| 1 | #| |
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| 2 | Library for logical analysis of the network structure of |
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| 3 | signal transduction networks |
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| 4 | |
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| 5 | Authors: Julio Saez-Rodriguez, Martin Ginkel, Rebecca Hemenway |
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| 6 | $Id$ |
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| 7 | |# |
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| 8 | |
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| 9 | (add-icon-dir "promot:kb;SignalTransd;libraries;") |
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| 10 | (add-icon-dir "promot:kb;SignalTransd;structure;") |
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| 11 | (add-mdl-dir "promot:kb;SignalTransd;structure;") |
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| 12 | |
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| 13 | |
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| 14 | (define-module |
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| 15 | :class "struct-library" |
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| 16 | :super-classes ("module")) |
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| 17 | |
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| 18 | (define-terminal |
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| 19 | :class "term-struct" |
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| 20 | :super-classes ("terminal") |
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| 21 | :geometry-width "13" |
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| 22 | :geometry-height "13" |
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| 23 | :link-color "blue" |
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| 24 | :variables |
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| 25 | (("a" |
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| 26 | :system-theoretic "state" |
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| 27 | :value "1"))) |
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| 28 | |
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| 29 | #| |
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| 30 | (define-variable |
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| 31 | :class "var-real-parameter" |
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| 32 | :super-classes ("variable") |
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| 33 | :system-theoretic "real-parameter") |
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| 34 | |
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| 35 | |
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| 36 | (define-variable |
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| 37 | :class "var-integer-parameter" |
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| 38 | :super-classes ("variable") |
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| 39 | :system-theoretic "integer-parameter") |
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| 40 | |# |
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| 41 | |
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| 42 | (define-terminal |
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| 43 | :class "term-struct-compound" |
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| 44 | :super-classes ("term-struct") |
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| 45 | :properties |
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| 46 | (("abstract" :value "no")) |
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| 47 | :icon "icons/struct/term-compound") |
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| 48 | |
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| 49 | |
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| 50 | (define-terminal |
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| 51 | :class "term-struct-gate" |
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| 52 | :super-classes ("term-struct")) |
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| 53 | |
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| 54 | |
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| 55 | (define-terminal |
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| 56 | :class "term-struct-input" |
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| 57 | :super-classes ("term-struct-gate") |
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| 58 | :properties |
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| 59 | (("abstract" :value "no")) |
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| 60 | :icon "icons/struct/term-input" |
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| 61 | :parameters |
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| 62 | (("a" |
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| 63 | :system-theoretic "input" |
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| 64 | :value "1"))) |
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| 65 | |
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| 66 | |
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| 67 | (define-terminal |
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| 68 | :class "term-struct-output" |
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| 69 | :super-classes ("term-struct-gate") |
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| 70 | :properties |
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| 71 | (("abstract" :value "no")) |
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| 72 | :icon "icons/struct/term-output" |
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| 73 | :parameters |
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| 74 | (("a" |
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| 75 | :system-theoretic "output" |
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| 76 | :value "1"))) |
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| 77 | |
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| 78 | |
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| 79 | (define-module |
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| 80 | :class "struct-adapter" |
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| 81 | :super-classes ("struct-library") |
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| 82 | :icon "icons/struct/struct-adapt" |
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| 83 | :terminals |
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| 84 | (("input" |
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| 85 | :is-a "term-struct" |
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| 86 | :geometry-side "top" |
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| 87 | :geometry-position "0.5") |
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| 88 | ("output" |
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| 89 | :is-a "term-struct" |
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| 90 | :geometry-side "bottom" |
