[CHNOSZ-commits] r510 - in pkg/CHNOSZ: . inst inst/extdata/cpetc man

Thu Oct 24 05:18:26 CEST 2019

Author: jedick
Date: 2019-10-24 05:18:25 +0200 (Thu, 24 Oct 2019)
New Revision: 510

Removed:
   pkg/CHNOSZ/inst/extdata/cpetc/RT71.csv
Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/man/examples.Rd
   pkg/CHNOSZ/man/extdata.Rd
   pkg/CHNOSZ/man/ionize.aa.Rd
Log:
remove RT71.csv (charge-pH curve for LYSC_CHICK)


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================

--- pkg/CHNOSZ/DESCRIPTION	2019-10-19 10:33:10 UTC (rev 509)
+++ pkg/CHNOSZ/DESCRIPTION	2019-10-24 03:18:25 UTC (rev 510)
@@ -1,6 +1,6 @@
-Date: 2019-10-19
+Date: 2019-10-24
 Package: CHNOSZ
-Version: 1.3.3-6
+Version: 1.3.3-7
 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/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2019-10-19 10:33:10 UTC (rev 509)
+++ pkg/CHNOSZ/inst/NEWS	2019-10-24 03:18:25 UTC (rev 510)
@@ -13,12 +13,12 @@
 - Fix bug in unexported function obigt2eos(): lambda (exponent in heat
   capacity equation) was incorrectly going through a units conversion.
 
-- Remove yeastgfp(), yeast.aa(), Sce.csv.xz, yeastgfp.csv.xz, and other
-  associated files. The data files and functions have been moved to the
-  JMDplots package (https://github.com/jedick/JMDplots).
+- Remove files Sce.csv.xz and yeastgfp.csv.xz and functions yeastgfp()
+  and yeast.aa(). These have been moved to the JMDplots package
+  (https://github.com/jedick/JMDplots).
 
-- Remove protein_refseq.csv.xz, which has been moved to
-  protein_refseq61.csv in JMDplots.
+- Remove protein_refseq.csv.xz (based on RefSeq release 61). An updated
+  version, based on RefSeq release 95, is available in JMDplots.
 
 CHANGES IN CHNOSZ 1.3.3 (2019-08-02)
 ------------------------------------

Deleted: pkg/CHNOSZ/inst/extdata/cpetc/RT71.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/cpetc/RT71.csv	2019-10-19 10:33:10 UTC (rev 509)
+++ pkg/CHNOSZ/inst/extdata/cpetc/RT71.csv	2019-10-24 03:18:25 UTC (rev 510)
@@ -1,28 +0,0 @@
-pH,Z
-1.291333,19.001552
-1.710776,19.043037
-1.947706,18.886528
-2.210429,18.808984
-2.632702,18.338036
-3.003823,17.630321
-3.216701,17.079503
-3.486171,15.780001
-3.755425,14.519916
-4.025984,13.023324
-4.133946,12.471989
-4.268573,11.841947
-4.562749,10.818501
-4.987852,9.835118
-5.35832,9.245657
-5.805951,8.93251
-6.411825,8.462466
-6.885684,8.149448
-7.386643,7.678888
-7.9923,7.248262
-8.440366,6.856279
-8.88865,6.424878
-9.312229,5.717421
-9.739725,4.300441
-9.955215,3.276606
-10.332213,1.504605
-10.440611,0.874434

Modified: pkg/CHNOSZ/man/examples.Rd
===================================================================
--- pkg/CHNOSZ/man/examples.Rd	2019-10-19 10:33:10 UTC (rev 509)
+++ pkg/CHNOSZ/man/examples.Rd	2019-10-24 03:18:25 UTC (rev 510)
@@ -14,11 +14,10 @@
 \usage{
   examples(save.png = FALSE)
   demos(which = c("sources", "protein.equil", "affinity", "NaCl",
-    "density", "ORP", "revisit", "findit", "ionize", "buffer",
-    "protbuff", "glycinate", "mosaic", "copper",
-    "arsenic", "solubility", "gold", "contour", "sphalerite", "wjd",
-    "bugstab", "Shh", "saturation", "adenine", "DEW", "lambda", "TCA",
-    "aluminum", "bison", "AkDi"),
+    "density", "ORP", "findit", "ionize", "buffer", "protbuff",
+    "glycinate", "mosaic", "copper", "arsenic", "solubility", "gold",
+    "contour", "sphalerite", "wjd", "bugstab", "Shh", "saturation",
+    "adenine", "DEW", "lambda", "TCA", "aluminum", "bison", "AkDi"),
     save.png=FALSE)
 }
 
@@ -37,7 +36,6 @@
     \code{NaCl} \tab Equilibrium constant for aqueous NaCl dissociation (Shock et al., 1992) \cr
     \code{density} \tab Density of \H2O, inverted from IAPWS-95 equations (\code{\link{rho.IAPWS95}}) \cr
     \code{ORP} \tab Temperature dependence of oxidation-reduction potential for redox standards \cr
-    \code{revisit} \tab Coefficient of variation of metastable equilibrium activities of proteins \cr
     \code{findit} \tab Minimize the standard deviation of logarithms of activities of sulfur species \cr
     \code{ionize} \tab ionize.aa(): contour plots of net charge and ionization properties of LYSC_CHICK \cr
     \code{buffer} \tab Minerals and aqueous species as buffers of hydrogen fugacity (Schulte and Shock, 1995) \cr

