info

info>   ## Don't show:
info> data(thermo)
thermo: loaded 1997 aqueous, 3089 total species to thermo$obigt
thermo: loaded 5264 proteins to thermo$ECO
thermo: loaded 6717 proteins to thermo$SGD
thermo: loaded 4155 localizations and 3570 abundances to thermo$yeastgfp

info> ## End Don't show
info>   ## basic operation
info>   ## Not run:
info> ##D   # view the license and news file
info> ##D   # marked dontrun because they open pagers
info> ##D   # that wait for the user to close them
info> ##D   info("licence")
info> ##D   info("CHNOSZ")
info> ##D   # run a consistency check on each species in the database
info> ##D   # (marked dontrun because it takes a while)
info> ##D   info()
info> ##D
info> ## End(Not run)
info>
info>   ## species information
info>   # search for something named (or whose formula is) "Fe"
info>   t <- info("Fe")
info: Fe available in cr1, cr2, cr3, cr4.
info: 2507 refers to Fe cr1 (RH95, CHNOSZ, 05.Aug.07).

info>   # use the number to get the full record
info>   info(t)
     name abbrv formula state source1 source2      date G H     S    Cp     V     a          b c d
2507   Fe  iron      Fe   cr1    RH95  CHNOSZ 05.Aug.07 0 0 6.475 5.994 7.092 7.162 -0.0069682 0 0
              e f lambda    T
2507 1.2294e-05 0      0 1043

info>   # it is possible to get a range of records
info>   info(t:(t+3))
info: Cp of Fe cr2 is NA; set by EOS parameters to 293.01.
info: Cp of Fe cr3 is NA; set by EOS parameters to 7.58.
info: Cp of Fe cr4 is NA; set by EOS parameters to 9.11.
     name abbrv formula state source1 source2      date        G        H         S         Cp
2507   Fe  iron      Fe   cr1    RH95  CHNOSZ 05.Aug.07      0.0      0.0    6.4750   5.994000
2508   Fe  iron      Fe   cr2    RH95  CHNOSZ 05.Aug.07 -32284.5 -87223.4 -177.7910 293.013353
2509   Fe  iron      Fe   cr3    RH95  CHNOSZ 05.Aug.07   1348.8   1843.8    8.1352   7.580456
2510   Fe  iron      Fe   cr4    RH95  CHNOSZ 05.Aug.07   3190.2   4835.6   11.9940   9.106491
         V        a          b      c d          e f lambda    T
2507 7.092   7.1620 -0.0069682      0 0 1.2294e-05 0      0 1043
2508 7.092 504.5770 -0.8072440      0 0 3.2754e-04 0      0 1185
2509 7.092   5.1938  0.0023381 150190 0 0.0000e+00 0      0 1667
2510 7.092  -4.0330  0.0080055 955840 0 0.0000e+00 0      0 1809

info>   ## dealing with states
info>   # default order of preference for names: aq > gas > cr,liq
info>   info(c("methane","ethanol","glycinate"))  # aq, aq, aq
info: methane (CH4) available in aq, liq, gas, gas.
info: ethanol (C2H5OH) available in aq, liq, gas.
info: 1291 refers to methane, CH4 aq (AH97b, SSW01, 1.Sep.06).
info: 1344 refers to ethanol, C2H5OH aq (AH97b, CHNOSZ, 1.Sep.06).
info: 563 refers to glycinate, C2H4NO2- aq (SK95, AH97a, 3.Sep.06).

info>   info(c("adenosine","alanine","hydroxyapatite"))  # aq, aq, cr
info: adenosine (C10H13N5O4) available in aq, cr.
info: alanine (C3H7NO2) available in aq, cr.
info: 1712 refers to adenosine, C10H13N5O4 aq (LH06a, 3.Feb.03).
info: 1618 refers to alanine, C3H7NO2 aq (AH97b, DLH06, 25.Aug.06).
info: 2426 refers to hydroxyapatite, Ca5(PO4)3OH cr (Ste01, 31.Aug.06).

info>   # state argument overrides the default
info>   info(c("ethanol","adenosine"),state=c("gas","cr"))
info: 2977 refers to ethanol, C2H5OH gas (HOK+98, 30.Aug.06).
info: 2453 refers to adenosine, C10H13N5O4 cr (LH06a, 14.Aug.06).

