saveSBMLR: Save an R model object of class SBMLR to a file.
In SBMLR: SBML-R Interface and Analysis Tools
Description
Usage
Arguments
Value
Warning
Note
Author(s)
References
See Also
Examples
Description
This function converts an SBMLR model object in R into an SBMLR model definition file.
Rate laws are provided only in string form. Redundancy is eliminated to make the file easier
to edit.
Usage
1
saveSBMLR(model,filename)
Arguments
model
The SBMLR model object to be mapped into the SBMLR model definition file.
filename
The file name of the destination SBMLR model definition file.
Value
No value returned.
Warning
SBML events and function definitions are NOT implemented.
Note
Similar to saveSBML, the file is written incrementally.
Author(s)
Tom Radivoyevitch
References
Radivoyevitch, T. A two-way interface between limited Systems Biology Markup Language and R. BMC Bioinformatics 5, 190 (2004).
See Also
Examples
1
2
3
4
5
6
7
Example output
Loading required package: XML
Loading required package: deSolve
$species
index initialConcentrations boundaryConditions
PRPP TRUE TRUE TRUE
IMP TRUE TRUE TRUE
SAMP TRUE TRUE TRUE
ATP TRUE TRUE TRUE
SAM TRUE TRUE TRUE
Ade TRUE TRUE TRUE
XMP TRUE TRUE TRUE
GTP TRUE TRUE TRUE
dATP TRUE TRUE TRUE
dGTP TRUE TRUE TRUE
RNA TRUE TRUE TRUE
DNA TRUE TRUE TRUE
HX TRUE TRUE TRUE
Xa TRUE TRUE TRUE
Gua TRUE TRUE TRUE
UA TRUE TRUE TRUE
R5P TRUE TRUE TRUE
Pi TRUE TRUE TRUE
$reactions
index Laws initialFluxes
ada TRUE TRUE TRUE
ade TRUE TRUE TRUE
adna TRUE TRUE TRUE
adrnr TRUE TRUE TRUE
ampd TRUE TRUE TRUE
aprt TRUE TRUE TRUE
arna TRUE TRUE TRUE
asuc TRUE TRUE TRUE
asli TRUE TRUE TRUE
dada TRUE TRUE TRUE
den TRUE TRUE TRUE
dgnuc TRUE TRUE TRUE
dnaa TRUE TRUE TRUE
dnag TRUE TRUE TRUE
gdna TRUE TRUE TRUE
gdrnr TRUE TRUE TRUE
gmpr TRUE TRUE TRUE
gmps TRUE TRUE TRUE
gnuc TRUE TRUE TRUE
gprt TRUE TRUE TRUE
grna TRUE TRUE TRUE
gua TRUE TRUE TRUE
hprt TRUE TRUE TRUE
hx TRUE TRUE TRUE
hxd TRUE TRUE TRUE
impd TRUE TRUE TRUE
inuc TRUE TRUE TRUE
mat TRUE TRUE TRUE
polyam TRUE TRUE TRUE
prpps TRUE TRUE TRUE
pyr TRUE TRUE TRUE
rnaa TRUE TRUE TRUE
rnag TRUE TRUE TRUE
trans TRUE TRUE TRUE
ua TRUE TRUE TRUE
x TRUE TRUE TRUE
xd TRUE TRUE TRUE
$nSpecies
[1] 18
$sIDs
[1] "PRPP" "IMP" "SAMP" "ATP" "SAM" "Ade" "XMP" "GTP" "dATP" "dGTP"
[11] "RNA" "DNA" "HX" "Xa" "Gua" "UA" "R5P" "Pi"
$S0
PRPP IMP SAMP ATP SAM Ade
5.01742e+00 9.82634e+01 1.98189e-01 2.47535e+03 3.99187e+00 9.84730e-01
