[CHNOSZ-commits] r414 - in pkg/CHNOSZ: . R inst inst/extdata/adds man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Mon Feb 25 14:16:28 CET 2019 

Author: jedick
Date: 2019-02-25 14:16:27 +0100 (Mon, 25 Feb 2019)
New Revision: 414

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/protein.info.R
   pkg/CHNOSZ/inst/CHECKLIST
   pkg/CHNOSZ/inst/extdata/adds/obigt_check.csv
   pkg/CHNOSZ/man/retrieve.Rd
Log:
update obigt_check.csv


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2019-02-25 11:28:33 UTC (rev 413)
+++ pkg/CHNOSZ/DESCRIPTION	2019-02-25 13:16:27 UTC (rev 414)
@@ -1,6 +1,6 @@
 Date: 2019-02-25
 Package: CHNOSZ
-Version: 1.2.0-21
+Version: 1.2.0-22
 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/protein.info.R
===================================================================
--- pkg/CHNOSZ/R/protein.info.R	2019-02-25 11:28:33 UTC (rev 413)
+++ pkg/CHNOSZ/R/protein.info.R	2019-02-25 13:16:27 UTC (rev 414)
@@ -16,9 +16,9 @@
   #   character `protein` and `organism`, e.g. 'LYSC', 'CHICK'
   # return the row(s) of thermo$protein (possibly per residue) for:
   #   numeric `protein` (the rownumber itself)
-  t_p <- get("thermo", CHNOSZ)$protein
   if(is.data.frame(protein)) out <- protein
   if(is.numeric(protein)) {
+    t_p <- get("thermo", CHNOSZ)$protein
     # drop NA matches to thermo$protein
     iproteins <- 1:nrow(t_p)
     protein[!protein %in% iproteins] <- NA
@@ -29,6 +29,7 @@
     # compute per-residue counts if requested
     if(residue) out[, 5:25] <- out[, 5:25]/rowSums(out[, 6:25])
   } else {
+    t_p <- get("thermo", CHNOSZ)$protein
     # search for protein by regular expression
     if(regexp) {
       iprotein <- grepl(protein, t_p$protein)

Modified: pkg/CHNOSZ/inst/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST	2019-02-25 11:28:33 UTC (rev 413)
+++ pkg/CHNOSZ/inst/CHECKLIST	2019-02-25 13:16:27 UTC (rev 414)
@@ -8,7 +8,7 @@
 
 - check output of demo("sources") to make sure all data sources are cited
 
-- recreate extdata/thermo/obigt_check.csv after all data updates:
+- recreate extdata/adds/obigt_check.csv after all data updates:
   co <- check.obigt()
   write.csv(co, "obigt_check.csv", row.names=FALSE, na="")
 

Modified: pkg/CHNOSZ/inst/extdata/adds/obigt_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/obigt_check.csv	2019-02-25 11:28:33 UTC (rev 413)
+++ pkg/CHNOSZ/inst/extdata/adds/obigt_check.csv	2019-02-25 13:16:27 UTC (rev 414)
