[CHNOSZ-commits] r118 - in pkg/CHNOSZ: . data inst inst/extdata/thermo man tests/testthat vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Dec 21 12:10:05 CET 2016
Author: jedick
Date: 2016-12-21 12:10:04 +0100 (Wed, 21 Dec 2016)
New Revision: 118
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/data/OBIGT.csv
pkg/CHNOSZ/data/refs.csv
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/inst/extdata/thermo/OBIGT-2.csv
pkg/CHNOSZ/inst/extdata/thermo/obigt_check.csv
pkg/CHNOSZ/man/protein.Rd
pkg/CHNOSZ/man/protein.info.Rd
pkg/CHNOSZ/man/read.expr.Rd
pkg/CHNOSZ/tests/testthat/test-affinity.R
pkg/CHNOSZ/tests/testthat/test-ionize.aa.R
pkg/CHNOSZ/tests/testthat/test-iprotein.R
pkg/CHNOSZ/tests/testthat/test-protein.info.R
pkg/CHNOSZ/tests/testthat/test-subcrt.R
pkg/CHNOSZ/tests/testthat/test-util.data.R
pkg/CHNOSZ/vignettes/equilibrium.Rnw
pkg/CHNOSZ/vignettes/equilibrium.lyx
pkg/CHNOSZ/vignettes/hotspring.Rnw
pkg/CHNOSZ/vignettes/hotspring.lyx
Log:
add citric acid cycle data from Canovas and Shock, 2016
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2016-12-19 04:17:18 UTC (rev 117)
+++ pkg/CHNOSZ/DESCRIPTION 2016-12-21 11:10:04 UTC (rev 118)
@@ -1,6 +1,6 @@
-Date: 2016-12-19
+Date: 2016-12-21
Package: CHNOSZ
-Version: 1.0.8-5
+Version: 1.0.8-6
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/data/OBIGT.csv
===================================================================
--- pkg/CHNOSZ/data/OBIGT.csv 2016-12-19 04:17:18 UTC (rev 117)
+++ pkg/CHNOSZ/data/OBIGT.csv 2016-12-21 11:10:04 UTC (rev 118)
@@ -1713,10 +1713,10 @@
dH2UTP-2,NA,C9H13N2O14P3-2,aq,LH06a,NA,4.Feb.03,-775114,-945072,95.02,97.96,191.34,2.4367,132.3092,-19.279,-2.6907,203.5,-29.52,5,-2
dH3UTP-,NA,C9H14N2O14P3-,aq,LH06a,NA,4.Feb.03,-777814,-943572,109.11,158.49,202.56,2.472,139.4108,-19.444,-2.9842,262.2,-29.07,4.9,-1
dH4UTP,NA,C9H15N2O14P3,aq,LH06a,NA,4.Feb.03,-779850,-940671,125.67,213.85,207.7,2.4888,142.7899,-19.522,-3.1239,315.8,-28.65,4.8,0
-"citric acid",NA,C6H8O7,aq,LH06a,NA,5.Feb.03,-297180,-364527,78.89,73.47,112.98,0,0,0,0,96.43,-11.57,-0.06,0
-H2-citrate,NA,C6H7O7-,aq,LH06a,NA,5.Feb.03,-292912,-363530,67.92,47.04,102.48,0,0,0,0,89.4,-14.12,1.5,-1
-H-citrate-2,NA,C6H6O7-2,aq,LH06a,NA,5.Feb.03,-286417,-362947,48.09,7.71,91.08,0,0,0,0,73.14,-21.06,2.4843,-2
-citrate-3,NA,C6H5O7-3,aq,LH06a,NA,5.Feb.03,-277690,-363750,16.13,-43.16,74.08,0,0,0,0,31.5,-24.41,2.75,-3
+"citric acid",NA,C6H8O7,aq,LH06a,CS16,21.Dec.16,-297180,-364527,78.89,73.47,112.98,17.2019,32.2622,-2.7285,-4.1127,96.43,-11.57,-0.06,0
+H2-citrate,NA,C6H7O7-,aq,LH06a,CS16,21.Dec.16,-292912,-363530,67.92,47.04,102.48,16.3576,30.3484,-2.2931,-4.0336,89.4,-14.12,1.5,-1
+H-citrate-2,NA,C6H6O7-2,aq,LH06a,CS16,21.Dec.16,-286417,-362947,48.09,7.71,91.08,15.1704,27.6579,-1.6828,-3.9224,73.14,-21.06,2.48,-2
+citrate-3,NA,C6H5O7-3,aq,LH06a,CS16,21.Dec.16,-277690,-363750,16.13,-43.16,74.08,12.9466,22.6175,-0.5371,-3.714,31.5,-24.41,2.75,-3
MgAMP,MgAMP,MgC10H12N5O7P,aq,LH06b,NA,10.Jun.03,-359729,-497815,41.69,115.391969407266,158.14,2.3212,109.107,-18.7412,-1.7315,191.66,-18.262,4.3,0
MgADP-,MgADP-,MgC10H12N5O10P2-,aq,LH06b,NA,21.May.03,-567524,-730933,55.74,139.985659655832,189.17,2.4109,127.142,-19.16,-2.477,175.24,-3.8947,3,-1
MgHADP,MgHADP,MgC10H13N5O10P2,aq,LH06b,NA,10.Jun.03,-574465,-731643,76.54,161.472275334608,199.93,2.4625,137.497,-19.3997,-2.9051,244.57,-19.376,4.8,0
@@ -1809,6 +1809,30 @@
"cis-1,2-dichloroethylene","cis-1,2-DCE",C2H2Cl2,aq,HS99,NA,01.May.12,6620,-7712,39.23,95,68.2,11.0468,19.1914,-1.7922,-3.5723,60.4606,16.3169,-0.15,0
"trans-1,2-dichloroethylene","trans-1,2-DCE",C2H2Cl2,aq,HS99,NA,01.May.12,7700,-6950,38.16,95,68.2,11.0468,19.1914,-1.7922,-3.5723,60.4606,16.3169,-0.15,0
"vinyl chloride",VC,C2H3Cl,aq,HS99,NA,01.May.12,12785,-4551,18.11,45,55.8,9.35,15.0507,-0.1702,-3.4011,31.1575,6.1319,-0.15,0
+"cis-aconitic acid",NA,C6H6O6,aq,CS16,NA,21.Dec.16,-236200,-291400,63.9,64,108.7,16.5766,30.8449,-2.4072,-4.0541,59.7379,1.3622,-0.164,0
