[CHNOSZ-commits] r588 - in pkg/CHNOSZ: . R demo inst inst/extdata/OBIGT inst/extdata/adds inst/extdata/thermo man tests/testthat
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Jul 27 06:02:40 CEST 2020
Author: jedick
Date: 2020-07-27 06:02:39 +0200 (Mon, 27 Jul 2020)
New Revision: 588
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/examples.R
pkg/CHNOSZ/R/makeup.R
pkg/CHNOSZ/demo/AkDi.R
pkg/CHNOSZ/demo/DEW.R
pkg/CHNOSZ/demo/NaCl.R
pkg/CHNOSZ/demo/ORP.R
pkg/CHNOSZ/demo/Shh.R
pkg/CHNOSZ/demo/TCA.R
pkg/CHNOSZ/demo/adenine.R
pkg/CHNOSZ/demo/affinity.R
pkg/CHNOSZ/demo/aluminum.R
pkg/CHNOSZ/demo/arsenic.R
pkg/CHNOSZ/demo/buffer.R
pkg/CHNOSZ/demo/carboxylase.R
pkg/CHNOSZ/demo/comproportionation.R
pkg/CHNOSZ/demo/contour.R
pkg/CHNOSZ/demo/copper.R
pkg/CHNOSZ/demo/dehydration.R
pkg/CHNOSZ/demo/density.R
pkg/CHNOSZ/demo/findit.R
pkg/CHNOSZ/demo/glycinate.R
pkg/CHNOSZ/demo/gold.R
pkg/CHNOSZ/demo/ionize.R
pkg/CHNOSZ/demo/lambda.R
pkg/CHNOSZ/demo/mosaic.R
pkg/CHNOSZ/demo/protbuff.R
pkg/CHNOSZ/demo/protein.equil.R
pkg/CHNOSZ/demo/saturation.R
pkg/CHNOSZ/demo/solubility.R
pkg/CHNOSZ/demo/sources.R
pkg/CHNOSZ/demo/sphalerite.R
pkg/CHNOSZ/inst/CHECKLIST
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv
pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
pkg/CHNOSZ/man/examples.Rd
pkg/CHNOSZ/tests/testthat/test-makeup.R
Log:
Add library(CHNOSZ) to demos and test for makeup() with unattached package
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/DESCRIPTION 2020-07-27 04:02:39 UTC (rev 588)
@@ -1,6 +1,6 @@
Date: 2020-07-27
Package: CHNOSZ
-Version: 1.3.6-61
+Version: 1.3.6-62
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 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/R/examples.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -33,7 +33,7 @@
demos <- function(which=c("sources", "protein.equil", "affinity", "NaCl", "density",
"ORP", "findit", "ionize", "buffer", "protbuff", "glycinate",
"mosaic", "copper", "arsenic", "solubility", "gold", "contour", "sphalerite",
- "bugstab", "Shh", "saturation", "adenine", "DEW", "lambda", "TCA", "aluminum",
+ "Shh", "saturation", "adenine", "DEW", "lambda", "TCA", "aluminum",
"AkDi", "comproportionation"), save.png=FALSE) {
# run one or more demos from CHNOSZ with ask=FALSE, and return the value of the last one
for(i in 1:length(which)) {
@@ -47,7 +47,6 @@
width <- 500
height <- 500
if(which[i]=="comproportionation") width <- 600
- if(which[i]=="bugstab") width <- 700
png(paste(which[i], "%d.png", sep=""), width = width, height = height, pointsize = 12)
}
out <- demo(which[i], package="CHNOSZ", character.only=TRUE, echo=FALSE, ask=FALSE)
Modified: pkg/CHNOSZ/R/makeup.R
===================================================================
--- pkg/CHNOSZ/R/makeup.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/R/makeup.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -59,7 +59,7 @@
# if the formula argument is numeric,
# and if the thermo object is available,
# get the formula of that numbered species from thermo()$OBIGT
- if(exists("CHNOSZ")) {
+ if("CHNOSZ" %in% .packages()) {
thermo <- get("thermo", CHNOSZ)
if(is.numeric(formula)) formula <- thermo$OBIGT$formula[formula]
}
@@ -87,7 +87,7 @@
# all done with the counting, now apply the multiplier
out <- out * multiplier
# complain if there are any elements that look strange
- if(exists("CHNOSZ")) {
+ if("CHNOSZ" %in% .packages()) {
are.elements <- names(out) %in% thermo$element$element
if(!all(are.elements)) warning(paste("element(s) not in thermo()$element:",
paste(names(out)[!are.elements], collapse=" ") ))
Modified: pkg/CHNOSZ/demo/AkDi.R
===================================================================
--- pkg/CHNOSZ/demo/AkDi.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/AkDi.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -1,6 +1,7 @@
# CHNOSZ/demo/AkDi.R
# calculations using the Akinfiev-Diamond model 20190220
# after Fig. 1 of Akinfiev and Diamond, 2003
+library(CHNOSZ)
# function to plot natural logarithm of Henry's constant
lines.KH <- function(name = "CO2", T = 1:373, P = "Psat", HKF = FALSE, altH2S = FALSE) {
Modified: pkg/CHNOSZ/demo/DEW.R
===================================================================
--- pkg/CHNOSZ/demo/DEW.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/DEW.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -1,4 +1,5 @@
# demo for the Deep Earth Water (DEW) model in CHNOSZ 20170927
+library(CHNOSZ)
# set up subplots
opar <- par(mfrow = c(2, 2), mar=c(3.0, 3.5, 2.5, 1.0), mgp=c(1.7, 0.3, 0), las=1, tcl=0.3, xaxs="i", yaxs="i")
Modified: pkg/CHNOSZ/demo/NaCl.R
===================================================================
--- pkg/CHNOSZ/demo/NaCl.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/NaCl.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -4,6 +4,7 @@
## Calculation of the thermodynamic properties of aqueous species at high pressures and temperatures:
## Effective electrostatic radii, dissociation constants and standard partial molal properties to 1000 degrees C and 5 kbar.
