[CHNOSZ-commits] r177 - in pkg/CHNOSZ: . R data demo inst inst/extdata/OBIGT man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Feb 27 12:09:54 CET 2017
Author: jedick
Date: 2017-02-27 12:09:54 +0100 (Mon, 27 Feb 2017)
New Revision: 177
Added:
pkg/CHNOSZ/vignettes/obigt.Rmd
pkg/CHNOSZ/vignettes/obigt.bib
pkg/CHNOSZ/vignettes/obigt.css
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/basis.R
pkg/CHNOSZ/data/refs.csv
pkg/CHNOSZ/demo/00Index
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/inst/extdata/OBIGT/Amend_aq.csv
pkg/CHNOSZ/inst/extdata/OBIGT/CHNOSZ_aq.csv
pkg/CHNOSZ/inst/extdata/OBIGT/CHNOSZ_cr.csv
pkg/CHNOSZ/inst/extdata/OBIGT/Dick_aq.csv
pkg/CHNOSZ/inst/extdata/OBIGT/Helgeson_cr.csv
pkg/CHNOSZ/inst/extdata/OBIGT/LaRowe_aq.csv
pkg/CHNOSZ/inst/extdata/OBIGT/LaRowe_liq.csv
pkg/CHNOSZ/inst/extdata/OBIGT/Other_cr.csv
pkg/CHNOSZ/inst/extdata/OBIGT/Other_gas.csv
pkg/CHNOSZ/inst/extdata/OBIGT/Richard_cr.csv
pkg/CHNOSZ/inst/extdata/OBIGT/Richard_gas.csv
pkg/CHNOSZ/inst/extdata/OBIGT/Richard_liq.csv
pkg/CHNOSZ/inst/extdata/OBIGT/Shock_aq.csv
pkg/CHNOSZ/inst/extdata/OBIGT/Shock_cr.csv
pkg/CHNOSZ/inst/extdata/OBIGT/Shock_gas.csv
pkg/CHNOSZ/man/basis.Rd
pkg/CHNOSZ/man/data.Rd
pkg/CHNOSZ/man/examples.Rd
pkg/CHNOSZ/vignettes/anintro.Rmd
Log:
add obigt.Rmd
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-02-25 02:08:42 UTC (rev 176)
+++ pkg/CHNOSZ/DESCRIPTION 2017-02-27 11:09:54 UTC (rev 177)
@@ -1,6 +1,6 @@
-Date: 2017-02-25
+Date: 2017-02-27
Package: CHNOSZ
-Version: 1.0.8-66
+Version: 1.0.8-67
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/R/basis.R
===================================================================
--- pkg/CHNOSZ/R/basis.R 2017-02-25 02:08:42 UTC (rev 176)
+++ pkg/CHNOSZ/R/basis.R 2017-02-27 11:09:54 UTC (rev 177)
@@ -203,9 +203,10 @@
# logarithms of activities for preset basis definitions
preset.logact <- function(species) {
bases <- c("H2O", "CO2", "NH3", "H2S", "oxygen", "H+", "e-", "Fe2O3",
- "cysteine", "glutamic acid", "glutamine")
+ "glutamine", "glutamic acid", "cysteine")
+ # values for QEC amino acids from Dick, 2017 (http://doi.org/10.1101/097667)
logact <- c(0, -3, -4, -7, -80, -7, -7, 0,
- -4, -4, -4)
+ -3.2, -4.5, -3.6)
ibase <- match(species, bases)
logact <- logact[ibase]
# any unmatched species gets a logarithm of activity of -3
Modified: pkg/CHNOSZ/data/refs.csv
===================================================================
--- pkg/CHNOSZ/data/refs.csv 2017-02-25 02:08:42 UTC (rev 176)
+++ pkg/CHNOSZ/data/refs.csv 2017-02-27 11:09:54 UTC (rev 177)
@@ -1,71 +1,87 @@
-key,author,year,citation,URL
-AH97b,"J. P. Amend and H. C. Helgeson",1997,"J. Chem. Soc., Faraday Trans. 93, 1927-1941",http://dx.doi.org/10.1039/A608126F
-AML10,"M. Accornero, L. Marini and M. Lelli",2010,"Appl. Geochem. 25, 242-260",http://dx.doi.org/10.1016/j.apgeochem.2009.11.010
-AP01,"J. P. Amend and A. V. Plyasunov",2001,"Geochim. Cosmochim. Acta 65, 3901-3917",http://dx.doi.org/10.1016/S0016-7037(01)00707-4
-AS01,"J. P. Amend and E. L. Shock",2001,"FEMS Microbiol. Rev. 25, 175-243",http://dx.doi.org/10.1016/S0168-6445(00)00062-0
-BH83a,"T. S. Bowers and H. C. Helgeson",1983,"Geochim. Cosmochim. Acta 47, 1247-1275",http://dx.doi.org/10.1016/0016-7037(83)90066-2
-CHNOSZ,"J. M. Dick",2007,"CHNOSZ package documentation",http://chnosz.net
-CS16,"P. A. Canovas III and E. L. Shock",2016,"Geochim. Cosmochim. Acta 195, 293-322",http://dx.doi.org/10.1016/j.gca.2016.08.028
-CWM89,"J. D. Cox, D. D. Wagman and V. A. Medvedev, eds.",1989,"CODATA Key Values for Thermodynamics",http://www.worldcat.org/oclc/18559968
-DEH+13,"J. M. Dick, K. A. Evans et al.",2013,"Geochim. Cosmochim. Acta 122, 247-266",http://dx.doi.org/10.1016/j.gca.2013.08.020
-DLH06,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Biogeosciences 3, 311-336",http://dx.doi.org/10.5194/bg-3-311-2006
-DSM+97,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024",http://dx.doi.org/10.1016/S0016-7037(97)00212-3
-Dic07,"J. M. Dick",2007,"Ph.D. Dissertation, U.C. Berkeley",