+H2-cis-aconitate,NA,C6H5O6-,aq,CS16,NA,21.Dec.16,-233600,-290480,58.2,37.6,98.2,15.4873,28.376,-1.8452,-3.9521,51.8298,-3.6503,0.7477,-1
+H-cis-aconitate-2,NA,C6H4O6-2,aq,CS16,NA,21.Dec.16,-227700,-289900,40.4,-1.7,86.8,14.6306,26.4342,-1.4046,-3.8718,30.3757,-4.1266,2.601,-2
+cis-aconitate-3,NA,C6H3O6-3,aq,CS16,NA,21.Dec.16,-218970,-290700,8.4,-52.6,69.8,13.0954,22.9544,-0.6139,-3.7279,-0.2807,-4.7435,4.6843,-3
+"isocitric acid",NA,C6H8O7,aq,CS16,NA,21.Dec.16,-295880,-363960,76.4,74.5,114.3,17.3743,32.653,-2.817,-4.1289,68.8768,2.3996,-0.082,0
+H2-isocitrate,NA,C6H7O7-,aq,CS16,NA,21.Dec.16,-291390,-362960,64.7,48.1,103.8,16.2126,30.0199,-2.2197,-4.02,61.1741,-3.523,0.6493,-1
+H-isocitrate-2,NA,C6H6O7-2,aq,CS16,NA,21.Dec.16,-284960,-362380,45.1,8.8,92.4,15.3672,28.1034,-1.783,-3.9408,39.977,-3.9993,2.5298,-2
+isocitrate-3,NA,C6H5O7-3,aq,CS16,NA,21.Dec.16,-276230,-363180,13.1,-42.1,75.4,13.8316,24.623,-0.9928,-3.7969,9.3108,-4.6163,4.6132,-3
+"a-ketoglutaric acid",NA,C5H6O5,aq,CS16,NA,21.Dec.16,-201800,-245700,76.1,39.9,95.7,14.8287,26.8831,-1.5061,-3.8903,41.2055,-1.0189,-0.084,0
+H-a-ketoglutarate,NA,C5H5O5-,aq,CS16,NA,21.Dec.16,-198800,-242300,77.1,2.9,88.9,14.1054,25.2437,-1.1337,-3.8226,15.3765,-4.0709,0.4615,-1
+a-ketoglutarate-2,NA,C5H4O5-2,aq,CS16,NA,21.Dec.16,-191800,-240400,60.1,-49.9,82.7,13.9562,24.9058,-1.057,-3.8086,-19.3472,-4.7108,2.3026,-2
+H-succinate,NA,C4H5O4-,aq,CS16,NA,21.Dec.16,-172060,-217350,45.2,9.3,69.99,11.6617,19.7057,0.1226,-3.5935,26.1173,-3.9932,0.9446,-1
+succinate-2,NA,C4H4O4-2,aq,CS16,NA,21.Dec.16,-164380,-217350,19.5,-50.5,56.32,10.4577,15.8622,3.5716,-3.4346,-14.0383,-4.718,2.917,-2
+"fumaric acid",NA,C4H4O4,aq,CS16,NA,21.Dec.16,-154820,-186260,60.62,47,77.9,12.3542,21.2748,-0.2318,-3.6585,45.951,-0.3174,-0.186,0
+H-fumarate,NA,C4H3O4-,aq,CS16,NA,21.Dec.16,-150600,-186150,46.83,10,65.4,11.0637,18.3498,0.4327,-3.5376,26.4785,-3.9848,0.9199,-1
+fumarate-2,NA,C4H2O4-2,aq,CS16,NA,21.Dec.16,-144320,-186830,23.48,-42.8,51.7,9.9248,15.7683,1.0191,-3.4309,-7.3722,-4.6247,2.8572,-2
+"malic acid",NA,C4H6O5,aq,CS16,NA,21.Dec.16,-213530,-259310,68.21,56.43,82.22,12.9644,22.6577,-0.5461,-3.7157,53.9427,0.6143,-0.136,0
+H-malate,NA,C4H5O5-,aq,CS16,NA,21.Dec.16,-208810,-258610,54.75,19.4,75.4,12.3867,21.3482,-0.249,-3.6615,34.5541,-3.8709,0.8,-1
+malate-2,NA,C4H4O5-2,aq,CS16,NA,21.Dec.16,-201860,-258890,30.48,-33.4,69.19,12.2779,21.1017,-0.1928,-3.6513,0.8264,-4.5108,2.7512,-2
+"oxaloacetic acid",NA,C4H4O5,aq,CS16,NA,21.Dec.16,-200000,-235100,72.9,29.1,79.1,12.5492,21.7168,-0.3324,-3.6768,32.3818,-2.0859,-0.105,0
+H-oxaloacetate,NA,C4H3O5-,aq,CS16,NA,21.Dec.16,-196600,-231300,74,-7.9,72.3,11.8516,20.1357,0.0269,-3.6114,5.2703,-4.2017,0.5084,-1
+oxaloacetate-2,NA,C4H2O5-2,aq,CS16,NA,21.Dec.16,-190600,-230300,57.2,-60.7,66.1,11.7014,19.7949,0.1041,-3.5973,-29.4812,-4.8417,2.3465,-2
+"pyruvic acid",NA,CH3COCOOH,aq,CS16,NA,21.Dec.16,-117000,-140300,62.1,36.3,64.6,10.5381,17.1584,0.7032,-3.4883,37.4903,-1.3746,-0.176,0
+pyruvate,NA,CH3COCOO-,aq,CS16,NA,21.Dec.16,-113600,-137400,60.4,-3.7,51.5,9.0836,13.862,1.4526,-3.3521,11.2428,-4.1508,0.7144,-1
acanthite,Acn,Ag2S,cr1,HDN+78,NA,5.May.78,-9446,-7550,34.3,NA,34.2,15.63,8.6,0,0,0,0,0,450
acanthite,Acn,Ag2S,cr2,HDN+78,NA,5.May.78,-9235.197,-7024.866,35.3543,NA,34.2,1.819,53,0,0,0,0,0,620
acanthite,Acn,Ag2S,cr3,HDN+78,NA,5.May.78,-8227.324,-4960.457,38.898,NA,34.2,21.6,0,0,0,0,0,0,1000
Modified: pkg/CHNOSZ/data/refs.csv
===================================================================
--- pkg/CHNOSZ/data/refs.csv 2016-12-19 04:17:18 UTC (rev 117)
+++ pkg/CHNOSZ/data/refs.csv 2016-12-21 11:10:04 UTC (rev 118)
@@ -15,6 +15,7 @@
BZA10,"E. F. Bazarkina, A. V. Zotov and N. N. Akinfiev",2010,"Geol. Ore Deposits 52, 167-178",http://dx.doi.org/10.1134/S1075701510020054
CGM+81,"S. Cabani, P. Gianni, V. Mollica and L. Lepori",1981,"J. Solution Chem. 10, 563-595",http://dx.doi.org/10.1007/BF00646936
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