## J. Chem. Soc. Faraday Trans. 88, 803-826. https://doi.org/10.1039/FT9928800803 )
+library(CHNOSZ)
## uncomment these lines to make the plot with the g-function disabled
#mod.OBIGT("Cl-", z=0)
Modified: pkg/CHNOSZ/demo/ORP.R
===================================================================
--- pkg/CHNOSZ/demo/ORP.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/ORP.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -1,5 +1,6 @@
# CHNOSZ/demo/ORP.R
# first version 20100715 jmd
+library(CHNOSZ)
# calculate the temperature dependence of
# potentials vs. standard hydrogen electrode (SHE) of various electrodes (Ag/AgCl)
Modified: pkg/CHNOSZ/demo/Shh.R
===================================================================
--- pkg/CHNOSZ/demo/Shh.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/Shh.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -1,5 +1,6 @@
# 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)
+library(CHNOSZ)
# to reproduce the calculations in the paper, use superseded data for [Gly] and [UPBB] 20190206
add.OBIGT("OldAA", c("[Gly]", "[UPBB]"))
Modified: pkg/CHNOSZ/demo/TCA.R
===================================================================
--- pkg/CHNOSZ/demo/TCA.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/TCA.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -2,6 +2,7 @@
# Reproduce Fig. 6 in Canovas and Shock, 2016:
# Plots of the standard partial molal Gibbs energy of reaction for each step in
# the citric acid cycle for temperatures to 500 degrees C and pressures to 5 kbar.
+library(CHNOSZ)
# species in reactions
NADox <- "NAD(ox)-"; NADred <- "NAD(red)-2"
Modified: pkg/CHNOSZ/demo/adenine.R
===================================================================
--- pkg/CHNOSZ/demo/adenine.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/adenine.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -1,5 +1,6 @@
# CHNOSZ/demos/adenine.R
# plot thermodynamic data and model fits for aqueous adenine 20170725
+library(CHNOSZ)
# notable functions in this demo:
# EOSregress() - to regress HKF coefficients from Cp data
Modified: pkg/CHNOSZ/demo/affinity.R
===================================================================
--- pkg/CHNOSZ/demo/affinity.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/affinity.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -2,6 +2,8 @@
## after Amend and Shock, 2001, Fig. 7
## Amend, J. P. and Shock, E. L. (2001) Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and Bacteria.
## FEMS Microbiol. Rev. 25, 175--243. https://doi.org/10.1016/S0168-6445(00)00062-0
+library(CHNOSZ)
+
# use aq state for all basis species (including O2)
basis(c("CO2", "H2", "NH3", "O2", "H2S", "H+"), "aq")
# we're going to make H2O
Modified: pkg/CHNOSZ/demo/aluminum.R
===================================================================
--- pkg/CHNOSZ/demo/aluminum.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/aluminum.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -1,6 +1,7 @@
# CHNOSZ/demo/aluminum.R
# 20171018 comparisons with calculations of SUPCRTBL
# 20190415 add diagrams from Tutolo et al., 2014
+library(CHNOSZ)
## set up plotting area
opar <- par(mfrow = c(2, 2))
Modified: pkg/CHNOSZ/demo/arsenic.R
===================================================================
--- pkg/CHNOSZ/demo/arsenic.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/arsenic.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -1,8 +1,8 @@
# CHNOSZ/demo/arsenic.R
# Eh-pH diagram for the system As-O-H-S,
# after Lu and Zhu, 2011 (doi:10.1007/s12665-010-0652-x)
-
# 20190415 extracted from go-IU.R; use retrieve()
+library(CHNOSZ)
# define temperature (degrees C), pressure (bar), grid resolution
res <- 500
Modified: pkg/CHNOSZ/demo/buffer.R
===================================================================
--- pkg/CHNOSZ/demo/buffer.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/buffer.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -1,6 +1,7 @@
# demos/buffer.R
# calculate buffered activities of basis species using two methods
# reproduces Figure 6 of Schulte and Shock, 1995 (doi:10.1007/BF01581580)
+library(CHNOSZ)
