[CHNOSZ-commits] r804 - in pkg/CHNOSZ: . inst inst/extdata/OBIGT inst/extdata/adds inst/extdata/thermo vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Sep 11 05:10:54 CEST 2023
Author: jedick
Date: 2023-09-11 05:10:54 +0200 (Mon, 11 Sep 2023)
New Revision: 804
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv
pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
pkg/CHNOSZ/vignettes/OBIGT.bib
Log:
Update charged amino acids with parameters from Kitadai (2015)
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2023-09-08 13:50:04 UTC (rev 803)
+++ pkg/CHNOSZ/DESCRIPTION 2023-09-11 03:10:54 UTC (rev 804)
@@ -1,6 +1,6 @@
-Date: 2023-09-08
+Date: 2023-09-11
Package: CHNOSZ
-Version: 2.0.0-23
+Version: 2.0.0-24
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.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2023-09-08 13:50:04 UTC (rev 803)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2023-09-11 03:10:54 UTC (rev 804)
@@ -12,7 +12,7 @@
% links to vignettes 20220723
\newcommand{\viglink}{\ifelse{html}{\out{<a href="../CHNOSZ/doc/#1.html"><strong>#1.Rmd</strong></a>}}{\bold{#1.Rmd}}}
-\section{Changes in CHNOSZ version 2.0.0-23 (2023-09-08)}{
+\section{Changes in CHNOSZ version 2.0.0-24 (2023-09-11)}{
\itemize{
@@ -54,6 +54,11 @@
\file{inorganic_cr.csv} so that \code{info("Fe2O3")} matches hematite
rather than maghemite.
+ \item Add 36 charged amino acids from
+ \href{https://doi.org/10.1007/s11084-015-9428-3}{Kitadai (2015)} and
+ update several others (Arg\S{+}, Arg\S{-}, Asp\S{-}, Glu\S{-}, His\S{+},
+ Lys\S{+}, Lys\S{-}, and Tyr\S{-}). Thanks to Grayson Boyer.
+
}
}
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv 2023-09-08 13:50:04 UTC (rev 803)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv 2023-09-11 03:10:54 UTC (rev 804)
@@ -831,24 +831,24 @@
NADP(ox)-3,NADP(ox)-3,C21H25N7O17P3-3,aq,LH06b,NA,2017-03-08,HKF,cal,-729596,-1015662,113.1,112.19,323.92,-28.7966,312.7727,-19.6642,-6.9367,297.97,-41.06,11.23,-3
alanine,Ala,C3H7NO2,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-88810,-132500,38.83,33.6,60.4,14.9,1.74,7.16,-3.69,49.5,-7,0.18,0
arginine,Arg,C6H14N4O2,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-57360,-143060,80.06,67.4,123.9,28.83,8.21,7.2,-5.95,94.8,-12.5,0.22,0
-argininium,Arg+,C6H15N4O2+,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-69930,-154880,82.57,77.6,122.5,31.72,0.22,5.46,-5.15,103.8,-9.6,0.73,0
-argininate,Arg-,C6H13N4O2-,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-40340,-129420,68.72,81.1,143,31.28,13.76,32.12,-9.94,141.9,-19.6,2.3,0
+argininium,Arg+,C6H15N4O2+,aq,Kit15.1,DLH06.1,2023-09-07,HKF,cal,-69630,-153860,84.98,77.6,122.5,31.72,0.22,5.46,-5.15,103.8,-9.6,0.73,1
