[6974] | 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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[6969] | 14 | (define-module |
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| 15 | :class "struct-library" |
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[8688] | 16 | :super-classes ("module")) |
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[3935] | 17 | |
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[6969] | 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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[4520] | 28 | |
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[7078] | 29 | #| |
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[4520] | 30 | (define-variable |
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[4125] | 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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[3935] | 34 | |
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[5872] | 35 | |
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[6969] | 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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[7078] | 40 | |# |
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[6969] | 41 | |
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| 42 | (define-terminal |
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| 43 | :class "term-struct-compound" |
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[6590] | 44 | :super-classes ("term-struct") |
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[7565] | 45 | :properties |
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| 46 | (("abstract" :value "no")) |
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[8527] | 47 | :icon "icons/struct/term-compound") |
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[6590] | 48 | |
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[6969] | 49 | |
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| 50 | (define-terminal |
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| 51 | :class "term-struct-gate" |
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[8527] | 52 | :super-classes ("term-struct")) |
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[6590] | 53 | |
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| 54 | |
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[6969] | 55 | (define-terminal |
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[6061] | 56 | :class "term-struct-input" |
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[6590] | 57 | :super-classes ("term-struct-gate") |
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[7565] | 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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[4028] | 65 | |
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[6969] | 66 | |
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| 67 | (define-terminal |
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| 68 | :class "term-struct-output" |
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[6590] | 69 | :super-classes ("term-struct-gate") |
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[7565] | 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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[3864] | 77 | |
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| 78 | |
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[5872] | 79 | (define-module |
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| 80 | :class "struct-adapter" |
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[3864] | 81 | :super-classes ("struct-library") |
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[5872] | 82 | :icon "icons/struct/struct-adapt" |
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[6969] | 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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[3864] | 92 | |
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[6969] | 93 | |
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[5872] | 94 | (define-module |
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[6590] | 95 | :class "struct-adapter-compound" |
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| 96 | :super-classes ("struct-adapter") |
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[7565] | 97 | :properties |
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| 98 | (("abstract" :value "no")) |
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[6590] | 99 | :icon "icons/struct/struct-adapt" |
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[6969] | 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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[6590] | 105 | |
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[6969] | 106 | |
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[6590] | 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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[7565] | 111 | :properties |
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| 112 | (("abstract" :value "no")) |
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[6969] | 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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[6590] | 118 | |
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[6969] | 119 | |
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[6590] | 120 | (define-module |
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[6061] | 121 | :class "gate" |
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[5872] | 122 | :super-classes ("struct-library") |
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[6969] | 123 | :variables |
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| 124 | (("conf" |
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[7565] | 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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[6969] | 127 | :value "1") |
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| 128 | ("defval" |
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[6985] | 129 | :system-theoretic "integer-parameter" |
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[7565] | 130 | :documentation "Default value of the logical state of the reaction. empty = undefined") |
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[6969] | 131 | ("time" |
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[7565] | 132 | :system-theoretic "real-parameter" |
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[6969] | 133 | :documentation "parameter determining the time-scale, 1 being the fastest" |
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[6985] | 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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[7618] | 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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[8054] | 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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[8052] | 151 | :system-theoretic "integer-parameter" |
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[8055] | 152 | :documentation "parameter determining the map in CellNetAnalyzer. Should be a positive int, default is 1." |
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[8054] | 153 | :value "1") |
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| 154 | ("textbox_type" |
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| 155 | :system-theoretic "integer-parameter" |
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[8055] | 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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[8054] | 157 | :value "1") |
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[6985] | 158 | )) |
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[5676] | 159 | |
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[6969] | 160 | |
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| 161 | (define-module |
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[6061] | 162 | :class "gate-2" |
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| 163 | :super-classes ("gate") |
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[6969] | 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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[3935] | 179 | (define-module |
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[6061] | 180 | :class "gate-2-2" |