-GM09,"K.-D. Grevel and J. Majzlan",2009,"Geochim. Cosmochim. Acta 73, 6805 - 6815",http://dx.doi.org/10.1016/j.gca.2009.08.005
-Gur96,"S. Gurrieri",1996,"personal communication",
-HDN+78,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229",http://www.worldcat.org/oclc/13594862
-Hel85b,"H. C. Helgeson",1985,"Am. J. Sci. 285, 845-855",http://dx.doi.org/10.2475/ajs.285.9.845
-HOK+98,"H. C. Helgeson, C. E. Owens et al.",1998,"Geochim. Cosmochim. Acta 62, 985-1081",http://dx.doi.org/10.1016/S0016-7037(97)00219-6
-HPT06,"B. Hawrylak, R. Palepu and P. R. Tremaine",2006,"J. Chem. Thermodynamics 38, 988-1007",http://dx.doi.org.ezproxy1.lib.asu.edu/10.1016/j.jct.2005.10.013
-HRM+09,"H. C. Helgeson, L. Richard et al.",2009,"Geochim. Cosmochim. Acta 73, 594-695",http://dx.doi.org/10.1016/j.gca.2008.03.004
-HS99,"J. R. Haas and E. L. Shock",1998,"Geochim. Cosmochim. Acta 63, 3429-3441",http://dx.doi.org/10.1016/S0016-7037(99)00276-8
-HSS95,"J. R. Haas, E. L. Shock and D. C. Sassani",1995,"Geochim. Cosmochim. Acta 59, 4329-4350",http://dx.doi.org/10.1016/0016-7037(95)00314-P
-JH85b,"K. J. Jackson and H. C. Helgeson",1985,"Econ. Geol. 80, 1365-1378",http://dx.doi.org/10.2113/gsecongeo.80.5.1365
-Joh92,"J. W. Johnson",1992,"personal communication",
-Kel60,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584",http://www.worldcat.org/oclc/693388901
-LD12,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91",http://10.1016/j.gca.2011.11.041
-LH06a,"D. E. LaRowe and H. C. Helgeson",2006,"Geochim. Cosmochim. Acta 70, 4680-4724",http://dx.doi.org/10.1016/j.gca.2006.04.010
-LH06b,"D. E. LaRowe and H. C. Helgeson",2006,"Thermochim. Acta 448, 82-106",http://dx.doi.org/10.1016/j.tca.2006.06.008
-MA07,"L. Marini and M. Accornero",2007,"Environ. Geol. 52, 1343-1363",http://dx.doi.org/10.1007/s00254-006-0578-5
-MA10,"L. Marini and M. Accornero",2010,"Environ. Earth Sci. 59, 1601-1606",http://dx.doi.org/10.1007/s12665-009-0369-x
-MGN03,"J. Majzlan, K.-D. Grevel and A. Navrotsky",2003,"Am. Mineral. 88, 855-859",http://dx.doi.org/10.2138/am-2003-5-614
-MLS+03,"J. Majzlan, B. E. Lang et al.",2003,"Am. Mineral. 88, 846-854",http://dx.doi.org/10.2138/am-2003-5-613
-MNM+06,"J. Majzlan, A. Navrotsky et al.",2006,"Eur. J. Mineral. 18, 175-186",http://dx.doi.org/10.1127/0935-1221/2006/0018-0175
-MS97,"T. M. McCollom and E. L. Shock",1997,"Geochim. Cosmochim. Acta 61, 4375-4391",http://dx.doi.org/10.1016/S0016-7037(97)00241-X
-MSB+04,"J. Majzlan, R. Stevens et al.",2004,"Phys. Chem. Mineral. 31, 518-531",http://dx.doi.org/10.1007/s00269-004-0405-z
-MVT01,"L. Mercury, P. Vieillard. and Y. Tardy",2001,"Appl. Geochem. 16, 161-181",http://dx.doi.org/10.1016/S0883-2927(00)00025-1
-Nei86,"F. C. Neidhardt",1986,"Escherichia coli and Salmonella typhimurium, 3-5",http://www.worldcat.org/oclc/15280827
-Pan70,"L. B. Pankratz",1970,"U. S. Bureau of Mines Report of Investigations 7430",http://www.worldcat.org/oclc/14154245
-PB82,"L. N. Plummer and E. Busenberg",1982,"Geochim. Cosmochim. Acta 46, 1011-1040",http://dx.doi.org/10.1016/0016-7037(82)90056-4
-PK70,"L. B. Pankratz and E. G. King",1970,"U. S. Bureau of Mines Report of Investigations 7435",http://www.worldcat.org/oclc/14154292
-PK95,"V. B. Parker and I. L. Khodakovskii",1995,"J. Phys. Chem. Ref. Data 24, 1699-1745",http://dx.doi.org/10.1063/1.555964
-PS01,"A. V. Plyasunov and E. L. Shock",2001,"Geochim. Cosmochim. Acta 65, 3879-3900",http://dx.doi.org/10.1016/S0016-7037(01)00678-0
-PSK99,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"Geochim. Cosmochim. Acta 63, 2547-2577",http://dx.doi.org/10.1016/S0016-7037(99)00146-5
-RG11,"L. Richard and X. Gaona",2011,"Geochim. Cosmochim. Acta 75, 7304-7350",http://dx.doi.org/10.1016/j.gca.2011.07.030
-RH95,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131",http://pubs.er.usgs.gov/publication/b2131
-RH98,"L. Richard and H. C. Helgeson",1998,"Geochim. Cosmochim. Acta 62, 3591-3636",http://dx.doi.org/10.1016/S0016-7037(97)00345-1
-RHF79,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"U. S. Geological Survey Bull. 1452",http://pubs.er.usgs.gov/publication/b1452
