makeup

makeup>   ## Don't show:
makeup> 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

makeup> ## End Don't show
makeup>   ## makeups (nrow = number of elements)
makeup>   # the composition of a single compound (ncol=1)
makeup>   makeup("CO2")
  count
C     1
O     2

makeup>   # negative coefficients
makeup>   makeup("C-4O2") # minus four C's
  count
C    -4
O     2

makeup>   makeup("C-4O-2")  # interpreted as having charge -2
  count
C    -4
O     1
Z    -2

makeup>   makeup("C-4O-2+0") # no charge
  count
C    -4
O    -2

makeup>   # sum the compositions
makeup>   makeup(c("CO2","CH4"))
  count
C     2
O     2
H     4

makeup>   # sum with coefficients
makeup>   makeup(info(c("CO2","CH4")),c(-1,1))
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: CH4 (methane) available in aq, liq, gas, gas.
info: 69 refers to CO2 aq (SSW01, SHS89, 11.Oct.07).
info: 1291 refers to methane aq (AH97b, SSW01, 1.Sep.06).
  count
C     0
O    -2
H     4

makeup>   # this one adds up to zero
makeup>   makeup(c("C6H12O6","C2H5OH","CO2"),c(-1,2,2))
  count
C     0
H     0
O     0

makeup>   ## formulas (ncol = number of elements)
makeup>   # as a dataframe
makeup>   makeup("Zn(CH3CH2CH2CH2CO2)2","")
 Zn  C  H O
  1 10 18 4

makeup>   print( t <- makeup(c("HCl","H2O"),"") )
 H Cl O
 3  1 1

makeup>   # as a character formula
makeup>   makeup(makeup(info("glycinium"),""),"")
info: 1631 refers to glycinium, C2H6NO2+ aq (AH97b, DLH06, 25.Aug.06).
[1] "C2H6NO2+1"

makeup>   makeup(t,"")
[1] "H3ClO"

makeup>   # C6H12O6
makeup>   makeup(makeup(makeup("CHO6H11C5"),""),"")
[1] "C6H12O6"

makeup>   ## charged species, electron
makeup>   # these return the same:
makeup>   makeup("NH4+")
  count
N     1
H     4
Z     1

makeup>   makeup("NH4Z")
  count
N     1
H     4
Z     1

makeup>   # constitution of the electron
makeup>   makeup(info("e-"))
info: 2 refers to e-, Z-1 aq (CHNOSZ, 28.Oct.06).
  count
Z    -1

makeup>   # this produce an INcorrect makeup for the electron,
makeup>   # and gives a warning because "e" is not in the
makeup>   # table of elements.
makeup>   makeup("e-")
  count
e     1
Z    -1

makeup>   # compositions of made-up compounds
makeup>   makeup("CHNOS")
  count
C     1
H     1
N     1
O     1
S     1

makeup>   makeup("CHNOSZ")
  count
C     1
H     1
N     1
O     1
S     1
Z     1

makeup>   makeup("CHNOSe")  # Se is an element
   count
C      1
H      1
N      1
O      1
Se     1