+argininate,Arg-,C6H13N4O2-,aq,Kit15.1,DLH06.1,2023-09-07,HKF,cal,-41070,-142650,26.82,81.1,143,31.28,13.76,32.12,-9.94,141.9,-19.6,2.3,-1
asparagine,Asn,C4H8N2O3,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-125490,-182700,57.88,30.8,77.4,19.83,2.37,3.76,-4.81,56.5,-11.7,0.21,0
"aspartic acid",Asp,C4H7NO4,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-172510,-226340,55.22,32.4,74.7,18.96,3.05,-6.62,-2.23,58.1,-11.9,0.17,0
-aspartate,Asp-,C4H6NO4-,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-167170,-224540,43.34,2.7,64.8,16.96,5.77,10.11,-6.37,56.3,-15.3,2.47,0
+aspartate,Asp-,C4H6NO4-,aq,Kit15.1,DLH06.1,2023-09-07,HKF,cal,-167380,-225180,41.9,2.7,64.8,16.96,5.77,10.11,-6.37,56.3,-15.3,2.47,-1
cysteine,Cys,C3H7NO2S,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-80330,-124070,46.32,47.1,73.5,18.14,2.4,9.31,-4.97,59.8,-5.6,0.15,0
cysteinate,Cys-,C3H6NO2S-,aq,AH97b,DLH06.1,2006-11-28,HKF,cal,-68920,-115440,37.01,19.1,60.6,14.44,5.08,12.24,-3.68,61,-9.5,2.59,0
glutamine,Gln,C5H10N2O3,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-126280,-191860,62.41,43.8,93.7,23.22,3.58,5.44,-5.23,68.6,-11.4,0.18,0
"glutamic acid",Glu,C5H9NO4,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-173050,-234820,61.2,43.5,90.2,22.3,4.23,6.55,-5.84,65.2,-10,0.15,0
-glutamate,Glu-,C5H8NO4-,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-167210,-234150,43.86,7.6,80,20.49,6.96,10.86,-7.02,47.6,-7.8,2.65,0
+glutamate,Glu-,C5H8NO4-,aq,Kit15.1,DLH06.1,2023-09-11,HKF,cal,-167250,-233860,44.97,7.6,80,20.49,6.96,10.86,-7.02,47.6,-7.8,2.65,-1
glycine,Gly,C2H5NO2,aq,Kit14,DLH06.3,2019-02-06,HKF,cal,-88620,-122830,37.89,9.3,43.2,11.3,0.71,3.99,-3.04,28.5,-8.4,0.23,0
histidine,His,C6H9N3O2,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-48420,-108200,66,56.2,99.3,24.32,4.8,7.52,-6.05,81.6,-11.3,0.27,0
-histidinium,His+,C6H10N3O2+,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-56700,-115250,70.13,59.1,97,26.64,-3.4,-0.88,-3.07,88,-12,0.5,0
+histidinium,His+,C6H10N3O2+,aq,Kit15.1,DLH06.1,2023-09-07,HKF,cal,-56570,-115300,69.5,59.1,97,26.64,-3.4,-0.88,-3.07,88,-12,0.5,1
isoleucine,Ile,C6H13NO2,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-81990,-151600,49.7,91.6,105.8,24.49,6.55,18.16,-7.76,99.7,-3.6,0.09,0
leucine,Leu,C6H13NO2,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-84200,-153600,50.41,95.2,107.8,24.68,7.51,19.93,-8.37,102.7,-3.3,0.09,0
lysine,Lys,C6H14N2O2,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-80680,-159330,57.91,63.8,108.6,24.56,8.3,24.43,-9.53,86.6,-10.9,0.07,0
-lysinium,Lys+,C6H15N2O2+,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-92890,-170370,61.82,67.9,107.5,28.62,-1.51,4.47,-3.99,95.2,-8,1.21,0