XMP GTP dATP dGTP RNA DNA
2.47930e+01 4.10223e+02 6.01413e+00 3.02581e+00 2.86805e+04 5.17934e+03
HX Xa Gua UA R5P Pi
9.51785e+00 5.05941e+00 5.50638e+00 1.00293e+02 1.80000e+01 1.40000e+03
$BC
PRPP IMP SAMP ATP SAM Ade XMP GTP dATP dGTP RNA DNA HX
FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
Xa Gua UA R5P Pi
FALSE FALSE FALSE TRUE TRUE
$nStates
[1] 16
$y0
PRPP IMP SAMP ATP SAM Ade
5.01742e+00 9.82634e+01 1.98189e-01 2.47535e+03 3.99187e+00 9.84730e-01
XMP GTP dATP dGTP RNA DNA
2.47930e+01 4.10223e+02 6.01413e+00 3.02581e+00 2.86805e+04 5.17934e+03
HX Xa Gua UA
9.51785e+00 5.05941e+00 5.50638e+00 1.00293e+02
$nReactions
[1] 37
$rIDs
[1] "ada" "ade" "adna" "adrnr" "ampd" "aprt" "arna" "asuc"
[9] "asli" "dada" "den" "dgnuc" "dnaa" "dnag" "gdna" "gdrnr"
[17] "gmpr" "gmps" "gnuc" "gprt" "grna" "gua" "hprt" "hx"
[25] "hxd" "impd" "inuc" "mat" "polyam" "prpps" "pyr" "rnaa"
[33] "rnag" "trans" "ua" "x" "xd"
$rLaws
ada
"aada*ATP^fada4"
ade
"aade*Ade^fade6"
adna
"aadna*dATP^fdnap9*dGTP^fdnap10"
adrnr
"aadrnr*ATP^fadrnr4*dATP^fadrnr9*dGTP^fadrnr10"
ampd
"aampd*ATP^fampd4*GTP^fampd8*Pi^fampd18"
aprt
"aaprt*PRPP^faprt1*ATP^faprt4*Ade^faprt6"
arna
"aarna*ATP^frnap4*GTP^frnap8"
asuc
"aasuc*IMP^fasuc2*ATP^fasuc4*GTP^fasuc8*Pi^fasuc18"
asli
"aasli*SAMP^fasli3*ATP^fasli4"
dada
"adada*dATP^fdada9"
den
"aden*PRPP^fden1*IMP^fden2*ATP^fden4*GTP^fden8*Pi^fden18"
dgnuc
"adgnuc*dGTP^fdgnuc10"
dnaa
"adnaa*DNA^fdnan12"
dnag
"adnag*DNA^fdnan12"
gdna
"agdna*dATP^fdnap9*dGTP^fdnap10"
gdrnr
"agdrnr*GTP^fgdrnr8*dATP^fgdrnr9*dGTP^fgdrnr10"
gmpr
"agmpr*IMP^fgmpr2*ATP^fgmpr4*XMP^fgmpr7*GTP^fgmpr8"
gmps
"agmps*ATP^fgmps4*XMP^fgmps7"
gnuc
"agnuc*GTP^fgnuc8*Pi^fgnuc18"
gprt
"agprt*PRPP^fgprt1*GTP^fgprt8*Gua^fgprt15"
grna
"agrna*ATP^frnap4*GTP^frnap8"
gua
"agua*Gua^fgua15"
hprt
"ahprt*PRPP^fhprt1*IMP^fhprt2*HX^fhprt13"
hx
"ahx*HX^fhx13"
hxd
"ahxd*HX^fhxd13"
impd
"aimpd*IMP^fimpd2*XMP^fimpd7*GTP^fimpd8"
inuc
"ainuc*IMP^finuc2*Pi^finuc18"
mat
"amat*ATP^fmat4*SAM^fmat5"
polyam
"apolyam*SAM^fpolyam5"
prpps
"aprpps*PRPP^fprpps1*ATP^fprpps4*GTP^fprpps8*R5P^fprpps17*Pi^fprpps18"
pyr
"apyr*PRPP^fpyr1"
rnaa
"arnaa*RNA^frnan11"
rnag
"arnag*RNA^frnan11"
trans
"atrans*SAM^ftrans5"
ua
"aua*UA^fua16"
x
"ax*Xa^fx14"
xd
"axd*Xa^fxd14"
$V0
ada ade adna adrnr ampd aprt
2.079467e+00 9.915724e-03 1.003826e+01 2.011595e-01 5.640728e+00 9.980753e-01
arna asuc asli dada den dgnuc
1.985621e+03 8.003186e+00 8.003185e+00 2.004510e-01 2.403008e+00 1.008502e-01