CSM+07,"M. Censky, J. Sedlbauer et al.",2007,"Geochim. Cosmochim. Acta 71, 580-603",http://dx.doi.org/10.1016/j.gca.2006.10.022
CWM89,"J. D. Cox, D. D. Wagman and V. A. Medvedev, eds.",1989,"CODATA Key Values for Thermodynamics",http://www.worldcat.org/oclc/18559968
Dic07,"J. M. Dick",2007,"Ph.D. Dissertation, U.C. Berkeley",
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2016-12-19 04:17:18 UTC (rev 117)
+++ pkg/CHNOSZ/inst/NEWS 2016-12-21 11:10:04 UTC (rev 118)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.8-5 (2016-12-19)
+CHANGES IN CHNOSZ 1.0.8-6 (2016-12-21)
--------------------------------------
- Add "AA" as a keyword for preset species in basis() (cysteine,
@@ -9,12 +9,19 @@
- More flexible parsing of chemical formulas for ZC() and other
functions; e.g. ZC(colMeans(protein.formula(1:4))) now works.
-- supcrt() now returns 'loggam' using the common logarithm; add
+- subcrt() now returns 'loggam' using the common logarithm; add
test-nonideal.R to check for consistency between loggam and logK
- values returned by supcrt(). Thanks to David T. Wang for the bug
- report and test. (This also fixes the bug previously noted for the
- first example in ?nonideal.)
+ values returned by subcrt(). This also fixes the issue previously
+ noted for the first example in ?nonideal. Thanks to David T. Wang for
+ the bug report and test.
+- OBIGT.csv: Add data for citric acid cycle metabolites from Canovas and
+ Shock, 2016.
+
+- Clean up OBIGT-2.csv: remove data from Dalla-Betta and Schulte, 2009
+ (citric acid cycle metabolites; thioester species have been kept) and
+ from Dick et al., 2006 (methionine and [Met]).
+
CHANGES IN CHNOSZ 1.0.8 (2016-05-28)
------------------------------------
Modified: pkg/CHNOSZ/inst/extdata/thermo/OBIGT-2.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/thermo/OBIGT-2.csv 2016-12-19 04:17:18 UTC (rev 117)
+++ pkg/CHNOSZ/inst/extdata/thermo/OBIGT-2.csv 2016-12-21 11:10:04 UTC (rev 118)
@@ -134,29 +134,9 @@
m-diaminobenzene,NA,C6H8N2,aq,CSM+07,NA,12.Sep.07,56238,29995,90.94,75.76,96.9,2.0467,11.1955,149.555,-8.2091,79.8375,-1.8372,0.0342,0
p-diaminobenzene,NA,C6H8N2,aq,CSM+07,NA,12.Sep.07,56238,29995,90.94,75.76,96.9,2.0467,11.1955,149.555,-8.2091,79.8375,-1.8372,0.0342,0
aminophenols,NA,C6H7NO,aq,CSM+07,NA,12.Sep.07,5712,-17734,86.33,70.27,93,1.9788,10.4161,144.173,-7.7925,75.4541,-2.4763,0.1868,0
-"pyruvic acid",NA,CH3COCOOH,aq,DS09,NA,30.Jun.10,-116898,NA,43,27.39,54.6,9.3442,13.7309,0.5923,-3.348,5.8903,9.1799,-0.3088,0
-pyruvate,NA,CH3COCOO-,aq,DS09,NA,30.Jun.10,-113504,NA,40.99,-12.62,41.5,7.7918,10.0868,4.2106,-3.1973,5.3246,-4.261,0.1009,-1
-"oxaloacetic acid",NA,C4H4O5,aq,DS09,NA,30.Jun.10,-200359,NA,68.71,25.98,72.4,11.7108,17.158,5.9003,-3.4896,6.5026,9.0247,-0.1247,0
-H-oxaloacetate,NA,C4H3O5-,aq,DS09,NA,30.Jun.10,-196869,NA,55.71,-18.57,60.3,10.288,15.9467,2.5031,-3.4396,-2.5335,-4.3332,0.7902,-1
-oxaloacetate-2,NA,C4H2O5-2,aq,DS09,NA,30.Jun.10,-190894,NA,25.79,-78.42,46.7,9.1083,13.1771,3.3102,-3.3251,-42.12,-5.0583,2.7237,-2
-"malic acid",NA,C4H6O5,aq,DS09,NA,30.Jun.10,-213098,NA,67.83,54.42,82.8,13.1508,20.272,5.1675,-3.6184,28.0217,12.1772,-0.1801,0
-H-malate,NA,C4H5O5-,aq,DS09,NA,30.Jun.10,-208509,NA,54.42,9.85,69.4,11.5282,18.858,1.6549,-3.5599,25.3824,-3.9885,0.8233,-1
-malate-2,NA,C4H4O5-2,aq,DS09,NA,30.Jun.10,-201506,NA,30.31,-49.98,55.7,10.3188,16.0191,2.4821,-3.4426,-15.0136,-4.7137,2.7969,-2
-"fumaric acid",NA,C4H4O4,aq,DS09,NA,30.Jun.10,-154350,NA,62.4,36.97,78.8,12.6212,21.4233,9.5284,-3.666,14.0502,10.2418,-0.2286,0
-H-fumarate,NA,C4H3O4-,aq,DS09,NA,30.Jun.10,-150120,NA,48.59,-7.6,65.4,11.012,17.646,2.0079,-3.5098,9.1659,-4.2001,0.8937,-1
-fumarate-2,NA,C4H2O4-2,aq,DS09,NA,30.Jun.10,-143858,NA,25.19,-67.42,51.7,9.7988,14.7985,2.8377,-3.3921,-31.3293,-4.9252,2.8324,-2
-"a-ketoglutaric acid",NA,C5H6O5,aq,DS09,NA,30.Jun.10,-201315,NA,75.31,41.44,89,13.963,22.0282,5.7667,-3.691,18.8537,10.7384,-0.0839,0