info>   # formulas default to aqueous species, if available
info>   info(c("CH4","CO2","CS2","MgO"))  # aq, aq, gas, cr
info: CH4 (methane) available in aq, liq, gas, gas.
info: CO2 matches these species:
               name          abbrv formula state source1
69              CO2 carbon dioxide     CO2    aq   SSW01
81              CO2            CO2     CO2    aq   SHS89
2844 carbon dioxide            CO2     CO2   gas  WEP+82
info: CS2 (carbon disulfide) available in liq, gas.
info: 1291 refers to methane aq (AH97b, SSW01, 1.Sep.06).
info: 69 refers to CO2 aq (SSW01, SHS89, 11.Oct.07).
info: 2754 refers to carbon disulfide liq (Ric01, 1.Sep.06).
info: 2190 refers to periclase cr (HDN+78, 5.May.78).

info>   # state argument overrides the default
info>   info(c("CH4","CO2","MgO"),"gas")  # gas, gas, NA
info: CH4 (methane) available in gas, gas.
info: no match for MgO gas, and no approximate matches.
info: 2843 refers to methane gas (WEP+82, Kel60, 15.Dec.87).
info: 2870 refers to methane gas (HOK+98, 30.Aug.06).
info: 2844 refers to carbon dioxide gas (WEP+82, Kel60, 27.Dec.89).

info>   # exceptions to the aqueous default is O2
info>   info("O2")  # gas
info: O2 matches these species:
       name  abbrv formula state source1
2852 oxygen     O2      O2   gas  WEP+82
67       O2 oxygen      O2    aq   SHS89
info: 2852 refers to oxygen gas (WEP+82, Kel60, 27.Dec.89).

info>   ## partial name or formula searches
info>   info("ATP")
info: no match for ATP.
info: similar species names, abbreviations, or formulas are:
 [1] "AMYA-PYRFU"    "RNT1-ASPOR"    "AMP-2"         "HAMP-"         "H2AMP"         "dAMP-2"
 [7] "dHAMP-"        "dH2AMP"        "ADP-3"         "HADP-2"        "H2ADP-"        "H3ADP"
[13] "dADP-3"        "dHADP-2"       "dH2ADP-"       "dH3ADP"        "ATP-4"         "HATP-3"
[19] "H2ATP-2"       "H3ATP-"        "H4ATP"         "CTP-4"         "HCTP-3"        "H2CTP-2"
[25] "H3CTP-"        "H4CTP"         "GTP-4"         "HGTP-3"        "H2GTP-2"       "H3GTP-"
[31] "H4GTP"         "TTP-4"         "HTTP-3"        "H2TTP-2"       "H3TTP-"        "H4TTP"
[37] "UTP-4"         "HUTP-3"        "H2UTP-2"       "H3UTP-"        "H4UTP"         "dATP-4"
[43] "dHATP-3"       "dH2ATP-2"      "dH3ATP-"       "dH4ATP"        "dCTP-4"        "dHCTP-3"
[49] "dH2CTP-2"      "dH3CTP-"       "dH4CTP"        "dGTP-4"        "dHGTP-3"       "dH2GTP-2"
[55] "dH3GTP-"       "dH4GTP"        "dTTP-4"        "dHTTP-3"       "dH2TTP-2"      "dH3TTP-"
[61] "dH4TTP"        "dUTP-4"        "dHUTP-3"       "dH2UTP-2"      "dH3UTP-"       "dH4UTP"
[67] "MgAMP"         "MgADP-"        "MgHADP"        "Mg2ADP+"       "MgATP-2"       "MgHATP-"
[73] "MgH2ATP"       "Mg2ATP"        "H4NADP(red)"   "H3NADP(red)-"  "H2NADP(red)-2" "HNADP(red)-3"
[79] "NADP(red)-4"   "H4NADP(ox)+"   "H3NADP(ox)"    "H2NADP(ox)-"   "HNADP(ox)-2"   "NADP(ox)-3"