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| 181 | :super-classes ("gate-2") |
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[5872] | 182 | :terminals |
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| 183 | (("input1" |
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[6061] | 184 | :is-eq-to "gate_2.input1" |
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[5872] | 185 | :geometry-side "TOP" |
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| 186 | :geometry-position "0.1") |
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| 187 | ("input2" |
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| 188 | :is-eq-to "struct_adapter.input" |
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| 189 | :geometry-side "TOP" |
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| 190 | :geometry-position "0.5") |
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| 191 | ("input3" |
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[6061] | 192 | :is-eq-to "gate_2b.input2" |
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[5872] | 193 | :geometry-side "TOP" |
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| 194 | :geometry-position "0.9") |
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| 195 | ("output" |
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| 196 | :is-eq-to "struct_adapterb.output" |
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| 197 | :geometry-side "BOTTOM" |
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| 198 | :geometry-position "0.5")) |
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| 199 | :modules |
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[6061] | 200 | (("gate_2" |
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| 201 | :is-a "gate-2" |
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[5872] | 202 | :geometry-x "48" |
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| 203 | :geometry-y "147") |
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[6061] | 204 | ("gate_2b" |
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| 205 | :is-a "gate-2" |
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[5872] | 206 | :geometry-x "228" |
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| 207 | :geometry-y "147") |
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| 208 | ("struct_adapter" |
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[6616] | 209 | :is-a "struct-adapter-gate" |
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[5872] | 210 | :geometry-x "137" |
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| 211 | :geometry-y "82") |
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| 212 | ("struct_adapterb" |
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[6616] | 213 | :is-a "struct-adapter-gate" |
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[5872] | 214 | :geometry-x "138" |
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| 215 | :geometry-y "209")) |
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| 216 | :links |
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[6061] | 217 | (("struct_adapterbinput_gate_2output" |
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| 218 | :terminals ("struct_adapterb.input" "gate_2.output" "gate_2b.output") |
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[5872] | 219 | :nodes (("138" "158")) |
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| 220 | :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil))) |
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[6061] | 221 | ("struct_adapteroutput_gate_2input2" |
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| 222 | :terminals ("struct_adapter.output" "gate_2.input2" "gate_2b.input1") |
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[5872] | 223 | :nodes (("138" "136")) |
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| 224 | :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))) |
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| 225 | :variables |
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| 226 | (("visibility" |
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[8013] | 227 | :value "1")) |
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| 228 | :parameters( |
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| 229 | ("gate_2.ignore_in_export" |
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| 230 | :value "parent.ignore_in_export") |
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| 231 | ("gate_2b.ignore_in_export" |
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| 232 | :value "parent.ignore_in_export") |
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| 233 | ("struct_adapter.ignore_in_export" |
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| 234 | :value "parent.ignore_in_export") |
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| 235 | ("struct_adapterb.ignore_in_export" |
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| 236 | :value "parent.ignore_in_export"))) |
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[5872] | 237 | |
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[6969] | 238 | |
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[5872] | 239 | (define-module |
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[6061] | 240 | :class "gate-3" |
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[7565] | 241 | :super-classes ("gate") |
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[6969] | 242 | :terminals |
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| 243 | (("input1" |
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[7565] | 244 | :is-a "term-struct-input" |
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| 245 | :geometry-side "top" |
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[6969] | 246 | :geometry-position "0.1") |
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| 247 | ("input2" |
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[7565] | 248 | :is-a "term-struct-input" |
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| 249 | :geometry-side "top" |
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[6969] | 250 | :geometry-position "0.5") |
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| 251 | ("input3" |
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| 252 | :is-a "term-struct-input" |
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| 253 | :geometry-side "top" |
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[7565] | 254 | :geometry-position "0.9") |
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| 255 | ("output" |
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| 256 | :is-a "term-struct-output" |
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| 257 | :geometry-side "bottom" |
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| 258 | :geometry-position "0.5"))) |
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[6969] | 259 | |
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| 260 | |
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[5676] | 261 | (define-module |
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[6061] | 262 | :class "gate-4" |
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[7565] | 263 | :super-classes ("gate") |
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[6969] | 264 | :terminals |
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| 265 | (("input1" |
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[7565] | 266 | :is-a "term-struct-input" |
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[6969] | 267 | :geometry-side "left" |
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| 268 | :geometry-position "0.5") |
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| 269 | ("input2" |
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[7565] | 270 | :is-a "term-struct-input" |
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[6969] | 271 | :geometry-side "top" |
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| 272 | :geometry-position "0.25") |
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| 273 | ("input3" |
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[7565] | 274 | :is-a "term-struct-input" |
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[6969] | 275 | :geometry-side "top" |
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| 276 | :geometry-position "0.77") |