-lysinate,Lys-,C6H13N2O2-,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-66310,-146340,53.27,72.8,112.2,28.29,10.53,2.97,-7.61,133.7,-18,2.67,0
+lysinium,Lys+,C6H15N2O2+,aq,Kit15.1,DLH06.1,2023-09-07,HKF,cal,-93080,-168720,68,67.9,107.5,28.62,-1.51,4.47,-3.99,95.2,-8,1.21,1
+lysinate,Lys-,C6H13N2O2-,aq,Kit15.1,DLH06.1,2023-09-07,HKF,cal,-65810,-148950,42.87,72.8,112.2,28.29,10.53,2.97,-7.61,133.7,-18,2.67,-1
methionine,Met,C5H11NO2S,aq,LD12.2,DLH06.4,2015-07-10,HKF,cal,-76959.8,-135210.3,62.81,70.7,105.4,24.95,6.9,13.59,-7.77,85.3,-6.6,0.13,0
phenylalanine,Phe,C9H11NO2,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-49430,-108900,56.6,93.8,122.1,28.27,8.8,19.34,-9.38,108.1,-6.5,0.12,0
proline,Pro,C5H9NO2,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-73560,-124100,49.83,43,82.6,19.39,4.87,11.88,-5.68,63.6,-9.5,0.14,0
@@ -856,7 +856,7 @@
threonine,Thr,C4H9NO3,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-119830,-178940,44.23,50.1,77.6,18.94,2.83,8.87,-4.87,65.5,-7.1,0.11,0
tryptophan,Trp,C11H12N2O2,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-26820,-97590,59.96,99.6,143.6,33.91,9.21,14.78,-9.36,116.8,-7.8,0.15,0
tyrosine,Tyr,C9H11NO3,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-91800,-157740,59.41,80.2,124.5,30.06,8.49,8.36,-8.58,106.2,-12.4,0.09,0
-tyrosinate,Tyr-,C9H10NO3-,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-79380,-149420,45.66,51.2,111.8,26.34,10.49,16.42,-7.59,109,-16,2.78,0
+tyrosinate,Tyr-,C9H10NO3-,aq,Kit15.1,DLH06.1,2023-09-11,HKF,cal,-79400,-148090,50.19,51.2,111.8,26.34,10.49,16.42,-7.59,109,-16,2.78,-1
valine,Val,C5H11NO2,aq,AH97b,DLH06.1,2006-08-25,HKF,cal,-85330,-146420,45.68,74,90.9,21.35,4.48,14.58,-6.12,83.8,-4.3,0.12,0
[Ala],NA,CH3,aq,DLH06,NA,2006-08-25,HKF,cal,-3936,-13290,16.85,35.671,26.864,5.43,3.6,4.39,-1.92,27.9,3.6,-0.05,0
[Arg],NA,C4H10N3,aq,DLH06,NA,2006-08-25,HKF,cal,31624,-20730,54.75,74.167,105.825,18.08,13.39,50.81,-10.09,73.2,-1.9,-0.53,0
@@ -1021,3 +1021,39 @@
"diaminopimelic acid",NA,C7H14N2O4,aq,LA16,OBIGT.9,2021-04-07,HKF,J,-644060,-977667,436.9,111.5,142.7,92.1,131.5,-37.7,12.2,276.1,-72.5,1.9,0
putrescine,NA,C4H12N2,aq,LA16,OBIGT.9,2021-04-07,HKF,J,77630,-151478,230.2,268,93.9,83.1,26,38.6,-9.5,321.9,-29.4,-0.6,0
spermidine,NA,C7H19N3,aq,LA16,OBIGT.9,2021-04-07,HKF,J,144361,-222539,338.4,378.6,147.4,130.8,38.8,67,-15.6,465.6,-46.7,-0.8,0
+alaninium,Ala+,C3H8NO2+,aq,Kit15,NA,2023-09-07,HKF,cal,-92000,-133200,47.18,64.5,67.9,20.02,-6.38,-7.07,-0.88,61.6,0.46,-0.21,1
+alaninate,Ala-,C3H6NO2-,aq,Kit15,NA,2023-09-07,HKF,cal,-75360,-121590,30.3,18,59.5,12.55,4.99,18.91,-5.78,28.9,-5.87,-0.32,-1