dnaa dnag gdna gdrnr gmpr gmps
1.003756e+01 6.826370e+00 6.825859e+00 1.003440e-01 5.138721e-01 1.595763e+00
gnuc gprt grna gua hprt hx
4.807078e+00 3.753642e+00 1.323532e+03 1.154277e+00 3.683827e+00 4.730928e-02
hxd impd inuc mat polyam prpps
1.191281e+00 1.595762e+00 2.642505e+00 1.498849e+01 1.007991e+00 2.088274e+01
pyr rnaa rnag trans ua x
1.004416e+01 1.985551e+03 1.323605e+03 1.398050e+01 2.314825e+00 3.071716e-02
xd
2.314841e+00
$globalVec
NULL
$incid
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
PRPP 0 0 0 0 0 -1 0 0 0 0 -1 0 0 0
IMP 0 0 0 0 1 0 0 -1 0 0 1 0 0 0
SAMP 0 0 0 0 0 0 0 1 -1 0 0 0 0 0
ATP -1 0 0 -1 -1 1 -1 0 1 0 0 0 0 0
SAM 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Ade 0 -1 0 0 0 -1 0 0 0 0 0 0 0 0
XMP 0 0 0 0 0 0 0 0 0 0 0 0 0 0
GTP 0 0 0 0 0 0 0 0 0 0 0 0 0 0
dATP 0 0 -1 1 0 0 0 0 0 -1 0 0 1 0
dGTP 0 0 0 0 0 0 0 0 0 0 0 -1 0 1
RNA 0 0 0 0 0 0 1 0 0 0 0 0 0 0
DNA 0 0 1 0 0 0 0 0 0 0 0 0 -1 -1
HX 1 0 0 0 0 0 0 0 0 1 0 0 0 0
Xa 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Gua 0 0 0 0 0 0 0 0 0 0 0 1 0 0
UA 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26]
PRPP 0 0 0 0 0 -1 0 0 -1 0 0 0
IMP 0 0 1 0 0 0 0 0 1 0 0 -1
SAMP 0 0 0 0 0 0 0 0 0 0 0 0
ATP 0 0 0 0 0 0 0 0 0 0 0 0
SAM 0 0 0 0 0 0 0 0 0 0 0 0
Ade 0 0 0 0 0 0 0 0 0 0 0 0
XMP 0 0 0 -1 0 0 0 0 0 0 0 1
GTP 0 -1 -1 1 -1 1 -1 0 0 0 0 0
dATP 0 0 0 0 0 0 0 0 0 0 0 0
dGTP -1 1 0 0 0 0 0 0 0 0 0 0
RNA 0 0 0 0 0 0 1 0 0 0 0 0
DNA 1 0 0 0 0 0 0 0 0 0 0 0
HX 0 0 0 0 0 0 0 0 -1 -1 -1 0
Xa 0 0 0 0 0 0 0 1 0 0 1 0
Gua 0 0 0 0 1 -1 0 -1 0 0 0 0
UA 0 0 0 0 0 0 0 0 0 0 0 0
[,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37]
PRPP 0 0 0 1 -1 0 0 0 0 0 0
IMP -1 0 0 0 0 0 0 0 0 0 0
SAMP 0 0 0 0 0 0 0 0 0 0 0
ATP 0 -1 0 0 0 1 0 1 0 0 0
SAM 0 1 -1 0 0 0 0 -1 0 0 0
Ade 0 0 1 0 0 0 0 0 0 0 0
XMP 0 0 0 0 0 0 0 0 0 0 0
GTP 0 0 0 0 0 0 1 0 0 0 0
dATP 0 0 0 0 0 0 0 0 0 0 0
dGTP 0 0 0 0 0 0 0 0 0 0 0
RNA 0 0 0 0 0 -1 -1 0 0 0 0
DNA 0 0 0 0 0 0 0 0 0 0 0
HX 1 0 0 0 0 0 0 0 0 0 0
Xa 0 0 0 0 0 0 0 0 0 -1 -1
Gua 0 0 0 0 0 0 0 0 0 0 0
UA 0 0 0 0 0 0 0 0 -1 0 1
$nRules
[1] 0
$ruleIDs
NULL
$species
index initialConcentrations boundaryConditions
PRPP 1 5.01742e+00 FALSE
IMP 2 9.82634e+01 FALSE
SAMP 3 1.98189e-01 FALSE
ATP 4 2.47535e+03 FALSE
SAM 5 3.99187e+00 FALSE
Ade 6 9.84730e-01 FALSE
XMP 7 2.47930e+01 FALSE
GTP 8 4.10223e+02 FALSE
dATP 9 6.01413e+00 FALSE
dGTP 10 3.02581e+00 FALSE
RNA 11 2.86805e+04 FALSE