info>   info("thiol")
info: no match for thiol.
info: similar species names, abbreviations, or formulas are:
 [1] "methanethiol"                "ethanethiol"                 "n-propanethiol"
 [4] "n-butanethiol"               "n-pentanethiol"              "n-hexanethiol"
 [7] "n-heptanethiol"              "n-octanethiol"               "n-nonanethiol"
[10] "n-decanethiol"               "n-undecanethiol"             "n-dodecanethiol"
[13] "methionine"                  "glutathione"                 "glutathione,ox"
[16] "benzenethiol"                "poly(thio-1,4-phenylene)"    "thiophene"
[19] "benzo[b]thiophene"           "dibenzo[b,d]thiophene"       "n-tridecanethiol"
[22] "n-tetradecanethiol"          "n-pentadecanethiol"          "n-hexadecanethiol"
[25] "n-heptadecanethiol"          "n-octadecanethiol"           "n-nonadecanethiol"
[28] "n-eicosanethiol"             "thiophenol"                  "2-propanethiol"
[31] "2-butanethiol"               "2-methyl-1-propanethiol"     "2-methyl-2-propanethiol"
[34] "2-methyl-1-butanethiol"      "2-methyl-2-butanethiol"      "3-methyl-1-butanethiol"
[37] "3-methyl-2-butanethiol"      "2,2-dimethyl-1-propanethiol" "2-methyl-2-pentanethiol"
[40] "2,3-dimethyl-2-butanethiol"  "cyclopentanethiol"           "cyclohexanethiol"
[43] "phenylmethanethiol"          "2-methylthiophene"           "3-methylthiophene"
[46] "2,5-dimethylthiophene"       "2-isopropylthiophene"

info>   info("MgC")
info: no match for MgC.
info: similar species names, abbreviations, or formulas are:
  [1] "Mg+2"                         "Mg(Ac)+"                      "Mg(Ac)2"
  [4] "Mg(For)+"                     "Mg(For)2"                     "Mg(Prop)+"
  [7] "Mg(Prop)2"                    "Mg(But)+"                     "Mg(But)2"
 [10] "Mg(Pent)+"                    "Mg(Pent)2"                    "Mg(Glyc)+"
 [13] "Mg(Glyc)2"                    "Mg(Lac)+"                     "Mg(Lac)2"
 [16] "Mg(Gly)+"                     "Mg(Gly)2"                     "Mg(Alan)+"
 [19] "Mg(Alan)2"                    "Mg(HCO3)+"                    "MgSO4"
 [22] "AgCl"                         "AgCl2-"                       "MgCl+"
 [25] "MgF+"                         "MgCO3"                        "MnCl+"
 [28] "AgCl3-2"                      "AgCl4-3"                      "HgCl+"
 [31] "HgCl2"                        "HgCl3-"                       "HgCl4-2"
 [34] "Mg(HSiO3)+"                   "MgOH+"                        "Mg(Mal)"
 [37] "Mg(Oxal)"                     "Mg(Succ)"                     "Mg(Glut)"
 [40] "Mg(Adip)"                     "MgAMP"                        "MgADP-"
 [43] "MgHADP"                       "Mg2ADP+"                      "MgATP-2"
 [46] "MgHATP-"                      "MgH2ATP"                      "Mg2ATP"
 [49] "MgH2AsO4+"                    "MgHAsO4"                      "MgAsO4-"
 [52] "MgH2AsO3+"                    "Hydro-Mgs"                    "Mg-Hs"
 [55] "Mg-Rbk"                       "Mgs"                          "MgCH3COO+"
 [58] "MnCH3COO+"                    "HgCH3COO+"                    "AgCH3COO"
 [61] "Mg(CH3COO)2"                  "MgCHO2+"                      "Mg(CHO2)2"
 [64] "MnCHO2+"                      "MgCH3CH2CO2+"                 "Mg(CH3CH2CO2)2"
 [67] "MnCH3CH2CO2+"                 "MgCH3(CH2)2CO2+"              "Mg(CH3CH2CH2CO2)2"
 [70] "MnCH3(CH2)2CO2+"              "MgCH3(CH2)3CO2+1"             "Mg(CH3CH2CH2CH2CO2)2"
 [73] "MnCH3(CH2)3CO2+"              "MgCH3OCO2+"                   "Mg(CH3OCO2)2"
 [76] "MnCH3OCO2+"                   "MgCH3CH2OCO2+"                "Mg(CH3CH2OCO2)2"
 [79] "MnCH3CH2OCO2+"                "Mg(C2H4NO2)+"                 "Mg(C2H4NO2)2"
 [82] "Mg(C3H6NO2)+"                 "Mg(C3H6NO2)2"                 "MnC2O4"
 [85] "MgC3H2O4"                     "MnC4H4O4"                     "MgC2O4"
 [88] "HgC2O4"                       "MnC3H2O4"                     "MgC4H4O4"
 [91] "MnC5H6O4"                     "MgC5H6O4"                     "MgC6H8O4"
 [94] "MnC6H8O4"                     "MgC10H12N5O7P"                "MgC10H12N5O10P2-"
 [97] "MgC10H13N5O10P2"              "Mg2C10H12N5O10P2+"            "MgC10H12N5O13P3-2"
[100] "MgC10H13N5O13P3-"             "MgC10H14N5O13P3"              "Mg2C10H12N5O13P3"
[103] "Ca2MgSi2O7"                   "Mg4Al2(Al2Si2)O10(OH)8"       "Mg2Al(AlSi)O5(OH)4"
[106] "Mg7Si8O22(OH)2"               "Mg48Si34O85(OH)62"            "Mg2(OH)2(CO3)*3H2O"
[109] "Mg(OH)2"                      "K(MgAl)Si4O10(OH)2"           "Mg3Si2O5(OH)4"
[112] "Mg5Al(AlSi3)O10(OH)8"         "Mg2Al3(AlSi5)O18"             "Mg2Al3(AlSi5)O18*H2O"
[115] "CaMg(SiO3)2"                  "CaMg(CO3)2"                   "Na(Ca2Mg5)(AlSi7)O22(OH2)"
[118] "MgSiO3"                       "Na(Ca2Mg5)(AlSi7)O22(F)2"     "KMg3(AlSi3)O10(F)2"
[121] "(Ca2Mg5)Si8O22(F)2"           "Mg2SiO4"                      "Na2(Mg3Al2)Si8O22(OH)2"
[124] "CaMg3(CO3)4"                  "Mg5(OH)2(CO3)4*4H2O"          "Na(Ca2Mg4Fe)(Al2Si6)O22(OH)2"
[127] "Na2(Mg3Fe2)Si8O22(OH)2"       "Ca3Mg(SiO4)2"                 "CaMgSiO4"
[130] "MgCO3*3H2O"                   "Na(Ca2Mg4Al)(Al2Si6)O22(OH)2" "MgO"
[133] "KMg3(AlSi3)O10(OH)2"          "Mg3Al2Si3O12"                 "MnCO3"
[136] "Na2(CaMg5)Si8O22(OH)2"        "Mg4Si6O15(OH)2(H2O)2*4H2O"    "MgAl2O4"
[139] "Mg3Si4O10(OH)2"               "(Ca2Mg5)Si8O22(OH)2"