+argininium+2,Arg+2,C6H16N4O2+2,aq,Kit15,NA,2023-09-07,HKF,cal,-72110,-154860,89.96,105.5,132.6,38.92,-8.28,-15.7,-2.21,120.3,-3.25,0.9,2
+asparaginium,Asn+,C4H9N2O3+,aq,Kit15,NA,2023-09-07,HKF,cal,-128440,-183630,64.65,60.7,85.7,24.64,-4.5,-4.58,-2.24,68,0.06,0.81,1
+asparaginate,Asn-,C4H7N2O3-,aq,Kit15,NA,2023-09-07,HKF,cal,-113250,-172960,49.51,16.5,77.1,17.8,6.85,23.16,-7.12,44.6,-4.36,2.1,-1
+aspartinium,Asp+,C4H8NO4+,aq,Kit15,NA,2023-09-07,HKF,cal,-175170,-227970,58.68,58.1,84.9,22.74,-4.58,0.19,-2.18,58.9,-3.66,-0.73,1
+aspartate-2,Asp-2,C4H5NO4-2,aq,Kit15,NA,2023-09-07,HKF,cal,-153520,-215330,28.43,-9.9,64.8,15.19,9.1,23.54,-8.14,44.4,-12.45,3.16,-2
+cysteinium,Cys+,C3H8NO2S+,aq,Kit15,NA,2023-09-07,HKF,cal,-82660,-123930,54.63,76.3,81.7,22.85,-4.92,2.05,-1.93,71.6,6.86,1.01,1
+cysteinate-2,Cys-2,C3H5NO2S-2,aq,Kit15,NA,2023-09-07,HKF,cal,-54250,-107290,15.16,4.6,60.7,12.26,8.67,37.49,-7.83,49.6,-7.55,3.23,-2
+glutaminium,Gln+,C5H11N2O3+,aq,Kit15,NA,2023-09-07,HKF,cal,-129240,-192540,70.05,73.1,102.7,28.42,-2.72,-2.17,-3.52,81.4,0.02,0.9,1
+glutaminate,Gln-,C5H9N2O3-,aq,Kit15,NA,2023-09-07,HKF,cal,-113720,-182180,52.75,28.7,93.1,21.44,8.52,24.95,-8.33,58,-4.48,2.19,-1
+glutamic-acid+1,Glu+,C5H10NO4+,aq,Kit15,NA,2023-09-07,HKF,cal,-176050,-235700,68.31,65.7,98.1,25.66,-3.2,-5.05,-3.17,54.4,-4.36,-2.2,1
+glutamate-2,Glu-2,C5H7NO4-2,aq,Kit15,NA,2023-09-07,HKF,cal,-153650,-224900,29.42,-5.3,79.7,19.02,10.67,22.11,-9.27,34.8,-5.11,3.24,-2
+histidinate,His-,C6H8N3O2-,aq,Kit15,NA,2023-09-07,HKF,cal,-35760,-97700,58.75,37.9,97.7,21.36,9,25.83,-8.67,61.9,-7.79,0.62,-1
+histidinium+2,His+2,C6H11N3O2+2,aq,Kit15,NA,2023-09-07,HKF,cal,-58750,-116300,73.47,87.8,106.1,32.48,-11.06,-16.13,-0.21,102.9,-4.28,0.69,2
+isoleucinium,Ile+,C6H14NO2+,aq,Kit15,NA,2023-09-07,HKF,cal,-85190,-151830,59.64,120.5,115.1,31.68,-1.42,-6.57,-4.46,121,1.49,0.39,1
+isoleucinate,Ile-,C6H12NO2-,aq,Kit15,NA,2023-09-07,HKF,cal,-68750,-140690,41.92,77.6,106.1,24.15,9.89,21.15,-9.31,96,-4.9,0.75,-1
+leucinium,Leu+,C6H14NO2+,aq,Kit15,NA,2023-09-07,HKF,cal,-87380,-153990,59.75,122.4,117.3,31.28,-1.18,3.94,-4.63,119.1,7.09,1.22,1
+leucinate,Leu-,C6H12NO2-,aq,Kit15,NA,2023-09-07,HKF,cal,-70910,-142750,42.22,77,106.9,24.18,9.97,30.41,-9.37,95.5,2.2,2.51,-1
+lysinium+2,Lys+2,C6H16N2O2+2,aq,Kit15,NA,2023-09-07,HKF,cal,-95610,-168800,76.2,96.2,117,35.18,-9.91,-13.36,-1.03,110.8,-0.83,1.41,2
+methioninium,Met+,C5H12NO2S+,aq,Kit15,NA,2023-09-07,HKF,cal,-80000,-135510,72.13,95.1,114.4,30.54,-1.48,-3.31,-4.41,90.2,0.61,-0.4,1
+methionate,Met-,C5H10NO2S-,aq,Kit15,NA,2023-09-07,HKF,cal,-64410,-124840,55.51,51.8,105.7,24.39,9.85,19.31,-9.28,77.2,-7.41,0.87,-1
