transfer

trnsfr>   ## Don't show:
trnsfr> 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

trnsfr> ## End Don't show
trnsfr>   ## react potassium feldspar in a closed system
trnsfr>   ## after Steinmann et al., 1994 and Helgeson et al., 1969
trnsfr>   basis(c("Al+3","H4SiO4","K+","H2O","H+","O2"),c(0,-6,-6,0,0,0))
       Al H K O Si Z ispecies logact state
Al+3    1 0 0 0  0 3      990      0    aq
H4SiO4  0 4 0 4  1 0     1587     -6    aq
K+      0 0 1 0  0 1        6     -6    aq
H2O     0 2 0 1  0 0        1      0   liq
H+      0 1 0 0  0 1        3      0    aq
O2      0 0 0 2  0 0     2852      0   gas

trnsfr>   species(c("k-feldspar","muscovite","pyrophyllite","kaolinite","gibbsite"))

trnsfr>   a <- affinity(H4SiO4=c(-6,-2),"K+"=c(-3,8))
affinity: temperature is 25 C
energy.args: pressure is Psat
energy.args: variable 1 is H4SiO4 at 128 increments from -6 to -2
energy.args: variable 2 is K+ at 128 increments from -3 to 8
subcrt: 11 species at 298.15 K and 1 bar (wet)

trnsfr>   diagram(a)
diagram: immobile component is Al+3
diagram: conservation coefficients are 1 3 2 2 1

trnsfr>   basis("pH",4)
       Al H K O Si Z ispecies logact state
Al+3    1 0 0 0  0 3      990      0    aq
H4SiO4  0 4 0 4  1 0     1587     -6    aq
K+      0 0 1 0  0 1        6     -6    aq
H2O     0 2 0 1  0 0        1      0   liq
H+      0 1 0 0  0 1        3     -4    aq
O2      0 0 0 2  0 0     2852      0   gas

trnsfr>   species(1:5,c(-4,rep(-999,4)))

trnsfr>   t <- transfer(550,dmode="coupled",plot=c(2,3),devmax=0.2)
--- step 1 ---
transfer: destruction exponent is -10
transfer: destruction is coupled ( coupled )
transfer: formation is one species, balanced on Al+3
affinity: temperature is 25 C
energy.args: pressure is Psat
subcrt: 11 species at 298.15 K and 1 bar (wet)
transfer: coupling: nothing to react
transfer: failed step ( would form gibbsite )
--- step 2 ---
transfer: destruction exponent is -10
transfer: destruction is coupled ( all )
transfer: formation is one species, balanced on Al+3
affinity: temperature is 25 C
energy.args: pressure is Psat
transfer: reacting 1e-14 moles of k-feldspar (primary)
transfer: forming 1e-14 moles of gibbsite
--- step 3 ---
transfer: destruction exponent is -9
transfer: destruction is coupled ( coupled )
transfer: formation is one species, balanced on Al+3
transfer: coupling: no conservant
transfer: failed step ( would form gibbsite )
--- step 4 ---
transfer: destruction exponent is -9
transfer: destruction is coupled ( all )
transfer: formation is one species, balanced on Al+3
affinity: temperature is 25 C
energy.args: pressure is Psat
transfer: reacting 1e-13 moles of k-feldspar (primary)
transfer: reacting 1e-14 moles of gibbsite
transfer: forming 1.1e-13 moles of gibbsite

[... MUCH OUTPUT REMOVED ...]