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| 91 | :geometry-position "0.5"))) |
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| 92 | |
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| 93 | |
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| 94 | (define-module |
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| 95 | :class "struct-adapter-compound" |
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| 96 | :super-classes ("struct-adapter") |
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| 97 | :properties |
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| 98 | (("abstract" :value "no")) |
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| 99 | :icon "icons/struct/struct-adapt" |
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| 100 | :terminals |
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| 101 | (("input" |
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| 102 | :is-a "term-struct-compound") |
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| 103 | ("output" |
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| 104 | :is-a "term-struct-compound"))) |
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| 105 | |
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| 106 | |
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| 107 | (define-module |
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| 108 | :class "struct-adapter-gate" |
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| 109 | :super-classes ("struct-adapter") |
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| 110 | :icon "icons/struct/struct-adapt" |
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| 111 | :properties |
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| 112 | (("abstract" :value "no")) |
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| 113 | :terminals |
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| 114 | (("input" |
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| 115 | :is-a "term-struct-input") |
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| 116 | ("output" |
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| 117 | :is-a "term-struct-output"))) |
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| 118 | |
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| 119 | |
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| 120 | (define-module |
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| 121 | :class "gate" |
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| 122 | :super-classes ("struct-library") |
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| 123 | :variables |
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| 124 | (("conf" |
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| 125 | :system-theoretic "real-parameter" |
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| 126 | :documentation "confidency level of this element: 1-most established (values between 0 and 1)" |
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| 127 | :value "1") |
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| 128 | ("defval" |
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| 129 | :system-theoretic "integer-parameter" |
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| 130 | :documentation "Default value of the logical state of the reaction. empty = undefined") |
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| 131 | ("time" |
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| 132 | :system-theoretic "real-parameter" |
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| 133 | :documentation "parameter determining the time-scale, 1 being the fastest" |
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| 134 | :value "1") |
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| 135 | ("logexcl" |
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| 136 | :system-theoretic "integer-parameter" |
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| 137 | :documentation "parameter defining the gate to be excluded from logical |
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| 138 | analysis. Allowed Values 0 (included) or 1 (excluded), default 0." |
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| 139 | :value "0") |
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| 140 | ("ignore_in_export" |
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| 141 | :system-theoretic "integer-parameter" |
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| 142 | :documentation "parameter determining whether the gate is exported to the |
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| 143 | CellNetAnalyzer. Allowed Values 0 (exported) or 1 (ignored in export), default |
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| 144 | 0." |
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| 145 | :value "0") |
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| 146 | ("monotone" |
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| 147 | :system-theoretic "real-parameter" |
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| 148 | :documentation "parameter defining the gate to be monotone. Allowed Values 0 (non monotone) or 1 (monotone), default 0." |
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| 149 | :value "0.01") |
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| 150 | ("map_number" |
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| 151 | :system-theoretic "integer-parameter" |
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| 152 | :documentation "parameter determining the map in CellNetAnalyzer. Should be a positive int, default is 1." |
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| 153 | :value "1") |
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| 154 | ("textbox_type" |
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| 155 | :system-theoretic "integer-parameter" |
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| 156 | :documentation "parameter determining if the textbox in CellNetAnalyzer is editable (1), not-editable (2) or non-visible (3). The default value is 1." |
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| 157 | :value "1") |
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| 158 | )) |
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| 159 | |
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| 160 | |
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| 161 | (define-module |
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| 162 | :class "gate-2" |
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| 163 | :super-classes ("gate") |
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| 164 | :terminals |
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| 165 | (("input1" |
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| 166 | :is-a "term-struct-input" |
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| 167 | :geometry-side "top" |
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| 168 | :geometry-position "0.1") |
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| 169 | ("input2" |
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| 170 | :is-a "term-struct-input" |