info>   # add an extra character to refine a search
info>   # or to search using terms that have exact matches
info>   info("MgC ")
info: no match for MgC .
info: similar species names, abbreviations, or formulas are:
 [1] "MgCl+"             "MgCO3"             "MgCH3COO+"         "MgCHO2+"
 [5] "MgCH3CH2CO2+"      "MgCH3(CH2)2CO2+"   "MgCH3(CH2)3CO2+1"  "MgCH3OCO2+"
 [9] "MgCH3CH2OCO2+"     "MgC3H2O4"          "MgC2O4"            "MgC4H4O4"
[13] "MgC5H6O4"          "MgC6H8O4"          "MgC10H12N5O7P"     "MgC10H12N5O10P2-"
[17] "MgC10H13N5O10P2"   "MgC10H12N5O13P3-2" "MgC10H13N5O13P3-"  "MgC10H14N5O13P3"
[21] "MgCO3*3H2O"

info>   info("acetate ")
info: no match for acetate .
info: approximately matching species are:
              name abbrv      formula state
109   ethylacetate  <NA> CH3COOCH2CH3    aq
511        acetate  <NA>      C2H3O2-    aq
2707 ethyl acetate  <NA>       C4H8O2   liq
3019 ethyl acetate  <NA>       C4H8O2   gas