--- step 547 ---
transfer: destruction exponent is -12
transfer: destruction is coupled ( all )
transfer: formation is one species, balanced on Al+3
transfer: change of H4SiO4 by -2.47853507262895 exceeds deviation limit
 transfer: change of K+ by -2.004290158239 exceeds deviation limit
 transfer: change of H+ by 4.13910764852734 exceeds deviation limit
transfer: failed step ( would form k-feldspar )
--- step 548 ---
transfer: destruction exponent is -13
transfer: destruction is coupled ( coupled )
transfer: formation is one species, balanced on Al+3
transfer: found two secondary conservants
transfer: coupling on -0.0002999782 H4SiO4 -9.999274e-05 K+
transfer: fall back to one secondary conservant (negative species used)
transfer: coupling: no conservant
transfer: failed step ( would form k-feldspar )
--- step 549 ---
transfer: destruction exponent is -13
transfer: destruction is coupled ( all )
transfer: formation is one species, balanced on Al+3
transfer: change of H4SiO4 by -2.478535072629 exceeds deviation limit
 transfer: change of K+ by -2.00429015823901 exceeds deviation limit
 transfer: change of H+ by 4.13910764852734 exceeds deviation limit
transfer: failed step ( would form k-feldspar )
--- step 550 ---
transfer: destruction exponent is -14
transfer: destruction is coupled ( coupled )
transfer: formation is one species, balanced on Al+3
transfer: coupling: no conservant
transfer: failed step ( would form k-feldspar )
transfer:  227 of 550 steps succeeded ( 149.99912111 % overall progress)

trnsfr>   # plot the output from transfer
trnsfr>   draw.transfer(t)

trnsfr>   # reset the plot layout
trnsfr>   layout(matrix(1))

trnsfr>   # note, the same calculation can be performed using
trnsfr>   # feldspar("closed")

trnsfr>   ## react APC2 from Saccharomyces cerevisiae
trnsfr>   ## to other proteins in the anaphase-promoting complex
trnsfr>   basis(c("CO2","H2O","NH3","H2","H2S"),c(-10,0,-4,-10,-7))
    C H N O S ispecies logact state
CO2 1 0 0 2 0       69    -10    aq
H2O 0 2 0 1 0        1      0   liq
NH3 0 3 1 0 0       68     -4    aq
H2  0 2 0 0 0       66    -10    aq
H2S 0 2 0 0 1       70     -7    aq

trnsfr>   species(c("APC1","APC2","APC5","CDC16","APC10","SWM1"),"YEAST")
protein: found APC1_YEAST (C8788H13856N2304O2662S55, 1748 residues)
protein: found APC2_YEAST (C4534H7069N1175O1311S30, 853 residues)
protein: found APC5_YEAST (C3564H5608N908O1071S30, 685 residues)
protein: found CDC16_YEAST (C4179H6559N1143O1310S38, 840 residues)
protein: found APC10_YEAST (C1290H1980N350O377S11, 250 residues)
protein: found SWM1_YEAST (C830H1257N253O276S5, 170 residues)

trnsfr>   a <- affinity(CO2=c(-10,0),H2=c(-10,0))
affinity: temperature is 25 C
energy.args: pressure is Psat
energy.args: variable 1 is CO2 at 128 increments from -10 to 0
energy.args: variable 2 is H2 at 128 increments from -10 to 0
subcrt: 11 species at 298.15 K and 1 bar (wet)

trnsfr>   diagram(a,as.residue=TRUE)
diagram: immobile component is protein backbone group
diagram: conservation coefficients are 1748 853 685 840 250 170
diagram: using residue equivalents

trnsfr>   species(1:nrow(species()),-999)

trnsfr>   species("APC2_YEAST",0)