DNA 12 5.17934e+03 FALSE
HX 13 9.51785e+00 FALSE
Xa 14 5.05941e+00 FALSE
Gua 15 5.50638e+00 FALSE
UA 16 1.00293e+02 FALSE
R5P 17 1.80000e+01 TRUE
Pi 18 1.40000e+03 TRUE
$reactions
index
ada 1
ade 2
adna 3
adrnr 4
ampd 5
aprt 6
arna 7
asuc 8
asli 9
dada 10
den 11
dgnuc 12
dnaa 13
dnag 14
gdna 15
gdrnr 16
gmpr 17
gmps 18
gnuc 19
gprt 20
grna 21
gua 22
hprt 23
hx 24
hxd 25
impd 26
inuc 27
mat 28
polyam 29
prpps 30
pyr 31
rnaa 32
rnag 33
trans 34
ua 35
x 36
xd 37
Laws
ada aada*ATP^fada4
ade aade*Ade^fade6
adna aadna*dATP^fdnap9*dGTP^fdnap10
adrnr aadrnr*ATP^fadrnr4*dATP^fadrnr9*dGTP^fadrnr10
ampd aampd*ATP^fampd4*GTP^fampd8*Pi^fampd18
aprt aaprt*PRPP^faprt1*ATP^faprt4*Ade^faprt6
arna aarna*ATP^frnap4*GTP^frnap8
asuc aasuc*IMP^fasuc2*ATP^fasuc4*GTP^fasuc8*Pi^fasuc18
asli aasli*SAMP^fasli3*ATP^fasli4
dada adada*dATP^fdada9
den aden*PRPP^fden1*IMP^fden2*ATP^fden4*GTP^fden8*Pi^fden18
dgnuc adgnuc*dGTP^fdgnuc10
dnaa adnaa*DNA^fdnan12
dnag adnag*DNA^fdnan12
gdna agdna*dATP^fdnap9*dGTP^fdnap10
gdrnr agdrnr*GTP^fgdrnr8*dATP^fgdrnr9*dGTP^fgdrnr10
gmpr agmpr*IMP^fgmpr2*ATP^fgmpr4*XMP^fgmpr7*GTP^fgmpr8
gmps agmps*ATP^fgmps4*XMP^fgmps7
gnuc agnuc*GTP^fgnuc8*Pi^fgnuc18
gprt agprt*PRPP^fgprt1*GTP^fgprt8*Gua^fgprt15
grna agrna*ATP^frnap4*GTP^frnap8
gua agua*Gua^fgua15
hprt ahprt*PRPP^fhprt1*IMP^fhprt2*HX^fhprt13
hx ahx*HX^fhx13
hxd ahxd*HX^fhxd13
impd aimpd*IMP^fimpd2*XMP^fimpd7*GTP^fimpd8
inuc ainuc*IMP^finuc2*Pi^finuc18
mat amat*ATP^fmat4*SAM^fmat5
polyam apolyam*SAM^fpolyam5
prpps aprpps*PRPP^fprpps1*ATP^fprpps4*GTP^fprpps8*R5P^fprpps17*Pi^fprpps18
pyr apyr*PRPP^fpyr1
rnaa arnaa*RNA^frnan11
rnag arnag*RNA^frnan11
trans atrans*SAM^ftrans5
ua aua*UA^fua16
x ax*Xa^fx14
xd axd*Xa^fxd14
initialFluxes
ada 2.079467e+00
ade 9.915724e-03
adna 1.003826e+01
adrnr 2.011595e-01
ampd 5.640728e+00
aprt 9.980753e-01
arna 1.985621e+03
asuc 8.003186e+00
asli 8.003185e+00
dada 2.004510e-01
den 2.403008e+00
dgnuc 1.008502e-01
dnaa 1.003756e+01
dnag 6.826370e+00
gdna 6.825859e+00
gdrnr 1.003440e-01
gmpr 5.138721e-01
gmps 1.595763e+00
gnuc 4.807078e+00
gprt 3.753642e+00
grna 1.323532e+03
gua 1.154277e+00
hprt 3.683827e+00
hx 4.730928e-02
hxd 1.191281e+00
impd 1.595762e+00
inuc 2.642505e+00
mat 1.498849e+01
polyam 1.007991e+00
prpps 2.088274e+01
pyr 1.004416e+01
rnaa 1.985551e+03
rnag 1.323605e+03
trans 1.398050e+01
ua 2.314825e+00
x 3.071716e-02
xd 2.314841e+00
SBMLR documentation built on Nov. 8, 2020, 6:50 p.m.