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| 171 | :geometry-side "top" |
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| 172 | :geometry-position "0.9") |
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| 173 | ("output" |
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| 174 | :is-a "term-struct-output" |
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| 175 | :geometry-side "bottom" |
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| 176 | :geometry-position "0.5"))) |
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| 177 | |
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| 178 | |
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| 179 | (define-module |
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| 180 | :class "gate-2-lr" |
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| 181 | :super-classes ("gate-2") |
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| 182 | :terminals |
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| 183 | (("input1" |
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| 184 | :geometry-side "left") |
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| 185 | ("input2" |
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| 186 | :geometry-side "left") |
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| 187 | ("output" |
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| 188 | :geometry-side "right"))) |
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| 189 | |
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| 190 | (define-module |
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| 191 | :class "gate-2-rl" |
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| 192 | :super-classes ("gate-2") |
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| 193 | :terminals |
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| 194 | (("input1" |
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| 195 | :geometry-side "right") |
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| 196 | ("input2" |
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| 197 | :geometry-side "right") |
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| 198 | ("output" |
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| 199 | :geometry-side "left"))) |
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| 200 | |
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| 201 | (define-module |
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| 202 | :class "gate-2-du" |
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| 203 | :super-classes ("gate-2") |
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| 204 | :terminals |
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| 205 | (("input1" |
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| 206 | :geometry-side "bottom") |
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| 207 | ("input2" |
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| 208 | :geometry-side "bottom") |
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| 209 | ("output" |
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| 210 | :geometry-side "top"))) |
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| 211 | |
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| 212 | (define-module |
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| 213 | :class "gate-2-2" |
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| 214 | :super-classes ("gate-2") |
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| 215 | :terminals |
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| 216 | (("input1" |
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| 217 | :is-eq-to "gate_2.input1" |
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| 218 | :geometry-side "TOP" |
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| 219 | :geometry-position "0.1") |
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| 220 | ("input2" |
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| 221 | :is-eq-to "struct_adapter.input" |
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| 222 | :geometry-side "TOP" |
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| 223 | :geometry-position "0.5") |
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| 224 | ("input3" |
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| 225 | :is-eq-to "gate_2b.input2" |
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| 226 | :geometry-side "TOP" |
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| 227 | :geometry-position "0.9") |
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| 228 | ("output" |
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| 229 | :is-eq-to "struct_adapterb.output" |
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| 230 | :geometry-side "BOTTOM" |
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| 231 | :geometry-position "0.5")) |
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| 232 | :modules |
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| 233 | (("gate_2" |
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| 234 | :is-a "gate-2" |
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| 235 | :geometry-x "48" |
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| 236 | :geometry-y "147") |
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| 237 | ("gate_2b" |
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| 238 | :is-a "gate-2" |
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| 239 | :geometry-x "228" |
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| 240 | :geometry-y "147") |
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| 241 | ("struct_adapter" |
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| 242 | :is-a "struct-adapter-gate" |
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| 243 | :geometry-x "137" |
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| 244 | :geometry-y "82") |
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| 245 | ("struct_adapterb" |
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| 246 | :is-a "struct-adapter-gate" |
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| 247 | :geometry-x "138" |
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| 248 | :geometry-y "209")) |
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| 249 | :links |
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| 250 | (("struct_adapterbinput_gate_2output" |
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| 251 | :terminals ("struct_adapterb.input" "gate_2.output" "gate_2b.output") |
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| 252 | :nodes (("138" "158")) |
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| 253 | :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil))) |
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| 254 | ("struct_adapteroutput_gate_2input2" |
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| 255 | :terminals ("struct_adapter.output" "gate_2.input2" "gate_2b.input1") |
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| 256 | :nodes (("138" "136")) |
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| 257 | :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))) |