b.species <- c("Fe", "CO2", "H2O", "N2", "H2", "H2S", "SiO2")
b.state <- c("cr", "gas", "liq", "gas", "gas", "aq", "aq")
Modified: pkg/CHNOSZ/demo/carboxylase.R
===================================================================
--- pkg/CHNOSZ/demo/carboxylase.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/carboxylase.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -2,6 +2,8 @@
# animate rank-activity diagrams over a temperature
# and logaH2 gradient, or plot a single one for a single temperature
# first version ca. 200903; packaged anim.carboxylase() 20110818; converted to demo 20171030
+library(CHNOSZ)
+
T <- 25:125
ntop <- 5
lcex <- 0.8
Modified: pkg/CHNOSZ/demo/comproportionation.R
===================================================================
--- pkg/CHNOSZ/demo/comproportionation.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/comproportionation.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -2,6 +2,7 @@
# Gibbs energy of sulfur comproportionation,
# after Fig. 1 of Amend et al., 2020 (doi:10.1111/1462-2920.14982)
# 20191112 jmd first version
+library(CHNOSZ)
# set basis species and activities
basis(c("H2S", "SO4-2", "H2O", "H+"))
Modified: pkg/CHNOSZ/demo/contour.R
===================================================================
--- pkg/CHNOSZ/demo/contour.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/contour.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -1,11 +1,11 @@
# CHNOSZ/demo/contour.R
# gold solubility contours on logfO2-pH diagram
+# After Williams-Jones et al., 2009, Fig. 3
+# doi:10.2113/gselements.5.5.281
# 20181107 initial version
# 20190415 cleanup for demo
+library(CHNOSZ)
-# After Williams-Jones et al., 2009, Fig. 3
-# doi:10.2113/gselements.5.5.281
-
# define temperature (degrees C), pressure (bar), grid resolution
T <- 250
P <- 500
Modified: pkg/CHNOSZ/demo/copper.R
===================================================================
--- pkg/CHNOSZ/demo/copper.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/copper.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -2,6 +2,7 @@
## After Fig. 2 of Aksu and Doyle, 2001
## (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)
+library(CHNOSZ)
# we need superseded data for Cu-Gly complexes 20190206
add.OBIGT("OldAA")
Modified: pkg/CHNOSZ/demo/dehydration.R
===================================================================
--- pkg/CHNOSZ/demo/dehydration.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/dehydration.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -1,4 +1,5 @@
# plot temperature dependence of log K for some dehydration reactions
+library(CHNOSZ)
# the RSVGTipsDevice package allows us to create an SVG file with
# tooltips and hyperlinks
Modified: pkg/CHNOSZ/demo/density.R
===================================================================
--- pkg/CHNOSZ/demo/density.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/density.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -1,4 +1,5 @@
# make T-P diagram for H2O, colored according to density
+library(CHNOSZ)
# IAPWS95 or SUPCRT92
method <- "IAPWS95"
Modified: pkg/CHNOSZ/demo/findit.R
===================================================================
--- pkg/CHNOSZ/demo/findit.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/findit.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -1,4 +1,6 @@
## findit() calculations for sulfur species
+library(CHNOSZ)
+
basis("CHNOS+")
basis("pH", 5)
species(c("H2S", "S2-2", "S3-2", "S2O3-2", "S2O4-2", "S3O6-2",
Modified: pkg/CHNOSZ/demo/glycinate.R
===================================================================
--- pkg/CHNOSZ/demo/glycinate.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/glycinate.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -1,6 +1,7 @@
# CHNOSZ/demo/glycinate.R
# plot logK of metal-glycinate complexes
# 20190207
+library(CHNOSZ)
# divalent metals
di <- c("Cu+2", "Ni+2", "Co+2", "Mn+2", "Zn+2", "Cd+2")
Modified: pkg/CHNOSZ/demo/gold.R
===================================================================
