printASM

Synopsis: Read the AdvanceSyn model specification file and print out its details before processing into model objects.

Usage: python astools.py printASM [option]

where [option] can be

• modelfile: Relative path to the model specification file.
• readertype: Reader type for AdvanceSyn Model specification. Allowable types are 'basic' and 'extended'.

For example:

python astools.py printASM --modelfile=models/asm/glycolysis.modelspec --readertype=extended

Working example:

D:\Dropbox\MyProjects\astoolkit>python astools.py printASM --modelfile=models/asm/glycolysis.modelspec --readertype=extended
Specification/type = 1
Identifiers/name = glycolysis
Identifiers/author = Maurice Ling
Objects/glucose = D-glucose
Objects/atp = adenosine-triphosphate
Objects/adp = adenosine-diphosphate
Objects/proton = proton
Objects/nad = NAD
Objects/pi = phosphate
Objects/nadh = NADH
Objects/water = water
Objects/g6p = a-D-Glucose-6-phosphate
Objects/f6p = b-D-Fructose-6-phosphate
Objects/f16p = b-D-Fructose-1,6-phosphate
Objects/gadp = D-glyceraldehyde 3-phosphate
Objects/dhap = Dihydroxyacetone phosphate
Objects/bpg13 = D-1,3-bisphosphoglycerate
Objects/pg3 = 3-phosphoglycerate
Objects/pg2 = 2-phosphoglycerate
Objects/pep = phosphoenolpyruvate
Objects/pyr = pyruvate
Objects/hk.rna = hexokinase
Objects/hk = hexokinase
Objects/pgi = Phosphoglucose isomerase
Objects/pfk = phosphofructokinase
Objects/aldo = fructose-bisphosphate aldolase
Objects/tpi = triosephosphate isomerase
Objects/gapdh = glyceraldehyde phosphate dehydrogenase
Objects/pkg = phosphoglycerate kinase
Objects/pgm = phosphoglycerate mutase
Objects/eno = enolase
Objects/pk = pyruvate kinase
Initials/glucose = 1e-5
Initials/atp = 1e-5
Initials/adp = 1e-5
Initials/proton = 1e-5
Initials/nad = 1e-5
Initials/pi = 1e-5
Initials/nadh = 1e-5
Initials/water = 1e-5
Initials/g6p = 1e-9
Initials/f6p = 1e-9
Initials/f16p = 1e-9
Initials/gadp = 1e-9
Initials/dhap = 1e-9
Initials/bpg13 = 1e-9
Initials/pg3 = 1e-9
Initials/pg2 = 1e-9
Initials/pep = 1e-9
Initials/pyr = 1e-9
Initials/hk.rna = 0
Initials/hk = 0
Initials/pgi = 1e-6
Initials/pfk = 1e-6
Initials/aldo = 1e-6
Initials/tpi = 1e-6
Initials/gapdh = 1e-6
Initials/pkg = 1e-6
Initials/pgm = 1e-6
Initials/eno = 1e-6
Initials/pk = 1e-6
Variables/hk.promoter = 1e-7
Variables/hk.rbs = 1e-5
Variables/hk.kcat = 1e-6
Variables/hk.km = 1e-6
Variables/pgi.kcat = 1e-6
Variables/pgi.km = 1e-6
Variables/pfk.kcat = 1e-6
Variables/pfk.km = 1e-6
Variables/aldo.kcat = 1e-6
Variables/aldo.km = 1e-6
Variables/tpi.kcat = 1e-6
Variables/tpi.km = 1e-6
Variables/gapdh.kcat = 1e-6
Variables/gapdh.km = 1e-6
Variables/pkg.kcat = 1e-6
Variables/pkg.km = 1e-6
Variables/pgm.kcat = 1e-6
Variables/pgm.km = 1e-6
Variables/eno.kcat = 1e-6
Variables/eno.km = 1e-6
Variables/pk.kcat = 1e-6
Variables/pk.km = 1e-6
Reactions/e1.rna = -> hk.rna | 1e-7
Reactions/e1 = -> hk | 1e-5 * hk.rna
Reactions/r1 = glucose + atp -> g6p + adp + proton | (1e-6 * hk * glucose)/(1e-6 + (hk * glucose))
Reactions/r2 = g6p -> f6p | (1e-6 * pgi * g6p)/(1e-6 + (pgi * g6p))
Reactions/r3 = f6p + atp -> f16p + adp + proton | (1e-6 * pfk * f6p)/(1e-6 + (pfk * f6p))
Reactions/r4 = f16p -> gadp + dhap | (1e-6 * aldo * f16p)/(1e-6 + (aldo * f16p))
Reactions/r5 = dhap -> gadp | (1e-6 * tpi * dhap)/(1e-6 + (tpi * dhap))
Reactions/r6 = gadp + nad + pi -> bpg13 + nadh + proton | (1e-6 * gapdh * gadp)/(1e-6 + (gapdh * gadp))
Reactions/r7 = bpg13 + adp -> pg3 + atp | (1e-6 * pkg * bpg13)/(1e-6 + (pkg * bpg13))
Reactions/r8 = pg3 -> pg2 | (1e-6 * pgm * pg3)/(1e-6 + (pgm * pg3))
Reactions/r9 = pg2 -> pep + water | (1e-6 * eno * pg2)/(1e-6 + (eno * pg2))
Reactions/r10 = pep + adp + proton -> pyr + atp | (1e-6 * pk * pep)/(1e-6 + (pk * pep))