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| 277 | ("input4" |
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| 278 | :is-a "term-struct-input" |
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| 279 | :geometry-side "right" |
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[7565] | 280 | :geometry-position "0.5") |
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| 281 | ("output" |
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| 282 | :is-a "term-struct-output" |
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| 283 | :geometry-side "bottom" |
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[6969] | 284 | :geometry-position "0.5"))) |
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[5676] | 285 | |
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[6969] | 286 | |
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[5676] | 287 | (define-module |
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[6061] | 288 | :class "gate-5" |
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[7565] | 289 | :super-classes ("gate") |
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[6969] | 290 | :terminals |
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[7565] | 291 | (("input1" |
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| 292 | :is-a "term-struct-input" |
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[6969] | 293 | :geometry-side "left" |
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| 294 | :geometry-position "0.9") |
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| 295 | ("input2" |
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[7565] | 296 | :is-a "term-struct-input" |
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[6969] | 297 | :geometry-side "left" |
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| 298 | :geometry-position "0.1") |
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| 299 | ("input3" |
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[7565] | 300 | :is-a "term-struct-input" |
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[6969] | 301 | :geometry-side "top" |
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| 302 | :geometry-position "0.5") |
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| 303 | ("input4" |
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[7565] | 304 | :is-a "term-struct-input" |
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[6969] | 305 | :geometry-side "right" |
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| 306 | :geometry-position "0.1") |
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| 307 | ("input5" |
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| 308 | :is-a "term-struct-input" |
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| 309 | :geometry-side "right" |
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[7565] | 310 | :geometry-position "0.9") |
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| 311 | ("output" |
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| 312 | :is-a "term-struct-output" |
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| 313 | :geometry-side "bottom" |
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| 314 | :geometry-position "0.5"))) |
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[5676] | 315 | |
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| 316 | (define-module |
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[6061] | 317 | :class "gate-6" |
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[7565] | 318 | :super-classes ("gate") |
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[5872] | 319 | :terminals |
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| 320 | (("input1" |
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[7565] | 321 | :is-a "term-struct-input" |
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[6969] | 322 | :geometry-side "left" |
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[5872] | 323 | :geometry-position "0.9") |
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| 324 | ("input2" |
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[7565] | 325 | :is-a "term-struct-input" |
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[5872] | 326 | :geometry-side "left" |
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| 327 | :geometry-position "0.1") |
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| 328 | ("input3" |
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[7565] | 329 | :is-a "term-struct-input" |
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[5872] | 330 | :geometry-side "top" |
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| 331 | :geometry-position "0.5") |
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| 332 | ("input4" |
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[7565] | 333 | :is-a "term-struct-input" |
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[5872] | 334 | :geometry-side "right" |
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| 335 | :geometry-position "0.1") |
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| 336 | ("input5" |
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[7565] | 337 | :is-a "term-struct-input" |
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[5872] | 338 | :geometry-side "right" |
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| 339 | :geometry-position "0.5") |
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| 340 | ("input6" |
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| 341 | :is-a "term-struct-input" |
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| 342 | :geometry-side "right" |
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[7565] | 343 | :geometry-position "0.9") |
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| 344 | ("output" |
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| 345 | :is-a "term-struct-output" |
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| 346 | :geometry-side "bottom" |
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| 347 | :geometry-position "0.5"))) |
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[6969] | 348 | |
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[6061] | 349 | (define-module |
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| 350 | :class "activ" |
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| 351 | :super-classes ("gate") |
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[8727] | 352 | :properties |
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| 353 | (("abstract" |
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| 354 | :value "no")) |
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[6061] | 355 | :icon "icons/struct/activ" |
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| 356 | :terminals |
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| 357 | (("input1" |
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| 358 | :is-a "term-struct-input" |
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| 359 | :geometry-side "top" |
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| 360 | :geometry-position "0.5") |
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[7565] | 361 | ("output" |
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[6061] | 362 | :is-a "term-struct-output" |
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[7574] | 363 | :geometry-side "bottom" |
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[6061] | 364 | :geometry-position "0.5"))) |
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[5872] | 365 | |
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| 366 | (define-module |
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[6061] | 367 | :class "and" |
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| 368 | :super-classes ("gate") |
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[6969] | 369 | :icon "icons/struct/and") |
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[6061] | 370 | |
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[6969] | 371 | (define-module |
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[6061] | 372 | :class "and-2" |
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[8727] | 373 | :super-classes ("and" "gate-2") |
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[7565] | 374 | :properties |
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[8727] | 375 | (("abstract" |
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| 376 | :value "no"))) |
