initial commit
This commit is contained in:
a2390yu
commit
ed37e11581
24
daniels-strats/dg.py
Normal file
24
daniels-strats/dg.py
Normal file
@ -0,0 +1,24 @@
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import os
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include("common.py")
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filename = "dg.dg"
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nogMols = (Pi, AcP, G3P, DHAP, E4P, R5P, Ru5P, F6P, S7P, FBP)
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if os.path.isfile(prefixFilename(filename)):
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dg = DG.load(inputGraphs, inputRules, filename)
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else:
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stratBFS = (
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addSubset(nogMols)
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>> rightPredicate[
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lambda d: all(a.vLabelCount("C") <= 8 for a in d.right)
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](
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repeat(nogRules)
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)
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)
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dg = DG(graphDatabase=inputGraphs)
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dg.build().execute(stratBFS)
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outFile = dg.dump()
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post("cp \"" + outFile + "\" \"" + prefixFilename(filename) + "\"")
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print("|V| =", dg.numVertices)
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print("|E| =", dg.numEdges)
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renameGraphs(dg.graphDatabase)
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27
graphs/AcP.gml
Normal file
27
graphs/AcP.gml
Normal file
@ -0,0 +1,27 @@
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graph [
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node [ id 0 label "O" ]
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node [ id 1 label "P" ]
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node [ id 2 label "O" ]
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node [ id 3 label "O" ]
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node [ id 4 label "O" ]
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node [ id 5 label "C" ]
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node [ id 6 label "O" ]
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node [ id 7 label "C" ]
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node [ id 8 label "H" ]
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node [ id 9 label "H" ]
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node [ id 10 label "H" ]
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node [ id 11 label "H" ]
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node [ id 12 label "H" ]
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edge [ source 2 target 1 label "-" ]
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edge [ source 3 target 1 label "=" ]
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edge [ source 1 target 0 label "-" ]
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edge [ source 4 target 1 label "-" ]
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edge [ source 6 target 5 label "=" ]
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edge [ source 5 target 4 label "-" ]
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edge [ source 7 target 5 label "-" ]
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edge [ source 8 target 0 label "-" ]
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edge [ source 9 target 2 label "-" ]
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edge [ source 10 target 7 label "-" ]
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edge [ source 11 target 7 label "-" ]
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edge [ source 12 target 7 label "-" ]
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]
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35
graphs/DHAP.gml
Normal file
35
graphs/DHAP.gml
Normal file
@ -0,0 +1,35 @@
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graph [
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node [ id 0 label "O" ]
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node [ id 1 label "P" ]
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node [ id 2 label "O" ]
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node [ id 3 label "O" ]
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node [ id 4 label "O" ]
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node [ id 5 label "C" ]
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node [ id 6 label "C" ]
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node [ id 7 label "O" ]
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node [ id 8 label "C" ]
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node [ id 9 label "O" ]