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| 258 | :variables |
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| 259 | (("visibility" |
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| 260 | :value "1")) |
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| 261 | :parameters( |
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| 262 | ("gate_2.ignore_in_export" |
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| 263 | :value "parent.ignore_in_export") |
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| 264 | ("gate_2b.ignore_in_export" |
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| 265 | :value "parent.ignore_in_export") |
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| 266 | ("struct_adapter.ignore_in_export" |
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| 267 | :value "parent.ignore_in_export") |
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| 268 | ("struct_adapterb.ignore_in_export" |
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| 269 | :value "parent.ignore_in_export"))) |
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| 270 | |
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| 271 | |
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| 272 | (define-module |
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| 273 | :class "gate-3" |
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| 274 | :super-classes ("gate") |
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| 275 | :terminals |
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| 276 | (("input1" |
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| 277 | :is-a "term-struct-input" |
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| 278 | :geometry-side "top" |
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| 279 | :geometry-position "0.1") |
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| 280 | ("input2" |
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| 281 | :is-a "term-struct-input" |
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| 282 | :geometry-side "top" |
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| 283 | :geometry-position "0.5") |
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| 284 | ("input3" |
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| 285 | :is-a "term-struct-input" |
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| 286 | :geometry-side "top" |
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| 287 | :geometry-position "0.9") |
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| 288 | ("output" |
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| 289 | :is-a "term-struct-output" |
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| 290 | :geometry-side "bottom" |
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| 291 | :geometry-position "0.5"))) |
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| 292 | |
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| 293 | (define-module |
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| 294 | :class "gate-3-lr" |
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| 295 | :super-classes ("gate-3") |
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| 296 | :terminals |
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| 297 | (("input1" |
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| 298 | :geometry-side "left") |
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| 299 | ("input2" |
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| 300 | :geometry-side "left") |
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| 301 | ("input3" |
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| 302 | :geometry-side "left") |
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| 303 | ("output" |
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| 304 | :geometry-side "right"))) |
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| 305 | |
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| 306 | (define-module |
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| 307 | :class "gate-3-rl" |
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| 308 | :super-classes ("gate-3") |
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| 309 | :terminals |
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| 310 | (("input1" |
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| 311 | :geometry-side "right") |
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| 312 | ("input2" |
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| 313 | :geometry-side "right") |
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| 314 | ("input3" |
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| 315 | :geometry-side "right") |
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| 316 | ("output" |
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| 317 | :geometry-side "left"))) |
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| 318 | |
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| 319 | (define-module |
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| 320 | :class "gate-3-du" |
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| 321 | :super-classes ("gate-3") |
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| 322 | :terminals |
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| 323 | (("input1" |
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| 324 | :geometry-side "bottom") |
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| 325 | ("input2" |
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| 326 | :geometry-side "bottom") |
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| 327 | ("input3" |
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| 328 | :geometry-side "bottom") |
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| 329 | ("output" |
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| 330 | :geometry-side "top"))) |
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| 331 | |
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| 332 | (define-module |
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| 333 | :class "gate-4" |
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| 334 | :super-classes ("gate") |
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| 335 | :terminals |
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| 336 | (("input1" |
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| 337 | :is-a "term-struct-input" |
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| 338 | :geometry-side "left" |
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| 339 | :geometry-position "0.5") |
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| 340 | ("input2" |
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| 341 | :is-a "term-struct-input" |
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| 342 | :geometry-side "top" |
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| 343 | :geometry-position "0.25") |
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| 344 | ("input3" |
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| 345 | :is-a "term-struct-input" |
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| 346 | :geometry-side "top" |