@@ -1,9 +1,9 @@
 "table","ispecies","name","state","DCp","DV","DG"
 "OBIGT",14,"CO3-2","aq",,-1.04,
 "OBIGT",20,"HPO4-2","aq",,-1.02,
-"OBIGT",49,"BO2-","aq",,-19.31,
-"OBIGT",61,"Cu+2","aq",3.62,,
-"OBIGT",65,"NH3","aq",2.75,,
+"OBIGT",48,"BO2-","aq",,-19.31,
+"OBIGT",60,"Cu+2","aq",3.62,,
+"OBIGT",64,"NH3","aq",2.75,,
 "OBIGT",73,"SO2","aq",11.1,,
 "OBIGT",91,"LaSO4+","aq",-6.02,,
 "OBIGT",134,"NdF2+","aq",16.64,6.19,
@@ -15,203 +15,197 @@
 "OBIGT",185,"EuCl2","aq",-9.84,40.4,
 "OBIGT",186,"EuCl3-","aq",-17.19,64.47,
 "OBIGT",187,"EuCl4-2","aq",-26.15,91.04,
-"OBIGT",341,"UO4-2","aq",,-1.11,
-"OBIGT",378,"Ag(CO3)2-3","aq",,-1.56,
-"OBIGT",396,"AgCl4-3","aq",,-1.31,
-"OBIGT",444,"CuCl4-2","aq",,-1.07,
-"OBIGT",446,"ReO4-","aq",-1.26,,
-"OBIGT",455,"PO4-3","aq",,-1.72,
-"OBIGT",463,"UO2+2","aq",-1.1,,
-"OBIGT",464,"Th+4","aq",,-1.14,
-"OBIGT",483,"P2O7-4","aq",,-2.11,
-"OBIGT",484,"HP2O7-3","aq",,-1.42,
-"OBIGT",498,"SO3-2","aq",,-1.02,
-"OBIGT",532,"VO4-3","aq",,-1.63,
-"OBIGT",544,"Zr+4","aq",,-1.18,
-"OBIGT",551,"Hf+4","aq",,-1.18,
-"OBIGT",554,"U+4","aq",,-1.13,
-"OBIGT",570,"Ce+4","aq",,-1.13,
-"OBIGT",571,"Pr+4","aq",,-1.12,
-"OBIGT",572,"Nd+4","aq",,-1.12,
-"OBIGT",573,"Pm+4","aq",,-1.13,
-"OBIGT",574,"Sm+4","aq",,-1.14,
-"OBIGT",575,"Eu+4","aq",,-1.14,
-"OBIGT",576,"Gd+4","aq",,-1.16,
-"OBIGT",577,"Tb+4","aq",,-1.15,
-"OBIGT",578,"Dy+4","aq",,-1.15,
-"OBIGT",579,"Ho+4","aq",,-1.15,
-"OBIGT",580,"Er+4","aq",,-1.15,
-"OBIGT",581,"Tm+4","aq",,-1.16,
-"OBIGT",582,"Yb+4","aq",,-1.16,
-"OBIGT",583,"Lu+4","aq",,-1.17,
-"OBIGT",592,"BeO2-2","aq",,-1.17,
-"OBIGT",635,"MnO2-2","aq",,-1.05,
-"OBIGT",646,"CoO2-2","aq",,-1.14,
-"OBIGT",651,"NiO2-2","aq",,-1.16,
-"OBIGT",655,"CuO2-2","aq",,-1.09,
-"OBIGT",659,"ZnO2-2","aq",,-1.17,
-"OBIGT",674,"CdO2-2","aq",,-1.08,
-"OBIGT",692,"RuCl4-2","aq",,-1.09,
-"OBIGT",695,"Ru(SO4)3-4","aq",,-1.8,
-"OBIGT",702,"RuCl5-2","aq",,-1.49,
-"OBIGT",703,"RuCl6-3","aq",,-2.39,
-"OBIGT",706,"Ru(SO4)3-3","aq",,-1.3,
-"OBIGT",712,"RhCl4-2","aq",,-1.14,
-"OBIGT",715,"Rh(SO4)3-4","aq",,-1.82,
-"OBIGT",719,"RhCl2+","aq",,4.67,
-"OBIGT",724,"Rh(SO4)3-3","aq",,-1.33,
-"OBIGT",730,"PdCl4-2","aq",,-1.05,
-"OBIGT",733,"Pd(SO4)3-4","aq",,-1.8,
-"OBIGT",736,"PtCl+","aq",-3.52,1.25,
-"OBIGT",737,"PtCl2","aq",-7.11,2.29,
-"OBIGT",738,"PtCl3-","aq",-10.48,1.78,
-"OBIGT",739,"PtCl4-2","aq",-13.86,,
-"OBIGT",742,"Pt(SO4)3-4","aq",,-1.79,
-"OBIGT",745,"CF4","aq",5.9,,