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node [ id 10 label "H" ]
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node [ id 11 label "H" ]
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node [ id 12 label "H" ]
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node [ id 13 label "H" ]
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node [ id 14 label "H" ]
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node [ id 15 label "H" ]
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node [ id 16 label "H" ]
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edge [ source 2 target 1 label "-" ]
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edge [ source 3 target 1 label "=" ]
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edge [ source 1 target 0 label "-" ]
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edge [ source 4 target 1 label "-" ]
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edge [ source 5 target 4 label "-" ]
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edge [ source 7 target 6 label "=" ]
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edge [ source 6 target 5 label "-" ]
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edge [ source 8 target 6 label "-" ]
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edge [ source 9 target 8 label "-" ]
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edge [ source 10 target 0 label "-" ]
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edge [ source 11 target 2 label "-" ]
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edge [ source 12 target 5 label "-" ]
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edge [ source 13 target 5 label "-" ]
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edge [ source 14 target 8 label "-" ]
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edge [ source 15 target 8 label "-" ]
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edge [ source 16 target 9 label "-" ]
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]
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43
graphs/E4P.gml
Normal file
43
graphs/E4P.gml
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@ -0,0 +1,43 @@
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graph [
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node [ id 0 label "O" ]
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node [ id 1 label "P" ]
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node [ id 2 label "O" ]
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node [ id 3 label "O" ]
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node [ id 4 label "O" ]
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node [ id 5 label "C" ]
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node [ id 6 label "C" ]
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node [ id 7 label "O" ]
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node [ id 8 label "C" ]
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node [ id 9 label "O" ]
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node [ id 10 label "C" ]
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node [ id 11 label "O" ]
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node [ id 12 label "H" ]
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node [ id 13 label "H" ]
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node [ id 14 label "H" ]
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node [ id 15 label "H" ]
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node [ id 16 label "H" ]
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node [ id 17 label "H" ]
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node [ id 18 label "H" ]
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node [ id 19 label "H" ]
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node [ id 20 label "H" ]
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edge [ source 2 target 1 label "-" ]
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edge [ source 3 target 1 label "=" ]
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edge [ source 1 target 0 label "-" ]
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edge [ source 4 target 1 label "-" ]
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edge [ source 5 target 4 label "-" ]
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edge [ source 7 target 6 label "-" ]
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edge [ source 6 target 5 label "-" ]
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edge [ source 9 target 8 label "-" ]
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edge [ source 8 target 6 label "-" ]
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edge [ source 10 target 8 label "-" ]
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edge [ source 11 target 10 label "=" ]
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edge [ source 12 target 0 label "-" ]
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edge [ source 13 target 2 label "-" ]
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edge [ source 14 target 5 label "-" ]
