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info

## Don't show: data(thermo)
thermo$obigt: 1809 aqueous, 3368 total species
## End(Don't show) ## summary of available data info()
info: 'species' is NULL; summarizing information about thermodynamic data... thermo$obigt has 1809 aqueous, 3368 total species number of literature sources: 116, elements: 130, buffers: 26 number of proteins in thermo$protein is 453 from 98 organisms more.aa: extdata/protein/Sce.csv.xz has data for 6719 proteins more.aa: extdata/protein/Eco.csv.xz has data for 4407 proteins yeastgfp: extdata/abundance/yeastgfp.csv.xz has 4155 localizations and 3570 abundances NULL
## Not run: ##D ## run a consistency check on each species in the database ##D # (marked dontrun because it takes a while) ##D info(check=TRUE) ## End(Not run) ## species information # search for something named (or whose formula is) "Fe" si <- info("Fe")
info.character: found Fe(cr1), also available in cr2, cr3, cr4
# use the number to get the full record info(si)
name abbrv formula state ref1 ref2 date G H S Cp V a b c d e f 2535 Fe iron Fe cr1 RH95 CHNOSZ 05.Aug.07 0 0 6.475 5.994 7.092 7.162 -0.0069682 0 0 1.2294e-05 0 lambda T 2535 0 1043
# it is possible to get a range of records info(si:(si+3))
info.numeric: Cp of Fe(cr2) is NA; set by EOS parameters to 293.01 info.numeric: Cp of Fe(cr3) is NA; set by EOS parameters to 7.58 info.numeric: Cp of Fe(cr4) is NA; set by EOS parameters to 9.11 name abbrv formula state ref1 ref2 date G H S Cp V a 2535 Fe iron Fe cr1 RH95 CHNOSZ 05.Aug.07 0.0 0.0 6.4750 5.994000 7.092 7.1620 2536 Fe iron Fe cr2 RH95 CHNOSZ 05.Aug.07 -32284.5 -87223.4 -177.7910 293.013353 7.092 504.5770 2537 Fe iron Fe cr3 RH95 CHNOSZ 05.Aug.07 1348.8 1843.8 8.1352 7.580456 7.092 5.1938 2538 Fe iron Fe cr4 RH95 CHNOSZ 05.Aug.07 3190.2 4835.6 11.9940 9.106491 7.092 -4.0330 b c d e f lambda T 2535 -0.0069682 0 0 1.2294e-05 0 0 1043 2536 -0.8072440 0 0 3.2754e-04 0 0 1185 2537 0.0023381 150190 0 0.0000e+00 0 0 1667 2538 0.0080055 955840 0 0.0000e+00 0 0 1809
## 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] 80 112 592
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 info.approx: 'hydroxyapatite' has no approximate matches [1] 1585 1504 NA
# state argument overrides the default info(c("ethanol","adenosine"),state=c("gas","cr"))
[1] 3219 2480
# 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 [1] 80 69 2972 2002
# state argument overrides the default info(c("CH4","CO2","MgO"),"gas") # gas, gas, NA
info.character: requested state 'gas' for MgO but only 'cr' is available info.approx: 'MgO' has no approximate matches [1] 3086 3087 NA
# exceptions to the aqueous default is O2 info("O2") # gas
info.character: found O2(aq), also available in gas [1] 67
## partial name or formula searches info("ATP")
info.approx: 'ATP' is ambiguous; has approximate matches to 83 species (showing first 25) [1] "AMP-2" "HAMP-" "H2AMP" "dAMP-2" "dHAMP-" "dH2AMP" "ADP-3" "HADP-2" "H2ADP-" "H3ADP" [11] "dADP-3" "dHADP-2" "dH2ADP-" "dH3ADP" "ATP-4" "HATP-3" "H2ATP-2" "H3ATP-" "H4ATP" "CTP-4" [21] "HCTP-3" "H2CTP-2" "H3CTP-" "H4CTP" "GTP-4" [1] NA
info("thiol")
info.approx: 'thiol' is ambiguous; has approximate matches to 105 species (showing first 25) [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" [1] NA
info("MgC")
info.approx: 'MgC' is ambiguous; has approximate matches to 122 species (showing first 25) [1] "Mg+2" "Mg(Ac)+" "Mg(Ac)2" "Mg(For)+" "Mg(For)2" "Mg(Prop)+" "Mg(Prop)2" "Mg(But)+" [9] "Mg(But)2" "Mg(Pent)+" "Mg(Pent)2" "Mg(Glyc)+" "Mg(Glyc)2" "Mg(Lac)+" "Mg(Lac)2" "Mg(Gly)+" [17] "Mg(Gly)2" "Mg(Alan)+" "Mg(Alan)2" "Mg(HCO3)+" "MgSO4" "AgCl" "AgCl2-" "MgCl+" [25] "MgF+" [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 23 species: [1] "MgCl+" "MgCO3" "Mg(Ac)+" "Mg(For)+" "Mg(Prop)+" "Mg(But)+" [7] "Mg(Pent)+" "Mg(Glyc)+" "Mg(Lac)+" "Mg(Mal)" "Mg(Oxal)" "Mg(Succ)" [13] "Mg(Glut)" "Mg(Adip)" "MgAMP" "MgADP-" "MgHADP" "MgATP-2" [19] "MgHATP-" "MgH2ATP" "magnesite" "nesquehonite" "nesquehonite" [1] NA
info("acetate ")
info.approx: 'acetate ' is ambiguous; has approximate matches to 4 species: [1] "ethylacetate" "acetate" "ethyl acetate" "ethyl acetate" [1] NA
info(" H2O")
info.approx: ' H2O' is ambiguous; has approximate matches to 105 species (showing first 25) [1] "H2O2" "[-CH2OH]" "steam" "water" "oxalic acid" "malonate" "Na(Lac)" [8] "Na(Lac)2-" "K(Lac)" "K(Lac)2-" "Ca(Lac)+" "Ca(Lac)2" "Mg(Lac)+" "Mg(Lac)2" [15] "Sr(Lac)+" "Sr(Lac)2" "Ba(Lac)+" "Ba(Lac)2" "Mn(Lac)+" "Mn(Lac)2" "Fe(Lac)+" [22] "Fe(Lac)2" "Ni(Lac)+" "Ni(Lac)2" "Cu(Lac)+" [1] NA


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Next: [1] protein.info Up: CHNOSZ examples Previous: taxonomy