-Ric01,"L. Richard",2001,"Geochim. Cosmochim. Acta 65, 3827-3877",http://dx.doi.org/10.1016/S0016-7037(01)00761-X
-Ric08,"L. Richard",2008,"personal communication",
-SAJ00,"R. E. Stoffregen, C. N. Alpers and J. L. Jambor",2000,"Rev. Mineral. Geochem. 40, 453-479",http://dx.doi.org/10.2138/rmg.2000.40.9
-Sch10,"M. Schulte",2010,"Aquat. Geochem. 16, 621-637",http://dx.doi.org/10.1007/s10498-010-9102-3
-SH88,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036",http://dx.doi.org/10.1016/0016-7037(88)90181-0
-SH90,"E. L. Shock and H. C. Helgeson",1990,"Geochim. Cosmochim. Acta 54, 915-945",http://dx.doi.org/10.1016/0016-7037(90)90429-O
-Sho92,"E. L. Shock",1992,"Geochim. Cosmochim. Acta 56, 3481-3491",http://dx.doi.org/10.1016/0016-7037(92)90392-V
-Sho93,"E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3341-3349",http://dx.doi.org/10.1016/0016-7037(93)90542-5
-Sho95,"E. L. Shock",1990,"Am. J. Sci. 295, 496-580",http://dx.doi.org/10.2475/ajs.295.5.496
-SHS89,"E. L. Shock, H. C. Helgeson and D. A. Sverjensky",1989,"Geochim. Cosmochim. Acta 53, 2157-2183",http://dx.doi.org/10.1016/0016-7037(89)90341-4
-SK93,"E. L. Shock and C. M. Koretsky",1993,"Geochim. Cosmochim. Acta 57, 4899-4922",http://dx.doi.org/10.1016/0016-7037(93)90128-J
-SK95,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532",http://dx.doi.org/10.1016/0016-7037(95)00058-8
-SLOP98,"E. L. Shock et al.",1998,"slop98.dat computer data file",http://geopig.asu.edu/?q=tools
-SM93,"E. L. Shock and W. B. McKinnon",1993,"Icarus 106, 464-477",http://dx.doi.org/10.1006/icar.1993.1185
-SR04,"M. D. Schulte and K. L. Rogers",2004,"Geochim. Cosmochim. Acta 68, 1087-1097",http://dx.doi.org/10.1016/j.gca.2003.06.001
-SS93,"M. D. Schulte and E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3835-3846",http://dx.doi.org/10.1016/0016-7037(93)90337-V
-SS98,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671",http://dx.doi.org/10.1016/S0016-7037(98)00049-0
-SSB97,"E. L. Shock, D. C. Sassani and H. Betz",1997,"Geochim. Cosmochim. Acta 61, 4245-4266",http://dx.doi.org/10.1016/S0016-7037(97)00240-8
-SSH97,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412",http://dx.doi.org/10.1016/S0016-7037(97)00009-4
-SSW+97,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950",http://dx.doi.org/10.1016/S0016-7037(96)00339-0
-SSW01,"M. D. Schulte, E. L. Shock and R. H. Wood",2001,"Geochim. Cosmochim. Acta 65, 3919-3930",http://dx.doi.org/10.1016/S0016-7037(01)00717-7
-TSD97,"Y. Tardy, R. Schaul, J. Duplay",1997,"C. R. Acad. Sci. Paris 324, 969-976",http://dx.doi.org/10.1016/S1251-8050(97)83981-X
-UniProt,"The UniProt Consortium",2017,"The UniProt knowledgebase",http://www.uniprot.org/
-WEP+82,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, 1-392",http://dx.doi.org/10.1063/1.555661
+key,author,year,note,citation,URL
+Kel60,"K. K. Kelley",1960,"gases Cp","U. S. Bureau of Mines Bull. 584",http://www.worldcat.org/oclc/693388901
+Kel60.1,"K. K. Kelley",1960,larnite,"U. S. Bureau of Mines Bull. 584",http://www.worldcat.org/oclc/693388901
+Kel60.2,"K. K. Kelley",1960,"gypsum Cp","U. S. Bureau of Mines Bull. 584",http://www.worldcat.org/oclc/693388901
+Pan70,"L. B. Pankratz",1970,chlorargyrite,"U. S. Bureau of Mines Report of Investigations 7430",http://www.worldcat.org/oclc/14154245
+PK70,"L. B. Pankratz and E. G. King",1970,"bornite and chalcopyrite","U. S. Bureau of Mines Report of Investigations 7435",http://www.worldcat.org/oclc/14154292
+HDNB78,"H. C. Helgeson, J. M. Delany et al.",1978,minerals,"Am. J. Sci. 278A, 1-229",http://www.worldcat.org/oclc/13594862
+RHF79,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"chlorargyrite, rutile, and titanite","U. S. Geological Survey Bull. 1452",http://pubs.er.usgs.gov/publication/b1452
+RHF79.1,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1979,"dickite, fluorphlogopite, halloysite, and pyrope","U. S. Geological Survey Bull. 1452",http://pubs.er.usgs.gov/publication/b1452