-H-a-ketoglutarate,NA,C5H5O5-,aq,DS09,NA,30.Jun.10,-198231,NA,58.2,-3.13,75.6,12.3535,20.7952,1.0903,-3.64,12.1953,-4.1458,0.6982,-1
-a-ketoglutarate-2,NA,C5H4O5-2,aq,DS09,NA,30.Jun.10,-191683,NA,32.5,-62.95,61.9,11.1522,17.9751,1.912,-3.5234,-27.9773,-4.8709,2.6719,-2
-"citric acid",NA,C6H8O7,aq,DS09,NA,30.Jun.10,-297180,NA,78.73,77.08,113.6,17.3131,29.2727,9.5366,-3.9905,46.7151,14.6883,-0.0558,0
-H2-citrate,NA,C6H7O7-,aq,DS09,NA,30.Jun.10,-293093,NA,68.4,44.91,98.1,15.3786,27.8965,-0.979,-3.9336,57.6138,-3.5638,0.5938,-1
-H-citrate-2,NA,C6H6O7-2,aq,DS09,NA,30.Jun.10,-286616,NA,48.35,0.2,88.5,14.7041,26.3129,-0.5174,-3.8681,31.407,-4.1055,2.4817,-2
-citrate-3,NA,C6H5O7-3,aq,DS09,NA,30.Jun.10,-277892,NA,22.01,-60.9,72,13.1248,22.6059,0.5629,-3.7148,-9.7775,-4.8461,4.4801,-3
"succinyl thioester",NA,C6H10O3S,aq,DS09,NA,30.Jun.10,-118690,NA,94.29,51.65,140.5,20.9773,37.1962,27.6083,-4.318,27.2302,11.8701,-0.0331,0
"succinyl thioester-1",NA,C6H9O3S-,aq,DS09,NA,30.Jun.10,-112070,NA,69.79,18.64,133.7,20.2297,39.2837,-4.2971,-4.4043,31.8088,-3.882,0.4476,-1
"acetyl thioester",NA,C4H8OS,aq,DS09,NA,30.Jun.10,-33485,NA,95.63,61.07,107.3,16.5664,24.6312,8.8162,-3.7986,40.8944,8.1836,-0.3839,0
-methionine,Met,C5H11NO2S,aq,AH97b,DLH06,25.Aug.06,-120120,-178520,62.36,70.7,105.4,24.95,6.9,13.59,-7.77,85.3,-6.6,0.13,0
-[Met],NA,C3H7S,aq,DLH06,NA,25.Aug.06,-35245,-59310,40.38,72.739,71.832,15.48,8.76,10.82,-6,63.7,4,-0.1,0
LiCrO4-,NA,LiCrO4-,aq,AML10,NA,03.Jul.10,-246189,-276987,23.021,-1.86,25.17,5.6394,5.9909,2.9644,-3.0267,16.8298,-3.4143,1.2728,-1
NaCrO4-,NA,NaCrO4-,aq,AML10,NA,03.Jul.10,-239025,-266828,38.364,-3.93,24.95,5.5308,5.7256,3.0783,-3.0157,13.4846,-3.8343,1.0404,-1
KCrO4-,NA,KCrO4-,aq,AML10,NA,03.Jul.10,-243870,-269706,48.161,-16.63,33.98,6.7157,8.6197,1.8358,-3.1354,4.6973,-6.4214,0.8921,-1
Modified: pkg/CHNOSZ/inst/extdata/thermo/obigt_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/thermo/obigt_check.csv 2016-12-19 04:17:18 UTC (rev 117)
+++ pkg/CHNOSZ/inst/extdata/thermo/obigt_check.csv 2016-12-21 11:10:04 UTC (rev 118)
@@ -175,10 +175,6 @@
"OBIGT",1495,"n-butanethiol","aq",2.19,,
"OBIGT",1621,"dH2TMP","aq",,-1,
"OBIGT",1623,"dHUMP-","aq",1.84,,
-"OBIGT",1715,"citric acid","aq",,-112.81,
-"OBIGT",1716,"H2-citrate","aq",,-106.64,
-"OBIGT",1717,"H-citrate-2","aq",,-97.98,
-"OBIGT",1718,"citrate-3","aq",,-81.71,
"OBIGT",1731,"HNicMP(ox)","aq",,9.54,
"OBIGT",1739,"ribose-5-phosphate","aq",,7.48,
"OBIGT",1742,"H4NADP(red)","aq",1.73,,
@@ -194,52 +190,52 @@
"OBIGT",1760,"fructose","aq",1.3,,
"OBIGT",1761,"sorbose","aq",1.3,,
"OBIGT",1762,"cyclohexane","aq",9.35,6.64,
-"OBIGT",1787,"Gly-Ala-Gly","aq",,-126.09,
-"OBIGT",1788,"Gly-Arg+-Gly","aq",,-182.01,
-"OBIGT",1789,"Gly-Asn-Gly","aq",,-145.77,
-"OBIGT",1790,"Gly-Asp-Gly","aq",,-139.16,
-"OBIGT",1791,"Gly-Cys-Gly","aq",,-139.2,
-"OBIGT",1792,"Gly-Gln-Gly","aq",,-158.09,
-"OBIGT",1793,"Gly-Glu-Gly","aq",,-155.4,
-"OBIGT",1794,"Gly-Gly-Gly","aq",,-107.83,
-"OBIGT",1795,"Gly-His-Gly","aq",,-167.84,
-"OBIGT",1796,"Gly-Ile-Gly","aq",,-172.24,
-"OBIGT",1797,"Gly-Leu-Gly","aq",,-171.74,
-"OBIGT",1798,"Gly-Lys+-Gly","aq",,-175.45,
-"OBIGT",1799,"Gly-Met-Gly","aq",,-172.45,
-"OBIGT",1800,"Gly-Phe-Gly","aq",,-188.52,
-"OBIGT",1801,"Gly-Pro-Gly","aq",,-140.68,
-"OBIGT",1802,"Gly-Ser-Gly","aq",,-125.79,
-"OBIGT",1803,"Gly-Thr-Gly","aq",,-141.19,
-"OBIGT",1804,"Gly-Tyr-Gly","aq",,-190.24,
-"OBIGT",1805,"Gly-Val-Gly","aq",,-155.72,
-"OBIGT",1806,"[GXGBB]","aq",,-98.93,
-"OBIGT",1844,"antigorite","cr1",,,812
-"OBIGT",1878,"clinochlore,7a","cr1",,,666
-"OBIGT",1897,"daphnite,14a","cr",,,-836
-"OBIGT",1922,"ferrosilite","cr1",,,694
-"OBIGT",1923,"ferrosilite","cr2",,,694
-"OBIGT",1938,"greenalite","cr",,,142507
-"OBIGT",1953,"hydromagnesite","cr",,,-2569
-"OBIGT",2090,"n-octadecane","cr",-2.63,,
-"OBIGT",2091,"n-nonadecane","cr",-13.32,,
-"OBIGT",2092,"n-eicosane","cr",-2.79,,
-"OBIGT",2093,"n-heneicosane","cr",-8.61,,
-"OBIGT",2094,"n-docosane","cr",-2.63,,