--- pkg/CHNOSZ/demo/gold.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/gold.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -2,6 +2,7 @@
# 20181101 jmd first version
# 20181109 add calculation of K+ molality
# 20190127 update Au species in OBIGT, not here
+library(CHNOSZ)
# set up system
# use H2S here: it's the predominant species at the pH of the QMK buffer -- see sulfur()
Modified: pkg/CHNOSZ/demo/ionize.R
===================================================================
--- pkg/CHNOSZ/demo/ionize.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/ionize.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -1,4 +1,6 @@
## ionize.aa(): Contour plots of net charge and ionization properties of LYSC_CHICK
+library(CHNOSZ)
+
aa <- pinfo(pinfo("LYSC_CHICK"))
pH <- seq(0, 14, 0.2)
T <- seq(0, 200, 2)
Modified: pkg/CHNOSZ/demo/lambda.R
===================================================================
--- pkg/CHNOSZ/demo/lambda.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/lambda.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -1,5 +1,7 @@
# plot effects of lambda transition in quartz
# after Berman 1988 Figs. 1 and 2
+library(CHNOSZ)
+
opar <- par(no.readonly = TRUE)
layout(matrix(c(1, 4:2, 1, 7:5), nrow=4), heights=c(0.7, 3, 3, 3))
# plot title first
Modified: pkg/CHNOSZ/demo/mosaic.R
===================================================================
--- pkg/CHNOSZ/demo/mosaic.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/mosaic.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -1,5 +1,6 @@
# CHNOSZ/demo/mosaic.R
# 20141221 first version
+library(CHNOSZ)
# Fe-minerals and aqueous species in Fe-S-O-H-C system
# after Garrels and Christ, 1965 Figure 7.21
Modified: pkg/CHNOSZ/demo/protbuff.R
===================================================================
--- pkg/CHNOSZ/demo/protbuff.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/protbuff.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -2,6 +2,8 @@
## thiol peroxidases from model bactera
## (ECOLI, BACSU mesophile; AQUAE thermophile,
## THIDA acidophile, BACHD alkaliphile)
+library(CHNOSZ)
+
basis("CHNOS+")
organisms <- c("ECOLI", "AQUAE", "BACSU", "BACHD", "THIDA")
species("TPX", organisms)
Modified: pkg/CHNOSZ/demo/protein.equil.R
===================================================================
--- pkg/CHNOSZ/demo/protein.equil.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/protein.equil.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -1,5 +1,7 @@
## steps in calculation of chemical activities of two proteins
## in metastable equilibrium, after Dick and Shock, 2011
+library(CHNOSZ)
+
protein <- pinfo(c("CSG_METVO", "CSG_METJA"))
# use superseded properties of [Met], [Gly], and [UPBB] (Dick et al., 2006)
add.OBIGT("OldAA")
Modified: pkg/CHNOSZ/demo/saturation.R
===================================================================
--- pkg/CHNOSZ/demo/saturation.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/saturation.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -1,10 +1,10 @@
# CHNOSZ/demo/saturation.R
+## Make equilibrium activity diagrams including saturation limits
+## and using activity ratios as variables
# first version (activity_ratios.R) 20170217
# keep one diagram and add saturation lines 20190127
+library(CHNOSZ)
-## Make equilibrium activity diagrams including saturation limits
-## and using activity ratios as variables
-
# The ratios are calculated with pH = 0 (activity of H+ = 1), so (activity of the ion) is equal to
# (activity of the ion) / [(activity of H+) ^ (charge of the ion)]
Modified: pkg/CHNOSZ/demo/solubility.R
===================================================================
--- pkg/CHNOSZ/demo/solubility.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/solubility.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -1,6 +1,7 @@
# CHNOSZ/demo/solubility.R: solubility of CO2 and calcite
# 20150306 jmd first version; used uniroot() to find zero affinity
# 20181031 use new vectorized, non-uniroot solubility(); add T-pH plots
+library(CHNOSZ)