trnsfr>   t <- transfer(510,ibalance="PBB",plot=c(1,4),dmode="coupled",devmax=0.15)
transfer: balancing reactions on PBB
--- step 1 ---
transfer: destruction exponent is -10
transfer: destruction is coupled ( coupled )
transfer: formation is one species, balanced on PBB
affinity: temperature is 25 C
energy.args: pressure is Psat
subcrt: 11 species at 298.15 K and 1 bar (wet)
transfer: coupling: nothing to react
transfer: failed step ( would form SWM1_YEAST )
--- step 2 ---
transfer: destruction exponent is -10
transfer: destruction is coupled ( all )
transfer: formation is one species, balanced on PBB
transfer: change of CO2 by 2.56861579797273 exceeds deviation limit
 transfer: change of H2 by 3.12426633724316 exceeds deviation limit
transfer: failed step ( would form SWM1_YEAST )
--- step 3 ---
transfer: destruction exponent is -11
transfer: destruction is coupled ( coupled )
transfer: formation is one species, balanced on PBB
transfer: coupling: nothing to react
transfer: failed step ( would form SWM1_YEAST )
--- step 4 ---
transfer: destruction exponent is -11
transfer: destruction is coupled ( all )
transfer: formation is one species, balanced on PBB
transfer: change of CO2 by 1.57904345555907 exceeds deviation limit
 transfer: change of H2 by 2.1271924872559 exceeds deviation limit
transfer: failed step ( would form SWM1_YEAST )
--- step 5 ---
transfer: destruction exponent is -12
transfer: destruction is coupled ( coupled )
transfer: formation is one species, balanced on PBB
transfer: coupling: nothing to react
transfer: failed step ( would form SWM1_YEAST )
--- step 6 ---
transfer: destruction exponent is -12
transfer: destruction is coupled ( all )
transfer: formation is one species, balanced on PBB
transfer: change of CO2 by 0.671499543694811 exceeds deviation limit
 transfer: change of H2 by 1.15541820799696 exceeds deviation limit
transfer: failed step ( would form SWM1_YEAST )
--- step 7 ---
transfer: destruction exponent is -13
transfer: destruction is coupled ( coupled )
transfer: formation is one species, balanced on PBB
transfer: coupling: nothing to react
transfer: failed step ( would form SWM1_YEAST )
--- step 8 ---
transfer: destruction exponent is -13
transfer: destruction is coupled ( all )
transfer: formation is one species, balanced on PBB
transfer: change of H2 by 0.367406353710287 exceeds deviation limit
transfer: failed step ( would form SWM1_YEAST )
--- step 9 ---
transfer: destruction exponent is -14
transfer: destruction is coupled ( coupled )
transfer: formation is one species, balanced on PBB
transfer: coupling: nothing to react
transfer: failed step ( would form SWM1_YEAST )
--- step 10 ---
transfer: destruction exponent is -14
transfer: destruction is coupled ( all )
transfer: formation is one species, balanced on PBB
affinity: temperature is 25 C
energy.args: pressure is Psat
transfer: reacting 1e-14 moles of APC2_YEAST (primary)
transfer: forming 5.01764705882353e-14 moles of SWM1_YEAST

[... MUCH OUTPUT REMOVED ...]

--- step 508 ---
transfer: destruction exponent is -9
transfer: destruction is coupled ( all )
transfer: formation is one species, balanced on PBB
transfer: change of H2S by -0.510228268590472 exceeds deviation limit
transfer: failed step ( would form APC5_YEAST )
--- step 509 ---
transfer: destruction exponent is -10
transfer: destruction is coupled ( coupled )
transfer: formation is one species, balanced on PBB
transfer: coupling: no conservant
transfer: failed step ( would form APC5_YEAST )
--- step 510 ---
transfer: destruction exponent is -10
transfer: destruction is coupled ( all )
transfer: formation is one species, balanced on PBB
affinity: temperature is 25 C
energy.args: pressure is Psat
transfer: reacting 1e-10 moles of APC2_YEAST (primary)
transfer: reacting 1.51228432262774e-08 moles of APC5_YEAST
transfer: forming 1.52473687737226e-08 moles of APC5_YEAST
transfer:  131 of 510 steps succeeded ( 1.224437e-06 % overall progress)
Time elapsed:  340.501 1.484 343.77 0.036 0.036
Warning messages:
1: reaction was unbalanced!!!
2: In makeup("e-") : 'e' is not a recognized element.
3: In yeastgfp(names[i]) :
  yeastgfp: no exclusive localization found for bud ... using non-exclusive localizations

4: In yeastgfp(names[i]) :
  yeastgfp: no exclusive localization found for bud ... using non-exclusive localizations

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