-"OBIGT",2095,"n-tricosane","cr",-5.22,,
-"OBIGT",2096,"n-tetracosane","cr",-2.02,,
-"OBIGT",2097,"n-pentacosane","cr",-2.93,,
-"OBIGT",2098,"n-hexacosane","cr",-1.29,,
-"OBIGT",2099,"n-heptacosane","cr",-1.23,,
-"OBIGT",2151,"carbazole","cr",-43.39,,
-"OBIGT",2192,"triphenylene","cr",,,541
-"OBIGT",2487,"deoxyadenosine","cr",,,-2977
-"OBIGT",2494,"acetamide","cr",-67.91,,
-"OBIGT",2610,"n-nonacontane","liq",,,635
-"OBIGT",2617,"2-methyloctane","liq",10,,
-"OBIGT",3030,"5,6-dithiadecane","liq",2,,
-"OBIGT",3104,"ethylene","gas",-4.59,,
-"OBIGT",3114,"3,5-dimethylphenol","gas",,,628
+"OBIGT",1785,"Gly-Ala-Gly","aq",,-126.09,
+"OBIGT",1786,"Gly-Arg+-Gly","aq",,-182.01,
+"OBIGT",1787,"Gly-Asn-Gly","aq",,-145.77,
+"OBIGT",1788,"Gly-Asp-Gly","aq",,-139.16,
+"OBIGT",1789,"Gly-Cys-Gly","aq",,-139.2,
+"OBIGT",1790,"Gly-Gln-Gly","aq",,-158.09,
+"OBIGT",1791,"Gly-Glu-Gly","aq",,-155.4,
+"OBIGT",1792,"Gly-Gly-Gly","aq",,-107.83,
+"OBIGT",1793,"Gly-His-Gly","aq",,-167.84,
+"OBIGT",1794,"Gly-Ile-Gly","aq",,-172.24,
+"OBIGT",1795,"Gly-Leu-Gly","aq",,-171.74,
+"OBIGT",1796,"Gly-Lys+-Gly","aq",,-175.45,
+"OBIGT",1797,"Gly-Met-Gly","aq",,-172.45,
+"OBIGT",1798,"Gly-Phe-Gly","aq",,-188.52,
+"OBIGT",1799,"Gly-Pro-Gly","aq",,-140.68,
+"OBIGT",1800,"Gly-Ser-Gly","aq",,-125.79,
+"OBIGT",1801,"Gly-Thr-Gly","aq",,-141.19,
+"OBIGT",1802,"Gly-Tyr-Gly","aq",,-190.24,
+"OBIGT",1803,"Gly-Val-Gly","aq",,-155.72,
+"OBIGT",1804,"[GXGBB]","aq",,-98.93,
+"OBIGT",1866,"antigorite","cr1",,,812
+"OBIGT",1900,"clinochlore,7a","cr1",,,666
+"OBIGT",1919,"daphnite,14a","cr",,,-836
+"OBIGT",1944,"ferrosilite","cr1",,,694
+"OBIGT",1945,"ferrosilite","cr2",,,694
+"OBIGT",1960,"greenalite","cr",,,142507
+"OBIGT",1975,"hydromagnesite","cr",,,-2569
+"OBIGT",2112,"n-octadecane","cr",-2.63,,
+"OBIGT",2113,"n-nonadecane","cr",-13.32,,
+"OBIGT",2114,"n-eicosane","cr",-2.79,,
+"OBIGT",2115,"n-heneicosane","cr",-8.61,,
+"OBIGT",2116,"n-docosane","cr",-2.63,,
+"OBIGT",2117,"n-tricosane","cr",-5.22,,
+"OBIGT",2118,"n-tetracosane","cr",-2.02,,
+"OBIGT",2119,"n-pentacosane","cr",-2.93,,
+"OBIGT",2120,"n-hexacosane","cr",-1.29,,
+"OBIGT",2121,"n-heptacosane","cr",-1.23,,
+"OBIGT",2173,"carbazole","cr",-43.39,,
+"OBIGT",2214,"triphenylene","cr",,,541
+"OBIGT",2509,"deoxyadenosine","cr",,,-2977
+"OBIGT",2516,"acetamide","cr",-67.91,,
+"OBIGT",2633,"n-nonacontane","liq",,,635
+"OBIGT",2640,"2-methyloctane","liq",10,,
+"OBIGT",3053,"5,6-dithiadecane","liq",2,,
+"OBIGT",3127,"ethylene","gas",-4.59,,
+"OBIGT",3137,"3,5-dimethylphenol","gas",,,628
"OBIGT-2",33,"AgCl2-","aq",1.65,,
"OBIGT-2",36,"AgCl","aq",,-1.88,
"OBIGT-2",39,"Cu+","aq",-5.84,-1.78,
@@ -249,14 +245,9 @@
"OBIGT-2",100,"MnAsO4-","aq",-1.45,,
"OBIGT-2",119,"methyldiethanolamine","aq",1.61,,
"OBIGT-2",135,"aminophenols","aq",-1.55,,
-"OBIGT-2",137,"pyruvate","aq",8.37,2.23,
-"OBIGT-2",140,"oxaloacetate-2","aq",1.21,,
-"OBIGT-2",144,"fumaric acid","aq",,6.38,
-"OBIGT-2",150,"citric acid","aq",,2.62,
-"OBIGT-2",153,"citrate-3","aq",,-1.34,
-"OBIGT-2",154,"succinyl thioester","aq",,13.76,
-"OBIGT-2",155,"succinyl thioester-1","aq",1.2,,
-"OBIGT-2",254,"realgar","cr",3.14,,
-"OBIGT-2",262,"Tb(OH)3","cr",,,-777
-"OBIGT-2",294,"jarosite","cr",,,20697
-"OBIGT-2",295,"natrojarosite","cr",,,17554
+"OBIGT-2",136,"succinyl thioester","aq",,13.76,
+"OBIGT-2",137,"succinyl thioester-1","aq",1.2,,
+"OBIGT-2",236,"realgar","cr",3.14,,
+"OBIGT-2",244,"Tb(OH)3","cr",,,-777
+"OBIGT-2",276,"jarosite","cr",,,20697
+"OBIGT-2",277,"natrojarosite","cr",,,17554
Modified: pkg/CHNOSZ/man/protein.Rd
===================================================================
--- pkg/CHNOSZ/man/protein.Rd 2016-12-19 04:17:18 UTC (rev 117)
+++ pkg/CHNOSZ/man/protein.Rd 2016-12-21 11:10:04 UTC (rev 118)
@@ -57,7 +57,7 @@
## as a function of oxygen fugacity, after Dick, 2008, Fig. 5b
# use old properties of [Met] to reproduce this example
data(thermo)
-add.obigt()
+mod.obigt("[Met]", G=-35245, H=-59310)
