info

## Don't show: data(thermo)
thermo$obigt: 1911 aqueous, 3588 total species
## End(Don't show) ## summary of available data info()
info: 'species' is NULL; summarizing information about thermodynamic data... thermo$obigt has 1911 aqueous, 3588 total species number of literature sources: 161, elements: 130, buffers: 26 number of proteins in thermo$protein is 506 from 97 organisms yeast.aa: extdata/protein/Sce.csv.xz has data for 6719 proteins yeastgfp: extdata/abundance/yeastgfp.csv.xz has 4155 localizations and 3570 abundances NULL
## species information # search for something named (or whose formula is) "Fe" si <- info("Fe")
info.character: found Fe(cr) with 3 phase transitions
# use the number to get the full record info(si)
info.numeric: Cp of iron(cr) is NA; set by EOS parameters to 5.97 name abbrv formula state ref1 ref2 date G H S Cp V a b 2054 iron Fe Fe cr RHF78.2 [S92] Kel60.2 [S92] 5.May.78 0 0 6.52 5.974943 7.092 3.04 0.00758 c d e f lambda T 2054 60000 0 0 0 0 1033
# it is possible to get a range of records info(si:(si+3))
info.numeric: Cp of iron(cr) is NA; set by EOS parameters to 5.97 info.numeric: Cp of iron(cr2) is NA; set by EOS parameters to 11.13 info.numeric: Cp of iron(cr3) is NA; set by EOS parameters to 6.39 info.numeric: Cp of iron(cr4) is NA; set by EOS parameters to 7.22 name abbrv formula state ref1 ref2 date G H S Cp V 2054 iron Fe Fe cr RHF78.2 [S92] Kel60.2 [S92] 5.May.78 0.000 0.000 6.520 5.974943 7.092 2055 iron Fe Fe cr2 RHF78.2 [S92] CHNOSZ.1 5.May.78 -618.237 -1768.418 2.662 11.130000 7.092 2056 iron Fe Fe cr3 RHF78.2 [S92] CHNOSZ.1 5.May.78 1293.526 1865.343 8.438 6.390337 7.092 2057 iron Fe Fe cr4 RHF78.2 [S92] CHNOSZ.1 5.May.78 979.290 1252.891 7.438 7.217040 7.092 a b c d e f lambda T 2054 3.04 0.00758 60000 0 0 0 0 1033 2055 11.13 0.00000 0 0 0 0 0 1183 2056 5.80 0.00198 0 0 0 0 0 1673 2057 6.74 0.00160 0 0 0 0 0 1812
## dealing with states # default order of preference for names: aq > gas > cr,liq info(c("methane","ethanol","glycinate")) # aq, aq, aq
info.character: found methane(aq), also available in liq, gas info.character: found ethanol(aq), also available in liq, gas [1] 859 890 1122
info(c("adenosine","alanine","hydroxyapatite")) # aq, aq, cr
info.character: found adenosine(aq), also available in cr info.character: found alanine(aq), also available in cr [1] 1682 1611 2761
# state argument overrides the default info(c("ethanol","adenosine"),state=c("gas","cr"))
[1] 3441 2637
# formulas default to aqueous species, if available info(c("CH4","CO2","CS2","MgO")) # aq, aq, gas, cr
info.character: found CH4(aq), also available in liq, gas info.character: found CO2(aq), also available in gas info.character: found CS2(liq), also available in gas info.character: found MgO(cr), also available in cr_Berman [1] 859 1576 3193 2108
# state argument overrides the default info(c("CH4","CO2","MgO"),"gas") # gas, gas, NA
info.character: requested state 'gas' for MgO but only 'cr' 'cr_Berman' are available info.approx: 'MgO' has no approximate matches [1] 3307 3308 NA
# exceptions to the aqueous default is O2 info("O2") # gas
info.character: found O2(aq), also available in gas [1] 65