+PB82,"L. N. Plummer and E. Busenberg",1982,"aragonite and calcite","Geochim. Cosmochim. Acta 46, 1011-1040",http://dx.doi.org/10.1016/0016-7037(82)90056-4
+WEP+82,"D. D. Wagman, W. H. Evans et al.",1982,"gases GHS","J. Phys. Chem. Ref. Data 11, 1-392",http://dx.doi.org/10.1063/1.555661
+WEP+82.1,"D. D. Wagman, W. H. Evans et al.",1982,manganosite,"J. Phys. Chem. Ref. Data 11, 1-392",http://dx.doi.org/10.1063/1.555661
+WEP+82.2,"D. D. Wagman, W. H. Evans et al.",1982,MgSO4,"J. Phys. Chem. Ref. Data 11, 1-392",http://dx.doi.org/10.1063/1.555661
+BH83,"T. S. Bowers and H. C. Helgeson",1983,rutile,"Geochim. Cosmochim. Acta 47, 1247-1275",http://dx.doi.org/10.1016/0016-7037(83)90066-2
+Hel85,"H. C. Helgeson",1985,"ferrosilite and siderite","Am. J. Sci. 285, 845-855",http://dx.doi.org/10.2475/ajs.285.9.845
+JH85,"K. J. Jackson and H. C. Helgeson",1985,"Sn minerals","Econ. Geol. 80, 1365-1378",http://dx.doi.org/10.2113/gsecongeo.80.5.1365
+Nei86,"F. C. Neidhardt",1986,,"Escherichia coli and Salmonella typhimurium, 3-5",http://www.worldcat.org/oclc/15280827
+SH88,"E. L. Shock and H. C. Helgeson",1988,"ionic species","Geochim. Cosmochim. Acta 52, 2009-2036",http://dx.doi.org/10.1016/0016-7037(88)90181-0
+SH88.1,"E. L. Shock and H. C. Helgeson",1988,"corrections for Ca-bearing minerals","Geochim. Cosmochim. Acta 52, 2009-2036",http://dx.doi.org/10.1016/0016-7037(88)90181-0
+SH88.2,"E. L. Shock and H. C. Helgeson",1988,titanite,"Geochim. Cosmochim. Acta 52, 2009-2036",http://dx.doi.org/10.1016/0016-7037(88)90181-0
+CWM89,"J. D. Cox, D. D. Wagman and V. A. Medvedev, eds.",1989,,"CODATA Key Values for Thermodynamics",http://www.worldcat.org/oclc/18559968
+SHS89,"E. L. Shock, H. C. Helgeson and D. A. Sverjensky",1989,"inorganic neutral species","Geochim. Cosmochim. Acta 53, 2157-2183",http://dx.doi.org/10.1016/0016-7037(89)90341-4
+SH90,"E. L. Shock and H. C. Helgeson",1990,"organic species","Geochim. Cosmochim. Acta 54, 915-945",http://dx.doi.org/10.1016/0016-7037(90)90429-O
+Joh92a,"J. W. Johnson",1992,"steam, Cp represented by Maier-Kelley equation","personal communication",
+Sho92,"E. L. Shock",1992,dipeptides,"Geochim. Cosmochim. Acta 56, 3481-3491",http://dx.doi.org/10.1016/0016-7037(92)90392-V
+Sho93,"E. L. Shock",1993,ethylacetate,"Geochim. Cosmochim. Acta 57, 3341-3349",http://dx.doi.org/10.1016/0016-7037(93)90542-5
+Sho93.1,"E. L. Shock",1993,"carbon monoxide and ethylene","Geochim. Cosmochim. Acta 57, 3341-3349",http://dx.doi.org/10.1016/0016-7037(93)90542-5
+SK93,"E. L. Shock and C. M. Koretsky",1993,"metal-acetate complexes","Geochim. Cosmochim. Acta 57, 4899-4922",http://dx.doi.org/10.1016/0016-7037(93)90128-J
+SM93,"E. L. Shock and W. B. McKinnon",1993,"CO, HCN, urea","Icarus 106, 464-477",http://dx.doi.org/10.1006/icar.1993.1185
+SS93,"M. D. Schulte and E. L. Shock",1993,aldehydes,"Geochim. Cosmochim. Acta 57, 3835-3846",http://dx.doi.org/10.1016/0016-7037(93)90337-V
+HSS95,"J. R. Haas, E. L. Shock and D. C. Sassani",1995,"REE complexes","Geochim. Cosmochim. Acta 59, 4329-4350",http://dx.doi.org/10.1016/0016-7037(95)00314-P
+PK95,"V. B. Parker and I. L. Khodakovskii",1995,melanterite,"J. Phys. Chem. Ref. Data 24, 1699-1745",http://dx.doi.org/10.1063/1.555964
+RH95,"R. A. Robie and B. S. Hemingway",1995,"gypsum GHS","U. S. Geological Survey Bull. 2131",http://pubs.er.usgs.gov/publication/b2131
+RH95.1,"R. A. Robie and B. S. Hemingway",1995,iron,"U. S. Geological Survey Bull. 2131",http://pubs.er.usgs.gov/publication/b2131
+SK95,"E. L. Shock and C. M. Koretsky",1995,"metal-organic acid complexes","Geochim. Cosmochim. Acta 59, 1497-1532",http://dx.doi.org/10.1016/0016-7037(95)00058-8
+Sho95,"E. L. Shock",1995,"carboxylic acids","Am. J. Sci. 295, 496-580",http://dx.doi.org/10.2475/ajs.295.5.496
+Gur96,"S. Gurrieri",1996,sulfur,"personal communication",
+AH97b,"J. P. Amend and H. C. Helgeson",1997,"amino acids GHS","J. Chem. Soc., Faraday Trans. 93, 1927-1941",http://dx.doi.org/10.1039/A608126F
+DSM+97,"J. D. Dale, E. L. Shock et al.",1997,alkylphenols,"Geochim. Cosmochim. Acta 61, 4017-4024",http://dx.doi.org/10.1016/S0016-7037(97)00212-3