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edge [ source 15 target 5 label "-" ]
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edge [ source 16 target 6 label "-" ]
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edge [ source 17 target 7 label "-" ]
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edge [ source 18 target 8 label "-" ]
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edge [ source 19 target 9 label "-" ]
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edge [ source 20 target 10 label "-" ]
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]
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59
graphs/F6P.gml
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59
graphs/F6P.gml
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@ -0,0 +1,59 @@
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graph [
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node [ id 0 label "O" ]
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node [ id 1 label "C" ]
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node [ id 2 label "C" ]
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node [ id 3 label "O" ]
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node [ id 4 label "C" ]
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node [ id 5 label "O" ]
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node [ id 6 label "C" ]
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node [ id 7 label "O" ]
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node [ id 8 label "C" ]
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node [ id 9 label "O" ]
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node [ id 10 label "C" ]
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node [ id 11 label "O" ]
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node [ id 12 label "P" ]
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node [ id 13 label "O" ]
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node [ id 14 label "O" ]
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node [ id 15 label "O" ]
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node [ id 16 label "H" ]
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node [ id 17 label "H" ]
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node [ id 18 label "H" ]
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node [ id 19 label "H" ]
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node [ id 20 label "H" ]
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node [ id 21 label "H" ]
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node [ id 22 label "H" ]
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node [ id 23 label "H" ]
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node [ id 24 label "H" ]
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node [ id 25 label "H" ]
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node [ id 26 label "H" ]
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node [ id 27 label "H" ]
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node [ id 28 label "H" ]
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edge [ source 1 target 0 label "-" ]
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edge [ source 3 target 2 label "=" ]
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edge [ source 2 target 1 label "-" ]
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edge [ source 5 target 4 label "-" ]
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edge [ source 4 target 2 label "-" ]
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edge [ source 7 target 6 label "-" ]
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edge [ source 6 target 4 label "-" ]
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edge [ source 9 target 8 label "-" ]
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edge [ source 8 target 6 label "-" ]
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edge [ source 10 target 8 label "-" ]
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edge [ source 11 target 10 label "-" ]
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edge [ source 13 target 12 label "=" ]
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edge [ source 14 target 12 label "-" ]
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edge [ source 12 target 11 label "-" ]
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edge [ source 15 target 12 label "-" ]
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edge [ source 16 target 0 label "-" ]
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edge [ source 17 target 1 label "-" ]
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edge [ source 18 target 1 label "-" ]
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edge [ source 19 target 4 label "-" ]
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edge [ source 20 target 5 label "-" ]
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edge [ source 21 target 6 label "-" ]
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edge [ source 22 target 7 label "-" ]
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edge [ source 23 target 8 label "-" ]