# for comparison with published CO2 solubility plot, see Fig. 4.5 in
# Stumm and Morgan, 1996, Aquatic Chemistry: Chemical Equilibria and Rates in Natural Waters
Modified: pkg/CHNOSZ/demo/sources.R
===================================================================
--- pkg/CHNOSZ/demo/sources.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/sources.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -1,4 +1,6 @@
## cross-checking sources
+library(CHNOSZ)
+
# the reference sources
ref.source <- thermo()$refs$key
# sources in the primary thermodynamic database
Modified: pkg/CHNOSZ/demo/sphalerite.R
===================================================================
--- pkg/CHNOSZ/demo/sphalerite.R 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/demo/sphalerite.R 2020-07-27 04:02:39 UTC (rev 588)
@@ -1,6 +1,7 @@
# CHNOSZ/demo/sphalerite.R
# sphalerite solubility after Akinfiev and Tagirov, 2014, Fig. 13
# 20190526 jmd initial version
+library(CHNOSZ)
# set up chemical system
basis(c("ZnS", "Cl-", "H2S", "H2O", "O2", "H+"))
Modified: pkg/CHNOSZ/inst/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/inst/CHECKLIST 2020-07-27 04:02:39 UTC (rev 588)
@@ -1,14 +1,14 @@
****************************
Release checklist for CHNOSZ
- (updated 2020-07-11)
+ (updated 2020-07-27)
****************************
- Run examples() and demos() and inspect their output (especially plots)
- Install the package with --install-tests and run
- testthat::test_package("CHNOSZ", reporter = "progress") to:
- - run *all* tests (long ones are skipped under R CMD check --as-cran)
- - find warnings from tests that aren't shown in R CMD check
+ library(CHNOSZ); testthat::test_package("CHNOSZ", reporter = "progress")
+ - runs *all* tests (long ones are skipped under R CMD check --as-cran)
+ - finds warnings from tests that aren't shown in R CMD check
- Check that uniprot.aa() works with current UniProt web pages
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2020-07-27 04:02:39 UTC (rev 588)
@@ -236,8 +236,6 @@
different units (cal, J) in OBIGT can be used in subcrt, diagrams, etc.
in CHNOSZ.
- \item TODO: add library(CHNOSZ) to all scripts in demo/.
-
}
}
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv 2020-07-27 04:02:39 UTC (rev 588)
@@ -773,11 +773,9 @@
ZrCrO4+2,NA,ZrCrO4+2,aq,AML10,NA,03.Jul.10,cal,-318046,-354803,-41.459,64.52,-10.25,0.758,-5.9319,8.0834,-2.5338,54.6888,10.109,1.1717,1
RuCrO4+2,NA,RuCrO4+2,aq,AML10,NA,03.Jul.10,cal,-141077,-167607,5.976,6.81,4.55,2.5404,-1.5785,6.2143,-2.7138,14.3488,-1.6477,0.4535,2
ThCrO4+2,NA,ThCrO4+2,aq,AML10,NA,03.Jul.10,cal,-355180,-388722,-27.615,85.52,-8.88,1.059,-5.1967,7.7678,-2.5642,70.0375,14.3862,1.5061,2
-H3AsO4,NA,H3AsO4,aq,NA03.1,NA,17.Oct.17,J,-766750,-903450,183.07,NA,NA,NA,NA,NA,NA,NA,NA,NA,0
H2AsO4-,NA,H2AsO4-,aq,NA03.1,NA,17.Oct.17,J,-753650,-911420,112.38,NA,NA,NA,NA,NA,NA,NA,NA,NA,-1
HAsO4-2,NA,HAsO4-2,aq,NA03.1,NA,17.Oct.17,J,-713730,-908410,-11.42,NA,NA,NA,NA,NA,NA,NA,NA,NA,-2
AsO4-3,NA,AsO4-3,aq,NA03.1,NA,17.Oct.17,J,-646360,-890210,-176.31,NA,NA,NA,NA,NA,NA,NA,NA,NA,-3
-H3AsO3,NA,H3AsO3,aq,NA03.1,NA,17.Oct.17,J,-640030,-742360,195.83,NA,NA,NA,NA,NA,NA,NA,NA,NA,0
H2AsO3-,NA,H2AsO3-,aq,NA03.1,NA,17.Oct.17,J,-587660,-714740,112.79,NA,NA,NA,NA,NA,NA,NA,NA,NA,-1
HAsO3-2,NA,HAsO3-2,aq,NA03.1,NA,17.Oct.17,J,-507400,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,-2
AsO3-3,NA,AsO3-3,aq,NA03.1,NA,17.Oct.17,J,-421800,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,-3
Modified: pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2020-07-27 00:52:35 UTC (rev 587)
+++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2020-07-27 04:02:39 UTC (rev 588)
@@ -105,168 +105,168 @@
"OBIGT",708,"CF4","aq","cal",5.9,,-2329
"OBIGT",715,"AsH3","aq","cal",-2.67,,
"OBIGT",776,"RuCrO4+2","aq","cal",,,-4659
-"OBIGT",800,"AgCl","aq","cal",,-1.88,
-"OBIGT",801,"AgCl2-","aq","cal",1.65,,
-"OBIGT",802,"AgCl3-2","aq","cal",,,-546
-"OBIGT",806,"CuHS","aq","cal",7.35,-16.2,
-"OBIGT",814,"ZnO2-2","aq","cal",,-1.17,
-"OBIGT",840,"S3-","aq","cal",,,661
-"OBIGT",843,"CH4","aq","cal",-2.61,,
-"OBIGT",848,"hexane","aq","cal",1.43,3.21,