+MS97,"T. M. McCollom and E. L. Shock",1997,"MgSO<sub>4</sub>, NaSO<sub>4</sub><sup>-</sup>, and HCl","Geochim. Cosmochim. Acta 61, 4375-4391",http://dx.doi.org/10.1016/S0016-7037(97)00241-X
+SSB97,"E. L. Shock, D. C. Sassani and H. Betz",1997,"uranium species","Geochim. Cosmochim. Acta 61, 4245-4266",http://dx.doi.org/10.1016/S0016-7037(97)00240-8
+SSH97,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"metal complexes","Geochim. Cosmochim. Acta 61, 1359-1412",http://dx.doi.org/10.1016/S0016-7037(97)00009-4
+SSW+97,"E. L. Shock, D. C. Sassani et al.",1997,"inorganic ions and hydroxide complexes","Geochim. Cosmochim. Acta 61, 907-950",http://dx.doi.org/10.1016/S0016-7037(96)00339-0
+TSD97,"Y. Tardy, R. Schaul, J. Duplay",1997,"humic acid, microflora, and plants","C. R. Acad. Sci. Paris 324, 969-976",http://dx.doi.org/10.1016/S1251-8050(97)83981-X
+HOKR98,"H. C. Helgeson, C. E. Owens et al.",1998,"organic molecules and groups","Geochim. Cosmochim. Acta 62, 985-1081",http://dx.doi.org/10.1016/S0016-7037(97)00219-6
+HS99,"J. R. Haas and E. L. Shock",1998,"chloroethylene species","Geochim. Cosmochim. Acta 63, 3429-3441",http://dx.doi.org/10.1016/S0016-7037(99)00276-8
+RH98,"L. Richard and H. C. Helgeson",1998,"organic molecules and groups","Geochim. Cosmochim. Acta 62, 3591-3636",http://dx.doi.org/10.1016/S0016-7037(97)00345-1
+SLOP98,"E. L. Shock et al.",1998,,"slop98.dat computer data file",http://geopig.asu.edu/?q=tools
+SS98a,"D. C. Sassani and E. L. Shock",1998,"platinum-group solids","Geochim. Cosmochim. Acta 62, 2643-2671",http://dx.doi.org/10.1016/S0016-7037(98)00049-0
+PSK99,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"metal-dicarboxylate complexes","Geochim. Cosmochim. Acta 63, 2547-2577",http://dx.doi.org/10.1016/S0016-7037(99)00146-5
+SAJ00,"R. E. Stoffregen, C. N. Alpers and J. L. Jambor",2000,"jarosite, natroalunite, and natrojarosite","Rev. Mineral. Geochem. 40, 453-479",http://dx.doi.org/10.2138/rmg.2000.40.9
+AP01,"J. P. Amend and A. V. Plyasunov",2001,carbohydrates,"Geochim. Cosmochim. Acta 65, 3901-3917",http://dx.doi.org/10.1016/S0016-7037(01)00707-4
+AS01,"J. P. Amend and E. L. Shock",2001,"NO and N<sub>2</sub>O","FEMS Microbiol. Rev. 25, 175-243",http://dx.doi.org/10.1016/S0168-6445(00)00062-0
+MVT01,"L. Mercury, P. Vieillard. and Y. Tardy",2001,"ice polymorphs","Appl. Geochem. 16, 161-181",http://dx.doi.org/10.1016/S0883-2927(00)00025-1
+PS01,"A. V. Plyasunov and E. L. Shock",2001,cyclohexane,"Geochim. Cosmochim. Acta 65, 3879-3900",http://dx.doi.org/10.1016/S0016-7037(01)00678-0
+Ric01,"L. Richard",2001,"organic sulfur compounds","Geochim. Cosmochim. Acta 65, 3827-3877",http://dx.doi.org/10.1016/S0016-7037(01)00761-X
+SSW01,"M. D. Schulte, E. L. Shock and R. H. Wood",2001,"nonelectrolytes HKF heat capacity parameters","Geochim. Cosmochim. Acta 65, 3919-3930",http://dx.doi.org/10.1016/S0016-7037(01)00717-7
+MGN03,"J. Majzlan, K.-D. Grevel and A. Navrotsky",2003,"goethite, lepidocrocite, and maghemite GHS","Am. Mineral. 88, 855-859",http://dx.doi.org/10.2138/am-2003-5-614
+MLS+03,"J. Majzlan, B. E. Lang et al.",2003,"goethite, lepidocrocite, and maghemite Cp","Am. Mineral. 88, 846-854",http://dx.doi.org/10.2138/am-2003-5-613
+MSB+04,"J. Majzlan, R. Stevens et al.",2004,"hydronium jarosite","Phys. Chem. Mineral. 31, 518-531",http://dx.doi.org/10.1007/s00269-004-0405-z
+SR04,"M. D. Schulte and K. L. Rogers",2004,"alkane thiols","Geochim. Cosmochim. Acta 68, 1087-1097",http://dx.doi.org/10.1016/j.gca.2003.06.001
+DLH06,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"amino acid, protein, and organic groups","Biogeosciences 3, 311-336",http://dx.doi.org/10.5194/bg-3-311-2006
+DLH06.1,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"amino acids HKF parameters","Biogeosciences 3, 311-336",http://dx.doi.org/10.5194/bg-3-311-2006
+DLH06.2,"J. M. Dick, D. E. LaRowe and H. C. Helgeson",2006,"Gly-X-Gly tripeptides","Biogeosciences 3, 311-336",http://dx.doi.org/10.5194/bg-3-311-2006