-"OBIGT",752,"AsH3","aq",-2.67,,
-"OBIGT",841,"MgAsO4-","aq",1.3,,
-"OBIGT",844,"MnAsO4-","aq",-1.45,,
-"OBIGT",926,"methane","aq",-2.61,,
-"OBIGT",931,"hexane","aq",1.43,3.21,
-"OBIGT",934,"ethylene","aq",6.12,-3.82,
-"OBIGT",958,"propanol","aq",-1.89,,
-"OBIGT",1091,"urea","aq",-23.26,23.32,
-"OBIGT",1104,"propanoic acid","aq",1.42,,
-"OBIGT",1127,"formate","aq",1.96,,
-"OBIGT",1129,"propanoate","aq",1.68,,
-"OBIGT",1136,"n-decanoate","aq",-1.93,,
-"OBIGT",1152,"oxalate-2","aq",-3.19,,
-"OBIGT",1419,"Li(Mal)-","aq",,-3.22,
-"OBIGT",1423,"Pb(Mal)","aq",,1.16,
-"OBIGT",1427,"Pb(Succ)","aq",,1.49,
-"OBIGT",1428,"Na(Oxal)-","aq",,-3.14,
-"OBIGT",1429,"K(Oxal)-","aq",,-2.75,
-"OBIGT",1430,"Fe(Oxal)+","aq",,-2.19,
-"OBIGT",1432,"Na(Mal)-","aq",,-3.11,
-"OBIGT",1433,"K(Mal)-","aq",,-2.63,
-"OBIGT",1435,"La(Mal)+","aq",,-1.92,
-"OBIGT",1436,"Gd(Mal)+","aq",,-1.73,
-"OBIGT",1437,"Lu(Mal)+","aq",,-2.25,
-"OBIGT",1438,"Yb(Mal)+","aq",,-2.05,
-"OBIGT",1439,"Th(Mal)+2","aq",-1.29,-4.79,
-"OBIGT",1441,"Ce(Mal)+","aq",,-1.75,
-"OBIGT",1442,"Nd(Mal)+","aq",4.52,,
-"OBIGT",1443,"Sm(Mal)+","aq",,-1.77,
-"OBIGT",1444,"Pr(Mal)+","aq",,-1.75,
-"OBIGT",1445,"Eu(Mal)+","aq",,-1.87,
-"OBIGT",1446,"Tb(Mal)+","aq",,-1.92,
-"OBIGT",1447,"Dy(Mal)+","aq",,-1.89,
-"OBIGT",1448,"Tm(Mal)+","aq",,-2.08,
-"OBIGT",1449,"Ho(Mal)+","aq",,-2.08,
-"OBIGT",1450,"Er(Mal)+","aq",,-2.11,
-"OBIGT",1451,"Sc(Mal)+","aq",,-1.97,
-"OBIGT",1452,"Fe(Mal)+","aq",,-1.97,
-"OBIGT",1453,"Na(Succ)-","aq",,-2.82,
-"OBIGT",1454,"K(Succ)-","aq",,-2.39,
-"OBIGT",1460,"Th(Succ)+2","aq",-1.21,-4.47,
-"OBIGT",1465,"NH4(Oxal)-","aq",,-2.62,
-"OBIGT",1470,"Yb(Oxal)+","aq",,-2.02,
-"OBIGT",1471,"Ce(Oxal)+","aq",,-1.8,
-"OBIGT",1472,"Nd(Oxal)+","aq",,-1.8,
-"OBIGT",1473,"Eu(Oxal)+","aq",,-1.89,
-"OBIGT",1474,"Gd(Oxal)+","aq",,-1.8,
-"OBIGT",1475,"Ru(Oxal)+","aq",,-2.41,
-"OBIGT",1476,"Pa(Oxal)+2","aq",-1.25,-4.63,
-"OBIGT",1477,"Th(Oxal)+2","aq",-1.27,-4.69,
-"OBIGT",1478,"U(Oxal)+2","aq",-1.25,-4.63,
-"OBIGT",1479,"Np(Oxal)+2","aq",-1.27,-4.69,
-"OBIGT",1482,"Am(Oxal)+","aq",,-1.8,
-"OBIGT",1483,"Cm(Oxal)+","aq",,-1.8,
-"OBIGT",1484,"Y(Oxal)+","aq",,-2.11,
-"OBIGT",1489,"La(Oxal)+","aq",,-1.87,
-"OBIGT",1490,"Tb(Oxal)+","aq",,-1.92,
-"OBIGT",1491,"Er(Oxal)+","aq",,-2.05,
-"OBIGT",1492,"Lu(Oxal)+","aq",,-2.19,
-"OBIGT",1493,"Cr(Oxal)+","aq",,-2.58,
-"OBIGT",1494,"Ga(Oxal)+","aq",,-2.66,
-"OBIGT",1495,"Sc(Oxal)+","aq",,-2.13,
-"OBIGT",1496,"In(Oxal)+","aq",,-2.19,