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Description Usage Arguments Value Warning Note Author(s) References See Also Examples
Description
This function converts an SBMLR model object in R into an SBMLR model definition file.
Rate laws are provided only in string form. Redundancy is eliminated to make the file easier
to edit.
Usage
1 | saveSBMLR(model,filename)
|
Arguments
model |
The |
filename |
The file name of the destination SBMLR model definition file. |
Value
No value returned.
Warning
SBML events and function definitions are NOT implemented.
Note
Similar to saveSBML, the file is written incrementally.
Author(s)
Tom Radivoyevitch
References
Radivoyevitch, T. A two-way interface between limited Systems Biology Markup Language and R. BMC Bioinformatics 5, 190 (2004).
See Also
Examples
1 2 3 4 5 6 7 |
Example output
Loading required package: XML
Loading required package: deSolve
$species
index initialConcentrations boundaryConditions
PRPP TRUE TRUE TRUE
IMP TRUE TRUE TRUE
SAMP TRUE TRUE TRUE
ATP TRUE TRUE TRUE
SAM TRUE TRUE TRUE
Ade TRUE TRUE TRUE
XMP TRUE TRUE TRUE
GTP TRUE TRUE TRUE
dATP TRUE TRUE TRUE
dGTP TRUE TRUE TRUE
RNA TRUE TRUE TRUE
DNA TRUE TRUE TRUE
HX TRUE TRUE TRUE
Xa TRUE TRUE TRUE
Gua TRUE TRUE TRUE
UA TRUE TRUE TRUE
R5P TRUE TRUE TRUE
Pi TRUE TRUE TRUE
$reactions
index Laws initialFluxes
ada TRUE TRUE TRUE
ade TRUE TRUE TRUE
adna TRUE TRUE TRUE
adrnr TRUE TRUE TRUE
ampd TRUE TRUE TRUE
aprt TRUE TRUE TRUE
arna TRUE TRUE TRUE
asuc TRUE TRUE TRUE
asli TRUE TRUE TRUE
dada TRUE TRUE TRUE
den TRUE TRUE TRUE
dgnuc TRUE TRUE TRUE
dnaa TRUE TRUE TRUE
dnag TRUE TRUE TRUE
gdna TRUE TRUE TRUE
gdrnr TRUE TRUE TRUE
gmpr TRUE TRUE TRUE
gmps TRUE TRUE TRUE
gnuc TRUE TRUE TRUE
gprt TRUE TRUE TRUE
grna TRUE TRUE TRUE
gua TRUE TRUE TRUE
hprt TRUE TRUE TRUE
hx TRUE TRUE TRUE
hxd TRUE TRUE TRUE
impd TRUE TRUE TRUE
inuc TRUE TRUE TRUE
mat TRUE TRUE TRUE
polyam TRUE TRUE TRUE
prpps TRUE TRUE TRUE
pyr TRUE TRUE TRUE
rnaa TRUE TRUE TRUE
rnag TRUE TRUE TRUE
trans TRUE TRUE TRUE
ua TRUE TRUE TRUE
x TRUE TRUE TRUE
xd TRUE TRUE TRUE
$nSpecies
[1] 18
$sIDs
[1] "PRPP" "IMP" "SAMP" "ATP" "SAM" "Ade" "XMP" "GTP" "dATP" "dGTP"
[11] "RNA" "DNA" "HX" "Xa" "Gua" "UA" "R5P" "Pi"
$S0
PRPP IMP SAMP ATP SAM Ade
5.01742e+00 9.82634e+01 1.98189e-01 2.47535e+03 3.99187e+00 9.84730e-01
XMP GTP dATP dGTP RNA DNA
2.47930e+01 4.10223e+02 6.01413e+00 3.02581e+00 2.86805e+04 5.17934e+03