+phenylalaninium,Phe+,C9H12NO2+,aq,Kit15,NA,2023-09-07,HKF,cal,-52430,-109500,64.65,121,132.2,35.42,0.38,-0.44,-5.75,125.1,3.12,1.13,1
+phenylalanate,Phe-,C9H10NO2-,aq,Kit15,NA,2023-09-07,HKF,cal,-36730,-98200,49.89,75.7,120.9,28.15,11.44,25.73,-10.43,101.5,-1.74,2.42,-1
+prolinium,Pro+,C5H10NO2+,aq,Kit15,NA,2023-09-07,HKF,cal,-76220,-124440,57.61,73,88.5,24.19,-4.21,-4.18,-2.45,70.1,-2.05,-0.77,1
+prolinate,Pro-,C5H8NO2-,aq,Kit15,NA,2023-09-07,HKF,cal,-59040,-113790,35.72,40.8,82.9,16.94,7.45,32.3,-7.55,59.9,-5.41,0.7,-1
+serinium,Ser+,C3H8NO3+,aq,Kit15,NA,2023-09-07,HKF,cal,-126910,-173740,52.86,58.7,68.5,19.13,-6.3,-2.53,-0.94,56.3,-2.52,-0.82,1
+serinate,Ser-,C3H6NO3-,aq,Kit15,NA,2023-09-07,HKF,cal,-111370,-162070,39.82,12.3,60.4,13.15,5.09,19.39,-5.85,37.1,-9.2,0.35,-1
+threoninium,Thr+,C4H10NO3+,aq,Kit15,NA,2023-09-07,HKF,cal,-122910,-179820,51.61,78.4,86.1,23.15,-4.46,0.49,-2.27,77.2,-1.57,-0.48,1
+threonate,Thr-,C4H8NO3-,aq,Kit15,NA,2023-09-07,HKF,cal,-107330,-169020,35.59,34.7,75.8,15.31,6.71,27.6,-7.02,46.9,-6.02,-0.22,-1
+tryptophanium,Trp+,C11H13N2O2+,aq,Kit15,NA,2023-09-07,HKF,cal,-30050,-97520,71.04,126.6,154.5,41.24,2.72,-4.16,-7.44,134.7,0.62,1.02,1
+tryptophanate,Trp-,C11H11N2O2-,aq,Kit15,NA,2023-09-07,HKF,cal,-14050,-86880,42.99,81.1,141.9,33.75,13.65,21.44,-12.02,111,-4.28,2.31,-1
+tyrosinium,Tyr+,C9H12NO3+,aq,Kit15,NA,2023-09-07,HKF,cal,-94580,-157400,69.88,108,134.7,37.25,0.64,-8.74,-5.94,123,-1.88,1.22,1
+tyrosinate-2,Tyr-2,C9H9NO3-2,aq,Kit15,NA,2023-09-07,HKF,cal,-64820,-136740,39.35,15.3,101.6,24.63,12.97,20.83,-10.93,91.4,-21.73,3.48,-2
+valinium,Val+,C5H12NO2+,aq,Kit15,NA,2023-09-07,HKF,cal,-88450,-146590,55.57,103.5,100.4,27.2,-2.96,-1.29,-3.35,102.5,0.87,0.08,1
+valinate,Val-,C5H10NO2-,aq,Kit15,NA,2023-09-07,HKF,cal,-72070,-138360,28.23,54.8,88.8,20.38,8.07,18.6,-8,76.8,-6.27,0.79,-1
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2023-09-08 13:50:04 UTC (rev 803)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2023-09-11 03:10:54 UTC (rev 804)
@@ -200,6 +200,8 @@
SHA14.2,"D. A. Sverjensky et al.",2014,"Geochim. Cosmochim. Acta 129, 125-145","BO(OH): Revised May 2013",https://doi.org/10.1016/j.gca.2013.12.019
SHA14.3,"D. A. Sverjensky et al.",2014,"Geochim. Cosmochim. Acta 129, 125-145","Fitted to @HP97 data with a<sub>1</sub> pred. from the sum of the ions and used to predict the volume",https://doi.org/10.1016/j.gca.2013.12.019
SHA14.4,"D. A. Sverjensky et al.",2014,"Geochim. Cosmochim. Acta 129, 125-145","BO<sub>2</sub><sup>-</sup>: revised a<sub>1</sub>-a<sub>4</sub> using delkappan for BO<sub>2</sub><sup>-</sup> instead of B(OH)<sub>4</sub><sup>-</sup> used by @SH88; @SSWS97",https://doi.org/10.1016/j.gca.2013.12.019