+HPT06,"B. Hawrylak, R. Palepu and P. R. Tremaine",2006,"methyldiethanolamine and methyldiethanolammonium chloride","J. Chem. Thermodynamics 38, 988-1007",http://dx.doi.org.ezproxy1.lib.asu.edu/10.1016/j.jct.2005.10.013
+LH06a,"D. E. LaRowe and H. C. Helgeson",2006,"nucleic-acid bases, nucleosides, and nucleotides","Geochim. Cosmochim. Acta 70, 4680-4724",http://dx.doi.org/10.1016/j.gca.2006.04.010
+LH06b,"D. E. LaRowe and H. C. Helgeson",2006,"Mg-complexed adenosine nucleotides (ATP), NAD, and NADP","Thermochim. Acta 448, 82-106",http://dx.doi.org/10.1016/j.tca.2006.06.008
+LH06b.1,"D. E. LaRowe and H. C. Helgeson",2006,"pyridine and piperidine","Thermochim. Acta 448, 82-106",http://dx.doi.org/10.1016/j.tca.2006.06.008
+MNM+06,"J. Majzlan, A. Navrotsky et al.",2006,"coquimbite, ferricopiapite, rhomboclase","Eur. J. Mineral. 18, 175-186",http://dx.doi.org/10.1127/0935-1221/2006/0018-0175
+CHNOSZ.1,"J. M. Dick",2007,"recalculated GHS","CHNOSZ package documentation",http://chnosz.net
+CHNOSZ.2,"J. M. Dick",2007,"calculated Cp coefficients","CHNOSZ package documentation",http://chnosz.net
+CHNOSZ.3,"J. M. Dick",2007,pseudo-H<sub>4</sub>SiO<sub>4</sub>,"CHNOSZ package documentation",http://chnosz.net
+Dic07,"J. M. Dick",2007,"glutathione, cystine, and cystine sidechain","Ph.D. Dissertation, U.C. Berkeley",
+MA07,"L. Marini and M. Accornero",2007,"metal-arsenate and metal-arsenite complexes","Environ. Geol. 52, 1343-1363",http://dx.doi.org/10.1007/s00254-006-0578-5
+Ric08,"L. Richard",2008,alkenes,"personal communication",
+GM09,"K.-D. Grevel and J. Majzlan",2009,"kieserite, starkeyite, hexahydrite, and epsomite","Geochim. Cosmochim. Acta 73, 6805 - 6815",http://dx.doi.org/10.1016/j.gca.2009.08.005
+HRMNS09,"H. C. Helgeson, L. Richard et al.",2009,kerogens,"Geochim. Cosmochim. Acta 73, 594-695",http://dx.doi.org/10.1016/j.gca.2008.03.004
+AML10,"M. Accornero, L. Marini and M. Lelli",2010,"metal-chromate complexes","Appl. Geochem. 25, 242-260",http://dx.doi.org/10.1016/j.apgeochem.2009.11.010
+MA10,"L. Marini and M. Accornero",2010,"corrected values","Environ. Earth Sci. 59, 1601-1606",http://dx.doi.org/10.1007/s12665-009-0369-x
+Sch10,"M. Schulte",2010,"organic sulfides","Aquat. Geochem. 16, 621-637",http://dx.doi.org/10.1007/s10498-010-9102-3
+RG11,"L. Richard and X. Gaona",2011,"organic iodine compounds","Geochim. Cosmochim. Acta 75, 7304-7350",http://dx.doi.org/10.1016/j.gca.2011.07.030
+LD12,"D. E. LaRowe and J. M. Dick",2012,"amino acids and protein groups","Geochim. Cosmochim. Acta 80, 70-91",http://10.1016/j.gca.2011.11.041
+LD12.1,"D. E. LaRowe and J. M. Dick",2012,"methionine and methionine sidechain GHS","Geochim. Cosmochim. Acta 80, 70-91",http://10.1016/j.gca.2011.11.041
+DEH+13,"J. M. Dick, K. A. Evans et al.",2013,"phenanthrene and isomers of methylphenanthrene","Geochim. Cosmochim. Acta 122, 247-266",http://dx.doi.org/10.1016/j.gca.2013.08.020
+CS16,"P. A. Canovas III and E. L. Shock",2016,"citric acid cycle metabolites","Geochim. Cosmochim. Acta 195, 293-322",http://dx.doi.org/10.1016/j.gca.2016.08.028
+CS16.1,"P. A. Canovas III and E. L. Shock",2016,"citric acid species HKF a1-a4 parameters and corrected Cp and V","Geochim. Cosmochim. Acta 195, 293-322",http://dx.doi.org/10.1016/j.gca.2016.08.028
+UniProt,"The UniProt Consortium",2017,,"The UniProt knowledgebase",http://www.uniprot.org/
Modified: pkg/CHNOSZ/demo/00Index
===================================================================
--- pkg/CHNOSZ/demo/00Index 2017-02-25 02:08:42 UTC (rev 176)
+++ pkg/CHNOSZ/demo/00Index 2017-02-27 11:09:54 UTC (rev 177)
@@ -3,13 +3,13 @@
affinity affinities of metabolic reactions and amino acid synthesis
NaCl equilibrium constant for aqueous NaCl dissociation
density density of H2O, inverted from IAPWS-95 equations
-ORP oxidation-reduction potential of redox standards as a function of temperature
+ORP temperature dependence of oxidation-reduction potential for redox standards
revisit coefficient of variation of metastable equilibrium activities of proteins
findit minimize the standard deviation of logarithms of activities of sulfur species