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| 347 | :geometry-position "0.77") |
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| 348 | ("input4" |
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| 349 | :is-a "term-struct-input" |
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| 350 | :geometry-side "right" |
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| 351 | :geometry-position "0.5") |
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| 352 | ("output" |
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| 353 | :is-a "term-struct-output" |
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| 354 | :geometry-side "bottom" |
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| 355 | :geometry-position "0.5"))) |
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| 356 | |
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| 357 | |
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| 358 | (define-module |
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| 359 | :class "gate-5" |
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| 360 | :super-classes ("gate") |
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| 361 | :terminals |
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| 362 | (("input1" |
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| 363 | :is-a "term-struct-input" |
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| 364 | :geometry-side "left" |
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| 365 | :geometry-position "0.9") |
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| 366 | ("input2" |
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| 367 | :is-a "term-struct-input" |
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| 368 | :geometry-side "left" |
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| 369 | :geometry-position "0.1") |
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| 370 | ("input3" |
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| 371 | :is-a "term-struct-input" |
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| 372 | :geometry-side "top" |
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| 373 | :geometry-position "0.5") |
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| 374 | ("input4" |
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| 375 | :is-a "term-struct-input" |
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| 376 | :geometry-side "right" |
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| 377 | :geometry-position "0.1") |
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| 378 | ("input5" |
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| 379 | :is-a "term-struct-input" |
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| 380 | :geometry-side "right" |
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| 381 | :geometry-position "0.9") |
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| 382 | ("output" |
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| 383 | :is-a "term-struct-output" |
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| 384 | :geometry-side "bottom" |
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| 385 | :geometry-position "0.5"))) |
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| 386 | |
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| 387 | (define-module |
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| 388 | :class "gate-6" |
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| 389 | :super-classes ("gate") |
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| 390 | :terminals |
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| 391 | (("input1" |
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| 392 | :is-a "term-struct-input" |
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| 393 | :geometry-side "left" |
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| 394 | :geometry-position "0.9") |
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| 395 | ("input2" |
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| 396 | :is-a "term-struct-input" |
|---|
| 397 | :geometry-side "left" |
|---|
| 398 | :geometry-position "0.1") |
|---|
| 399 | ("input3" |
|---|
| 400 | :is-a "term-struct-input" |
|---|
| 401 | :geometry-side "top" |
|---|
| 402 | :geometry-position "0.5") |
|---|
| 403 | ("input4" |
|---|
| 404 | :is-a "term-struct-input" |
|---|
| 405 | :geometry-side "right" |
|---|
| 406 | :geometry-position "0.1") |
|---|
| 407 | ("input5" |
|---|
| 408 | :is-a "term-struct-input" |
|---|
| 409 | :geometry-side "right" |
|---|
| 410 | :geometry-position "0.5") |
|---|
| 411 | ("input6" |
|---|
| 412 | :is-a "term-struct-input" |
|---|
| 413 | :geometry-side "right" |
|---|
| 414 | :geometry-position "0.9") |
|---|
| 415 | ("output" |
|---|
| 416 | :is-a "term-struct-output" |
|---|
| 417 | :geometry-side "bottom" |
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| 418 | :geometry-position "0.5"))) |
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| 419 | |
|---|
| 420 | (define-module |
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| 421 | :class "activ" |
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| 422 | :super-classes ("gate") |
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| 423 | :icon "icons/struct/activ" |
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| 424 | :terminals |
|---|
| 425 | (("input1" |
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| 426 | :is-a "term-struct-input" |
|---|
| 427 | :geometry-side "top" |
|---|
| 428 | :geometry-position "0.5") |
|---|
| 429 | ("output" |
|---|
| 430 | :is-a "term-struct-output" |
|---|
| 431 | :geometry-side "bottom" |
|---|
| 432 | :geometry-position "0.5"))) |
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| 433 | |
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| 434 | (define-module |
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| 435 | :class "activ-ud" |
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| 436 | :super-classes ("activ") |
|---|
| 437 | :properties |
|---|
| 438 | (("abstract" :value "no"))) |
|---|
| 439 | |
|---|
| 440 | (define-module |
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| 441 | :class "activ-du" |
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| 442 | :super-classes ("activ") |
|---|
| 443 | :properties |
|---|
| 444 | (("abstract" :value "no")) |
|---|
| 445 | :icon "icons/struct/activ-du" |
|---|
| 446 | :terminals |
|---|
| 447 | (("input1" |
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| 448 | :geometry-side "bottom") |
|---|
| 449 | ("output" |
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| 450 | :geometry-side "top"))) |
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| 451 | |
|---|
| 452 | (define-module |
|---|
| 453 | :class "activ-lr" |
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| 454 | :super-classes ("activ") |
|---|
| 455 | :properties |
|---|
| 456 | (("abstract" :value "no")) |
|---|
| 457 | :icon "icons/struct/activ-lr" |
|---|
| 458 | :terminals |
|---|
| 459 | (("input1" |
|---|
| 460 | :geometry-side "left") |
|---|
| 461 | ("output" |