+Kit15,"N. Kitadai",2015,"Origins Life Evol. Biospheres 45, 377-409","charged amino acids",https://doi.org/10.1007/s11084-015-9428-3
+Kit15.1,"N. Kitadai",2015,"Origins Life Evol. Biospheres 45, 377-409","charged amino acids GHS (Arg<sup>+</sup>, Arg<sup>-</sup>, Asp<sup>-</sup>, Glu<sup>-</sup>, His<sup>+</sup>, Lys<sup>+</sup>, Lys<sup>-</sup>, and Tyr<sup>-</sup>)",https://doi.org/10.1007/s11084-015-9428-3
PD15,"G. S. Pokrovski and J. Dubessy",2015,"Earth Planet. Sci. Lett. 411, 298-309","trisulfur radical ion",https://doi.org/10.1016/j.epsl.2014.11.035
LA16,"D. E. LaRowe and J. P. Amend",2016,"ISME J. 10, 1285-1295","fatty acids, saccharides, and other species",https://doi.org/10.1038/ismej.2015.227
SLOP16.1,"E. L. Shock et al.",2016,"slop16.dat computer data file",""Enthalpy changed to be compatible with the equation ΔH=ΔG+TΔS for the formation reaction from elements."",https://doi.org/10.5281/zenodo.2630820
Modified: pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2023-09-08 13:50:04 UTC (rev 803)
+++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2023-09-11 03:10:54 UTC (rev 804)
@@ -257,33 +257,42 @@
"OBIGT",1897,"heptose","aq","J",,,-75027
"OBIGT",1901,"N-acetylmuramic acid","aq","J",,,-38589
"OBIGT",1902,"ethanolamine","aq","J",,,4598
-"OBIGT",1942,"hydromagnesite","cr","cal",,,-2569
-"OBIGT",2019,"jarosite","cr","cal",,,20697
-"OBIGT",2020,"natrojarosite","cr","cal",,,17554
-"OBIGT",2028,"realgar,alpha","cr","J",,,768
-"OBIGT",2029,"realgar,beta","cr","J",,,989
-"OBIGT",2030,"orpiment","cr","J",,,-1036
-"OBIGT",2038,"dawsonite","cr","J",,,19466
-"OBIGT",2040,"ferberite","cr","J",1.21,,
-"OBIGT",2056,"willemite","cr","J",-1.47,,
-"OBIGT",2078,"octadecane","cr","cal",-2.63,,
-"OBIGT",2079,"nonadecane","cr","cal",-13.32,,
-"OBIGT",2080,"eicosane","cr","cal",-2.79,,
-"OBIGT",2081,"heneicosane","cr","cal",-8.61,,
-"OBIGT",2082,"docosane","cr","cal",-2.63,,
-"OBIGT",2083,"tricosane","cr","cal",-5.22,,
-"OBIGT",2084,"tetracosane","cr","cal",-2.02,,
-"OBIGT",2085,"pentacosane","cr","cal",-2.93,,
-"OBIGT",2086,"hexacosane","cr","cal",-1.29,,
-"OBIGT",2087,"heptacosane","cr","cal",-1.23,,
-"OBIGT",2139,"carbazole","cr","cal",-43.39,,
-"OBIGT",2180,"triphenylene","cr","cal",,,541
-"OBIGT",2493,"deoxyadenosine","cr","cal",,,-2977
-"OBIGT",2652,"ethylene","gas","cal",-4.59,,
-"OBIGT",2662,"3,5-dimethylphenol","gas","cal",,,628
-"OBIGT",2972,"nonacontane","liq","cal",,,635
-"OBIGT",2979,"2-methyloctane","liq","cal",10,,
-"OBIGT",3392,"5,6-dithiadecane","liq","cal",2,,
+"OBIGT",1907,"alaninate","aq","cal",1.89,,
+"OBIGT",1919,"histidinate","aq","cal",2.52,,
+"OBIGT",1922,"isoleucinate","aq","cal",1.61,,
+"OBIGT",1927,"methionate","aq","cal",2.42,,