ionize ionize.aa(): contour plots of net charge and ionization properties of LYSC_CHICK
buffer minerals and aqueous species as buffers of hydrogen fugacity
protbuff chemical activities buffered by thiol peroxidases or sigma factors
-yeastgfp YeastGFP locations: log fO2 - log aH2O and log a - log fO2 diagrams
+yeastgfp subcellular locations: log fO2 - log aH2O and log a - log fO2 diagrams
mosaic Eh-pH diagram for iron oxides, sulfides and carbonate with two sets of changing basis species
copper another example of mosaic(): complexation of copper with glycine species
solubility solubility of calcite or CO2(gas) as a function of pH
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2017-02-25 02:08:42 UTC (rev 176)
+++ pkg/CHNOSZ/inst/NEWS 2017-02-27 11:09:54 UTC (rev 177)
@@ -1,11 +1,13 @@
-CHANGES IN CHNOSZ 1.0.8-66 (2017-02-25)
+CHANGES IN CHNOSZ 1.0.8-67 (2017-02-27)
---------------------------------------
DOCUMENTATION:
-- Replace anintro.Rnw (using Sweave) with rewritten anintro.Rmd (using
- knitr with Tufte style).
+- Replace anintro.Rnw (Sweave) with rewritten anintro.Rmd (using knitr
+ with Tufte style).
+- Add obigt.Rmd (Thermodynamic data in CHNOSZ).
+
- Add eos-regress.Rmd (Regressing thermodynamic data), including
section on Making a pseudospecies: H4SiO4.
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/Amend_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/Amend_aq.csv 2017-02-25 02:08:42 UTC (rev 176)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/Amend_aq.csv 2017-02-27 11:09:54 UTC (rev 177)
@@ -1,4 +1,33 @@
name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
+alanine,Ala,C3H7NO2,aq,AH97b,DLH06.1,25.Aug.06,-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,DLH06.1,25.Aug.06,-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,DLH06.1,25.Aug.06,-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,DLH06.1,25.Aug.06,-40340,-129420,68.72,81.1,143,31.28,13.76,32.12,-9.94,141.9,-19.6,2.3,0
+asparagine,Asn,C4H8N2O3,aq,AH97b,DLH06.1,25.Aug.06,-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,DLH06.1,25.Aug.06,-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,DLH06.1,25.Aug.06,-167170,-224540,43.34,2.7,64.8,16.96,5.77,10.11,-6.37,56.3,-15.3,2.47,0
+cysteine,Cys,C3H7NO2S,aq,AH97b,DLH06.1,25.Aug.06,-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,DLH06.1,25.Aug.06,-68920,-115440,37.01,19.1,60.6,14.43,5.11,12.35,-3.71,61,-9.5,2.48,0
+glutamine,Gln,C5H10N2O3,aq,AH97b,DLH06.1,25.Aug.06,-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,DLH06.1,25.Aug.06,-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,DLH06.1,25.Aug.06,-167210,-234150,43.86,7.6,80,20.49,6.96,10.86,-7.02,47.6,-7.8,2.65,0
+glycine,Gly,C2H5NO2,aq,AH97b,DLH06.1,25.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,DLH06.1,25.Aug.06,-94160,-125720,46.91,40,56.4,19.57,-7.58,-40.35,5.41,49,-1.8,0.59,0
+histidine,His,C6H9N3O2,aq,AH97b,DLH06.1,25.Aug.06,-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,DLH06.1,25.Aug.06,-56700,-115250,70.13,59.1,97,26.64,-3.4,-0.88,-3.07,88,-12,0.5,0
+isoleucine,Ile,C6H13NO2,aq,AH97b,DLH06.1,25.Aug.06,-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,DLH06.1,25.Aug.06,-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,DLH06.1,25.Aug.06,-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,DLH06.1,25.Aug.06,-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,DLH06.1,25.Aug.06,-66310,-146340,53.27,72.8,112.2,28.29,10.53,2.97,-7.61,133.7,-18,2.67,0
+phenylalanine,Phe,C9H11NO2,aq,AH97b,DLH06.1,25.Aug.06,-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,DLH06.1,25.Aug.06,-73560,-124100,49.83,43,82.6,19.39,4.87,11.88,-5.68,63.6,-9.5,0.14,0
+serine,Ser,C3H7NO3,aq,AH97b,DLH06.1,25.Aug.06,-123930,-172420,47.24,27.8,60.6,15.69,0.73,3.87,-3.49,48.5,-9.4,0.18,0
+threonine,Thr,C4H9NO3,aq,AH97b,DLH06.1,25.Aug.06,-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,DLH06.1,25.Aug.06,-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,DLH06.1,25.Aug.06,-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,DLH06.1,25.Aug.06,-79380,-149420,45.66,51.2,111.8,26.34,10.49,16.42,-7.59,109,-16,2.78,0
