine proteins
-## as a function of temperature along a glutathione redox buffer
-mod.buffer("GSH-GSSG", c("GSH","GSSG"), logact=c(-3, -7))
-basis(c("CO2", "H2O", "NH4+", "SO4-2", "H2", "H+"),
- c(-1, 0, -4, -4, 999, -7))
-basis("H2", "GSH-GSSG")
-basis("CO2", "gas")
-prot <- c("CYC", "RNAS1", "BPT1", "ALBU", "INS", "PRIO")
-species(prot, "BOVIN")
-a <- affinity(T=c(0, 200))
-# set line colors according to oxidation state of carbon
-ZC <- ZC(species()$ispecies)
-col <- ZC.col(ZC)
-e <- equilibrate(a, normalize=TRUE)
-d <- diagram(e, col=col, lwd=3)
-title(main="Bovine proteins, GSH/GSSG redox buffer")
-}
-
-\concept{Protein properties}
Modified: pkg/CHNOSZ/man/protein.info.Rd
===================================================================
--- pkg/CHNOSZ/man/protein.info.Rd 2020-07-25 05:27:55 UTC (rev 579)
+++ pkg/CHNOSZ/man/protein.info.Rd 2020-07-25 05:47:15 UTC (rev 580)
@@ -70,10 +70,9 @@
\examples{\dontshow{reset()}
# search by name in thermo()$protein
+# these are the same: ip1 == ip2
ip1 <- pinfo("LYSC_CHICK")
ip2 <- pinfo("LYSC", "CHICK")
-# these are the same
-stopifnot(all.equal(ip1, ip2))
# two organisms with the same protein name
ip3 <- pinfo("MYG", c("HORSE", "PHYCA"))
# their amino acid compositions
@@ -81,9 +80,8 @@
# their thermodynamic properties by group additivity
protein.OBIGT(ip3)
-# an example of an unrecognized protein name
+# an unknown protein name gives NA
ip4 <- pinfo("MYGPHYCA")
-stopifnot(is.na(ip4))
## example for chicken lysozyme C
# index in thermo()$protein
@@ -99,13 +97,7 @@
# calculation of standard thermodynamic properties
# (subcrt uses the species name, not ip)
subcrt("LYSC_CHICK")
-# affinity calculation, protein identified by ip
-basis("CHNOS+")
-affinity(iprotein=ip)
-# affinity calculation, protein loaded as a species
-species("LYSC_CHICK")
-affinity()
-# NB: subcrt() only shows the properties of the non-ionized
+# NOTE: subcrt() only shows the properties of the non-ionized
# protein, but affinity() uses the properties of the ionized
# protein if the basis species have H+
@@ -113,49 +105,12 @@
protein.formula("P53_PIG")
protein.formula(pinfo("P53_PIG"))
protein.formula(pinfo(pinfo("P53_PIG")))
-
-\dontshow{opar <- par(no.readonly=TRUE)}
-# using pinfo() with regexp=TRUE:
-# plot ZC and nH2O/residue of HOX proteins
-# basis species: glutamine-glutamic acid-cysteine-O2-H2O
-basis("QEC")
-# device setup
-par(mfrow=c(2, 2))
-# a red-blue scale from 1-13
-col <- ZC.col(1:13)
-# axis labels
-ZClab <- axis.label("ZC")
-nH2Olab <- expression(bar(italic(n))[H[2]*O])
-# loop over HOX gene clusters
-for(cluster in c("A", "B", "C", "D")) {
- # get protein indices
- pattern <- paste0("^HX", cluster)
- ip <- pinfo(pattern, "HUMAN", regexp=TRUE)
- # calculate ZC and nH2O/residue
- thisZC <- ZC(protein.formula(ip))
- thisH2O <- protein.basis(ip)[, "H2O"] / protein.length(ip)
- # plot lines
- plot(thisZC, thisH2O, type="l", xlab=ZClab, ylab=nH2Olab)
- # the number of the HOX gene
- pname <- pinfo(ip)$protein
- nHOX <- as.numeric(gsub("[A-Za-z]*", "", pname))
- # plot colored points
- points(thisZC, thisH2O, pch=19, col=col[nHOX], cex=3.5)
- points(thisZC, thisH2O, pch=19, col="white", cex=2.5)
- # plot the number of the HOX gene
- text(thisZC, thisH2O, nHOX)
- # add title
- title(main=paste0("HOX", cluster))
}
-\dontshow{par(opar)}
-}
\references{
Dick, J. M., LaRowe, D. E. and Helgeson, H. C. (2006) Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins. \emph{Biogeosciences} \bold{3}, 311--336. \url{https://doi.org/10.5194/bg-3-311-2006}
LaRowe, D. E. and Dick, J. M. (2012) Calculation of the standard molal thermodynamic properties of crystalline peptides. \emph{Geochim. Cosmochim. Acta} \bold{80}, 70--91. \url{https://doi.org/10.1016/j.gca.2011.11.041}
-
- Dick, J. M. (2014) Average oxidation state of carbon in proteins. \emph{J. R. Soc. Interface} \bold{11}, 20131095. \url{https://doi.org/10.1098/rsif.2013.1095}
}
\concept{Protein properties}
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