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edge [ source 24 target 9 label "-" ]
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edge [ source 25 target 10 label "-" ]
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edge [ source 26 target 10 label "-" ]
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edge [ source 27 target 14 label "-" ]
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edge [ source 28 target 15 label "-" ]
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]
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69
graphs/FBP.gml
Normal file
69
graphs/FBP.gml
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@ -0,0 +1,69 @@
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graph [
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node [ id 0 label "O" ]
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node [ id 1 label "C" ]
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node [ id 2 label "C" ]
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node [ id 3 label "O" ]
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node [ id 4 label "P" ]
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node [ id 5 label "O" ]
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node [ id 6 label "O" ]
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node [ id 7 label "O" ]
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node [ id 8 label "C" ]
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node [ id 9 label "O" ]
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node [ id 10 label "C" ]
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node [ id 11 label "O" ]
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node [ id 12 label "C" ]
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node [ id 13 label "C" ]
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||||
node [ id 14 label "O" ]
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node [ id 15 label "P" ]
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node [ id 16 label "O" ]
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node [ id 17 label "O" ]
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node [ id 18 label "O" ]
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node [ id 19 label "O" ]
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node [ id 20 label "H" ]
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node [ id 21 label "H" ]
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node [ id 22 label "H" ]
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node [ id 23 label "H" ]
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node [ id 24 label "H" ]
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node [ id 25 label "H" ]
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node [ id 26 label "H" ]
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node [ id 27 label "H" ]
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||||
node [ id 28 label "H" ]
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||||
node [ id 29 label "H" ]
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node [ id 30 label "H" ]
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node [ id 31 label "H" ]
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node [ id 32 label "H" ]
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node [ id 33 label "H" ]
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||||
edge [ source 2 target 1 label "-" ]
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||||
edge [ source 3 target 2 label "-" ]
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||||
edge [ source 5 target 4 label "-" ]
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edge [ source 6 target 4 label "-" ]
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edge [ source 4 target 3 label "-" ]
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edge [ source 7 target 4 label "=" ]
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edge [ source 1 target 0 label "-" ]
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edge [ source 9 target 8 label "-" ]
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edge [ source 8 target 1 label "-" ]
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edge [ source 11 target 10 label "-" ]
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edge [ source 10 target 8 label "-" ]
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edge [ source 13 target 12 label "-" ]
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edge [ source 14 target 13 label "-" ]
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edge [ source 16 target 15 label "-" ]
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edge [ source 17 target 15 label "-" ]
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edge [ source 15 target 14 label "-" ]
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edge [ source 18 target 15 label "=" ]
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edge [ source 12 target 10 label "-" ]
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edge [ source 19 target 12 label "=" ]
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||||