-"OBIGT",851,"ethylene","aq","cal",6.12,-3.82,
-"OBIGT",875,"propanol","aq","cal",-1.89,,
-"OBIGT",922,"La(Ac)2+","aq","cal",,,-779
-"OBIGT",925,"Sm(Ac)+2","aq","cal",,,-660
-"OBIGT",926,"Sm(Ac)2+","aq","cal",,,-621
-"OBIGT",939,"Ca(Ac)2","aq","cal",,,-1006
-"OBIGT",955,"La(Ac)3","aq","cal",,,-564
-"OBIGT",975,"Ce(Ac)+2","aq","cal",,,797
-"OBIGT",976,"Ce(Ac)2+","aq","cal",,,567
-"OBIGT",1004,"urea","aq","cal",-23.26,23.32,
-"OBIGT",1017,"propanoic acid","aq","cal",1.42,,
-"OBIGT",1036,"pimelic acid","aq","cal",,,-19931
-"OBIGT",1040,"formate","aq","cal",1.96,,
-"OBIGT",1042,"propanoate","aq","cal",1.68,,
-"OBIGT",1049,"n-decanoate","aq","cal",-1.93,,
-"OBIGT",1065,"oxalate-2","aq","cal",-3.19,,
-"OBIGT",1106,"Fe(For)+","aq","cal",,,587
-"OBIGT",1107,"Fe(For)2","aq","cal",,,639
-"OBIGT",1179,"Mg(But)2","aq","cal",,,-3347811
-"OBIGT",1208,"Yb(But)+2","aq","cal",,,665
-"OBIGT",1227,"Fe(Pent)2","aq","cal",,,532
-"OBIGT",1312,"Ba(HCO3)+","aq","cal",,,-5800
-"OBIGT",1332,"Li(Mal)-","aq","cal",,-3.22,
-"OBIGT",1336,"Pb(Mal)","aq","cal",,1.16,
-"OBIGT",1340,"Pb(Succ)","aq","cal",,1.49,
-"OBIGT",1341,"Na(Oxal)-","aq","cal",,-3.14,
-"OBIGT",1342,"K(Oxal)-","aq","cal",,-2.75,
-"OBIGT",1343,"Fe(Oxal)+","aq","cal",,-2.19,
-"OBIGT",1345,"Na(Mal)-","aq","cal",,-3.11,17018
-"OBIGT",1346,"K(Mal)-","aq","cal",,-2.63,17013
-"OBIGT",1348,"La(Mal)+","aq","cal",,-1.92,
-"OBIGT",1349,"Gd(Mal)+","aq","cal",,-1.73,
-"OBIGT",1350,"Lu(Mal)+","aq","cal",,-2.25,
-"OBIGT",1351,"Yb(Mal)+","aq","cal",,-2.05,
-"OBIGT",1352,"Th(Mal)+2","aq","cal",-1.29,-4.79,
-"OBIGT",1354,"Ce(Mal)+","aq","cal",,-1.75,
-"OBIGT",1355,"Nd(Mal)+","aq","cal",4.52,,
-"OBIGT",1356,"Sm(Mal)+","aq","cal",,-1.77,
-"OBIGT",1357,"Pr(Mal)+","aq","cal",,-1.75,
-"OBIGT",1358,"Eu(Mal)+","aq","cal",,-1.87,
-"OBIGT",1359,"Tb(Mal)+","aq","cal",,-1.92,
-"OBIGT",1360,"Dy(Mal)+","aq","cal",,-1.89,
-"OBIGT",1361,"Tm(Mal)+","aq","cal",,-2.08,
-"OBIGT",1362,"Ho(Mal)+","aq","cal",,-2.08,
-"OBIGT",1363,"Er(Mal)+","aq","cal",,-2.11,
-"OBIGT",1364,"Sc(Mal)+","aq","cal",,-1.97,
-"OBIGT",1365,"Fe(Mal)+","aq","cal",,-1.97,
-"OBIGT",1366,"Na(Succ)-","aq","cal",,-2.82,
-"OBIGT",1367,"K(Succ)-","aq","cal",,-2.39,
-"OBIGT",1373,"Th(Succ)+2","aq","cal",-1.21,-4.47,
-"OBIGT",1378,"NH4(Oxal)-","aq","cal",,-2.62,
-"OBIGT",1383,"Yb(Oxal)+","aq","cal",,-2.02,
-"OBIGT",1384,"Ce(Oxal)+","aq","cal",,-1.8,
-"OBIGT",1385,"Nd(Oxal)+","aq","cal",,-1.8,
-"OBIGT",1386,"Eu(Oxal)+","aq","cal",,-1.89,
-"OBIGT",1387,"Gd(Oxal)+","aq","cal",,-1.8,
-"OBIGT",1388,"Ru(Oxal)+","aq","cal",,-2.41,
-"OBIGT",1389,"Pa(Oxal)+2","aq","cal",-1.25,-4.63,
-"OBIGT",1390,"Th(Oxal)+2","aq","cal",-1.27,-4.69,
-"OBIGT",1391,"U(Oxal)+2","aq","cal",-1.25,-4.63,
-"OBIGT",1393,"Y(Oxal)+","aq","cal",,-2.11,
-"OBIGT",1398,"La(Oxal)+","aq","cal",,-1.87,
-"OBIGT",1399,"Tb(Oxal)+","aq","cal",,-1.92,
-"OBIGT",1400,"Er(Oxal)+","aq","cal",,-2.05,
-"OBIGT",1401,"Lu(Oxal)+","aq","cal",,-2.19,
-"OBIGT",1402,"Cr(Oxal)+","aq","cal",,-2.58,
-"OBIGT",1403,"Ga(Oxal)+","aq","cal",,-2.66,
-"OBIGT",1404,"Sc(Oxal)+","aq","cal",,-2.13,
-"OBIGT",1405,"In(Oxal)+","aq","cal",,-2.19,
-"OBIGT",1406,"Sm(Oxal)+","aq","cal",,-1.84,
-"OBIGT",1407,"Cs(Mal)-","aq","cal",,-2.39,
-"OBIGT",1408,"NH4(Mal)-","aq","cal",,-2.54,
-"OBIGT",1413,"In(Mal)+","aq","cal",,-2.11,
-"OBIGT",1414,"Y(Mal)+","aq","cal",,-2.02,29999
-"OBIGT",1422,"La(Succ)+","aq","cal",,-1.52,
-"OBIGT",1423,"NH4(Succ)-","aq","cal",,-2.26,
-"OBIGT",1425,"Fe(Succ)+","aq","cal",,-1.92,
-"OBIGT",1426,"Sc(Succ)+","aq","cal",,-1.77,
-"OBIGT",1428,"Sm(Succ)+","aq","cal",,-1.48,
-"OBIGT",1429,"Er(Succ)+","aq","cal",,-1.68,
-"OBIGT",1430,"U(Succ)+2","aq","cal",-1.15,-4.27,
-"OBIGT",1434,"La(Glut)+","aq","cal",,-1.23,
-"OBIGT",1435,"Y(Glut)+","aq","cal",,-1.46,
-"OBIGT",1436,"Sc(Glut)+","aq","cal",,-1.5,
-"OBIGT",1437,"Th(Glut)+2","aq","cal",-1.09,-4.05,
-"OBIGT",1440,"Fe(Glut)+","aq","cal",,-1.05,
-"OBIGT",1441,"Sm(Glut)+","aq","cal",,-1.2,
-"OBIGT",1443,"Er(Glut)+","aq","cal",,-1.4,-4673
-"OBIGT",1445,"Ba(Adip)","aq","cal",,1.19,
-"OBIGT",1452,"Pb(Adip)","aq","cal",,1.25,
-"OBIGT",1453,"Sc(Adip)+","aq","cal",,-1.22,
-"OBIGT",1455,"Th(Adip)+2","aq","cal",-1.02,-3.76,