Modified: pkg/CHNOSZ/man/extdata.Rd
===================================================================
--- pkg/CHNOSZ/man/extdata.Rd	2019-10-19 10:33:10 UTC (rev 509)
+++ pkg/CHNOSZ/man/extdata.Rd	2019-10-24 03:18:25 UTC (rev 510)
@@ -38,7 +38,6 @@
   \itemize{
     \item \code{PM90.csv} Heat capacities of four unfolded aqueous proteins taken from Privalov and Makhatadze, 1990. Temperature in \degC is in the first column, and heat capacities of the proteins in J mol\eqn{^{-1}}{^-1} K\eqn{^{-1}}{^-1} in the remaining columns. See \code{\link{ionize.aa}} and the vignette \code{anintro.Rmd} for examples that use this file.
     \item \code{RH95.csv} Heat capacity data for iron taken from Robie and Hemingway, 1995. Temperature in Kelvin is in the first column, heat capacity in J K\eqn{^{-1}}{^-1} mol\eqn{^{-1}}{^-1} in the second. See \code{\link{subcrt}} for an example that uses this file.
-    \item \code{RT71.csv} pH titration measurements for unfolded lysozyme (\samp{LYSC_CHICK}) taken from Roxby and Tanford, 1971. pH is in the first column, net charge in the second. See \code{\link{ionize.aa}} for an example that uses this file.
     \item \code{SOJSH.csv} Experimental equilibrium constants for the reaction NaCl(aq) = Na+ + Cl- as a function of temperature and pressure taken from Fig. 1 of Shock et al., 1992. See \code{demo("NaCl")} for an example that uses this file.
     \item \code{Cp.CH4.HW97.csv}, \code{V.CH4.HWM96.csv} Apparent molar heat capacities and volumes of CH4 in dilute aqueous solutions reported by Hnědkovský and Wood, 1997 and Hnědkovský et al., 1996. See \code{\link{EOSregress}} and the vignette \code{eos-regress.Rmd} for examples that use these files.
     \item \code{SC10_Rainbow.csv} Values of temperature (\degC, pH and logarithms of activity of \CO2, \H2, \NH4plus, \H2S and \CH4 for mixing of seawater and hydrothermal fluid at Rainbow field (Mid-Atlantic Ridge), taken from Shock and Canovas, 2010. See the vignette \code{anintro.Rmd} for an example that uses this file.
@@ -157,10 +156,6 @@
 
 Robie, R. A. and Hemingway, B. S. (1995) \emph{Thermodynamic Properties of Minerals and Related Substances at 298.15 K and 1 Bar (\eqn{10^5} Pascals) Pressure and at Higher Temperatures}. U. S. Geol. Surv., Bull. 2131, 461 p. \url{http://www.worldcat.org/oclc/32590140}
 
-Roxby, R. and Tanford, C. (1971) Hydrogen ion titration curve of lysozyme in 6 M guanidine hydrochloride. \emph{Biochemistry} \bold{10}, 3348--3352. \url{https://doi.org/10.1021/bi00794a005}
-
-SGD project. \emph{Saccharomyces} Genome Database, \url{http://www.yeastgenome.org}
-
 Shock, E. and Canovas, P. (2010) The potential for abiotic organic synthesis and biosynthesis at seafloor hydrothermal systems. \emph{Geofluids} \bold{10}, 161--192. \url{https://doi.org/10.1111/j.1468-8123.2010.00277.x}
 
 Shock, E. L. and Koretsky, C. M. (1995) Metal-organic complexes in geochemical processes: Estimation of standard partial molal thermodynamic properties of aqueous complexes between metal cations and monovalent organic acid ligands at high pressures and temperatures. \emph{Geochim. Cosmochim. Acta} \bold{59}, 1497--1532. \url{https://doi.org/10.1016/0016-7037(95)00058-8}

Modified: pkg/CHNOSZ/man/ionize.aa.Rd
===================================================================
--- pkg/CHNOSZ/man/ionize.aa.Rd	2019-10-19 10:33:10 UTC (rev 509)
+++ pkg/CHNOSZ/man/ionize.aa.Rd	2019-10-24 03:18:25 UTC (rev 510)
@@ -34,32 +34,6 @@
 \seealso{ \code{\link{pinfo}}, \code{\link{affinity}} }
 
 \examples{\dontshow{reset()}
-## Charge of LYSC_CHICK as a function of pH and T
-# After Fig. 10 of Dick et al., 2006
-# the rownumber of the protein in thermo()$protein
-ip <- pinfo("LYSC_CHICK")
-# its amino acid composition
-aa <- pinfo(ip)
-# additive charges of unfolded protein at 25, 100, 150 degrees C
-# as a function of pH
-pH <- seq(0, 14, 0.1)
-Z.25 <- ionize.aa(aa, T=25, pH=pH)
-plot(pH, Z.25[, 1], type="l", xlab="pH", ylab="net charge (Z)")
-lines(pH, ionize.aa(aa, T=100, pH=pH)[, 1], col="red")
-lines(pH, ionize.aa(aa, T=150, pH=pH)[, 1], col="orange")
-text(c(12, 10, 9), c(-15, -16, -18),
-  labels=paste("T=", c(25, 100, 150), sep=""))
-# suppress ionization of cysteine as if it was oxidized 
-# (to form non-ionizable cystine disulfide bonds)
-lines(pH, ionize.aa(aa, T=25, pH=pH, suppress.Cys=TRUE)[, 1], lty=2)
-text(12, -7, "T=25, oxidized")
-# add experimental points
-RT71 <- read.csv(system.file("extdata/cpetc/RT71.csv", package="CHNOSZ"))
-points(RT71$pH, RT71$Z)
-legend("topright", pch=1, legend="Roxby and Tanford, 1971")
-title(main=paste("Ionization of unfolded LYSC_CHICK\n",
-  "After Dick et al., 2006"))
-
 ## Heat capacity of LYSC_CHICK as a function of T
 pH <- c(5, 9, 3)
 T <- seq(0, 100)