edge [ source 20 target 0 label "-" ]
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||||
edge [ source 21 target 1 label "-" ]
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||||
edge [ source 22 target 2 label "-" ]
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||||
edge [ source 23 target 2 label "-" ]
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||||
edge [ source 24 target 5 label "-" ]
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||||
edge [ source 25 target 6 label "-" ]
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||||
edge [ source 26 target 8 label "-" ]
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||||
edge [ source 27 target 9 label "-" ]
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||||
edge [ source 28 target 10 label "-" ]
|
||||
edge [ source 29 target 11 label "-" ]
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||||
edge [ source 30 target 13 label "-" ]
|
||||
edge [ source 31 target 13 label "-" ]
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edge [ source 32 target 16 label "-" ]
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edge [ source 33 target 17 label "-" ]
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]
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||||
35
graphs/G3P.gml
Normal file
35
graphs/G3P.gml
Normal file
@ -0,0 +1,35 @@
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graph [
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node [ id 0 label "C" ]
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node [ id 1 label "C" ]
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||||
node [ id 2 label "C" ]
|
||||
node [ id 3 label "O" ]
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||||
node [ id 4 label "O" ]
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||||
node [ id 5 label "O" ]
|
||||
node [ id 6 label "P" ]
|
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node [ id 7 label "O" ]
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node [ id 8 label "O" ]
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node [ id 9 label "O" ]
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node [ id 10 label "H" ]
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node [ id 11 label "H" ]
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node [ id 12 label "H" ]
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node [ id 13 label "H" ]
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node [ id 14 label "H" ]
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node [ id 15 label "H" ]
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node [ id 16 label "H" ]
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edge [ source 2 target 1 label "-" ]
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edge [ source 3 target 2 label "=" ]
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edge [ source 1 target 0 label "-" ]
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edge [ source 4 target 1 label "-" ]
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edge [ source 5 target 0 label "-" ]
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edge [ source 7 target 6 label "=" ]
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edge [ source 8 target 6 label "-" ]
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edge [ source 6 target 5 label "-" ]
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edge [ source 9 target 6 label "-" ]
|
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edge [ source 10 target 0 label "-" ]
|
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edge [ source 11 target 0 label "-" ]
|
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edge [ source 12 target 1 label "-" ]
|
||||
edge [ source 13 target 2 label "-" ]
|
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edge [ source 14 target 4 label "-" ]
|
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edge [ source 15 target 8 label "-" ]
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edge [ source 16 target 9 label "-" ]
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]
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||||
17
graphs/Pi.gml
Normal file
17
graphs/Pi.gml
Normal file
@ -0,0 +1,17 @@
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graph [
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node [ id 0 label "O" ]
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node [ id 1 label "P" ]
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node [ id 2 label "O" ]
|
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node [ id 3 label "O" ]
|
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node [ id 4 label "O" ]
|
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node [ id 5 label "H" ]
|
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node [ id 6 label "H" ]
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node [ id 7 label "H" ]
|
||||
edge [ source 2 target 1 label "-" ]
|
||||
edge [ source 3 target 1 label "-" ]
|
||||
edge [ source 1 target 0 label "=" ]
|
||||
edge [ source 4 target 1 label "-" ]
|
||||
edge [ source 5 target 2 label "-" ]
|