-"OBIGT",1497,"Pu(Oxal)+2","aq",-1.2,-4.44,
-"OBIGT",1498,"NpO2(Oxal)","aq",,-1.94,
-"OBIGT",1499,"Sm(Oxal)+","aq",,-1.84,
-"OBIGT",1500,"Cs(Mal)-","aq",,-2.39,
-"OBIGT",1501,"NH4(Mal)-","aq",,-2.54,
-"OBIGT",1506,"In(Mal)+","aq",,-2.11,
-"OBIGT",1507,"Y(Mal)+","aq",,-2.02,
-"OBIGT",1515,"La(Succ)+","aq",,-1.52,
-"OBIGT",1516,"NH4(Succ)-","aq",,-2.26,
-"OBIGT",1518,"Fe(Succ)+","aq",,-1.92,
-"OBIGT",1519,"Sc(Succ)+","aq",,-1.77,
-"OBIGT",1522,"NpO2(Succ)","aq",,-3.16,
-"OBIGT",1523,"Sm(Succ)+","aq",,-1.48,
-"OBIGT",1524,"Er(Succ)+","aq",,-1.68,
-"OBIGT",1525,"U(Succ)+2","aq",-1.15,-4.27,
-"OBIGT",1529,"La(Glut)+","aq",,-1.23,
-"OBIGT",1530,"Y(Glut)+","aq",,-1.46,
-"OBIGT",1531,"Sc(Glut)+","aq",,-1.5,
-"OBIGT",1532,"Th(Glut)+2","aq",-1.09,-4.05,
-"OBIGT",1535,"Fe(Glut)+","aq",,-1.05,
-"OBIGT",1536,"Sm(Glut)+","aq",,-1.2,
-"OBIGT",1539,"Er(Glut)+","aq",,-1.4,
-"OBIGT",1541,"Ba(Adip)","aq",,1.19,
-"OBIGT",1548,"Pb(Adip)","aq",,1.25,
-"OBIGT",1549,"Sc(Adip)+","aq",,-1.22,
-"OBIGT",1551,"Th(Adip)+2","aq",-1.02,-3.76,
-"OBIGT",1552,"U(Adip)+2","aq",-1,-3.71,
-"OBIGT",1554,"Li(Oxal)-","aq",,-3.3,
-"OBIGT",1558,"Li(Succ)-","aq",,-2.94,
-"OBIGT",1560,"Na(Glut)-","aq",,-2.34,
-"OBIGT",1561,"K(Glut)-","aq",,-2.05,
-"OBIGT",1562,"Li(Glut)-","aq",,-2.66,
-"OBIGT",1567,"Na(Adip)-","aq",,-2.05,
-"OBIGT",1568,"K(Adip)-","aq",,-1.76,
-"OBIGT",1569,"Li(Adip)-","aq",,-2.38,
-"OBIGT",1575,"cyclohexane","aq",9.35,6.64,
-"OBIGT",1576,"argon","aq",-1.24,-8.59,
-"OBIGT",1577,"benzene","aq",,-1.14,
-"OBIGT",1578,"CO2","aq",-4.94,,
-"OBIGT",1579,"xenon","aq",2.8,,
-"OBIGT",1589,"n-butanethiol","aq",2.19,,
-"OBIGT",1611,"methyldiethanolamine","aq",1.61,,
-"OBIGT",1621,"cysteinate","aq",-1,,
-"OBIGT",1647,"glucose","aq",1.11,,
-"OBIGT",1675,"guanine","aq",-4.26,,
-"OBIGT",1719,"dHUMP-","aq",-3.13,,
-"OBIGT",1816,"MgADP-","aq",-1.01,,
-"OBIGT",1827,"HNicMP(ox)","aq",,9.4,
-"OBIGT",1835,"ribose-5-phosphate","aq",,7.48,
-"OBIGT",1837,"ribose-5-phosphate-2","aq",1.53,,
-"OBIGT",1838,"H4NADP(red)","aq",1.73,,
-"OBIGT",1839,"H3NADP(red)-","aq",2.41,,
-"OBIGT",1840,"H2NADP(red)-2","aq",1.28,,
-"OBIGT",1841,"HNADP(red)-3","aq",2.09,,
-"OBIGT",1842,"NADP(red)-4","aq",1.09,,
-"OBIGT",1844,"H3NADP(ox)","aq",1.05,,
-"OBIGT",1915,"diglycine+","aq",-177.69,,
-"OBIGT",1916,"diglycine-","aq",-49.22,,
-"OBIGT",1917,"triglycine+","aq",,1.75,
-"OBIGT",1918,"triglycine-","aq",,1.78,
-"OBIGT",2048,"jarosite","cr",,,20697
-"OBIGT",2049,"natrojarosite","cr",,,17554