info>   info(" H2O")
info: no match for  H2O.
info: similar species names, abbreviations, or formulas are:
 [1] "H2O2"                           "[-CH2OH]"
 [3] "H2O"                            "C2H2O4"
 [5] "C3H2O4-2"                       "NaCH3CH2OCO2"
 [7] "Na(CH3CH2OCO2)2-"               "KCH3CH2OCO2"
 [9] "K(CH3CH2OCO2)2-"                "CaCH3CH2OCO2+"
[11] "Ca(CH3CH2OCO2)2"                "MgCH3CH2OCO2+"
[13] "Mg(CH3CH2OCO2)2"                "SrCH3CH2OCO2+"
[15] "Sr(CH3CH2OCO2)2"                "BaCH3CH2OCO2+"
[17] "Ba(CH3CH2OCO2)2"                "MnCH3CH2OCO2+"
[19] "Mn(CH3CH2OCO2)2"                "FeCH3CH2OCO2+"
[21] "Fe(CH3CH2OCO2)2"                "NiCH3CH2OCO2+"
[23] "Ni(CH3CH2OCO2)2"                "CuCH3CH2OCO2+"
[25] "Cu(CH3CH2OCO2)2"                "ZnCH3CH2OCO2+"
[27] "Zn(CH3CH2OCO2)2"                "PbCH3CH2OCO2+"
[29] "Pb(CH3CH2OCO2)2"                "CoCH3CH2OCO2+"
[31] "Co(CH3CH2OCO2)2"                "CdCH3CH2OCO2+"
[33] "Cd(CH3CH2OCO2)2"                "Eu(CH3CH2OCO2)+"
[35] "Eu(CH3CH2OCO2)2"                "LuCH3CH2OCO2+2"
[37] "LaCH3CH2OCO2+2"                 "LiCH3CH2OCO2"
[39] "LiC3H2O4-"                      "MgC3H2O4"
[41] "ZnC3H2O4"                       "CdC3H2O4"
[43] "AlC3H2O4+"                      "PbC3H2O4"
[45] "CuC3H2O4"                       "LaC3H2O4+"
[47] "GdC3H2O4+"                      "LuC3H2O4+"
[49] "YbC3H2O4+"                      "ThC3H2O4+2"
[51] "UO2C3H2O4"                      "CeC3H2O4+"
[53] "NdC3H2O4+"                      "SmC3H2O4+"
[55] "PrC3H2O4+"                      "EuC3H2O4+"
[57] "TbC3H2O4+"                      "DyCC3H2O4+"
[59] "TmC3H2O4+"                      "HoC3H2O4+"
[61] "ErC3H2O4+"                      "ScC3H2O4+"
[63] "FeC3H2O4+"                      "CsC3H2O4-"
[65] "NH4C3H2O4-"                     "SrC3H2O4"
[67] "CrC3H2O4"                       "BeC3H2O4"
[69] "FeC3H2O4"                       "InC3H2O4+"
[71] "YC3H2O4+"                       "CaC3H2O4"
[73] "BaC3H2O4"                       "MnC3H2O4"
[75] "CoC3H2O4"                       "NiC3H2O4"
[77] "C2H2O2-"                        "NaAlSi2O6*H2O"
[79] "Mg2(OH)2(CO3)*3H2O"             "Ca(Al2Si5)O14*5H2O"
[81] "Ca(Al2Si4)O12*6H2O"             "Mg2Al3(AlSi5)O18*H2O"
[83] "Ca(Al2Si6)O16*5H2O"             "Ca(Al2Si7)O18*6H2O"
[85] "Mg5(OH)2(CO3)4*4H2O"            "K2(Al2Si5)O14*5H2O"
[87] "Ca(Al2Si4)O12*4H2O"             "CaAl2Si2O7(OH)2*H2O"
[89] "Ca2(Al4Si8)O24*7H2O"            "Na2(Al2Si5)O14*5H2O"
[91] "Na2(Al2Si3)O10*2H2O"            "MgCO3*3H2O"
[93] "Mg4Si6O15(OH)2(H2O)2*4H2O"      "NaCa2(Al5Si13)O36*14H2O"
[95] "Ca(Al2Si4)O12*2H2O"             "FeSO4*7H2O"
[97] "Fe1.47Al0.53(SO4)3(H2O)9.65"    "Fe4.78(SO4)6(OH)2.34(H2O)20.71"
[99] "(H3O)1.34Fe(SO4)2.17(H2O)3.06"