||||
edge [ source 6 target 3 label "-" ]
|
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edge [ source 7 target 4 label "-" ]
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]
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51
graphs/R5P.gml
Normal file
51
graphs/R5P.gml
Normal file
@ -0,0 +1,51 @@
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graph [
|
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node [ id 0 label "O" ]
|
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node [ id 1 label "P" ]
|
||||
node [ id 2 label "O" ]
|
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node [ id 3 label "O" ]
|
||||
node [ id 4 label "O" ]
|
||||
node [ id 5 label "C" ]
|
||||
node [ id 6 label "C" ]
|
||||
node [ id 7 label "O" ]
|
||||
node [ id 8 label "C" ]
|
||||
node [ id 9 label "O" ]
|
||||
node [ id 10 label "C" ]
|
||||
node [ id 11 label "O" ]
|
||||
node [ id 12 label "C" ]
|
||||
node [ id 13 label "O" ]
|
||||
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" ]
|
||||
node [ id 24 label "H" ]
|
||||
edge [ source 2 target 1 label "-" ]
|
||||
edge [ source 3 target 1 label "=" ]
|
||||
edge [ source 1 target 0 label "-" ]
|
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edge [ source 4 target 1 label "-" ]
|
||||
edge [ source 5 target 4 label "-" ]
|
||||
edge [ source 7 target 6 label "-" ]
|
||||
edge [ source 6 target 5 label "-" ]
|
||||
edge [ source 9 target 8 label "-" ]
|
||||
edge [ source 8 target 6 label "-" ]
|
||||
edge [ source 11 target 10 label "-" ]
|
||||
edge [ source 10 target 8 label "-" ]
|
||||
edge [ source 12 target 10 label "-" ]
|
||||
edge [ source 13 target 12 label "=" ]
|
||||
edge [ source 14 target 0 label "-" ]
|
||||
edge [ source 15 target 2 label "-" ]
|
||||
edge [ source 16 target 5 label "-" ]
|
||||
edge [ source 17 target 5 label "-" ]
|
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edge [ source 18 target 6 label "-" ]
|
||||
edge [ source 19 target 7 label "-" ]
|
||||
edge [ source 20 target 8 label "-" ]
|
||||
edge [ source 21 target 9 label "-" ]
|
||||
edge [ source 22 target 10 label "-" ]
|
||||
edge [ source 23 target 11 label "-" ]
|
||||
edge [ source 24 target 12 label "-" ]
|
||||
]
|
||||
51
graphs/Ru5P-X5P.gml
Normal file
51
graphs/Ru5P-X5P.gml
Normal file
@ -0,0 +1,51 @@
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graph [
|
||||
node [ id 0 label "O" ]
|
||||
node [ id 1 label "C" ]
|
||||
node [ id 2 label "C" ]
|
||||
node [ id 3 label "O" ]
|
||||
node [ id 4 label "C" ]
|
||||
node [ id 5 label "O" ]
|
||||
node [ id 6 label "C" ]
|
||||
node [ id 7 label "O" ]
|
||||
node [ id 8 label "C" ]
|
||||
node [ id 9 label "O" ]
|
||||
node [ id 10 label "P" ]
|
||||
node [ id 11 label "O" ]
|
||||
node [ id 12 label "O" ]
|
||||
node [ id 13 label "O" ]
|
||||
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" ]
|
||||
node [ id 24 label "H" ]
|
||||
edge [ source 1 target 0 label "-" ]
|
||||
edge [ source 3 target 2 label "=" ]
|
||||
edge [ source 2 target 1 label "-" ]
|
||||
edge [ source 5 target 4 label "-" ]
|
||||
edge [ source 4 target 2 label "-" ]
|
||||
edge [ source 7 target 6 label "-" ]
|
||||
edge [ source 6 target 4 label "-" ]
|
||||
edge [ source 8 target 6 label "-" ]
|
||||
edge [ source 9 target 8 label "-" ]
|
||||
edge [ source 11 target 10 label "=" ]
|
||||
edge [ source 12 target 10 label "-" ]
|
||||
edge [ source 10 target 9 label "-" ]
|
||||
edge [ source 13 target 10 label "-" ]
|
||||
edge [ source 14 target 0 label "-" ]
|
||||
edge [ source 15 target 1 label "-" ]
|
||||
edge [ source 16 target 1 label "-" ]
|
||||
edge [ source 17 target 4 label "-" ]
|
||||
edge [ source 18 target 5 label "-" ]
|
||||
edge [ source 19 target 6 label "-" ]
|
||||
edge [ source 20 target 7 label "-" ]
|
||||
edge [ source 21 target 8 label "-" ]
|
||||
edge [ source 22 target 8 label "-" ]
|
||||
edge [ source 23 target 12 label "-" ]
|
||||
edge [ source 24 target 13 label "-" ]
|
||||
]
|
||||
67
graphs/S7P.gml
Normal file
67
graphs/S7P.gml
Normal file
@ -0,0 +1,67 @@
|
||||
graph [
|
||||
node [ id 0 label "O" ]
|
||||
node [ id 1 label "P" ]
|
||||
node [ id 2 label "O" ]
|
||||
node [ id 3 label "O" ]
|
||||
node [ id 4 label "C" ]
|
||||
node [ id 5 label "C" ]
|
||||
node [ id 6 label "O" ]
|
||||
node [ id 7 label "C" ]
|
||||
node [ id 8 label "O" ]
|
||||
node [ id 9 label "C" ]
|
||||
node [ id 10 label "O" ]
|
||||
node [ id 11 label "C" ]
|
||||
node [ id 12 label "O" ]
|
||||
node [ id 13 label "C" ]
|
||||
node [ id 14 label "O" ]
|
||||
node [ id 15 label "C" ]
|
||||
node [ id 16 label "O" ]
|
||||
node [ id 17 label "O" ]
|
||||
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" ]
|
||||
node [ id 24 label "H" ]
|
||||
node [ id 25 label "H" ]
|
||||
node [ id 26 label "H" ]
|
||||
node [ id 27 label "H" ]
|
||||
node [ id 28 label "H" ]
|
||||
node [ id 29 label "H" ]
|
||||
node [ id 30 label "H" ]
|
||||
node [ id 31 label "H" ]
|
||||
node [ id 32 label "H" ]
|
||||
edge [ source 2 target 1 label "-" ]
|
||||
edge [ source 3 target 1 label "-" ]
|
||||
edge [ source 4 target 3 label "-" ]
|
||||
edge [ source 6 target 5 label "-" ]
