diff --git a/mod/hydroxylation.py b/mod/hydroxylation.py index adfbe90..8e4c458 100644 --- a/mod/hydroxylation.py +++ b/mod/hydroxylation.py @@ -211,6 +211,30 @@ rule [ """ ) +#hydroxylation = Rule.fromGMLString( +""" +rule [ + left [ + node [ id 1 label "H" ] + edge [ source 1 target 2 label "-" ] + ] + context [ + node [ id 2 label "C" ] + node [ id 3 label "C" ] + node [ id 4 label "C" ] + edge [ source 2 target 3 label ":" ] + edge [ source 2 target 4 label ":" ] + ] + right [ + node [ id 5 label "O" ] + node [ id 6 label "H" ] + edge [ source 2 target 5 label "-" ] + edge [ source 5 target 6 label "-" ] + ] +] +""" +#) + #decarboxylation = Rule.fromGMLString( """ rule [ @@ -277,21 +301,19 @@ for a in inputRules: dg = DG(graphDatabase=inputGraphs) dg.build().execute( addSubset(inputGraphs) - >> rightPredicate[ - lambda d: all(g.vLabelCount("C") <= 30 for g in d.right) - ]( - repeat(inputRules) - ) + >>repeat(inputRules) ) + +#rightPredicate[ +# lambda d: all(g.vLabelCount("C") <= 30 for g in d.right) +# ]( 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.addSource(cinnamon) flowAutocata.addSink(vanilline) flowAutocata.findSolutions() flowAutocata.solutions.list() diff --git a/mod/n-methylation.py b/mod/n-methylation.py index 07b44dd..75d9026 100644 --- a/mod/n-methylation.py +++ b/mod/n-methylation.py @@ -114,6 +114,27 @@ nmethylation = Rule.fromGMLString( ]""" ) +#doublebondflip = Rule.fromGMLString( +"""rule [ + left [ + edge [ source 1 target 2 label "-" ] + edge [ source 2 target 3 label "-" ] + edge [ source 3 target 4 label "=" ] + ] + context [ + node [ id 1 label "H" ] + node [ id 2 label "N" ] + node [ id 3 label "C"] + node [ id 4 label "N"] + ] + right [ + edge [ source 1 target 4 label "-" ] + edge [ source 4 target 3 label "-" ] + edge [ source 3 target 2 label "=" ] + ] +]""" +#) + flowPrinter = FlowPrinter() flowPrinter.printUnfiltered = False @@ -127,11 +148,7 @@ for a in inputRules: dg = DG(graphDatabase=inputGraphs) dg.build().execute( addSubset(inputGraphs) - >> rightPredicate[ - lambda d: all(g.vLabelCount("C") <= 20 for g in d.right) - ]( - repeat(inputRules) - ) + >>repeat(inputRules) ) dg.print() postSection("Product Graphs") @@ -139,9 +156,7 @@ for a in dg.vertices: a.graph.print() flowAutocata = Flow(dg) -flowAutocata.overallAutocatalysis.enable() -for a in {xanthine}: - flowAutocata.addSource(a) +flowAutocata.addSource(xanthine) flowAutocata.addSink(caffeine) flowAutocata.findSolutions() flowAutocata.solutions.list() diff --git a/mod/summaryHydroxylation.pdf b/mod/summaryHydroxylation.pdf new file mode 100644 index 0000000..0e5249d Binary files /dev/null and b/mod/summaryHydroxylation.pdf differ diff --git a/mod/summaryNMeDBflip.pdf b/mod/summaryNMeDBflip.pdf new file mode 100644 index 0000000..a13f53b Binary files /dev/null and b/mod/summaryNMeDBflip.pdf differ