# make our protein list
organisms <- c("METSC", "METJA", "METFE", "HALJP", "METVO",
"METBU", "ACEKI", "GEOSE", "BACLI", "AERSA")
Modified: pkg/CHNOSZ/man/protein.info.Rd
===================================================================
--- pkg/CHNOSZ/man/protein.info.Rd 2016-12-19 04:17:18 UTC (rev 117)
+++ pkg/CHNOSZ/man/protein.info.Rd 2016-12-21 11:10:04 UTC (rev 118)
@@ -99,8 +99,8 @@
# clear out amino acid residues loaded by the example above
# ( in affinity(iprotein=ip) )
data(thermo)
-# load supplemental database to use "old" [Met] sidechain group
-add.obigt()
+# use properties of the "old" [Met] sidechain group (Dick et al., 2006)
+mod.obigt("[Met]", G=-35245, H=-59310)
# set up the basis species to those used in DS11
basis("CHNOS+")
# note this yields logaH2 = -4.657486
Modified: pkg/CHNOSZ/man/read.expr.Rd
===================================================================
--- pkg/CHNOSZ/man/read.expr.Rd 2016-12-19 04:17:18 UTC (rev 117)
+++ pkg/CHNOSZ/man/read.expr.Rd 2016-12-21 11:10:04 UTC (rev 118)
@@ -88,8 +88,8 @@
## speciation diagram for ER.to.Golgi proteins (COPII coat
## proteins) as a function of logfO2, after Dick, 2009
-# add old parameters for [Met] sidechain to database
-add.obigt()
+# use old parameters for [Met] sidechain group
+mod.obigt("[Met]", G=-35245, H=-59310)
y <- yeastgfp("ER.to.Golgi")
# don't use those with NA abundance
ina <- is.na(y$abundance)
Modified: pkg/CHNOSZ/tests/testthat/test-affinity.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-affinity.R 2016-12-19 04:17:18 UTC (rev 117)
+++ pkg/CHNOSZ/tests/testthat/test-affinity.R 2016-12-21 11:10:04 UTC (rev 118)
@@ -101,8 +101,8 @@
sites <- c("N", "S", "R", "Q", "P")
aa <- read.aa(system.file("extdata/protein/DS11.csv", package="CHNOSZ"))
ip <- add.protein(aa[1:5, ])
- # to reproduce, we need use the "old" parameters for [Met]
- add.obigt()
+ # to reproduce, we need use the "old" parameters for [Met] from Dick et al., 2006
+ mod.obigt("[Met]", G=-35245, H=-59310)
a <- affinity(T=T, pH=pH, H2=H2, iprotein=ip)
# divide A/2.303RT by protein length
pl <- protein.length(ip)
Modified: pkg/CHNOSZ/tests/testthat/test-ionize.aa.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-ionize.aa.R 2016-12-19 04:17:18 UTC (rev 117)
+++ pkg/CHNOSZ/tests/testthat/test-ionize.aa.R 2016-12-21 11:10:04 UTC (rev 118)
@@ -65,7 +65,7 @@
G.AMY_BACSU.25 <- c(-24.9, -24.9, -24.7, -24.5, -24.4, -23.9, -23.5, -23.2)
G.AMY_BACSU.100 <- c(-26.7, -26.7, -26.4, -26.1, -25.7, -25.1, -24.9, -24.9)
# calculate the Gibbs energies of the nonionized proteins using the same [Met] parameters as in the paper
- add.obigt()
+ mod.obigt("[Met]", G=-35245, H=-59310)
G.nonionized <- subcrt("AMY_BACSU", T=c(25, 100))$out[[1]]$G
aa <- ip2aa(iprotein("AMY_BACSU"))
G.ionization.25 <- ionize.aa(aa, "G", T=25, pH=seq(0, 14, 2))[,1]
Modified: pkg/CHNOSZ/tests/testthat/test-iprotein.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-iprotein.R 2016-12-19 04:17:18 UTC (rev 117)
+++ pkg/CHNOSZ/tests/testthat/test-iprotein.R 2016-12-21 11:10:04 UTC (rev 118)
@@ -29,10 +29,9 @@
Cp <- 6415.5
V <- 10421
formula <- "C613H959N193O185S10"
- # use add.obigt to load the parameters for [Met] sidechain group
- # from above reference instead of the updated values
- # from LaRowe and Dick, 2012 (Geochim Cosmochim Acta 80, 70-91)
- add.obigt()
+ # use parameters for [Met] sidechain group from above reference
+ # (OBIGT.csv uses updated values from LaRowe and Dick, 2012 (Geochim Cosmochim Acta 80, 70-91))
+ mod.obigt("[Met]", G=-35245, H=-59310)
lprop <- info(info("LYSC_CHICK"))
expect_equal(G, lprop$G)
expect_equal(Cp, lprop$Cp, tolerance=1e-5)
Modified: pkg/CHNOSZ/tests/testthat/test-protein.info.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-protein.info.R 2016-12-19 04:17:18 UTC (rev 117)
+++ pkg/CHNOSZ/tests/testthat/test-protein.info.R 2016-12-21 11:10:04 UTC (rev 118)
@@ -5,7 +5,7 @@
# test_that somehow affects capture.output so we set up the problem here
protein <- iprotein(c("CSG_METVO", "CSG_METJA"))