|
||||
edge [ source 5 target 4 label "-" ]
|
||||
edge [ source 8 target 7 label "-" ]
|
||||
edge [ source 7 target 5 label "-" ]
|
||||
edge [ source 10 target 9 label "-" ]
|
||||
edge [ source 9 target 7 label "-" ]
|
||||
edge [ source 12 target 11 label "-" ]
|
||||
edge [ source 11 target 9 label "-" ]
|
||||
edge [ source 14 target 13 label "=" ]
|
||||
edge [ source 13 target 11 label "-" ]
|
||||
edge [ source 15 target 13 label "-" ]
|
||||
edge [ source 16 target 15 label "-" ]
|
||||
edge [ source 1 target 0 label "=" ]
|
||||
edge [ source 17 target 1 label "-" ]
|
||||
edge [ source 18 target 2 label "-" ]
|
||||
edge [ source 19 target 4 label "-" ]
|
||||
edge [ source 20 target 4 label "-" ]
|
||||
edge [ source 21 target 5 label "-" ]
|
||||
edge [ source 22 target 6 label "-" ]
|
||||
edge [ source 23 target 7 label "-" ]
|
||||
edge [ source 24 target 8 label "-" ]
|
||||
edge [ source 25 target 9 label "-" ]
|
||||
edge [ source 26 target 10 label "-" ]
|
||||
edge [ source 27 target 11 label "-" ]
|
||||
edge [ source 28 target 12 label "-" ]
|
||||
edge [ source 29 target 15 label "-" ]
|
||||
edge [ source 30 target 15 label "-" ]
|
||||
edge [ source 31 target 16 label "-" ]
|
||||
edge [ source 32 target 17 label "-" ]
|
||||
]
|
||||
37
rules/aldolase.gml
Normal file
37
rules/aldolase.gml
Normal file
@ -0,0 +1,37 @@
|
||||
rule [
|
||||
ruleID "AL"
|
||||
left [
|
||||
edge [ source 1 target 4 label "-" ]
|
||||
|
||||
edge [ source 101 target 102 label "=" ]
|
||||
]
|
||||
context [
|
||||
node [ id 1 label "C" ]
|
||||
node [ id 2 label "C" ]
|
||||
node [ id 3 label "O" ]
|
||||
node [ id 4 label "H" ]
|
||||
|
||||
edge [ source 1 target 2 label "-" ]
|
||||
edge [ source 2 target 3 label "=" ]
|
||||
|
||||
node [ id 30 label "O" ]
|
||||
edge [ source 1 target 30 label "-" ]
|
||||
node [ id 31 label "H" ]
|
||||
edge [ source 30 target 31 label "-" ]
|
||||
node [ id 32 label "H" ]
|
||||
edge [ source 1 target 32 label "-" ]
|
||||
|
||||
|
||||
node [ id 101 label "C" ]
|
||||
node [ id 102 label "O" ]
|
||||
|
||||
node [ id 130 label "H" ]
|
||||
edge [ source 101 target 130 label "-" ]
|
||||
]
|
||||
right [
|
||||
edge [ source 102 target 4 label "-" ]
|
||||
edge [ source 101 target 102 label "-" ]
|
||||
|
||||
edge [ source 1 target 101 label "-" ]
|
||||
]
|
||||
]
|
||||
32
rules/aldose-ketose.gml
Normal file
32
rules/aldose-ketose.gml
Normal file
@ -0,0 +1,32 @@
|
||||
rule [
|
||||
ruleID "AlKe"
|
||||
left [
|
||||
edge [ source 1 target 2 label "-" ]
|
||||
edge [ source 1 target 5 label "-" ]
|
||||
edge [ source 2 target 6 label "-" ]
|
||||
edge [ source 3 target 4 label "=" ]
|
||||
]
|
||||
context [
|
||||
node [ id 1 label "O" ]
|
||||
node [ id 2 label "C" ]
|
||||
node [ id 3 label "C" ]
|
||||
node [ id 4 label "O" ]
|
||||
node [ id 5 label "H" ]
|
||||
node [ id 6 label "H" ]
|
||||
node [ id 7 label "H" ]
|
||||
edge [ source 2 target 3 label "-" ]
|
||||
edge [ source 3 target 7 label "-" ]
|
||||
]
|
||||
right [
|
||||
edge [ source 1 target 2 label "=" ]
|
||||
edge [ source 3 target 4 label "-" ]
|
||||
edge [ source 3 target 5 label "-" ]
|
||||
edge [ source 4 target 6 label "-" ]
|
||||
]
|
||||
constrainAdj [
|
||||
id 2
|
||||
op "="
|
||||
count 1
|
||||
nodeLabels [ label "O" ]
|
||||
]
|
||||
]
|
||||
32
rules/ketose-aldose.gml
Normal file
32
rules/ketose-aldose.gml
Normal file
@ -0,0 +1,32 @@
|
||||
rule [
|
||||
ruleID "KeAl"
|
||||
left [
|
||||
edge [ source 1 target 2 label "=" ]
|
||||
edge [ source 3 target 4 label "-" ]
|
||||
edge [ source 3 target 5 label "-" ]
|
||||
edge [ source 4 target 6 label "-" ]
|
||||
]
|
||||
context [
|
||||
node [ id 1 label "O" ]
|
||||
node [ id 2 label "C" ]
|
||||
node [ id 3 label "C" ]
|
||||
node [ id 4 label "O" ]
|
||||
node [ id 5 label "H" ]
|
||||
node [ id 6 label "H" ]
|
||||
node [ id 7 label "H" ]
|
||||
edge [ source 2 target 3 label "-" ]
|
||||
edge [ source 3 target 7 label "-" ]
|
||||
]
|
||||
right [
|
||||
edge [ source 1 target 2 label "-" ]
|
||||
edge [ source 1 target 5 label "-" ]
|
||||
edge [ source 2 target 6 label "-" ]
|
||||
edge [ source 3 target 4 label "=" ]
|
||||
]
|
||||
constrainAdj [
|
||||
id 2
|
||||
op "="
|
||||
count 1
|
||||
nodeLabels [ label "O" ]
|
||||
]
|
||||
]
|
||||
36
rules/phosphohydrolase.gml
Normal file
36
rules/phosphohydrolase.gml
Normal file
@ -0,0 +1,36 @@
|
||||
rule [
|
||||
ruleID "PHL"
|
||||
left [
|
||||
edge [ source 0 target 6 label "-" ]
|
||||
|
||||
edge [ source 100 target 101 label "-" ]
|
||||
]
|
||||
context [
|
||||
node [ id 0 label "P" ]
|
||||
node [ id 1 label "O" ]
|
||||
edge [ source 0 target 1 label "=" ]
|
||||
node [ id 2 label "O" ]
|
||||
edge [ source 0 target 2 label "-" ]
|
||||
node [ id 3 label "H" ]
|
||||
edge [ source 2 target 3 label "-" ]
|
||||
node [ id 4 label "O" ]
|
||||
edge [ source 0 target 4 label "-" ]
|
||||
node [ id 5 label "H" ]
|
||||
edge [ source 4 target 5 label "-" ]
|
||||
node [ id 6 label "O" ]
|
||||
|
||||
node [ id 7 label "C" ]
|
||||
edge [ source 6 target 7 label "-" ]
|
||||
|
||||
|
||||
node [ id 100 label "O" ]
|
||||
node [ id 101 label "H" ]