-"OBIGT",2068,"dawsonite","cr",,,4653
-"OBIGT",2089,"n-octadecane","cr",-2.63,,
-"OBIGT",2090,"n-nonadecane","cr",-13.32,,
-"OBIGT",2091,"n-eicosane","cr",-2.79,,
-"OBIGT",2092,"n-heneicosane","cr",-8.61,,
-"OBIGT",2093,"n-docosane","cr",-2.63,,
-"OBIGT",2094,"n-tricosane","cr",-5.22,,
-"OBIGT",2095,"n-tetracosane","cr",-2.02,,
-"OBIGT",2096,"n-pentacosane","cr",-2.93,,
-"OBIGT",2097,"n-hexacosane","cr",-1.29,,
-"OBIGT",2098,"n-heptacosane","cr",-1.23,,
-"OBIGT",2150,"carbazole","cr",-43.39,,
-"OBIGT",2191,"triphenylene","cr",,,541
-"OBIGT",2504,"deoxyadenosine","cr",,,-2977
-"OBIGT",2691,"n-nonacontane","liq",,,635
-"OBIGT",2698,"2-methyloctane","liq",10,,
-"OBIGT",3111,"5,6-dithiadecane","liq",2,,
-"OBIGT",3186,"ethylene","gas",-4.59,,
-"OBIGT",3196,"3,5-dimethylphenol","gas",,,628
+"OBIGT",340,"UO4-2","aq",,-1.11,
+"OBIGT",370,"Ag(CO3)2-3","aq",,-1.56,
+"OBIGT",386,"AgCl4-3","aq",,-1.31,
+"OBIGT",433,"CuCl4-2","aq",,-1.07,
+"OBIGT",435,"ReO4-","aq",-1.26,,
+"OBIGT",444,"PO4-3","aq",,-1.72,
+"OBIGT",451,"UO2+2","aq",-1.1,,
+"OBIGT",452,"Th+4","aq",,-1.14,
+"OBIGT",471,"P2O7-4","aq",,-2.11,
+"OBIGT",472,"HP2O7-3","aq",,-1.42,
+"OBIGT",486,"SO3-2","aq",,-1.02,
+"OBIGT",520,"VO4-3","aq",,-1.63,
+"OBIGT",531,"Zr+4","aq",,-1.18,
+"OBIGT",538,"Hf+4","aq",,-1.18,
+"OBIGT",542,"U+4","aq",,-1.13,
+"OBIGT",558,"Ce+4","aq",,-1.13,
+"OBIGT",559,"Pr+4","aq",,-1.12,
+"OBIGT",560,"Nd+4","aq",,-1.12,
+"OBIGT",561,"Pm+4","aq",,-1.13,
+"OBIGT",562,"Sm+4","aq",,-1.14,
+"OBIGT",563,"Eu+4","aq",,-1.14,
+"OBIGT",564,"Gd+4","aq",,-1.16,
+"OBIGT",565,"Tb+4","aq",,-1.15,
+"OBIGT",566,"Dy+4","aq",,-1.15,
+"OBIGT",567,"Ho+4","aq",,-1.15,
+"OBIGT",568,"Er+4","aq",,-1.15,
+"OBIGT",569,"Tm+4","aq",,-1.16,
+"OBIGT",570,"Yb+4","aq",,-1.16,
+"OBIGT",571,"Lu+4","aq",,-1.17,
+"OBIGT",580,"BeO2-2","aq",,-1.17,
+"OBIGT",623,"MnO2-2","aq",,-1.05,
+"OBIGT",634,"CoO2-2","aq",,-1.14,
+"OBIGT",639,"NiO2-2","aq",,-1.16,
+"OBIGT",643,"CuO2-2","aq",,-1.09,
+"OBIGT",657,"CdO2-2","aq",,-1.08,
+"OBIGT",673,"RuCl4-2","aq",,-1.09,
+"OBIGT",676,"Ru(SO4)3-4","aq",,-1.8,
+"OBIGT",683,"RuCl5-2","aq",,-1.49,
+"OBIGT",684,"RuCl6-3","aq",,-2.39,
+"OBIGT",687,"Ru(SO4)3-3","aq",,-1.3,
+"OBIGT",693,"RhCl4-2","aq",,-1.14,
+"OBIGT",696,"Rh(SO4)3-4","aq",,-1.82,
+"OBIGT",700,"RhCl2+","aq",,4.67,
+"OBIGT",705,"Rh(SO4)3-3","aq",,-1.33,
+"OBIGT",708,"CF4","aq",5.9,,
+"OBIGT",715,"AsH3","aq",-2.67,,
+"OBIGT",841,"AgCl","aq",,-1.88,