+"OBIGT",1931,"prolinate","aq","cal",1.73,,
+"OBIGT",1933,"serinate","aq","cal",2.92,,
+"OBIGT",1935,"threonate","aq","cal",1.97,,
+"OBIGT",1937,"tryptophanate","aq","cal",,,2998
+"OBIGT",1941,"valinate","aq","cal",2.06,,
+"OBIGT",2070,"hydromagnesite","cr","cal",,,-2569
+"OBIGT",2147,"jarosite","cr","cal",,,20697
+"OBIGT",2148,"natrojarosite","cr","cal",,,17554
+"OBIGT",2156,"realgar,alpha","cr","J",,,768
+"OBIGT",2157,"realgar,beta","cr","J",,,989
+"OBIGT",2158,"orpiment","cr","J",,,-1036
+"OBIGT",2166,"dawsonite","cr","J",,,19466
+"OBIGT",2168,"ferberite","cr","J",1.21,,
+"OBIGT",2184,"willemite","cr","J",-1.47,,
+"OBIGT",2206,"octadecane","cr","cal",-2.63,,
+"OBIGT",2207,"nonadecane","cr","cal",-13.32,,
+"OBIGT",2208,"eicosane","cr","cal",-2.79,,
+"OBIGT",2209,"heneicosane","cr","cal",-8.61,,
+"OBIGT",2210,"docosane","cr","cal",-2.63,,
+"OBIGT",2211,"tricosane","cr","cal",-5.22,,
+"OBIGT",2212,"tetracosane","cr","cal",-2.02,,
+"OBIGT",2213,"pentacosane","cr","cal",-2.93,,
+"OBIGT",2214,"hexacosane","cr","cal",-1.29,,
+"OBIGT",2215,"heptacosane","cr","cal",-1.23,,
+"OBIGT",2267,"carbazole","cr","cal",-43.39,,
+"OBIGT",2308,"triphenylene","cr","cal",,,541
+"OBIGT",2621,"deoxyadenosine","cr","cal",,,-2977
+"OBIGT",2688,"ethylene","gas","cal",-4.59,,
+"OBIGT",2698,"3,5-dimethylphenol","gas","cal",,,628
+"OBIGT",3008,"nonacontane","liq","cal",,,635
+"OBIGT",3015,"2-methyloctane","liq","cal",10,,
+"OBIGT",3428,"5,6-dithiadecane","liq","cal",2,,
"DEW",8,"AlO2(SiO2)-","aq","cal",,,-897
"DEW",17,"BO(OH)","aq","cal",,,-1111
"DEW",19,"CaHCO3+","aq","cal",,,-2971
Modified: pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
===================================================================
(Binary files differ)
Modified: pkg/CHNOSZ/vignettes/OBIGT.bib
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.bib 2023-09-08 13:50:04 UTC (rev 803)
+++ pkg/CHNOSZ/vignettes/OBIGT.bib 2023-09-11 03:10:54 UTC (rev 804)
@@ -296,6 +296,17 @@
doi = {10.1007/s00239-014-9616-1},
}
+ at Article{Kit15,
+ author = {Kitadai, Norio},
+ journal = {Origins of Life and Evolution of Biospheres},
+ title = {Energetics of amino acid synthesis in alkaline hydrothermal environments},
+ year = {2015},
+ number = {4},
+ pages = {377--409},
+ volume = {45},
+ doi = {10.1007/s11084-015-9428-3},
+}
+
@Article{LA16,
author = {LaRowe, Douglas E. and Amend, Jan P.},
journal = {The ISME Journal},
@@ -1378,8 +1389,8 @@
journal = {Trans. Inst. Min. Metall., Sect. B},
title = {{P}ressure-dependence of wolframite solubility for hydrothermal vein formation},
year = {1990},
+ pages = {B120--B124},
volume = {99},
- pages = {B120--B124},
}
@Article{AP14,
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