HX Xa Gua UA R5P Pi
9.51785e+00 5.05941e+00 5.50638e+00 1.00293e+02 1.80000e+01 1.40000e+03
$BC
PRPP IMP SAMP ATP SAM Ade XMP GTP dATP dGTP RNA DNA HX
FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
Xa Gua UA R5P Pi
FALSE FALSE FALSE TRUE TRUE
$nStates
[1] 16
$y0
PRPP IMP SAMP ATP SAM Ade
5.01742e+00 9.82634e+01 1.98189e-01 2.47535e+03 3.99187e+00 9.84730e-01
XMP GTP dATP dGTP RNA DNA
2.47930e+01 4.10223e+02 6.01413e+00 3.02581e+00 2.86805e+04 5.17934e+03
HX Xa Gua UA
9.51785e+00 5.05941e+00 5.50638e+00 1.00293e+02
$nReactions
[1] 37
$rIDs
[1] "ada" "ade" "adna" "adrnr" "ampd" "aprt" "arna" "asuc"
[9] "asli" "dada" "den" "dgnuc" "dnaa" "dnag" "gdna" "gdrnr"
[17] "gmpr" "gmps" "gnuc" "gprt" "grna" "gua" "hprt" "hx"
[25] "hxd" "impd" "inuc" "mat" "polyam" "prpps" "pyr" "rnaa"
[33] "rnag" "trans" "ua" "x" "xd"
$rLaws
ada
"aada*ATP^fada4"
ade
"aade*Ade^fade6"
adna
"aadna*dATP^fdnap9*dGTP^fdnap10"
adrnr
"aadrnr*ATP^fadrnr4*dATP^fadrnr9*dGTP^fadrnr10"
ampd
"aampd*ATP^fampd4*GTP^fampd8*Pi^fampd18"
aprt
"aaprt*PRPP^faprt1*ATP^faprt4*Ade^faprt6"
arna
"aarna*ATP^frnap4*GTP^frnap8"
asuc
"aasuc*IMP^fasuc2*ATP^fasuc4*GTP^fasuc8*Pi^fasuc18"
asli
"aasli*SAMP^fasli3*ATP^fasli4"
dada
"adada*dATP^fdada9"
den
"aden*PRPP^fden1*IMP^fden2*ATP^fden4*GTP^fden8*Pi^fden18"
dgnuc
"adgnuc*dGTP^fdgnuc10"
dnaa
"adnaa*DNA^fdnan12"
dnag
"adnag*DNA^fdnan12"
gdna
"agdna*dATP^fdnap9*dGTP^fdnap10"
gdrnr
"agdrnr*GTP^fgdrnr8*dATP^fgdrnr9*dGTP^fgdrnr10"
gmpr
"agmpr*IMP^fgmpr2*ATP^fgmpr4*XMP^fgmpr7*GTP^fgmpr8"
gmps
"agmps*ATP^fgmps4*XMP^fgmps7"
gnuc
"agnuc*GTP^fgnuc8*Pi^fgnuc18"
gprt
"agprt*PRPP^fgprt1*GTP^fgprt8*Gua^fgprt15"
grna
"agrna*ATP^frnap4*GTP^frnap8"
gua
"agua*Gua^fgua15"
hprt
"ahprt*PRPP^fhprt1*IMP^fhprt2*HX^fhprt13"
hx
"ahx*HX^fhx13"
hxd
"ahxd*HX^fhxd13"
impd
"aimpd*IMP^fimpd2*XMP^fimpd7*GTP^fimpd8"
inuc
"ainuc*IMP^finuc2*Pi^finuc18"
mat
"amat*ATP^fmat4*SAM^fmat5"
polyam
"apolyam*SAM^fpolyam5"
prpps
"aprpps*PRPP^fprpps1*ATP^fprpps4*GTP^fprpps8*R5P^fprpps17*Pi^fprpps18"
pyr
"apyr*PRPP^fpyr1"
rnaa
"arnaa*RNA^frnan11"
rnag
"arnag*RNA^frnan11"
trans
"atrans*SAM^ftrans5"
ua
"aua*UA^fua16"
x
"ax*Xa^fx14"
xd
"axd*Xa^fxd14"
$V0
ada ade adna adrnr ampd aprt
2.079467e+00 9.915724e-03 1.003826e+01 2.011595e-01 5.640728e+00 9.980753e-01
arna asuc asli dada den dgnuc
1.985621e+03 8.003186e+00 8.003185e+00 2.004510e-01 2.403008e+00 1.008502e-01
dnaa dnag gdna gdrnr gmpr gmps