-suppressMessages(add.obigt())
+suppressMessages(mod.obigt("[Met]", G=-35245, H=-59310))
basis("CHNOS+")
swap.basis("O2", "H2")
pequil <- capture.output(protein.equil(protein, loga.protein=-3))
Modified: pkg/CHNOSZ/tests/testthat/test-subcrt.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-subcrt.R 2016-12-19 04:17:18 UTC (rev 117)
+++ pkg/CHNOSZ/tests/testthat/test-subcrt.R 2016-12-21 11:10:04 UTC (rev 118)
@@ -9,8 +9,6 @@
test_that("unbalanced reactions are balanced given sufficient basis species", {
basis("CHNOS")
- # since it doesn't alter the species indices of the basis species, this can come second ...
- add.obigt()
s <- subcrt(c("malic acid", "citric acid"), c(-1, 1))
expect_equal(s$reaction$coeff, c(-1, 1, -2, -1, 1.5))
expect_equal(s$reaction$name, c("malic acid", "citric acid", "CO2", "water", "oxygen"))
Modified: pkg/CHNOSZ/tests/testthat/test-util.data.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-util.data.R 2016-12-19 04:17:18 UTC (rev 117)
+++ pkg/CHNOSZ/tests/testthat/test-util.data.R 2016-12-21 11:10:04 UTC (rev 118)
@@ -35,13 +35,13 @@
})
test_that("add.obigt() replaces existing entries without changing species index", {
- # store the original species index of citric acid
- icitric <- info("citric acid", "aq")
- # add supplemental database - includes citric acid
+ # store the original species index of Al+3
+ iAl <- info("Al+3", "aq")
+ # add supplemental database - includes Al+3
file <- system.file("extdata/thermo/OBIGT-2.csv", package="CHNOSZ")
isp <- add.obigt(file, force=TRUE)
- # species index of citric acid should not have changed
- expect_equal(info("citric acid", "aq"), icitric)
+ # species index of Al+3 should not have changed
+ expect_equal(info("Al+3", "aq"), iAl)
# check that names of species modified are same as in file
newdat <- read.csv(file, stringsAsFactors=FALSE)
# the order isn't guaranteed ... just make sure they're all there
Modified: pkg/CHNOSZ/vignettes/equilibrium.Rnw
===================================================================
--- pkg/CHNOSZ/vignettes/equilibrium.Rnw 2016-12-19 04:17:18 UTC (rev 117)
+++ pkg/CHNOSZ/vignettes/equilibrium.Rnw 2016-12-21 11:10:04 UTC (rev 118)
@@ -1,4 +1,4 @@
-%% LyX 2.1.4 created this file. For more info, see http://www.lyx.org/.
+%% LyX 2.2.2 created this file. For more info, see http://www.lyx.org/.
%% Do not edit unless you really know what you are doing.
\documentclass[english,round]{article}
\usepackage{mathpazo}
@@ -15,7 +15,7 @@
\usepackage[authoryear]{natbib}
\usepackage[unicode=true,pdfusetitle,
bookmarks=true,bookmarksnumbered=false,bookmarksopen=false,
- breaklinks=false,pdfborder={0 0 0},backref=false,colorlinks=true]
+ breaklinks=false,pdfborder={0 0 0},pdfborderstyle={},backref=false,colorlinks=true]
{hyperref}
\hypersetup{
citecolor=magenta, urlcolor=blue}
@@ -43,10 +43,8 @@
options(digits=3)
@
-
\title{Equilibrium in CHNOSZ}
-
\author{Jeffrey M. Dick}
\maketitle
@@ -56,7 +54,6 @@
diagrams) and includes an Appendix on details of the equilibration
calculations.
-
\section{Concepts}
\begin{description}
\item [{Species~of~interest}] Chemical species for which you want to
@@ -143,7 +140,6 @@
(also with a derivation of energetic distance from equilibrium using
the \textbf{starred affinity}).
-
\section{Organization}
The function sequences below assume you have already defined the basis
@@ -221,7 +217,6 @@
\section{Examples}
-
\subsection{Amino acids}
Basis species: $\mathrm{CO_{2}}$, $\mathrm{H_{2}O}$, $\mathrm{NH_{3}}$,
@@ -586,14 +581,12 @@
\clearpage
-
\section{Applications}
Many of the help-page examples and demos in CHNOSZ use these methods
to reproduce (or closely emulate) published figures. Below is not
a comprehensive list, but just some highlights.
-
\subsection{Maximum affinity method}
\begin{itemize}
\item The ``Aqueous Aluminum'' example in \texttt{?diagram} shows predominance
@@ -602,8 +595,8 @@
for minerals (balance $\ne$ 1, after \citealp{Hel70c}).