-"OBIGT",1456,"U(Adip)+2","aq","cal",-1,-3.71,
-"OBIGT",1458,"Li(Oxal)-","aq","cal",,-3.3,
-"OBIGT",1462,"Li(Succ)-","aq","cal",,-2.94,
-"OBIGT",1464,"Na(Glut)-","aq","cal",,-2.34,
-"OBIGT",1465,"K(Glut)-","aq","cal",,-2.05,
-"OBIGT",1466,"Li(Glut)-","aq","cal",,-2.66,
-"OBIGT",1471,"Na(Adip)-","aq","cal",,-2.05,
-"OBIGT",1472,"K(Adip)-","aq","cal",,-1.76,
-"OBIGT",1473,"Li(Adip)-","aq","cal",,-2.38,
-"OBIGT",1479,"cyclohexane","aq","cal",9.35,6.64,
-"OBIGT",1480,"Ar","aq","cal",-1.24,-8.59,
-"OBIGT",1481,"benzene","aq","cal",,-1.14,
-"OBIGT",1482,"CO2","aq","cal",-4.94,,
-"OBIGT",1483,"Xe","aq","cal",2.8,,
-"OBIGT",1491,"ethanethiol","aq","cal",,,753
-"OBIGT",1493,"n-butanethiol","aq","cal",2.19,,
-"OBIGT",1515,"methyldiethanolamine","aq","cal",1.61,,
-"OBIGT",1518,"dimethylamine","aq","J",-8.05,,
-"OBIGT",1532,"cysteinate","aq","cal",-1,,
-"OBIGT",1558,"glucose","aq","cal",1.11,,
-"OBIGT",1586,"guanine","aq","cal",-4.26,,
-"OBIGT",1630,"dHUMP-","aq","cal",-3.13,,
-"OBIGT",1727,"MgADP-","aq","cal",-1.01,,
-"OBIGT",1738,"HNicMP(ox)","aq","cal",,9.4,
-"OBIGT",1746,"ribose-5-phosphate","aq","cal",,7.48,
-"OBIGT",1748,"ribose-5-phosphate-2","aq","cal",1.53,,
-"OBIGT",1749,"H4NADP(red)","aq","cal",1.73,,
-"OBIGT",1750,"H3NADP(red)-","aq","cal",2.41,,
-"OBIGT",1751,"H2NADP(red)-2","aq","cal",1.28,,
-"OBIGT",1752,"HNADP(red)-3","aq","cal",2.09,,
-"OBIGT",1753,"NADP(red)-4","aq","cal",1.09,,
-"OBIGT",1755,"H3NADP(ox)","aq","cal",1.05,,
-"OBIGT",1826,"diglycine+","aq","cal",-177.69,,
-"OBIGT",1827,"diglycine-","aq","cal",-49.22,,565
-"OBIGT",1828,"triglycine+","aq","cal",,1.75,
-"OBIGT",1829,"triglycine-","aq","cal",,1.78,
-"OBIGT",1888,"hydromagnesite","cr","cal",,,-2569
-"OBIGT",1966,"jarosite","cr","cal",,,20697
-"OBIGT",1967,"natrojarosite","cr","cal",,,17554
-"OBIGT",1975,"realgar,alpha","cr","J",,,768
-"OBIGT",1976,"realgar,beta","cr","J",,,989
-"OBIGT",1977,"orpiment","cr","J",,,-1036
-"OBIGT",1985,"dawsonite","cr","J",,,19466
-"OBIGT",1987,"ferberite","cr","J",1.21,,
-"OBIGT",2009,"octadecane","cr","cal",-2.63,,
-"OBIGT",2010,"nonadecane","cr","cal",-13.32,,
-"OBIGT",2011,"eicosane","cr","cal",-2.79,,
-"OBIGT",2012,"heneicosane","cr","cal",-8.61,,
-"OBIGT",2013,"docosane","cr","cal",-2.63,,
-"OBIGT",2014,"tricosane","cr","cal",-5.22,,
-"OBIGT",2015,"tetracosane","cr","cal",-2.02,,
-"OBIGT",2016,"pentacosane","cr","cal",-2.93,,
-"OBIGT",2017,"hexacosane","cr","cal",-1.29,,
-"OBIGT",2018,"heptacosane","cr","cal",-1.23,,
-"OBIGT",2070,"carbazole","cr","cal",-43.39,,
-"OBIGT",2111,"triphenylene","cr","cal",,,541
-"OBIGT",2424,"deoxyadenosine","cr","cal",,,-2977
-"OBIGT",2582,"ethylene","gas","cal",-4.59,,
-"OBIGT",2592,"3,5-dimethylphenol","gas","cal",,,628
-"OBIGT",2902,"nonacontane","liq","cal",,,635
-"OBIGT",2909,"2-methyloctane","liq","cal",10,,
-"OBIGT",3322,"5,6-dithiadecane","liq","cal",2,,
+"OBIGT",798,"AgCl","aq","cal",,-1.88,
+"OBIGT",799,"AgCl2-","aq","cal",1.65,,
+"OBIGT",800,"AgCl3-2","aq","cal",,,-546
+"OBIGT",804,"CuHS","aq","cal",7.35,-16.2,
+"OBIGT",812,"ZnO2-2","aq","cal",,-1.17,
+"OBIGT",838,"S3-","aq","cal",,,661
+"OBIGT",841,"CH4","aq","cal",-2.61,,
+"OBIGT",846,"hexane","aq","cal",1.43,3.21,
+"OBIGT",849,"ethylene","aq","cal",6.12,-3.82,
+"OBIGT",873,"propanol","aq","cal",-1.89,,
+"OBIGT",920,"La(Ac)2+","aq","cal",,,-779
+"OBIGT",923,"Sm(Ac)+2","aq","cal",,,-660
+"OBIGT",924,"Sm(Ac)2+","aq","cal",,,-621
+"OBIGT",937,"Ca(Ac)2","aq","cal",,,-1006
+"OBIGT",953,"La(Ac)3","aq","cal",,,-564
+"OBIGT",973,"Ce(Ac)+2","aq","cal",,,797
+"OBIGT",974,"Ce(Ac)2+","aq","cal",,,567
+"OBIGT",1002,"urea","aq","cal",-23.26,23.32,
+"OBIGT",1015,"propanoic acid","aq","cal",1.42,,
+"OBIGT",1034,"pimelic acid","aq","cal",,,-19931
+"OBIGT",1038,"formate","aq","cal",1.96,,
+"OBIGT",1040,"propanoate","aq","cal",1.68,,
+"OBIGT",1047,"n-decanoate","aq","cal",-1.93,,
+"OBIGT",1063,"oxalate-2","aq","cal",-3.19,,
+"OBIGT",1104,"Fe(For)+","aq","cal",,,587
+"OBIGT",1105,"Fe(For)2","aq","cal",,,639
+"OBIGT",1177,"Mg(But)2","aq","cal",,,-3347811
+"OBIGT",1206,"Yb(But)+2","aq","cal",,,665
+"OBIGT",1225,"Fe(Pent)2","aq","cal",,,532
+"OBIGT",1310,"Ba(HCO3)+","aq","cal",,,-5800