+"OBIGT",842,"AgCl2-","aq",1.65,,
+"OBIGT",847,"CuHS","aq",7.35,-16.2,
+"OBIGT",855,"ZnO2-2","aq",,-1.17,
+"OBIGT",881,"methane","aq",-2.61,,
+"OBIGT",886,"hexane","aq",1.43,3.21,
+"OBIGT",889,"ethylene","aq",6.12,-3.82,
+"OBIGT",913,"propanol","aq",-1.89,,
+"OBIGT",1042,"urea","aq",-23.26,23.32,
+"OBIGT",1055,"propanoic acid","aq",1.42,,
+"OBIGT",1078,"formate","aq",1.96,,
+"OBIGT",1080,"propanoate","aq",1.68,,
+"OBIGT",1087,"n-decanoate","aq",-1.93,,
+"OBIGT",1103,"oxalate-2","aq",-3.19,,
+"OBIGT",1370,"Li(Mal)-","aq",,-3.22,
+"OBIGT",1374,"Pb(Mal)","aq",,1.16,
+"OBIGT",1378,"Pb(Succ)","aq",,1.49,
+"OBIGT",1379,"Na(Oxal)-","aq",,-3.14,
+"OBIGT",1380,"K(Oxal)-","aq",,-2.75,
+"OBIGT",1381,"Fe(Oxal)+","aq",,-2.19,
+"OBIGT",1383,"Na(Mal)-","aq",,-3.11,
+"OBIGT",1384,"K(Mal)-","aq",,-2.63,
+"OBIGT",1386,"La(Mal)+","aq",,-1.92,
+"OBIGT",1387,"Gd(Mal)+","aq",,-1.73,
+"OBIGT",1388,"Lu(Mal)+","aq",,-2.25,
+"OBIGT",1389,"Yb(Mal)+","aq",,-2.05,
+"OBIGT",1390,"Th(Mal)+2","aq",-1.29,-4.79,
+"OBIGT",1392,"Ce(Mal)+","aq",,-1.75,
+"OBIGT",1393,"Nd(Mal)+","aq",4.52,,
+"OBIGT",1394,"Sm(Mal)+","aq",,-1.77,
+"OBIGT",1395,"Pr(Mal)+","aq",,-1.75,
+"OBIGT",1396,"Eu(Mal)+","aq",,-1.87,
+"OBIGT",1397,"Tb(Mal)+","aq",,-1.92,
+"OBIGT",1398,"Dy(Mal)+","aq",,-1.89,
+"OBIGT",1399,"Tm(Mal)+","aq",,-2.08,
+"OBIGT",1400,"Ho(Mal)+","aq",,-2.08,
+"OBIGT",1401,"Er(Mal)+","aq",,-2.11,
+"OBIGT",1402,"Sc(Mal)+","aq",,-1.97,
+"OBIGT",1403,"Fe(Mal)+","aq",,-1.97,
+"OBIGT",1404,"Na(Succ)-","aq",,-2.82,
+"OBIGT",1405,"K(Succ)-","aq",,-2.39,
+"OBIGT",1411,"Th(Succ)+2","aq",-1.21,-4.47,
+"OBIGT",1416,"NH4(Oxal)-","aq",,-2.62,
+"OBIGT",1421,"Yb(Oxal)+","aq",,-2.02,
+"OBIGT",1422,"Ce(Oxal)+","aq",,-1.8,
+"OBIGT",1423,"Nd(Oxal)+","aq",,-1.8,
+"OBIGT",1424,"Eu(Oxal)+","aq",,-1.89,
+"OBIGT",1425,"Gd(Oxal)+","aq",,-1.8,
+"OBIGT",1426,"Ru(Oxal)+","aq",,-2.41,
+"OBIGT",1427,"Pa(Oxal)+2","aq",-1.25,-4.63,
+"OBIGT",1428,"Th(Oxal)+2","aq",-1.27,-4.69,
+"OBIGT",1429,"U(Oxal)+2","aq",-1.25,-4.63,
+"OBIGT",1430,"Np(Oxal)+2","aq",-1.27,-4.69,
+"OBIGT",1433,"Am(Oxal)+","aq",,-1.8,
+"OBIGT",1434,"Cm(Oxal)+","aq",,-1.8,
+"OBIGT",1435,"Y(Oxal)+","aq",,-2.11,
+"OBIGT",1440,"La(Oxal)+","aq",,-1.87,
+"OBIGT",1441,"Tb(Oxal)+","aq",,-1.92,
+"OBIGT",1442,"Er(Oxal)+","aq",,-2.05,
+"OBIGT",1443,"Lu(Oxal)+","aq",,-2.19,
+"OBIGT",1444,"Cr(Oxal)+","aq",,-2.58,
+"OBIGT",1445,"Ga(Oxal)+","aq",,-2.66,
+"OBIGT",1446,"Sc(Oxal)+","aq",,-2.13,
+"OBIGT",1447,"In(Oxal)+","aq",,-2.19,