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| 462 | :geometry-side "right"))) |
|---|
| 463 | |
|---|
| 464 | (define-module |
|---|
| 465 | :class "activ-rl" |
|---|
| 466 | :super-classes ("activ") |
|---|
| 467 | :properties |
|---|
| 468 | (("abstract" :value "no")) |
|---|
| 469 | :icon "icons/struct/activ-rl" |
|---|
| 470 | :terminals |
|---|
| 471 | (("input1" |
|---|
| 472 | :geometry-side "right") |
|---|
| 473 | ("output" |
|---|
| 474 | :geometry-side "left"))) |
|---|
| 475 | |
|---|
| 476 | (define-module |
|---|
| 477 | :class "and" |
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| 478 | :super-classes ("gate") |
|---|
| 479 | :icon "icons/struct/and") |
|---|
| 480 | |
|---|
| 481 | (define-module |
|---|
| 482 | :class "and-2" |
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| 483 | :super-classes ("and" "gate-2")) |
|---|
| 484 | |
|---|
| 485 | (define-module |
|---|
| 486 | :class "and-2-ud" |
|---|
| 487 | :super-classes ("and-2") |
|---|
| 488 | :properties |
|---|
| 489 | (("abstract" :value "no"))) |
|---|
| 490 | |
|---|
| 491 | (define-module |
|---|
| 492 | :class "and-2-lr" |
|---|
| 493 | :super-classes ("and-2" "gate-2-lr") |
|---|
| 494 | :properties |
|---|
| 495 | (("abstract" :value "no"))) |
|---|
| 496 | |
|---|
| 497 | (define-module |
|---|
| 498 | :class "and-2-rl" |
|---|
| 499 | :super-classes ("and-2" "gate-2-rl") |
|---|
| 500 | :properties |
|---|
| 501 | (("abstract" :value "no"))) |
|---|
| 502 | |
|---|
| 503 | (define-module |
|---|
| 504 | :class "and-2-du" |
|---|
| 505 | :super-classes ("and-2" "gate-2-du") |
|---|
| 506 | :properties |
|---|
| 507 | (("abstract" :value "no"))) |
|---|
| 508 | |
|---|
| 509 | (define-module |
|---|
| 510 | :class "and-2-2" |
|---|
| 511 | :super-classes ("and" "gate-2-2") |
|---|
| 512 | :properties |
|---|
| 513 | (("abstract" :value "no")) |
|---|
| 514 | :modules |
|---|
| 515 | (("gate_2" |
|---|
| 516 | :is-a "and-2") |
|---|
| 517 | ("gate_2b" |
|---|
| 518 | :is-a "and-2")) |
|---|
| 519 | :parameters( |
|---|
| 520 | ("gate_2.ignore_in_export" |
|---|
| 521 | :value "parent.ignore_in_export") |
|---|
| 522 | ("gate_2b.ignore_in_export" |
|---|
| 523 | :value "parent.ignore_in_export")) |
|---|
| 524 | ) |
|---|
| 525 | |
|---|
| 526 | (define-module |
|---|
| 527 | :class "and-3" |
|---|
| 528 | :super-classes ("and" "gate-3") |
|---|
| 529 | :properties |
|---|
| 530 | (("abstract" :value "no"))) |
|---|
| 531 | |
|---|
| 532 | |
|---|
| 533 | (define-module |
|---|
| 534 | :class "and-4" |
|---|
| 535 | :super-classes ("and" "gate-4") |
|---|
| 536 | :properties (("abstract" :value "no"))) |
|---|
| 537 | |
|---|
| 538 | |
|---|
| 539 | (define-module |
|---|
| 540 | :class "and-5" |
|---|
| 541 | :super-classes ("and" "gate-5") |
|---|
| 542 | :properties |
|---|
| 543 | (("abstract" :value "no"))) |
|---|
| 544 | |
|---|
| 545 | |
|---|
| 546 | (define-module |
|---|
| 547 | :class "and-6" |
|---|
| 548 | :super-classes ("and" "gate-6") |
|---|
| 549 | :properties |
|---|
| 550 | (("abstract" :value "no"))) |
|---|
| 551 | |
|---|
| 552 | (define-module |
|---|
| 553 | :class "compound" |
|---|
| 554 | :super-classes ("struct-library") |
|---|
| 555 | :icon "icons/struct/comp" |
|---|
| 556 | :parameters |
|---|
| 557 | (("input.a" |
|---|
| 558 | :system-theoretic "real-parameter")) |
|---|
| 559 | :terminals |
|---|
| 560 | (("input" |
|---|
| 561 | :is-a "term-struct-compound" |
|---|
| 562 | :geometry-side "top" |
|---|
| 563 | :geometry-position "0.5")) |
|---|
| 564 | :variables |
|---|
| 565 | (("defval" |
|---|
| 566 | :system-theoretic "integer-parameter" |
|---|
| 567 | :documentation "Default value of the logical state of the reaction. empty = |
|---|
| 568 | undefined") |
|---|
| 569 | ("ignore_in_export" |
|---|
| 570 | :system-theoretic "integer-parameter" |
|---|
| 571 | :documentation "parameter determining whether the compound is exported to the |
|---|
| 572 | CellNetAnalyzer. Allowed Values 0 (exported) or 1 (ignored in export), default |
|---|
| 573 | 0." |
|---|
| 574 | :value "0") |
|---|
| 575 | ("map_number" |
|---|
| 576 | :system-theoretic "integer-parameter" |
|---|
| 577 | :documentation "parameter determining the map in CellNetAnalyzer. Should be a positive int, default is 1." |
|---|
| 578 | :value "1") |
|---|
| 579 | ("textbox_type" |
|---|
| 580 | :system-theoretic "integer-parameter" |
|---|
| 581 | :documentation "parameter determining if the textbox in CellNetAnalyzer is editable (1), not-editable (2) or non-visible (3). The default value is 1." |
|---|
| 582 | :value "1") |
|---|
| 583 | )) |
|---|
| 584 | |
|---|
| 585 | (define-module |
|---|
| 586 | :class "receptor" |
|---|
| 587 | :super-classes ("compound") |
|---|
| 588 | :properties |
|---|
| 589 | (("abstract" :value "no")) |
|---|
| 590 | :icon "icons/struct/receptor") |
|---|
| 591 | |
|---|
| 592 | (define-module |
|---|
| 593 | :class "ligand" |
|---|
| 594 | :super-classes ("compound") |
|---|
| 595 | :properties |
|---|
| 596 | (("abstract" :value "no")) |
|---|
| 597 | :icon "icons/struct/ligand") |
|---|
| 598 | |
|---|
| 599 | (define-module |
|---|
| 600 | :class "kinase" |
|---|
| 601 | :super-classes ("compound") |
|---|
| 602 | :properties |
|---|
| 603 | (("abstract" :value "no")) |
|---|
| 604 | :icon "icons/struct/kinase") |
|---|
| 605 | |
|---|
| 606 | (define-module |
|---|
| 607 | :class "dummy" |
|---|
| 608 | :super-classes ("compound") |
|---|
| 609 | :properties |
|---|
| 610 | (("abstract" :value "no")) |
|---|
| 611 | :icon "icons/struct/dummy") |
|---|
| 612 | |
|---|
| 613 | (define-module |
|---|
| 614 | :class "phosphatase" |
|---|
| 615 | :super-classes ("compound") |
|---|
| 616 | :properties |
|---|
| 617 | (("abstract" :value "no")) |
|---|
| 618 | :icon "icons/struct/phosphatase") |
|---|
| 619 | |
|---|
| 620 | (define-module |
|---|
| 621 | :class "ubiquitin-ligase" |
|---|
| 622 | :super-classes ("compound") |
|---|
| 623 | :properties |
|---|
| 624 | (("abstract" :value "no")) |
|---|
| 625 | :icon "icons/struct/ubiquitinLigase") |
|---|
| 626 | |
|---|
| 627 | (define-module |
|---|
| 628 | :class "adapter" |
|---|
| 629 | :super-classes ("compound") |
|---|
| 630 | :properties |
|---|
| 631 | (("abstract" :value "no")) |
|---|
| 632 | :icon "icons/struct/adapter") |
|---|
| 633 | |
|---|
| 634 | (define-module |
|---|
| 635 | :class "transfactor" |
|---|
| 636 | :super-classes ("compound") |
|---|
| 637 | :properties |
|---|
| 638 | (("abstract" :value "no")) |
|---|
| 639 | :icon "icons/struct/transfactor") |
|---|
| 640 | |
|---|
| 641 | (define-module |
|---|
| 642 | :class "gtpase" |
|---|
| 643 | :super-classes ("compound") |
|---|
| 644 | :properties |
|---|
| 645 | (("abstract" :value "no")) |
|---|
| 646 | :icon "icons/struct/gpro") |
|---|
| 647 | |
|---|
| 648 | (define-module |
|---|
| 649 | :class "gprotein" |
|---|
| 650 | :super-classes ("compound") |
|---|
| 651 | :properties |
|---|
| 652 | (("abstract" :value "no")) |
|---|
| 653 | :icon "icons/struct/gpro") |
|---|
| 654 | |
|---|
| 655 | (define-module |
|---|
| 656 | :class "gef" |
|---|
| 657 | :super-classes ("compound") |
|---|
| 658 | :properties |
|---|
| 659 | (("abstract" :value "no")) |
|---|