|
||||
node [ id 102 label "H" ]
|
||||
edge [ source 100 target 102 label "-" ]
|
||||
]
|
||||
right [
|
||||
edge [ source 100 target 0 label "-" ]
|
||||
|
||||
edge [ source 101 target 6 label "-" ]
|
||||
]
|
||||
]
|
||||
49
rules/phosphoketolase.gml
Normal file
49
rules/phosphoketolase.gml
Normal file
@ -0,0 +1,49 @@
|
||||
rule [
|
||||
# The transition state is strange
|
||||
ruleID "PKL"
|
||||
left [
|
||||
edge [ source 4 target 7 label "-" ] # O-H (Pi)
|
||||
edge [ source 11 target 13 label "-" ] # C-C (Ketone)
|
||||
edge [ source 13 target 14 label "-" ] # C-O (Ketone)
|
||||
edge [ source 14 target 15 label "-" ] # O-H (Ketone)
|
||||
|
||||
edge [ source 10 target 16 label "-" ] # HO-C (Ketone)
|
||||
]
|
||||
context [
|
||||
# phosphate
|
||||
node [ id 0 label "P" ]
|
||||
node [ id 1 label "O" ]
|
||||
node [ id 2 label "O" ]
|
||||
node [ id 3 label "O" ]
|
||||
node [ id 4 label "O" ]
|
||||
node [ id 5 label "H" ]
|
||||
node [ id 6 label "H" ]
|
||||
node [ id 7 label "H" ]
|
||||
edge [ source 0 target 1 label "=" ]
|
||||
edge [ source 0 target 2 label "-" ]
|
||||
edge [ source 0 target 3 label "-" ]
|
||||
edge [ source 0 target 4 label "-" ]
|
||||
edge [ source 2 target 5 label "-" ]
|
||||
edge [ source 3 target 6 label "-" ]
|
||||
|
||||
# HO-C-C(=O)-COH
|
||||
node [ id 10 label "C" ]
|
||||
node [ id 11 label "C" ]
|
||||
node [ id 12 label "O" ]
|
||||
node [ id 13 label "C" ]
|
||||
node [ id 14 label "O" ]
|
||||
node [ id 15 label "H" ]
|
||||
node [ id 16 label "O" ]
|
||||
node [ id 17 label "H" ]
|
||||
edge [ source 10 target 11 label "-" ]
|
||||
edge [ source 11 target 12 label "=" ]
|
||||
edge [ source 16 target 17 label "-" ]
|
||||
]
|
||||
right [
|
||||
edge [ source 4 target 11 label "-" ] # C-O (Ketone-Pi)
|
||||
edge [ source 13 target 14 label "=" ] # C=O (Ketone)
|
||||
|
||||
edge [ source 15 target 16 label "-" ]
|
||||
edge [ source 10 target 7 label "-" ]
|
||||
]
|
||||
]
|
||||
56
rules/transaldolase.gml
Normal file
56
rules/transaldolase.gml
Normal file
@ -0,0 +1,56 @@
|
||||
rule [
|
||||
ruleID "TAL"
|
||||
left [
|
||||
edge [ source 8 target 15 label "-" ]
|
||||
edge [ source 10 target 8 label "-" ]
|
||||
|
||||
edge [ source 11 target 9 label "=" ]
|
||||
|
||||
edge [ source 12 target 10 label "-" ]
|
||||
]
|
||||
context [
|
||||
node [ id 1 label "H" ]
|
||||
node [ id 2 label "C" ]
|
||||
edge [ source 2 target 1 label "-" ]
|
||||
node [ id 3 label "H" ]
|
||||
edge [ source 3 target 2 label "-" ]
|
||||
node [ id 4 label "O" ]
|
||||
edge [ source 4 target 2 label "-" ]
|
||||
node [ id 5 label "H" ]
|
||||
edge [ source 5 target 4 label "-" ]
|
||||
node [ id 6 label "C" ]
|
||||
edge [ source 6 target 2 label "-" ]
|
||||
node [ id 7 label "O" ]
|
||||
edge [ source 7 target 6 label "=" ]
|
||||
|
||||
node [ id 15 label "C" ]
|
||||
edge [ source 15 target 6 label "-" ]
|
||||
node [ id 16 label "H" ]
|
||||
edge [ source 16 target 15 label "-" ]
|
||||
node [ id 17 label "O" ]
|
||||
edge [ source 17 target 15 label "-" ]
|
||||
node [ id 18 label "H" ]
|
||||
edge [ source 18 target 17 label "-" ]
|
||||
|
||||
|
||||
node [ id 8 label "C" ]
|
||||
node [ id 10 label "O" ]
|
||||
node [ id 13 label "H" ]
|
||||
edge [ source 13 target 8 label "-" ]
|
||||
|
||||
node [ id 9 label "C" ]
|
||||
node [ id 11 label "O" ]
|
||||
node [ id 14 label "H" ]
|
||||
edge [ source 14 target 9 label "-" ]
|
||||
|
||||
node [ id 12 label "H" ]
|
||||
]
|
||||
right [
|
||||
edge [ source 9 target 15 label "-" ]
|
||||
edge [ source 10 target 8 label "=" ]
|
||||
|
||||
edge [ source 11 target 9 label "-" ]
|
||||
|
||||
edge [ source 12 target 11 label "-" ]
|
||||
]
|
||||
]
|
||||
46
rules/transketolase.gml
Normal file
46
rules/transketolase.gml
Normal file
@ -0,0 +1,46 @@
|
||||
rule [
|
||||
ruleID "TKL"
|
||||
left [
|
||||
edge [ source 8 target 6 label "-" ]
|
||||
edge [ source 10 target 8 label "-" ]
|
||||
|
||||
edge [ source 11 target 9 label "=" ]
|
||||
|
||||
edge [ source 12 target 10 label "-" ]
|
||||
]
|
||||
context [
|
||||
node [ id 1 label "H" ]
|
||||
node [ id 2 label "C" ]
|
||||
edge [ source 2 target 1 label "-" ]
|
||||
node [ id 3 label "H" ]
|
||||
edge [ source 3 target 2 label "-" ]
|
||||
node [ id 4 label "O" ]
|
||||
edge [ source 4 target 2 label "-" ]
|
||||
node [ id 5 label "H" ]
|
||||
edge [ source 5 target 4 label "-" ]
|
||||
node [ id 6 label "C" ]
|
||||
edge [ source 6 target 2 label "-" ]
|
||||
node [ id 7 label "O" ]
|
||||
edge [ source 7 target 6 label "=" ]
|
||||
|
||||
node [ id 8 label "C" ]
|
||||
node [ id 10 label "O" ]
|
||||
node [ id 13 label "H" ]
|
||||
edge [ source 13 target 8 label "-" ]
|
||||
|
||||
node [ id 9 label "C" ]
|
||||
node [ id 11 label "O" ]
|
||||
node [ id 14 label "H" ]
|
||||
edge [ source 14 target 9 label "-" ]
|
||||
|
||||
node [ id 12 label "H" ]
|
||||
]
|
||||
right [
|
||||
edge [ source 9 target 6 label "-" ]
|
||||
edge [ source 10 target 8 label "=" ]
|
||||
|
||||
edge [ source 11 target 9 label "-" ]
|
||||
|
||||
edge [ source 12 target 11 label "-" ]
|
||||
]
|
||||
]
|
||||
Loading…
x
Reference in New Issue
Block a user