From 0c2eec0d9eb996c3673f92414a8e673a9a472e9d Mon Sep 17 00:00:00 2001 From: kilian Date: Thu, 9 Jul 2026 14:10:48 +0200 Subject: [PATCH] Dateien nach "mod" hochladen --- mod/hydroxylation.py | 317 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 317 insertions(+) create mode 100644 mod/hydroxylation.py diff --git a/mod/hydroxylation.py b/mod/hydroxylation.py new file mode 100644 index 0000000..adfbe90 --- /dev/null +++ b/mod/hydroxylation.py @@ -0,0 +1,317 @@ +config.ilp.solver="CPLEX" + +#phenylalanine = Graph.fromGMLString( +""" + graph [ + node [ id 1 label "C" ] + node [ id 2 label "C" ] + node [ id 3 label "C" ] + node [ id 4 label "C" ] + node [ id 5 label "C" ] + node [ id 6 label "C" ] + node [ id 7 label "H" ] + node [ id 8 label "H" ] + node [ id 9 label "H" ] + node [ id 10 label "H" ] + node [ id 11 label "H" ] + node [ id 12 label "C" ] + node [ id 13 label "H" ] + node [ id 14 label "H" ] + node [ id 15 label "C" ] + node [ id 16 label "C" ] + node [ id 17 label "O" ] + node [ id 18 label "O" ] + node [ id 19 label "H" ] + node [ id 20 label "N" ] + node [ id 21 label "H" ] + node [ id 22 label "H" ] + node [ id 23 label "H" ] + edge [ source 6 target 1 label ":" ] + edge [ source 1 target 7 label "-" ] + edge [ source 1 target 2 label ":" ] + edge [ source 2 target 8 label "-" ] + edge [ source 2 target 3 label ":" ] + edge [ source 3 target 9 label "-" ] + edge [ source 3 target 4 label ":" ] + edge [ source 4 target 10 label "-" ] + edge [ source 4 target 5 label ":" ] + edge [ source 5 target 11 label "-" ] + edge [ source 5 target 6 label ":" ] + edge [ source 6 target 12 label "-" ] + edge [ source 12 target 13 label "-" ] + edge [ source 12 target 14 label "-" ] + edge [ source 12 target 15 label "-" ] + edge [ source 15 target 16 label "-" ] + edge [ source 16 target 17 label "-" ] + edge [ source 16 target 18 label "=" ] + edge [ source 17 target 19 label "-" ] + edge [ source 21 target 20 label "-" ] + edge [ source 20 target 22 label "-" ] + edge [ source 20 target 15 label "-" ] + edge [ source 15 target 23 label "-" ] + ] +""" +# , name="Phenylalanine") + +#noradrenalin = Graph.fromGMLString( +""" + graph [ + node [ id 1 label "C" ] + node [ id 2 label "C" ] + node [ id 3 label "C" ] + node [ id 4 label "C" ] + node [ id 5 label "C" ] + node [ id 6 label "C" ] + node [ id 7 label "H" ] + node [ id 8 label "O" ] + node [ id 9 label "O" ] + node [ id 10 label "H" ] + node [ id 11 label "H" ] + node [ id 12 label "C" ] + node [ id 13 label "O" ] + node [ id 14 label "H" ] + node [ id 15 label "C" ] + node [ id 20 label "N" ] + node [ id 21 label "H" ] + node [ id 22 label "H" ] + node [ id 23 label "H" ] + node [ id 24 label "H" ] + node [ id 25 label "H" ] + node [ id 26 label "H" ] + node [ id 27 label "H" ] + edge [ source 6 target 1 label ":" ] + edge [ source 1 target 7 label "-" ] + edge [ source 1 target 2 label ":" ] + edge [ source 2 target 8 label "-" ] + edge [ source 2 target 3 label ":" ] + edge [ source 3 target 9 label "-" ] + edge [ source 3 target 4 label ":" ] + edge [ source 4 target 10 label "-" ] + edge [ source 4 target 5 label ":" ] + edge [ source 5 target 11 label "-" ] + edge [ source 5 target 6 label ":" ] + edge [ source 6 target 12 label "-" ] + edge [ source 12 target 13 label "-" ] + edge [ source 12 target 14 label "-" ] + edge [ source 12 target 15 label "-" ] + edge [ source 21 target 20 label "-" ] + edge [ source 20 target 22 label "-" ] + edge [ source 20 target 15 label "-" ] + edge [ source 15 target 23 label "-" ] + edge [ source 15 target 24 label "-" ] + edge [ source 13 target 25 label "-" ] + edge [ source 8 target 27 label "-" ] + edge [ source 9 target 26 label "-" ] + ]""" +#, name="Noradrenalin") + +vanilline = Graph.fromGMLString( +""" + graph [ + node [ id 1 label "C" ] + node [ id 2 label "C" ] + node [ id 3 label "C" ] + node [ id 4 label "C" ] + node [ id 