+"OBIGT",1448,"Pu(Oxal)+2","aq",-1.2,-4.44,
+"OBIGT",1449,"NpO2(Oxal)","aq",,-1.94,
+"OBIGT",1450,"Sm(Oxal)+","aq",,-1.84,
+"OBIGT",1451,"Cs(Mal)-","aq",,-2.39,
+"OBIGT",1452,"NH4(Mal)-","aq",,-2.54,
+"OBIGT",1457,"In(Mal)+","aq",,-2.11,
+"OBIGT",1458,"Y(Mal)+","aq",,-2.02,
+"OBIGT",1466,"La(Succ)+","aq",,-1.52,
+"OBIGT",1467,"NH4(Succ)-","aq",,-2.26,
+"OBIGT",1469,"Fe(Succ)+","aq",,-1.92,
+"OBIGT",1470,"Sc(Succ)+","aq",,-1.77,
+"OBIGT",1473,"NpO2(Succ)","aq",,-3.16,
+"OBIGT",1474,"Sm(Succ)+","aq",,-1.48,
+"OBIGT",1475,"Er(Succ)+","aq",,-1.68,
+"OBIGT",1476,"U(Succ)+2","aq",-1.15,-4.27,
+"OBIGT",1480,"La(Glut)+","aq",,-1.23,
+"OBIGT",1481,"Y(Glut)+","aq",,-1.46,
+"OBIGT",1482,"Sc(Glut)+","aq",,-1.5,
+"OBIGT",1483,"Th(Glut)+2","aq",-1.09,-4.05,
+"OBIGT",1486,"Fe(Glut)+","aq",,-1.05,
+"OBIGT",1487,"Sm(Glut)+","aq",,-1.2,
+"OBIGT",1490,"Er(Glut)+","aq",,-1.4,
+"OBIGT",1492,"Ba(Adip)","aq",,1.19,
+"OBIGT",1499,"Pb(Adip)","aq",,1.25,
+"OBIGT",1500,"Sc(Adip)+","aq",,-1.22,
+"OBIGT",1502,"Th(Adip)+2","aq",-1.02,-3.76,
+"OBIGT",1503,"U(Adip)+2","aq",-1,-3.71,
+"OBIGT",1505,"Li(Oxal)-","aq",,-3.3,
+"OBIGT",1509,"Li(Succ)-","aq",,-2.94,
+"OBIGT",1511,"Na(Glut)-","aq",,-2.34,
+"OBIGT",1512,"K(Glut)-","aq",,-2.05,
+"OBIGT",1513,"Li(Glut)-","aq",,-2.66,
+"OBIGT",1518,"Na(Adip)-","aq",,-2.05,
+"OBIGT",1519,"K(Adip)-","aq",,-1.76,
+"OBIGT",1520,"Li(Adip)-","aq",,-2.38,
+"OBIGT",1526,"cyclohexane","aq",9.35,6.64,
+"OBIGT",1527,"Ar","aq",-1.24,-8.59,
+"OBIGT",1528,"benzene","aq",,-1.14,
+"OBIGT",1529,"CO2","aq",-4.94,,
+"OBIGT",1530,"Xe","aq",2.8,,
+"OBIGT",1540,"n-butanethiol","aq",2.19,,
+"OBIGT",1562,"methyldiethanolamine","aq",1.61,,
+"OBIGT",1572,"cysteinate","aq",-1,,
+"OBIGT",1598,"glucose","aq",1.11,,
+"OBIGT",1626,"guanine","aq",-4.26,,
+"OBIGT",1670,"dHUMP-","aq",-3.13,,
+"OBIGT",1767,"MgADP-","aq",-1.01,,
+"OBIGT",1778,"HNicMP(ox)","aq",,9.4,
+"OBIGT",1786,"ribose-5-phosphate","aq",,7.48,
+"OBIGT",1788,"ribose-5-phosphate-2","aq",1.53,,
+"OBIGT",1789,"H4NADP(red)","aq",1.73,,
+"OBIGT",1790,"H3NADP(red)-","aq",2.41,,
+"OBIGT",1791,"H2NADP(red)-2","aq",1.28,,
+"OBIGT",1792,"HNADP(red)-3","aq",2.09,,
+"OBIGT",1793,"NADP(red)-4","aq",1.09,,
+"OBIGT",1795,"H3NADP(ox)","aq",1.05,,
+"OBIGT",1866,"diglycine+","aq",-177.69,,
+"OBIGT",1867,"diglycine-","aq",-49.22,,
+"OBIGT",1868,"triglycine+","aq",,1.75,
+"OBIGT",1869,"triglycine-","aq",,1.78,
+"OBIGT",1999,"jarosite","cr",,,20697
+"OBIGT",2000,"natrojarosite","cr",,,17554
