Restliche Files hochgeladen
Die restlichen Files vom Uni Rechner hochgeladen
This commit is contained in:
parent
016e30076b
commit
4b57f465da
BIN
CaffeineSynthesis.pdf
Normal file
BIN
CaffeineSynthesis.pdf
Normal file
Binary file not shown.
BIN
N-SelectivityEnzymes.pdf
Normal file
BIN
N-SelectivityEnzymes.pdf
Normal file
Binary file not shown.
191
n-methylation.py
Normal file
191
n-methylation.py
Normal file
@ -0,0 +1,191 @@
|
|||||||
|
config.ilp.solver="CPLEX"
|
||||||
|
|
||||||
|
xanthine = Graph.fromGMLString("""graph [
|
||||||
|
node [ id 0 label "N" ]
|
||||||
|
node [ id 1 label "C" ]
|
||||||
|
node [ id 2 label "N" ]
|
||||||
|
node [ id 3 label "C" ]
|
||||||
|
node [ id 4 label "C" ]
|
||||||
|
node [ id 5 label "C" ]
|
||||||
|
node [ id 6 label "N" ]
|
||||||
|
node [ id 7 label "C" ]
|
||||||
|
node [ id 8 label "N" ]
|
||||||
|
node [ id 9 label "O" ]
|
||||||
|
node [ id 10 label "O" ]
|
||||||
|
node [ id 11 label "H" ]
|
||||||
|
node [ id 12 label "H" ]
|
||||||
|
node [ id 13 label "H" ]
|
||||||
|
node [ id 14 label "H" ]
|
||||||
|
edge [ source 1 target 0 label "-" ]
|
||||||
|
edge [ source 2 target 1 label "-" ]
|
||||||
|
edge [ source 3 target 2 label "-" ]
|
||||||
|
edge [ source 4 target 3 label "=" ]
|
||||||
|
edge [ source 5 target 4 label "-" ]
|
||||||
|
edge [ source 0 target 5 label "-" ]
|
||||||
|
edge [ source 8 target 3 label "-" ]
|
||||||
|
edge [ source 7 target 8 label "=" ]
|
||||||
|
edge [ source 6 target 7 label "-" ]
|
||||||
|
edge [ source 4 target 6 label "-" ]
|
||||||
|
edge [ source 9 target 1 label "=" ]
|
||||||
|
edge [ source 10 target 5 label "=" ]
|
||||||
|
edge [ source 11 target 0 label "-" ]
|
||||||
|
edge [ source 12 target 2 label "-" ]
|
||||||
|
edge [ source 13 target 6 label "-" ]
|
||||||
|
edge [ source 14 target 7 label "-" ]
|
||||||
|
]""", name="Xanthine")
|
||||||
|
|
||||||
|
caffeine = Graph.fromGMLString("""graph [
|
||||||
|
node [ id 0 label "N" ]
|
||||||
|
node [ id 1 label "C" ]
|
||||||
|
node [ id 2 label "N" ]
|
||||||
|
node [ id 3 label "C" ]
|
||||||
|
node [ id 4 label "C" ]
|
||||||
|
node [ id 5 label "C" ]
|
||||||
|
node [ id 6 label "N" ]
|
||||||
|
node [ id 7 label "C" ]
|
||||||
|
node [ id 8 label "N" ]
|
||||||
|
node [ id 9 label "O" ]
|
||||||
|
node [ id 10 label "O" ]
|
||||||
|
node [ id 11 label "C" ]
|
||||||
|
node [ id 12 label "C" ]
|
||||||
|
node [ id 13 label "C" ]
|
||||||
|
node [ id 14 label "H" ]
|
||||||
|
node [ id 15 label "H" ]
|
||||||
|
node [ id 16 label "H" ]
|
||||||
|
node [ id 17 label "H" ]
|
||||||
|
node [ id 18 label "H" ]
|
||||||
|
node [ id 19 label "H" ]
|
||||||
|
node [ id 20 label "H" ]
|
||||||
|
node [ id 21 label "H" ]
|
||||||
|
node [ id 22 label "H" ]
|
||||||
|
node [ id 23 label "H" ]
|
||||||
|
edge [ source 1 target 0 label "-" ]
|
||||||
|
edge [ source 2 target 1 label "-" ]
|
||||||
|
edge [ source 3 target 2 label "-" ]
|
||||||
|
edge [ source 4 target 3 label "=" ]
|
||||||
|
edge [ source 5 target 4 label "-" ]
|
||||||
|
edge [ source 0 target 5 label "-" ]
|
||||||
|
edge [ source 8 target 3 label "-" ]
|
||||||
|
edge [ source 7 target 8 label "=" ]
|
||||||
|
edge [ source 6 target 7 label "-" ]
|
||||||
|
edge [ source 4 target 6 label "-" ]
|
||||||
|
edge [ source 9 target 1 label "=" ]
|
||||||
|
edge [ source 10 target 5 label "=" ]
|
||||||
|
edge [ source 11 target 0 label "-" ]
|
||||||
|
edge [ source 12 target 2 label "-" ]
|
||||||
|
edge [ source 13 target 6 label "-" ]
|
||||||
|
edge [ source 14 target 7 label "-" ]
|
||||||
|
edge [ source 11 target 15 label "-" ]
|
||||||
|
edge [ source 11 target 16 label "-" ]
|
||||||
|
edge [ source 11 target 17 label "-" ]
|
||||||
|
edge [ source 12 target 18 label "-" ]
|
||||||
|
edge [ source 12 target 19 label "-" ]
|
||||||
|