+valine,Val,C5H11NO2,aq,AH97b,DLH06.1,25.Aug.06,-85330,-146420,45.68,74,90.9,21.35,4.48,14.58,-6.12,83.8,-4.3,0.12,0
xylose,xylose,C5H10O5,aq,AP01,NA,24.Aug.06,-179371.414913958,-249937.858508604,48.7332695984704,65.9655831739962,95.7,22.5860420650096,0.90822179732314,4.78011472275335,-2.77246653919694,90.9177820267686,-17.5908221797323,-1.31453154875717,0
arabinose,arabinose,C5H10O5,aq,AP01,NA,24.Aug.06,-177397.227533461,-249471.797323136,43.6663479923518,67.1606118546845,93.3,22.538240917782,0.81261950286807,3.99139579349904,-3.48948374760994,93.7619502868069,-18.4034416826004,-1.31453154875717,0
lyxose,lyxose,C5H10O5,aq,AP01,NA,24.Aug.06,-179048.757170172,-250164.913957935,47.0841300191205,67.3996175908222,94.2,22.6577437858509,1.2906309751434,1.7925430210325,-3.10707456978967,93.9292543021032,-18.4034416826004,-1.31453154875717,0
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/CHNOSZ_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/CHNOSZ_aq.csv 2017-02-25 02:08:42 UTC (rev 176)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/CHNOSZ_aq.csv 2017-02-27 11:09:54 UTC (rev 177)
@@ -1,2 +1,2 @@
name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
-pseudo-H4SiO4,NA,H4SiO4,aq,CHNOSZ,NA,18.Feb.17,-312565,-346409,51.4246,-40.0964,52.1998,89.2031,-176.5071,-452.1431,101.36051,67.0854,-52.0776,0.1215745,0
+pseudo-H4SiO4,NA,H4SiO4,aq,CHNOSZ.3,NA,18.Feb.17,-312565,-346409,51.4246,-40.0964,52.1998,89.2031,-176.5071,-452.1431,101.36051,67.0854,-52.0776,0.1215745,0
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/CHNOSZ_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/CHNOSZ_cr.csv 2017-02-25 02:08:42 UTC (rev 176)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/CHNOSZ_cr.csv 2017-02-27 11:09:54 UTC (rev 177)
@@ -1,5 +1,5 @@
name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
-Fe,iron,Fe,cr1,RH95,CHNOSZ,05.Aug.07,0,0,6.475,5.994,7.092,7.162,-6.9682,0,0,1.2294,0,0,1043
-Fe,iron,Fe,cr2,RH95,CHNOSZ,05.Aug.07,-32284.5,-87223.4,-177.791,NA,7.092,504.577,-807.244,0,0,32.754,0,0,1185
-Fe,iron,Fe,cr3,RH95,CHNOSZ,05.Aug.07,1348.8,1843.8,8.1352,NA,7.092,5.1938,2.3381,1.5019,0,0,0,0,1667
-Fe,iron,Fe,cr4,RH95,CHNOSZ,05.Aug.07,3190.2,4835.6,11.994,NA,7.092,-4.033,8.0055,9.5584,0,0,0,0,1809
+Fe,iron,Fe,cr1,RH95.1,CHNOSZ.2,05.Aug.07,0,0,6.475,5.994,7.092,7.162,-6.9682,0,0,1.2294,0,0,1043
+Fe,iron,Fe,cr2,RH95.1,CHNOSZ.2,05.Aug.07,-32284.5,-87223.4,-177.791,NA,7.092,504.577,-807.244,0,0,32.754,0,0,1185
+Fe,iron,Fe,cr3,RH95.1,CHNOSZ.2,05.Aug.07,1348.8,1843.8,8.1352,NA,7.092,5.1938,2.3381,1.5019,0,0,0,0,1667
+Fe,iron,Fe,cr4,RH95.1,CHNOSZ.2,05.Aug.07,3190.2,4835.6,11.994,NA,7.092,-4.033,8.0055,9.5584,0,0,0,0,1809
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/Dick_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/Dick_aq.csv 2017-02-25 02:08:42 UTC (rev 176)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/Dick_aq.csv 2017-02-27 11:09:54 UTC (rev 177)
@@ -1,34 +1,5 @@
name,abbrv,formula,state,ref1,ref2,date,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
-alanine,Ala,C3H7NO2,aq,AH97b,DLH06,25.Aug.06,-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,DLH06,25.Aug.06,-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,DLH06,25.Aug.06,-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,DLH06,25.Aug.06,-40340,-129420,68.72,81.1,143,31.28,13.76,32.12,-9.94,141.9,-19.6,2.3,0
-asparagine,Asn,C4H8N2O3,aq,AH97b,DLH06,25.Aug.06,-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,DLH06,25.Aug.06,-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,DLH06,25.Aug.06,-167170,-224540,43.34,2.7,64.8,16.96,5.77,10.11,-6.37,56.3,-15.3,2.47,0
-cysteine,Cys,C3H7NO2S,aq,AH97b,DLH06,25.Aug.06,-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,DLH06,25.Aug.06,-68920,-115440,37.01,19.1,60.6,14.43,5.11,12.35,-3.71,61,-9.5,2.48,0
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 177
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