\item Next is an example of using \emph{unequal activities} of species (mineral
activity = 1; variable aqueous species activity indicated by the contours
-(logarithm of activity)) to plot aqueous species -- mineral stability
-boundaries (balance = 1, after Figure 14 of \citealp{Pou49}).
+(logarithm of activity)) to plot aqueous species \textendash{} mineral
+stability boundaries (balance = 1, after Figure 14 of \citealp{Pou49}).
\end{itemize}
<<Pourbaix, message=FALSE, results="hide", fig.width=4, fig.height=3, cache=TRUE>>=
basis(c("Cu+2", "H2O", "H+", "e-"))
@@ -620,7 +613,6 @@
@
-
\subsection{Equilibration method}
\begin{itemize}
\item Speciation of reduced and oxidized glutathione, after \citet{SB01}.
@@ -714,7 +706,6 @@
The results shows that two approaches are equivalent when the molar
formulas are normalized.
-
\section{Standard states, the ideal approximation and sources of data}
By chemical activity we mean the quantity $a_{i}$ that appears in
@@ -740,19 +731,15 @@
For the CSG examples below, we would like to reproduce exactly the
values appearing in publications. Because recent versions of CHNOSZ
incorporate data updates for the methionine sidechain group, we should
-therefore revert to the previous values before proceeding. The \texttt{add.obigt()}
-function does just that, as well as adds other species from the supplemental
-database provided with CHNOSZ:
+therefore revert to the previous values \citep{DLH06} before proceeding.
<<AddObigt>>=
data(thermo)
-add.obigt()
+mod.obigt("[Met]", G=-35245, H=-59310)
@
-
\section{Reaction-matrix approach}
-
\subsection{CSG Example: Whole formulas}
Let us calculate the equilibrium activities of two proteins in metastable
@@ -856,7 +843,6 @@
553\times a_{\mathrm{CSG\_METVO}}+530\times a_{\mathrm{CSG\_METJA}}=1.083\,.\label{eq:a_residue}
\end{equation}
-
At equilibrium, the affinities of the formation reactions, per conserved
quantity (in this case protein backbone groups) are equal. Therefore
$\boldsymbol{A}=\boldsymbol{A}_{3}/553=\boldsymbol{A}_{4}/530$ is
@@ -869,7 +855,7 @@
\begin{equation}
\boldsymbol{A}/2.303RT=\left(314.1877-\log a_{\mathrm{CSG\_METJA}}\right)/530\,.\label{eq:A_METJA}
\end{equation}
-Now we have three equations (\ref{eq:a_residue}--\ref{eq:A_METJA})
+Now we have three equations (\ref{eq:a_residue}\textendash \ref{eq:A_METJA})
with three unknowns. The solution can be displayed in CHNOSZ as follows.
Because the balancing coefficients differ from unity, the function
called by \texttt{equilibrate()} in this case is \texttt{equil.reaction()},
@@ -890,7 +876,6 @@
equilibrium. Later we explain the concept of using residue equivalents
of the proteins to achieve a different result.
-
\subsection{Implementing the reaction-matrix approach}
CHNOSZ implements a method for solving the system of equations that
@@ -925,7 +910,6 @@
and may give a warning about poor convergence if a certain tolerance
is not reached.
-
\subsection{CSG Example: normalized formulas (residue equivalents)}
Let us consider the formation reactions of the normalized formulas
@@ -992,10 +976,8 @@
normalize = TRUE)}. Instead, because balance = 1, the Boltzmann distribution,
which is faster, can be used.
-
\section{Boltzmann distribution}
-
\subsection{CSG Example: Normalized formulas}
An expression for Boltzmann distribution, relating equilibrium activities
@@ -1015,10 +997,8 @@
arrive at $a_{12}=0.3065982$ and $a_{13}=0.7764018$, the same result
as above.
-
\section{Notes on implementation}
-
\subsection{CSG example: another look}
All the tedium of writing reactions, calculating affinities, etc.,
@@ -1049,7 +1029,6 @@
can be multiplied by $\ln10$ to get the values shown above in Eqs.
\ref{eq:A_METVO_residue} and \ref{eq:A_METJA_residue}.)
-
\subsection{Visualizing the effects of normalization}
A comparison of equilibrium calculations that do and do not use normalized
@@ -1114,7 +1093,6 @@
might also be relevant to other systems where the molecules are in
various stages of polymerization.
-
\section*{Document history}
\begin{itemize}
\item 2009-11-29 Initial version containing CSG example (title: Calculating
Modified: pkg/CHNOSZ/vignettes/equilibrium.lyx
===================================================================
--- pkg/CHNOSZ/vignettes/equilibrium.lyx 2016-12-19 04:17:18 UTC (rev 117)
+++ pkg/CHNOSZ/vignettes/equilibrium.lyx 2016-12-21 11:10:04 UTC (rev 118)
@@ -1,7 +1,9 @@
-#LyX 2.1 created this file. For more info see http://www.lyx.org/
-\lyxformat 474
+#LyX 2.2 created this file. For more info see http://www.lyx.org/
+\lyxformat 508
\begin_document
\begin_header
+\save_transient_properties true
+\origin unavailable
\textclass article
\begin_preamble
%\VignetteIndexEntry{Equilibrium in CHNOSZ}
@@ -20,16 +22,16 @@
\language_package default
\inputencoding auto
\fontencoding global
-\font_roman palatino
-\font_sans lmss
-\font_typewriter lmtt
-\font_math auto
+\font_roman "palatino" "default"
+\font_sans "lmss" "default"
+\font_typewriter "lmtt" "default"
+\font_math "auto" "auto"
\font_default_family default
\use_non_tex_fonts false
\font_sc false
\font_osf false
-\font_sf_scale 100
-\font_tt_scale 100
+\font_sf_scale 100 100
+\font_tt_scale 100 100
\graphics default
\default_output_format default
\output_sync 0
@@ -557,6 +559,10 @@
\begin_layout Enumerate
Maximum affinity method, balance = 1
+\begin_inset Separator latexpar
+\end_inset
+
+
\end_layout
\begin_deeper
@@ -593,6 +599,10 @@
\end_deeper
\begin_layout Enumerate
Equilibration method, balance = 1
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/chnosz -r 118
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