| 660 | :documentation "guanine nucleotide exchange factor" |
|---|
| 661 | :icon "icons/struct/gef") |
|---|
| 662 | |
|---|
| 663 | (define-module |
|---|
| 664 | :class "gap" |
|---|
| 665 | :super-classes ("compound") |
|---|
| 666 | :properties |
|---|
| 667 | (("abstract" :value "no")) |
|---|
| 668 | :documentation "gtpase activating protein" |
|---|
| 669 | :icon "icons/struct/gap") |
|---|
| 670 | |
|---|
| 671 | (define-module |
|---|
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|---|
| 673 | :super-classes ("compound") |
|---|
| 674 | :properties |
|---|
| 675 | (("abstract" :value "no")) |
|---|
| 676 | :icon "icons/struct/reservoir") |
|---|
| 677 | |
|---|
| 678 | (define-module |
|---|
| 679 | :class "other" |
|---|
| 680 | :super-classes ("compound") |
|---|
| 681 | :properties |
|---|
| 682 | (("abstract" :value "no"))) |
|---|
| 683 | |
|---|
| 684 | (define-module |
|---|
| 685 | :class "drug" |
|---|
| 686 | :super-classes ("compound") |
|---|
| 687 | :properties |
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| 688 | (("abstract" :value "no")) |
|---|
| 689 | :icon "icons/struct/drug") |
|---|
| 690 | |
|---|
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|---|
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|---|
| 693 | :super-classes ("compound") |
|---|
| 694 | :properties |
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|---|
| 696 | :icon "icons/struct/externalStimulus") |
|---|
| 697 | |
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|---|
| 699 | :class "phenotype" |
|---|
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|---|
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|---|
| 703 | :icon "icons/struct/phenotype") |
|---|
| 704 | |
|---|
| 705 | |
|---|
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|---|
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|---|
| 708 | :super-classes ("gate")) |
|---|
| 709 | |
|---|
| 710 | |
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|---|
| 712 | :class "source" |
|---|
| 713 | :super-classes ("boundary") |
|---|
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| 721 | :geometry-position "0.5"))) |
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| 722 | |
|---|
| 723 | |
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|---|
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|---|
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|---|
| 727 | :properties |
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| 730 | :terminals |
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| 734 | :geometry-position "0.5"))) |
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| 735 | |
|---|
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| 740 | :terminals |
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|---|
| 755 | |
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| 756 | |
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|---|
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|---|
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|---|
| 797 | :terminals |
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| 798 | (("input" |
|---|
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| 800 | :geometry-side "right" |
|---|
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|---|
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|---|
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|---|
| 806 | |
|---|
| 807 | |
|---|
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|---|
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|---|
| 811 | :icon "icons/struct/or") |
|---|
| 812 | |
|---|
| 813 | |
|---|
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|---|
| 815 | :class "or-2" |
|---|
| 816 | :super-classes ("or" "gate-2") |
|---|
| 817 | :properties |
|---|
| 818 | (("abstract" :value "no")) |
|---|
| 819 | :terminals |
|---|
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|---|
| 821 | :is-eq-to "activ.input1") |
|---|
| 822 | ("input2" |
|---|
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|---|
| 824 | ("output" |
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|---|
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|---|
| 828 | :is-a "activ" |
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| 829 | :geometry-x "71" |
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| 830 | :geometry-y "81") |
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| 831 | ("activ2" |
|---|
| 832 | :is-a "activ" |
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| 833 | :geometry-x "202" |
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| 834 | :geometry-y "84") |
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| 835 | ("struct_adapter" |
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| 838 | :geometry-y "176")) |
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| 841 | :terminals ("struct_adapter.input" "activ2.output" "activ.output") |
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|---|
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| 845 | ("activ.ignore_in_export" |
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| 846 | :value "parent.ignore_in_export") |
|---|
| 847 | ("activ2.ignore_in_export" |
|---|
| 848 | :value "parent.ignore_in_export") |
|---|
| 849 | ("struct_adapter.ignore_in_export" |
|---|
| 850 | :value "parent.ignore_in_export"))) |
|---|
| 851 | |
|---|
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|---|
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|---|
| 854 | :super-classes ("or" "gate-3") |
|---|
| 855 | :properties |
|---|
| 856 | (("abstract" :value "no")) |
|---|
| 857 | :geometry-width "438" |
|---|
| 858 | :geometry-height "300" |
|---|
| 859 | :terminals |
|---|
| 860 | (("input1" |
|---|
| 861 | :is-eq-to "activ.input1") |
|---|
| 862 | ("input2" |
|---|
| 863 | :is-eq-to "activ2.input1") |
|---|
| 864 | ("input3" |
|---|
| 865 | :is-eq-to "activ0.input1") |
|---|
| 866 | ("output" |
|---|
| 867 | :is-eq-to "struct_adapter.output")) |
|---|
| 868 | :modules |
|---|
| 869 | (("activ" |
|---|
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|---|
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|---|
| 872 | :geometry-y "81") |
|---|
| 873 | ("activ0" |
|---|
| 874 | :is-a "activ" |
|---|
| 875 | :geometry-x "290" |
|---|
| 876 | :geometry-y "85") |
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| 877 | ("activ2" |
|---|
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|---|
| 879 | :geometry-x "202" |
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|---|
| 883 | :geometry-x "124" |
|---|
| 884 | :geometry-y "176")) |
|---|
| 885 | :links |
|---|
| 886 | (("struct_adapterinput_activ2output" |
|---|
| 887 | :terminals ("struct_adapter.input" "activ2.output" "activ.output" |
|---|
| 888 | "activ0.output") |
|---|
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| 890 | :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)))) |
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| 895 | :value "parent.ignore_in_export") |
|---|
| 896 | ("activ2.ignore_in_export" |
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| 897 | :value "parent.ignore_in_export") |
|---|