1.003756e+01 6.826370e+00 6.825859e+00 1.003440e-01 5.138721e-01 1.595763e+00
gnuc gprt grna gua hprt hx
4.807078e+00 3.753642e+00 1.323532e+03 1.154277e+00 3.683827e+00 4.730928e-02
hxd impd inuc mat polyam prpps
1.191281e+00 1.595762e+00 2.642505e+00 1.498849e+01 1.007991e+00 2.088274e+01
pyr rnaa rnag trans ua x
1.004416e+01 1.985551e+03 1.323605e+03 1.398050e+01 2.314825e+00 3.071716e-02
xd
2.314841e+00
$globalVec
NULL
$incid
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [,14]
PRPP 0 0 0 0 0 -1 0 0 0 0 -1 0 0 0
IMP 0 0 0 0 1 0 0 -1 0 0 1 0 0 0
SAMP 0 0 0 0 0 0 0 1 -1 0 0 0 0 0
ATP -1 0 0 -1 -1 1 -1 0 1 0 0 0 0 0
SAM 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Ade 0 -1 0 0 0 -1 0 0 0 0 0 0 0 0
XMP 0 0 0 0 0 0 0 0 0 0 0 0 0 0
GTP 0 0 0 0 0 0 0 0 0 0 0 0 0 0
dATP 0 0 -1 1 0 0 0 0 0 -1 0 0 1 0
dGTP 0 0 0 0 0 0 0 0 0 0 0 -1 0 1
RNA 0 0 0 0 0 0 1 0 0 0 0 0 0 0
DNA 0 0 1 0 0 0 0 0 0 0 0 0 -1 -1
HX 1 0 0 0 0 0 0 0 0 1 0 0 0 0
Xa 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Gua 0 0 0 0 0 0 0 0 0 0 0 1 0 0
UA 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25] [,26]
PRPP 0 0 0 0 0 -1 0 0 -1 0 0 0
IMP 0 0 1 0 0 0 0 0 1 0 0 -1
SAMP 0 0 0 0 0 0 0 0 0 0 0 0
ATP 0 0 0 0 0 0 0 0 0 0 0 0
SAM 0 0 0 0 0 0 0 0 0 0 0 0
Ade 0 0 0 0 0 0 0 0 0 0 0 0
XMP 0 0 0 -1 0 0 0 0 0 0 0 1
GTP 0 -1 -1 1 -1 1 -1 0 0 0 0 0
dATP 0 0 0 0 0 0 0 0 0 0 0 0
dGTP -1 1 0 0 0 0 0 0 0 0 0 0
RNA 0 0 0 0 0 0 1 0 0 0 0 0
DNA 1 0 0 0 0 0 0 0 0 0 0 0
HX 0 0 0 0 0 0 0 0 -1 -1 -1 0
Xa 0 0 0 0 0 0 0 1 0 0 1 0
Gua 0 0 0 0 1 -1 0 -1 0 0 0 0
UA 0 0 0 0 0 0 0 0 0 0 0 0
[,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37]
PRPP 0 0 0 1 -1 0 0 0 0 0 0
IMP -1 0 0 0 0 0 0 0 0 0 0
SAMP 0 0 0 0 0 0 0 0 0 0 0
ATP 0 -1 0 0 0 1 0 1 0 0 0
SAM 0 1 -1 0 0 0 0 -1 0 0 0
Ade 0 0 1 0 0 0 0 0 0 0 0
XMP 0 0 0 0 0 0 0 0 0 0 0
GTP 0 0 0 0 0 0 1 0 0 0 0
dATP 0 0 0 0 0 0 0 0 0 0 0
dGTP 0 0 0 0 0 0 0 0 0 0 0
RNA 0 0 0 0 0 -1 -1 0 0 0 0
DNA 0 0 0 0 0 0 0 0 0 0 0
HX 1 0 0 0 0 0 0 0 0 0 0
Xa 0 0 0 0 0 0 0 0 0 -1 -1
Gua 0 0 0 0 0 0 0 0 0 0 0
UA 0 0 0 0 0 0 0 0 -1 0 1
$nRules
[1] 0
$ruleIDs
NULL
$species
index initialConcentrations boundaryConditions
PRPP 1 5.01742e+00 FALSE
IMP 2 9.82634e+01 FALSE
SAMP 3 1.98189e-01 FALSE
ATP 4 2.47535e+03 FALSE
SAM 5 3.99187e+00 FALSE
Ade 6 9.84730e-01 FALSE
XMP 7 2.47930e+01 FALSE
GTP 8 4.10223e+02 FALSE
dATP 9 6.01413e+00 FALSE
dGTP 10 3.02581e+00 FALSE
RNA 11 2.86805e+04 FALSE
DNA 12 5.17934e+03 FALSE
