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a2390yu
2026-07-17 12:22:34 +02:00
commit ed37e11581
18 changed files with 766 additions and 0 deletions
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rules/aldolase.gml
+37
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@@ -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 "-" ]
]
]
rules/aldose-ketose.gml
+32
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@@ -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" ]
]
]
rules/ketose-aldose.gml
+32
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@@ -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" ]
]
]
rules/phosphohydrolase.gml
+36
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@@ -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 "-" ]
]
]
rules/phosphoketolase.gml
+49
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@@ -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 "-" ]
]
]
rules/transaldolase.gml
+56
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@@ -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 "-" ]
]
]
rules/transketolase.gml
+46
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@@ -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 "-" ]
]
]