+"OBIGT",2019,"dawsonite","cr",,,4653
+"OBIGT",2040,"octadecane","cr",-2.63,,
+"OBIGT",2041,"nonadecane","cr",-13.32,,
+"OBIGT",2042,"eicosane","cr",-2.79,,
+"OBIGT",2043,"heneicosane","cr",-8.61,,
+"OBIGT",2044,"docosane","cr",-2.63,,
+"OBIGT",2045,"tricosane","cr",-5.22,,
+"OBIGT",2046,"tetracosane","cr",-2.02,,
+"OBIGT",2047,"pentacosane","cr",-2.93,,
+"OBIGT",2048,"hexacosane","cr",-1.29,,
+"OBIGT",2049,"heptacosane","cr",-1.23,,
+"OBIGT",2101,"carbazole","cr",-43.39,,
+"OBIGT",2142,"triphenylene","cr",,,541
+"OBIGT",2455,"deoxyadenosine","cr",,,-2977
+"OBIGT",2642,"nonacontane","liq",,,635
+"OBIGT",2649,"2-methyloctane","liq",10,,
+"OBIGT",3062,"5,6-dithiadecane","liq",2,,
+"OBIGT",3142,"ethylene","gas",-4.59,,
+"OBIGT",3152,"3,5-dimethylphenol","gas",,,628
 "DEW",15,"BO(OH)","aq",,,-1111
 "DEW",19,"CaCl+","aq",,,-593
 "DEW",20,"CaCl2","aq",,,-7937
@@ -246,11 +240,23 @@
 "DEW",177,"SO3-2","aq",,-1.02,
 "DEW",186,"U+4","aq",,-1.13,
 "DEW",199,"ZnCl3-","aq",,,2264
-"SLOP98",4,"AuCl4-3","aq",,,117800
-"SLOP98",11,"AsO4-3","aq",,-1.65,
-"SLOP98",20,"Al+3","aq",1.74,,
-"SLOP98",27,"Al(Mal)+","aq",,-2.19,
-"SLOP98",28,"Al(Oxal)+","aq",,-2.62,
+"SLOP98",12,"PtCl+","aq",-3.52,1.25,
+"SLOP98",13,"PtCl2","aq",-7.11,2.29,
+"SLOP98",14,"PtCl3-","aq",-10.48,1.78,
+"SLOP98",15,"PtCl4-2","aq",-13.86,,
+"SLOP98",18,"Pt(SO4)3-4","aq",,-1.79,-2915
+"SLOP98",22,"Pd(SO4)3-4","aq",,-1.8,
+"SLOP98",26,"ZnCl3-","aq",,,2264
+"SLOP98",27,"Zn(Ac)+","aq",,,-4547
+"SLOP98",29,"Zn(Ac)3-","aq",,,-13968
+"SLOP98",44,"AsO4-3","aq",,-1.65,
+"SLOP98",51,"Al+3","aq",1.74,,
+"SLOP98",58,"ZnO2-2","aq",,-1.17,
+"SLOP98",62,"Al(Mal)+","aq",,-2.19,
+"SLOP98",63,"Al(Oxal)+","aq",,-2.62,
+"SLOP98",94,"MgAsO4-","aq",1.3,,
+"SLOP98",97,"MnAsO4-","aq",-1.45,,
+"SLOP98",119,"PdCl4-2","aq",,-1.05,
 "SUPCRT92",26,"antigorite","cr",,,812
 "SUPCRT92",43,"clinochlore,7a","cr",,,666
 "SUPCRT92",59,"daphnite,14a","cr",,,-836

Modified: pkg/CHNOSZ/man/retrieve.Rd
===================================================================
--- pkg/CHNOSZ/man/retrieve.Rd	2019-02-25 11:28:33 UTC (rev 413)
+++ pkg/CHNOSZ/man/retrieve.Rd	2019-02-25 13:16:27 UTC (rev 414)
@@ -7,7 +7,8 @@
 }
 
 \usage{
-  retrieve(..., state = NULL, add.charge = TRUE, hide.groups = TRUE, req1 = FALSE)
+  retrieve(..., state = NULL, add.charge = TRUE, hide.groups = TRUE,
+    req1 = FALSE)
 }
 
 \arguments{

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