edge [ source 12 target 20 label "-" ]
|
||||||
|
edge [ source 13 target 21 label "-" ]
|
||||||
|
edge [ source 13 target 22 label "-" ]
|
||||||
|
edge [ source 13 target 23 label "-" ]
|
||||||
|
]""", name="Caffeine")
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
nmethylation = Rule.fromGMLString(
|
||||||
|
"""rule [
|
||||||
|
left [
|
||||||
|
node [ id 1 label "H" ]
|
||||||
|
edge [ source 1 target 2 label "-" ]
|
||||||
|
]
|
||||||
|
context [
|
||||||
|
node [ id 2 label "N" ]
|
||||||
|
node [ id 3 label "C"]
|
||||||
|
node [ id 4 label "C"]
|
||||||
|
edge [ source 3 target 2 label "-" ]
|
||||||
|
edge [ source 4 target 2 label "-" ]
|
||||||
|
]
|
||||||
|
right [
|
||||||
|
node [ id 5 label "C" ]
|
||||||
|
node [ id 6 label "H" ]
|
||||||
|
node [ id 7 label "H" ]
|
||||||
|
node [ id 8 label "H" ]
|
||||||
|
edge [ source 2 target 5 label "-" ]
|
||||||
|
edge [ source 5 target 6 label "-" ]
|
||||||
|
edge [ source 5 target 7 label "-" ]
|
||||||
|
edge [ source 5 target 8 label "-" ]
|
||||||
|
]
|
||||||
|
]"""
|
||||||
|
)
|
||||||
|
|
||||||
|
ndemethylation = Rule.fromGMLString("""rule [
|
||||||
|
left [
|
||||||
|
node [ id 5 label "C" ]
|
||||||
|
node [ id 6 label "H" ]
|
||||||
|
node [ id 7 label "H" ]
|
||||||
|
node [ id 8 label "H" ]
|
||||||
|
edge [ source 2 target 5 label "-" ]
|
||||||
|
edge [ source 5 target 6 label "-" ]
|
||||||
|
edge [ source 5 target 7 label "-" ]
|
||||||
|
edge [ source 5 target 8 label "-" ]
|
||||||
|
]
|
||||||
|
context [
|
||||||
|
node [ id 2 label "N" ]
|
||||||
|
node [ id 3 label "C"]
|
||||||
|
node [ id 4 label "C"]
|
||||||
|
edge [ source 3 target 2 label "-" ]
|
||||||
|
edge [ source 4 target 2 label "-" ]
|
||||||
|
]
|
||||||
|
right [
|
||||||
|
node [ id 1 label "H" ]
|
||||||
|
edge [ source 1 target 2 label "-" ]
|
||||||
|
]
|
||||||
|
]""")
|
||||||
|
|
||||||
|
flowPrinter = FlowPrinter()
|
||||||
|
flowPrinter.printUnfiltered = False
|
||||||
|
|
||||||
|
postSection("Loaded Graphs")
|
||||||
|
for a in inputGraphs:
|
||||||
|
a.print()
|
||||||
|
postSection("Loaded Rules")
|
||||||
|
for a in inputRules:
|
||||||
|
a.print()
|
||||||
|
|
||||||
|
dg = DG(graphDatabase=inputGraphs)
|
||||||
|
dg.build().execute(
|
||||||
|
addSubset(inputGraphs)
|
||||||
|
>> rightPredicate[
|
||||||
|
lambda d: all(g.vLabelCount("C") <= 10 for g in d.right)
|
||||||
|
](
|
||||||
|
repeat(inputRules)
|
||||||
|
)
|
||||||
|
)
|
||||||
|
dg.print()
|
||||||
|
postSection("Product Graphs")
|
||||||
|
for a in dg.vertices:
|
||||||
|
a.graph.print()
|
||||||
|
|
||||||
|
flowAutocata = Flow(dg)
|
||||||
|
flowAutocata.overallAutocatalysis.enable()
|
||||||
|
for a in {xanthine}:
|
||||||
|
flowAutocata.addSource(a)
|
||||||
|
flowAutocata.addSink(caffeine)
|
||||||
|
flowAutocata.findSolutions()
|
||||||
|
flowAutocata.solutions.list()
|
||||||
|
flowAutocata.solutions.print(flowPrinter)
|
||||||
|
|
||||||
|
|
||||||
|
sys.exit(0)
|
||||||
|
|
||||||
|
rc = rcEvaluator(inputRules)
|
||||||
|
for dRef in dg.derivations:
|
||||||
|
der = dRef.derivation
|
||||||
|
educt = rcId(der.left[0])
|
||||||
|
for i in range(1, len(der.left)):
|
||||||
|
educt = educt *rcParallel* rcId(der.left[i])
|
||||||
|
product = rcId(der.right[0])
|
||||||
|
for i in range(1, len(der.right)):
|
||||||
|
product = product *rcParallel* rcId(der.right[i])
|
||||||
|
rcExp = educt *rcSuper(allowPartial=False)* der.rule *rcSuper(allowPartial=False)* product
|
||||||
|
res = rc.eval(rcExp)
|
||||||
|
dRef.print()
|
||||||
|
for a in res:
|
||||||
|
a.print()
|
||||||
|
a.printGML()
|
||||||
BIN
nucleotides.jpg
Normal file
BIN
nucleotides.jpg
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 75 KiB |
BIN
summary.pdf
Normal file
BIN
summary.pdf
Normal file
Binary file not shown.
Loading…
x
Reference in New Issue
Block a user