## partial name or formula searches info("ATP")
info.approx: 'ATP' is ambiguous; has approximate matches to 83 species: [1] "AMP-2" "HAMP-" "H2AMP" "dAMP-2" "dHAMP-" "dH2AMP" [7] "ADP-3" "HADP-2" "H2ADP-" "H3ADP" "dADP-3" "dHADP-2" [13] "dH2ADP-" "dH3ADP" "ATP-4" "HATP-3" "H2ATP-2" "H3ATP-" [19] "H4ATP" "CTP-4" "HCTP-3" "H2CTP-2" "H3CTP-" "H4CTP" [25] "GTP-4" "HGTP-3" "H2GTP-2" "H3GTP-" "H4GTP" "TTP-4" [31] "HTTP-3" "H2TTP-2" "H3TTP-" "H4TTP" "UTP-4" "HUTP-3" [37] "H2UTP-2" "H3UTP-" "H4UTP" "dATP-4" "dHATP-3" "dH2ATP-2" [43] "dH3ATP-" "dH4ATP" "dCTP-4" "dHCTP-3" "dH2CTP-2" "dH3CTP-" [49] "dH4CTP" "dGTP-4" "dHGTP-3" "dH2GTP-2" "dH3GTP-" "dH4GTP" [55] "dTTP-4" "dHTTP-3" "dH2TTP-2" "dH3TTP-" "dH4TTP" "dUTP-4" [61] "dHUTP-3" "dH2UTP-2" "dH3UTP-" "dH4UTP" "MgAMP" "MgADP-" [67] "MgHADP" "Mg2ADP+" "MgATP-2" "MgHATP-" "MgH2ATP" "Mg2ATP" [73] "H4NADP(red)" "H3NADP(red)-" "H2NADP(red)-2" "HNADP(red)-3" "NADP(red)-4" "H4NADP(ox)+" [79] "H3NADP(ox)" "H2NADP(ox)-" "HNADP(ox)-2" "NADP(ox)-3" "H2AMP" [1] NA
info("thiol")
info.approx: 'thiol' is ambiguous; has approximate matches to 105 species (showing first 100) [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] "methionine" "benzenethiol" "poly(thio-1,4-phenylene)" [19] "thiophene" "benzo[b]thiophene" "dibenzo[b,d]thiophene" [22] "methanethiol" "ethanethiol" "n-propanethiol" [25] "n-butanethiol" "n-pentanethiol" "n-hexanethiol" [28] "n-heptanethiol" "n-octanethiol" "n-nonanethiol" [31] "n-decanethiol" "n-undecanethiol" "n-dodecanethiol" [34] "n-tridecanethiol" "n-tetradecanethiol" "n-pentadecanethiol" [37] "n-hexadecanethiol" "n-heptadecanethiol" "n-octadecanethiol" [40] "n-nonadecanethiol" "n-eicosanethiol" "thiophenol" [43] "2-propanethiol" "2-butanethiol" "2-methyl-1-propanethiol" [46] "2-methyl-2-propanethiol" "2-methyl-1-butanethiol" "2-methyl-2-butanethiol" [49] "3-methyl-1-butanethiol" "3-methyl-2-butanethiol" "2,2-dimethyl-1-propanethiol" [52] "2-methyl-2-pentanethiol" "2,3-dimethyl-2-butanethiol" "cyclopentanethiol" [55] "cyclohexanethiol" "benzenethiol" "phenylmethanethiol" [58] "thiophene" "2-methylthiophene" "3-methylthiophene" [61] "2,5-dimethylthiophene" "2-isopropylthiophene" "benzo[b]thiophene" [64] "dibenzo[b,d]thiophene" "methanethiol" "ethanethiol" [67] "n-propanethiol" "n-butanethiol" "n-pentanethiol" [70] "n-hexanethiol" "n-heptanethiol" "n-octanethiol" [73] "n-nonanethiol" "n-decanethiol" "n-undecanethiol" [76] "n-dodecanethiol" "n-tridecanethiol" "n-tetradecanethiol" [79] "n-pentadecanethiol" "n-hexadecanethiol" "n-heptadecanethiol" [82] "n-octadecanethiol" "n-nonadecanethiol" "n-eicosanethiol" [85] "thiophenol" "2-propanethiol" "2-butanethiol" [88] "2-methyl-1-propanethiol" "2-methyl-2-propanethiol" "2-methyl-1-butanethiol" [91] "2-methyl-2-butanethiol" "3-methyl-1-butanethiol" "3-methyl-2-butanethiol" [94] "2,2-dimethyl-1-propanethiol" "2-methyl-2-pentanethiol" "2,3-dimethyl-2-butanethiol" [97] "cyclopentanethiol" "cyclohexanethiol" "benzenethiol" [100] "phenylmethanethiol" [1] NA
info("MgC")