HX 13 9.51785e+00 FALSE
Xa 14 5.05941e+00 FALSE
Gua 15 5.50638e+00 FALSE
UA 16 1.00293e+02 FALSE
R5P 17 1.80000e+01 TRUE
Pi 18 1.40000e+03 TRUE
$reactions
index
ada 1
ade 2
adna 3
adrnr 4
ampd 5
aprt 6
arna 7
asuc 8
asli 9
dada 10
den 11
dgnuc 12
dnaa 13
dnag 14
gdna 15
gdrnr 16
gmpr 17
gmps 18
gnuc 19
gprt 20
grna 21
gua 22
hprt 23
hx 24
hxd 25
impd 26
inuc 27
mat 28
polyam 29
prpps 30
pyr 31
rnaa 32
rnag 33
trans 34
ua 35
x 36
xd 37
Laws
ada aada*ATP^fada4
ade aade*Ade^fade6
adna aadna*dATP^fdnap9*dGTP^fdnap10
adrnr aadrnr*ATP^fadrnr4*dATP^fadrnr9*dGTP^fadrnr10
ampd aampd*ATP^fampd4*GTP^fampd8*Pi^fampd18
aprt aaprt*PRPP^faprt1*ATP^faprt4*Ade^faprt6
arna aarna*ATP^frnap4*GTP^frnap8
asuc aasuc*IMP^fasuc2*ATP^fasuc4*GTP^fasuc8*Pi^fasuc18
asli aasli*SAMP^fasli3*ATP^fasli4
dada adada*dATP^fdada9
den aden*PRPP^fden1*IMP^fden2*ATP^fden4*GTP^fden8*Pi^fden18
dgnuc adgnuc*dGTP^fdgnuc10
dnaa adnaa*DNA^fdnan12
dnag adnag*DNA^fdnan12
gdna agdna*dATP^fdnap9*dGTP^fdnap10
gdrnr agdrnr*GTP^fgdrnr8*dATP^fgdrnr9*dGTP^fgdrnr10
gmpr agmpr*IMP^fgmpr2*ATP^fgmpr4*XMP^fgmpr7*GTP^fgmpr8
gmps agmps*ATP^fgmps4*XMP^fgmps7
gnuc agnuc*GTP^fgnuc8*Pi^fgnuc18
gprt agprt*PRPP^fgprt1*GTP^fgprt8*Gua^fgprt15
grna agrna*ATP^frnap4*GTP^frnap8
gua agua*Gua^fgua15
hprt ahprt*PRPP^fhprt1*IMP^fhprt2*HX^fhprt13
hx ahx*HX^fhx13
hxd ahxd*HX^fhxd13
impd aimpd*IMP^fimpd2*XMP^fimpd7*GTP^fimpd8
inuc ainuc*IMP^finuc2*Pi^finuc18
mat amat*ATP^fmat4*SAM^fmat5
polyam apolyam*SAM^fpolyam5
prpps aprpps*PRPP^fprpps1*ATP^fprpps4*GTP^fprpps8*R5P^fprpps17*Pi^fprpps18
pyr apyr*PRPP^fpyr1
rnaa arnaa*RNA^frnan11
rnag arnag*RNA^frnan11
trans atrans*SAM^ftrans5
ua aua*UA^fua16
x ax*Xa^fx14
xd axd*Xa^fxd14
initialFluxes
ada 2.079467e+00
ade 9.915724e-03
adna 1.003826e+01
adrnr 2.011595e-01
ampd 5.640728e+00
aprt 9.980753e-01
arna 1.985621e+03
asuc 8.003186e+00
asli 8.003185e+00
dada 2.004510e-01
den 2.403008e+00
dgnuc 1.008502e-01
dnaa 1.003756e+01
dnag 6.826370e+00
gdna 6.825859e+00
gdrnr 1.003440e-01
gmpr 5.138721e-01
gmps 1.595763e+00
gnuc 4.807078e+00
gprt 3.753642e+00
grna 1.323532e+03
gua 1.154277e+00
hprt 3.683827e+00
hx 4.730928e-02
hxd 1.191281e+00
impd 1.595762e+00
inuc 2.642505e+00
mat 1.498849e+01
polyam 1.007991e+00
prpps 2.088274e+01
pyr 1.004416e+01
rnaa 1.985551e+03
rnag 1.323605e+03
trans 1.398050e+01
ua 2.314825e+00
x 3.071716e-02
xd 2.314841e+00
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