5 label "C" ] + node [ id 6 label "C" ] + node [ id 7 label "O" ] + node [ id 8 label "O" ] + node [ id 9 label "H" ] + node [ id 10 label "H" ] + node [ id 11 label "C" ] + node [ id 12 label "O" ] + node [ id 13 label "H" ] + node [ id 19 label "H" ] + node [ id 20 label "H" ] + node [ id 21 label "H" ] + edge [ source 9 target 8 label "-" ] + edge [ source 8 target 2 label "-" ] + edge [ source 10 target 7 label "-" ] + edge [ source 7 target 3 label "-" ] + edge [ source 3 target 2 label ":" ] + edge [ source 2 target 1 label ":" ] + edge [ source 1 target 6 label ":" ] + edge [ source 6 target 5 label ":" ] + edge [ source 5 target 4 label ":" ] + edge [ source 4 target 3 label ":" ] + edge [ source 6 target 11 label "-" ] + edge [ source 11 target 13 label "-" ] + edge [ source 11 target 12 label "=" ] + edge [ source 19 target 1 label "-" ] + edge [ source 5 target 21 label "-" ] + edge [ source 4 target 20 label "-" ] + ] +""" +, name="Vanilline") + +cinnamon = Graph.fromGMLString( +""" + graph [ + node [ id 1 label "C" ] + node [ id 2 label "C" ] + node [ id 3 label "C" ] + node [ id 4 label "C" ] + node [ id 5 label "C" ] + node [ id 6 label "C" ] + node [ id 7 label "H" ] + node [ id 8 label "H" ] + node [ id 9 label "H" ] + node [ id 10 label "H" ] + node [ id 11 label "H" ] + node [ id 12 label "C" ] + node [ id 15 label "C" ] + node [ id 28 label "H" ] + node [ id 29 label "H" ] + node [ id 30 label "C" ] + node [ id 31 label "O" ] + node [ id 32 label "O" ] + node [ id 33 label "H" ] + edge [ source 6 target 1 label ":" ] + edge [ source 1 target 7 label "-" ] + edge [ source 1 target 2 label ":" ] + edge [ source 2 target 8 label "-" ] + edge [ source 2 target 3 label ":" ] + edge [ source 3 target 9 label "-" ] + edge [ source 3 target 4 label ":" ] + edge [ source 4 target 10 label "-" ] + edge [ source 4 target 5 label ":" ] + edge [ source 5 target 11 label "-" ] + edge [ source 5 target 6 label ":" ] + edge [ source 6 target 12 label "-" ] + edge [ source 12 target 15 label "=" ] + edge [ source 12 target 28 label "-" ] + edge [ source 15 target 29 label "-" ] + edge [ source 15 target 30 label "-" ] + edge [ source 30 target 32 label "=" ] + edge [ source 30 target 31 label "-" ] + edge [ source 31 target 33 label "-" ] + ] +""" +, name="Cinnamon") + + + +hydroxylation = Rule.fromGMLString( +""" +rule [ + left [ + node [ id 1 label "H" ] + edge [ source 1 target 2 label "-" ] + ] + context [ + node [ id 2 label "C" ] + ] + right [ + node [ id 3 label "O" ] + node [ id 4 label "H" ] + edge [ source 2 target 3 label "-" ] + edge [ source 3 target 4 label "-" ] + ] +] +""" +) + +#decarboxylation = Rule.fromGMLString( +""" +rule [ + left [ + node [ id 1 label "C" ] + node [ id 2 label "O" ] + node [ id 3 label "O" ] + node [ id 4 label "H" ] + edge [ source 1 target 2 label "=" ] + edge [ source 1 target 3 label "-" ] + edge [ source 3 target 4 label "-" ] + edge [ source 1 target 5 label "-" ] + ] + context [ + node [ id 5 label "C" ] + ] + right [ + node [ id 6 label "H" ] + edge [ source 5 target 6 label "-" ] + ] +] +""" +#) + +aldehydation = Rule.fromGMLString( +""" +rule [ + left [ + node [ id 3 label "C" ] + node [ id 4 label "H" ] + node [ id 5 label "C" ] + node [ id 8 label "H" ] + node [ id 7 label "O" ] + node [ id 6 label "O" ] + edge [ source 1 target 3 label "=" ] + edge [ source 8 target 7 label "-" ] + edge [ source 7 target 5 label "-" ] + edge [ source 5 target 6 label "=" ] + edge [ source 5 target 3 label "-" ] + edge [ source 3 target 4 label "-" ] + ] + context [ + node [ id 1 label "C" ] + ] + right [ + node [ id 2 label "O" ] + 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") <= 30 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 {cinnamon}: + flowAutocata.addSource(a) +flowAutocata.addSink(vanilline) +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() \ No newline at end of file