info.approx: 'MgC' is ambiguous; has approximate matches to 157 species (showing first 100) [1] "Mg+2" "MgSO4" "AgCl" "AgCl2-" [5] "MgCl+" "MgF+" "MgCO3" "MnCl+" [9] "AgCl3-2" "AgCl4-3" "HgCl+" "HgCl2" [13] "HgCl3-" "HgCl4-2" "Mg(HSiO3)+" "MgOH+" [17] "MgCrO4" "MnCrO4" "Mg(Ac)+" "Mg(Ac)2" [21] "Mg(For)+" "Mg(For)2" "Mg(Prop)+" "Mg(Prop)2" [25] "Mg(But)+" "Mg(But)2" "Mg(Pent)+" "Mg(Pent)2" [29] "Mg(Glyc)+" "Mg(Glyc)2" "Mg(Lac)+" "Mg(Lac)2" [33] "Mg(Gly)+" "Mg(Gly)2" "Mg(Alan)+" "Mg(Alan)2" [37] "Mg(HCO3)+" "Mg(Mal)" "Mg(Oxal)" "Mg(Succ)" [41] "Mg(Glut)" "Mg(Adip)" "MgAMP" "MgADP-" [45] "MgHADP" "Mg2ADP+" "MgATP-2" "MgHATP-" [49] "MgH2ATP" "Mg2ATP" "MgSO4" "hydromagnesite" [53] "magnesiohastingsite" "magnesiohastingsite" "magnesiohastingsite" "magnesioriebeckite" [57] "magnesioriebeckite" "magnesioriebeckite" "magnesite" "Mn(Ac)+" [61] "Hg(Ac)+" "Ag(Ac)" "Mn(For)+" "Mn(Prop)+" [65] "Mn(But)+" "Mn(Pent)+" "Mn(Glyc)+" "Mn(Lac)+" [69] "Mn(Oxal)" "Mn(Succ)" "Hg(Oxal)" "Mn(Mal)" [73] "Mn(Glut)" "Mn(Adip)" "akermanite" "amesite,14a" [77] "amesite,14a" "amesite,7a" "anthophyllite" "anthophyllite" [81] "anthophyllite" "antigorite" "antigorite" "artinite" [85] "brucite" "celadonite" "chrysotile" "clinochlore,14a" [89] "clinochlore,7a" "clinochlore,7a" "cordierite,dry" "cordierite,hydrous" [93] "cummingtonite" "diopside" "dolomite" "dolomite,disordered" [97] "dolomite,ordered" "edenite" "edenite" "enstatite" [1] NA
# add an extra character to refine a search # or to search using terms that have exact matches info("MgC ")
info.approx: 'MgC ' is ambiguous; has approximate matches to 27 species: [1] "MgCl+" "MgCO3" "MgCrO4" "Mg(Ac)+" "Mg(For)+" "Mg(Prop)+" [7] "Mg(But)+" "Mg(Pent)+" "Mg(Glyc)+" "Mg(Lac)+" "Mg(Mal)" "Mg(Oxal)" [13] "Mg(Succ)" "Mg(Glut)" "Mg(Adip)" "MgAMP" "MgADP-" "MgHADP" [19] "MgATP-2" "MgHATP-" "MgH2ATP" "magnesite" "nesquehonite" "nesquehonite" [25] "diopside" "dolomite" "magnesite" [1] NA
info("acetate ")
info.approx: 'acetate ' is ambiguous; has approximate matches to 6 species: [1] "ethylacetate" "acetate" "H-oxaloacetate" "oxaloacetate-2" "ethyl acetate" "ethyl acetate" [1] NA
info(" H2O")
info.approx: ' H2O' is ambiguous; has approximate matches to 126 species (showing first 100) [1] "H2O2" "[-CH2OH]" "water" "Am(Lac)+2" [5] "Am(Lac)2+" "oxalic acid" "malonate" "Na(Lac)" [9] "Na(Lac)2-" "K(Lac)" "K(Lac)2-" "Ca(Lac)+" [13] "Ca(Lac)2" "Mg(Lac)+" "Mg(Lac)2" "Sr(Lac)+" [17] "Sr(Lac)2" "Ba(Lac)+" "Ba(Lac)2" "Mn(Lac)+" [21] "Mn(Lac)2" "Fe(Lac)+" "Fe(Lac)2" "Ni(Lac)+" [25] "Ni(Lac)2" "Cu(Lac)+" "Cu(Lac)2" "Zn(Lac)+" [29] "Zn(Lac)2" "Pb(Lac)+" "Pb(Lac)2" "Co(Lac)+" [33] "Co(Lac)2" "Cd(Lac)+" "Cd(Lac)2" "Eu(Lac)+" [37] "Eu(Lac)2" "Lu(Lac)+2" "La(Lac)+2" "Li(Lac)" [41] "Li(Mal)-" "Mg(Mal)" "Zn(Mal)" "Cd(Mal)" [45] "Al(Mal)+" "Pb(Mal)" "Cu(Mal)" "La(Mal)+" [49] "Gd(Mal)+" "Lu(Mal)+" "Yb(Mal)+" "Th(Mal)+2" [53] "UO2(Mal)" "Ce(Mal)+" "Nd(Mal)+" "Sm(Mal)+" [57] "Pr(Mal)+" "Eu(Mal)+" "Tb(Mal)+" "Dy(Mal)+" [61] "Tm(Mal)+" "Ho(Mal)+" "Er(Mal)+" "Sc(Mal)+" [65] "Fe(Mal)+" "Cs(Mal)-" "NH4(Mal)-" "Sr(Mal)" [69] "Cr(Mal)" "Be(Mal)" "Fe(Mal)" "In(Mal)+" [73] "Y(Mal)+" "Ca(Mal)" "Ba(Mal)" "Mn(Mal)" [77] "Co(Mal)" "Ni(Mal)" "fumarate-2" "oxaloacetate-2" [81] "[Asp-]" "analcime" "artinite" "Ca-phillipsite" [85] "Ca-phillipsite" "chabazite" "cordierite,hydrous" "epistilbite" [89] "epistilbite" "heulandite" "heulandite" "hydromagnesite" [93] "K-phillipsite" "K-phillipsite" "laumontite" "lawsonite" [97] "lawsonite" "leonhardite" "Na-phillipsite" "Na-phillipsite" [1] NA