+"OBIGT",1330,"Li(Mal)-","aq","cal",,-3.22,
+"OBIGT",1334,"Pb(Mal)","aq","cal",,1.16,
+"OBIGT",1338,"Pb(Succ)","aq","cal",,1.49,
+"OBIGT",1339,"Na(Oxal)-","aq","cal",,-3.14,
+"OBIGT",1340,"K(Oxal)-","aq","cal",,-2.75,
+"OBIGT",1341,"Fe(Oxal)+","aq","cal",,-2.19,
+"OBIGT",1343,"Na(Mal)-","aq","cal",,-3.11,17018
+"OBIGT",1344,"K(Mal)-","aq","cal",,-2.63,17013
+"OBIGT",1346,"La(Mal)+","aq","cal",,-1.92,
+"OBIGT",1347,"Gd(Mal)+","aq","cal",,-1.73,
+"OBIGT",1348,"Lu(Mal)+","aq","cal",,-2.25,
+"OBIGT",1349,"Yb(Mal)+","aq","cal",,-2.05,
+"OBIGT",1350,"Th(Mal)+2","aq","cal",-1.29,-4.79,
+"OBIGT",1352,"Ce(Mal)+","aq","cal",,-1.75,
+"OBIGT",1353,"Nd(Mal)+","aq","cal",4.52,,
+"OBIGT",1354,"Sm(Mal)+","aq","cal",,-1.77,
+"OBIGT",1355,"Pr(Mal)+","aq","cal",,-1.75,
+"OBIGT",1356,"Eu(Mal)+","aq","cal",,-1.87,
+"OBIGT",1357,"Tb(Mal)+","aq","cal",,-1.92,
+"OBIGT",1358,"Dy(Mal)+","aq","cal",,-1.89,
+"OBIGT",1359,"Tm(Mal)+","aq","cal",,-2.08,
+"OBIGT",1360,"Ho(Mal)+","aq","cal",,-2.08,
+"OBIGT",1361,"Er(Mal)+","aq","cal",,-2.11,
+"OBIGT",1362,"Sc(Mal)+","aq","cal",,-1.97,
+"OBIGT",1363,"Fe(Mal)+","aq","cal",,-1.97,
+"OBIGT",1364,"Na(Succ)-","aq","cal",,-2.82,
+"OBIGT",1365,"K(Succ)-","aq","cal",,-2.39,
+"OBIGT",1371,"Th(Succ)+2","aq","cal",-1.21,-4.47,
+"OBIGT",1376,"NH4(Oxal)-","aq","cal",,-2.62,
+"OBIGT",1381,"Yb(Oxal)+","aq","cal",,-2.02,
+"OBIGT",1382,"Ce(Oxal)+","aq","cal",,-1.8,
+"OBIGT",1383,"Nd(Oxal)+","aq","cal",,-1.8,
+"OBIGT",1384,"Eu(Oxal)+","aq","cal",,-1.89,
+"OBIGT",1385,"Gd(Oxal)+","aq","cal",,-1.8,
+"OBIGT",1386,"Ru(Oxal)+","aq","cal",,-2.41,
+"OBIGT",1387,"Pa(Oxal)+2","aq","cal",-1.25,-4.63,
+"OBIGT",1388,"Th(Oxal)+2","aq","cal",-1.27,-4.69,
+"OBIGT",1389,"U(Oxal)+2","aq","cal",-1.25,-4.63,
+"OBIGT",1391,"Y(Oxal)+","aq","cal",,-2.11,
+"OBIGT",1396,"La(Oxal)+","aq","cal",,-1.87,
+"OBIGT",1397,"Tb(Oxal)+","aq","cal",,-1.92,
+"OBIGT",1398,"Er(Oxal)+","aq","cal",,-2.05,
+"OBIGT",1399,"Lu(Oxal)+","aq","cal",,-2.19,
+"OBIGT",1400,"Cr(Oxal)+","aq","cal",,-2.58,
+"OBIGT",1401,"Ga(Oxal)+","aq","cal",,-2.66,
+"OBIGT",1402,"Sc(Oxal)+","aq","cal",,-2.13,
+"OBIGT",1403,"In(Oxal)+","aq","cal",,-2.19,
+"OBIGT",1404,"Sm(Oxal)+","aq","cal",,-1.84,
+"OBIGT",1405,"Cs(Mal)-","aq","cal",,-2.39,
+"OBIGT",1406,"NH4(Mal)-","aq","cal",,-2.54,
+"OBIGT",1411,"In(Mal)+","aq","cal",,-2.11,
+"OBIGT",1412,"Y(Mal)+","aq","cal",,-2.02,29999
+"OBIGT",1420,"La(Succ)+","aq","cal",,-1.52,
+"OBIGT",1421,"NH4(Succ)-","aq","cal",,-2.26,
+"OBIGT",1423,"Fe(Succ)+","aq","cal",,-1.92,
+"OBIGT",1424,"Sc(Succ)+","aq","cal",,-1.77,
+"OBIGT",1426,"Sm(Succ)+","aq","cal",,-1.48,
+"OBIGT",1427,"Er(Succ)+","aq","cal",,-1.68,
+"OBIGT",1428,"U(Succ)+2","aq","cal",-1.15,-4.27,
+"OBIGT",1432,"La(Glut)+","aq","cal",,-1.23,
+"OBIGT",1433,"Y(Glut)+","aq","cal",,-1.46,
+"OBIGT",1434,"Sc(Glut)+","aq","cal",,-1.5,
+"OBIGT",1435,"Th(Glut)+2","aq","cal",-1.09,-4.05,
+"OBIGT",1438,"Fe(Glut)+","aq","cal",,-1.05,
+"OBIGT",1439,"Sm(Glut)+","aq","cal",,-1.2,
+"OBIGT",1441,"Er(Glut)+","aq","cal",,-1.4,-4673
+"OBIGT",1443,"Ba(Adip)","aq","cal",,1.19,
+"OBIGT",1450,"Pb(Adip)","aq","cal",,1.25,
+"OBIGT",1451,"Sc(Adip)+","aq","cal",,-1.22,
+"OBIGT",1453,"Th(Adip)+2","aq","cal",-1.02,-3.76,
+"OBIGT",1454,"U(Adip)+2","aq","cal",-1,-3.71,
+"OBIGT",1456,"Li(Oxal)-","aq","cal",,-3.3,
+"OBIGT",1460,"Li(Succ)-","aq","cal",,-2.94,
+"OBIGT",1462,"Na(Glut)-","aq","cal",,-2.34,
+"OBIGT",1463,"K(Glut)-","aq","cal",,-2.05,
+"OBIGT",1464,"Li(Glut)-","aq","cal",,-2.66,
+"OBIGT",1469,"Na(Adip)-","aq","cal",,-2.05,
+"OBIGT",1470,"K(Adip)-","aq","cal",,-1.76,
+"OBIGT",1471,"Li(Adip)-","aq","cal",,-2.38,
+"OBIGT",1477,"cyclohexane","aq","cal",9.35,6.64,
+"OBIGT",1478,"Ar","aq","cal",-1.24,-8.59,
+"OBIGT",1479,"benzene","aq","cal",,-1.14,
+"OBIGT",1480,"CO2","aq","cal",-4.94,,
+"OBIGT",1481,"Xe","aq","cal",2.8,,
+"OBIGT",1489,"ethanethiol","aq","cal",,,753
+"OBIGT",1491,"n-butanethiol","aq","cal",2.19,,
+"OBIGT",1513,"methyldiethanolamine","aq","cal",1.61,,
+"OBIGT",1516,"dimethylamine","aq","J",-8.05,,
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 588
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