util.misc

utl.ms>   ## Don't show: 
utl.ms> data(thermo)
thermo$obigt has 1800 aqueous, 2925 total species

utl.ms> ## End Don't show
utl.ms>   ## calculate protein length
utl.ms>   protein.length("LYSC_CHICK")
[1] 129

utl.ms>   # another way to do it
utl.ms>   basis("CHNOS")
    C H N O S ispecies logact state
CO2 1 0 0 2 0       69     -3    aq
H2O 0 2 0 1 0        1      0   liq
NH3 0 3 1 0 0       68     -4    aq
H2S 0 2 0 0 1       70     -7    aq
O2  0 0 0 2 0     2691    -80   gas

utl.ms>   species("LYSC_CHICK")
protein: found LYSC_CHICK (C613H959N193O185S10, 129 residues)
  CO2 H2O NH3 H2S     O2 ispecies logact state       name
1 613 180 193  10 -610.5     2926     -3    aq LYSC_CHICK

utl.ms>   protein.length(species()$ispecies)
[1] 129

utl.ms>   # another way to do it
utl.ms>   ip <- protein("LYSC","CHICK")

utl.ms>   protein.length(-ip)
[1] 129

utl.ms>   ## heat capacity as a function of temperature
utl.ms>   ## (Makhatadze & Privalov, 1990) units: J mol-1
utl.ms>   MP90.cp(c(5,25,50,75,100,125),"LYSC_CHICK")
[1] 27536.9 29714.4 31570.3 32239.3 32967.6 33114.8

utl.ms>   ## properties of phase transitions
utl.ms>   si <- info("enstatite")
info: enstatite (MgSiO3) available in cr1, cr2, cr3.
info: 1897 refers to enstatite, MgSiO3 cr1 (HDN+78, 5.May.78)

utl.ms>   # (dP/dT) of transitions
utl.ms>   dPdTtr(si)  # first transition
[1] 384.5063

utl.ms>   dPdTtr(si+1) # second transition
[1] 11.90108

utl.ms>   # temperature of transitions (Ttr) as a function of P
utl.ms>   Ttr(si,P=c(1,10,100,1000))
[1] 903.0026 903.0260 903.2601 905.6007

utl.ms>   Ttr(si,P=c(1,10,100,1000))
[1] 903.0026 903.0260 903.2601 905.6007

utl.ms>   ## the basis stoichiometry of a made-up species
utl.ms>   # warns because P isn't in our basis
utl.ms>   basis("CHNOS")
    C H N O S ispecies logact state
CO2 1 0 0 2 0       69     -3    aq
H2O 0 2 0 1 0        1      0   liq
NH3 0 3 1 0 0       68     -4    aq
H2S 0 2 0 0 1       70     -7    aq
O2  0 0 0 2 0     2691    -80   gas

utl.ms>   basis.comp("SPONCH")
basis.comp: missing element P from species SPONCH.
        CO2 H2O NH3 H2S  O2
missing   1  -2   1   1 0.5

utl.ms>   ## describing the basis species
utl.ms>   basis("CHNOSe")
    C H N O S  Z ispecies logact state
CO2 1 0 0 2 0  0       69     -3    aq
H2O 0 2 0 1 0  0        1      0   liq
NH3 0 3 1 0 0  0       68     -4    aq
H2S 0 2 0 0 1  0       70     -7    aq
e-  0 0 0 0 0 -1        2     -7    aq
H+  0 1 0 0 0  1        3     -7    aq

utl.ms>   describe(thermo$basis)
[1] "25 C, 1 bar, aCO2(-3), aH2O(0), aNH3(-4), aH2S(-7), ae-(-7), aH+(-7)"

utl.ms>   describe(thermo$basis,T=NULL,P=NULL)
[1] "aCO2(-3), aH2O(0), aNH3(-4), aH2S(-7), ae-(-7), aH+(-7)"

utl.ms>   ## scale logarithms of activity
utl.ms>   ## suppose we have two proteins whose lengths
utl.ms>   ## are 100 and 200; what are the logarithms
utl.ms>   ## of activity of the proteins that are equal to
utl.ms>   ## each other and that give a total activity of
utl.ms>   ## residues equal to unity?
utl.ms>   logact <- c(-3,-3)  # could be any two equal numbers

utl.ms>   length <- c(100,200)

utl.ms>   logact.tot <- 0

utl.ms>   loga <- unitize(logact,length,logact.tot)

utl.ms>   # the proteins have equal activity
utl.ms>   stopifnot(identical(loga[1],loga[2]))

utl.ms>   # the sum of activity of the residues is unity
utl.ms>   stopifnot(isTRUE(all.equal(sum(10^loga * length),1)))

utl.ms>   ## now, what if the activity of protein 2 is ten
utl.ms>   ## times that of protein 1?
utl.ms>   logact <- c(-3,-2)


utl.ms>   loga <- unitize(logact,length,logact.tot)

utl.ms>   # the proteins have unequal activity
utl.ms>   stopifnot(isTRUE(all.equal(loga[2]-loga[1],1)))

utl.ms>   # but the activities of residues still add up to one
utl.ms>   stopifnot(isTRUE(all.equal(sum(10^loga * length),1)))