| 898 | ("struct_adapter.ignore_in_export" |
|---|
| 899 | :value "parent.ignore_in_export"))) |
|---|
| 900 | |
|---|
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|---|
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|---|
| 903 | :class "or-4" |
|---|
| 904 | :super-classes ("or" "gate-4") |
|---|
| 905 | :properties |
|---|
| 906 | (("abstract" :value "no")) |
|---|
| 907 | :geometry-width "407" |
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| 908 | :geometry-height "300" |
|---|
| 909 | :terminals |
|---|
| 910 | (("input1" |
|---|
| 911 | :is-eq-to "activ.input1") |
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| 912 | ("input2" |
|---|
| 913 | :is-eq-to "activ2.input1") |
|---|
| 914 | ("input3" |
|---|
| 915 | :is-eq-to "activ0.input1") |
|---|
| 916 | ("input4" |
|---|
| 917 | :is-eq-to "activ1.input1") |
|---|
| 918 | ("output" |
|---|
| 919 | :is-eq-to "struct_adapter.output")) |
|---|
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|---|
| 922 | :is-a "activ" |
|---|
| 923 | :geometry-x "55" |
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| 924 | :geometry-y "129") |
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| 925 | ("activ0" |
|---|
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| 928 | :geometry-y "77") |
|---|
| 929 | ("activ1" |
|---|
| 930 | :is-a "activ" |
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| 932 | :geometry-y "127") |
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| 933 | ("activ2" |
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| 936 | :geometry-y "76") |
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| 939 | :geometry-x "172" |
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| 940 | :geometry-y "176")) |
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|---|
| 943 | :terminals ("struct_adapter.input" "activ2.output" "activ.output" |
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| 944 | "activ0.output" "activ1.output") |
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| 947 | ("4" "-1" nil)))) |
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| 949 | ("activ.ignore_in_export" |
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| 950 | :value "parent.ignore_in_export") |
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| 951 | ("activ0.ignore_in_export" |
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| 952 | :value "parent.ignore_in_export") |
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| 953 | ("activ1.ignore_in_export" |
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| 954 | :value "parent.ignore_in_export") |
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| 955 | ("activ2.ignore_in_export" |
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| 956 | :value "parent.ignore_in_export") |
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| 957 | ("struct_adapter.ignore_in_export" |
|---|
| 958 | :value "parent.ignore_in_export"))) |
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| 959 | |
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| 960 | |
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| 961 | (define-module |
|---|
| 962 | :class "or-5" |
|---|
| 963 | :super-classes ("or" "gate-5") |
|---|
| 964 | :properties |
|---|
| 965 | (("abstract" :value "no")) |
|---|
| 966 | :geometry-width "407" |
|---|
| 967 | :geometry-height "300" |
|---|
| 968 | :terminals |
|---|
| 969 | (("input1" |
|---|
| 970 | :is-eq-to "activ.input1") |
|---|
| 971 | ("input2" |
|---|
| 972 | :is-eq-to "activ2.input1") |
|---|
| 973 | ("input3" |
|---|
| 974 | :is-eq-to "activ0.input1") |
|---|
| 975 | ("input4" |
|---|
| 976 | :is-eq-to "activ1.input1") |
|---|
| 977 | ("input5" |
|---|
| 978 | :is-eq-to "activ3.input1") |
|---|
| 979 | ("output" |
|---|
| 980 | :is-eq-to "struct_adapter.output")) |
|---|
| 981 | :modules |
|---|
| 982 | (("activ" |
|---|
| 983 | :is-a "activ" |
|---|
| 984 | :geometry-x "55" |
|---|
| 985 | :geometry-y "129") |
|---|
| 986 | ("activ0" |
|---|
| 987 | :is-a "activ" |
|---|
| 988 | :geometry-x "250" |
|---|
| 989 | :geometry-y "77") |
|---|
| 990 | ("activ1" |
|---|
| 991 | :is-a "activ" |
|---|
| 992 | :geometry-x "330" |
|---|
| 993 | :geometry-y "127") |
|---|
| 994 | ("activ2" |
|---|
| 995 | :is-a "activ" |
|---|
| 996 | :geometry-x "122" |
|---|
| 997 | :geometry-y "76") |
|---|
| 998 | ("activ3" |
|---|
| 999 | :is-a "activ" |
|---|
| 1000 | :geometry-x "165" |
|---|
| 1001 | :geometry-y "62") |
|---|
| 1002 | ("struct_adapter" |
|---|
| 1003 | :is-a "struct-adapter-gate" |
|---|
| 1004 | :geometry-x "172" |
|---|
| 1005 | :geometry-y "176")) |
|---|
| 1006 | :links |
|---|
| 1007 | (("struct_adapterinput_activ2output" |
|---|
| 1008 | :terminals ("struct_adapter.input" "activ2.output" "activ.output" |
|---|
| 1009 | "activ0.output" "activ1.output" "activ3.output") |
|---|
| 1010 | :nodes (("174" "104")) |
|---|
| 1011 | :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil) |
|---|
| 1012 | ("4" "-1" nil) ("5" "-1" nil)))) |
|---|
| 1013 | :parameters( |
|---|
| 1014 | ("activ.ignore_in_export" |
|---|
| 1015 | :value "parent.ignore_in_export") |
|---|
| 1016 | ("activ0.ignore_in_export" |
|---|
| 1017 | :value "parent.ignore_in_export") |
|---|
| 1018 | ("activ1.ignore_in_export" |
|---|
| 1019 | :value "parent.ignore_in_export") |
|---|
| 1020 | ("activ2.ignore_in_export" |
|---|
| 1021 | :value "parent.ignore_in_export") |
|---|
| 1022 | ("activ3.ignore_in_export" |
|---|
| 1023 | :value "parent.ignore_in_export") |
|---|
| 1024 | ("struct_adapter.ignore_in_export" |
|---|
| 1025 | :value "parent.ignore_in_export"))) |
|---|
| 1026 | |
|---|
| 1027 | |
|---|
| 1028 | (define-module |
|---|
| 1029 | :class "somehow" |
|---|
| 1030 | :super-classes ("gate") |
|---|
| 1031 | :documentation " classes to represent incomplete truth tables") |
|---|
| 1032 | |
|---|
| 1033 | |
|---|
| 1034 | (define-module |
|---|
| 1035 | :class "somehow-2" |
|---|
| 1036 | :super-classes ("gate-2" "somehow") |
|---|
| 1037 | :properties |
|---|
| 1038 | (("abstract" :value "no")) |
|---|
| 1039 | :icon "icons/struct/somehow") |
|---|
| 1040 | |
|---|
| 1041 | (define-module |
|---|
| 1042 | :class "somehow-3" |
|---|
| 1043 | :super-classes ("gate-3" "somehow") |
|---|
| 1044 | :properties |
|---|
| 1045 | (("abstract" :value "no")) |
|---|
| 1046 | :icon "icons/struct/somehow") |
|---|
| 1047 | |
|---|
| 1048 | (define-module |
|---|
| 1049 | :class "somehow-4" |
|---|
| 1050 | :super-classes ("gate-4" "somehow") |
|---|
| 1051 | :properties |
|---|
| 1052 | (("abstract" :value "no")) |
|---|
| 1053 | :icon "icons/struct/somehow") |
|---|
| 1054 | |
|---|
| 1055 | (define-module |
|---|
| 1056 | :class "somehow-5" |
|---|
| 1057 | :super-classes ("gate-5" "somehow") |
|---|
| 1058 | :properties |
|---|
| 1059 | (("abstract" :value "no")) |
|---|
| 1060 | :icon "icons/struct/somehow") |
|---|
| 1061 | |
|---|
| 1062 | (define-module |
|---|
| 1063 | :class "struct-model" |
|---|
| 1064 | :super-classes ("module") |
|---|
| 1065 | :documentation "superclass that must be used as a marker for all structural network modules opened in the visual editor") |
|---|
| 1066 | |
|---|
| 1067 | |
|---|
| 1068 | |
|---|