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[6969] | 377 | |
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[6061] | 378 | (define-module |
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| 379 | :class "and-2-2" |
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| 380 | :super-classes ("and" "gate-2-2") |
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[7565] | 381 | :properties |
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| 382 | (("abstract" :value "no")) |
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[6061] | 383 | :modules |
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[6969] | 384 | (("gate_2" |
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| 385 | :is-a "and-2") |
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| 386 | ("gate_2b" |
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[8013] | 387 | :is-a "and-2")) |
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| 388 | :parameters( |
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| 389 | ("gate_2.ignore_in_export" |
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| 390 | :value "parent.ignore_in_export") |
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| 391 | ("gate_2b.ignore_in_export" |
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[8727] | 392 | :value "parent.ignore_in_export"))) |
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[6061] | 393 | |
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| 394 | (define-module |
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| 395 | :class "and-3" |
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[7565] | 396 | :super-classes ("and" "gate-3") |
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| 397 | :properties |
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| 398 | (("abstract" :value "no"))) |
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[6969] | 399 | |
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| 400 | |
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[6061] | 401 | (define-module |
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| 402 | :class "and-4" |
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[7565] | 403 | :super-classes ("and" "gate-4") |
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| 404 | :properties (("abstract" :value "no"))) |
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[6061] | 405 | |
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[6969] | 406 | |
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[6061] | 407 | (define-module |
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| 408 | :class "and-5" |
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[7565] | 409 | :super-classes ("and" "gate-5") |
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| 410 | :properties |
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| 411 | (("abstract" :value "no"))) |
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[6061] | 412 | |
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[6969] | 413 | |
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[6061] | 414 | (define-module |
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| 415 | :class "and-6" |
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[7565] | 416 | :super-classes ("and" "gate-6") |
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| 417 | :properties |
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| 418 | (("abstract" :value "no"))) |
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[6061] | 419 | |
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| 420 | (define-module |
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[3864] | 421 | :class "compound" |
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| 422 | :super-classes ("struct-library") |
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[6590] | 423 | :icon "icons/struct/comp" |
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[6969] | 424 | :parameters |
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| 425 | (("input.a" |
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| 426 | :system-theoretic "real-parameter")) |
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| 427 | :terminals |
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| 428 | (("input" |
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| 429 | :is-a "term-struct-compound" |
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| 430 | :geometry-side "top" |
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| 431 | :geometry-position "0.5")) |
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| 432 | :variables |
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| 433 | (("defval" |
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[7078] | 434 | :system-theoretic "integer-parameter" |
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[6061] | 435 | :documentation "Default value of the logical state of the reaction. empty = |
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[7618] | 436 | undefined") |
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| 437 | ("ignore_in_export" |
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| 438 | :system-theoretic "integer-parameter" |
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| 439 | :documentation "parameter determining whether the compound is exported to the |
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| 440 | CellNetAnalyzer. Allowed Values 0 (exported) or 1 (ignored in export), default |
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| 441 | 0." |
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| 442 | :value "0") |
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[8055] | 443 | ("map_number" |
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| 444 | :system-theoretic "integer-parameter" |
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| 445 | :documentation "parameter determining the map in CellNetAnalyzer. Should be a positive int, default is 1." |
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| 446 | :value "1") |
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| 447 | ("textbox_type" |
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| 448 | :system-theoretic "integer-parameter" |
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| 449 | :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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| 450 | :value "1") |
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[7618] | 451 | )) |
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[6061] | 452 | |
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[3864] | 453 | (define-module |
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[6969] | 454 | :class "receptor" |
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[5872] | 455 | :super-classes ("compound") |
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[7565] | 456 | :properties |
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| 457 | (("abstract" :value "no")) |
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[6969] | 458 | :icon "icons/struct/receptor") |
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[5872] | 459 | |
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| 460 | (define-module |
---|
[6969] | 461 | :class "ligand" |
---|
[6061] | 462 | :super-classes ("compound") |
---|
[7565] | 463 | :properties |
---|
| 464 | (("abstract" :value "no")) |
---|
[6969] | 465 | :icon "icons/struct/ligand") |
---|
[6061] | 466 | |
---|
| 467 | (define-module |
---|
[6969] | 468 | :class "kinase" |
---|
[5872] | 469 | :super-classes ("compound") |
---|
[7565] | 470 | :properties |
---|
| 471 | (("abstract" :value "no")) |
---|
[6969] | 472 | :icon "icons/struct/kinase") |
---|
[5872] | 473 | |
---|
| 474 | (define-module |
---|
[6969] | 475 | :class "dummy" |
---|
[5872] | 476 | :super-classes ("compound") |
---|
[7565] | 477 | :properties |
---|
| 478 | (("abstract" :value "no")) |
---|
[6969] | 479 | :icon "icons/struct/dummy") |
---|
[5872] | 480 | |
---|
| 481 | (define-module |
---|
[6969] | 482 | :class "phosphatase" |
---|
[5872] | 483 | :super-classes ("compound") |
---|
[7565] | 484 | :properties |
---|
| 485 | (("abstract" :value "no")) |
---|
[6969] | 486 | :icon "icons/struct/phosphatase") |
---|
[5872] | 487 | |
---|
| 488 | (define-module |
---|
[8010] | 489 | :class "ubiquitin-ligase" |
---|
| 490 | :super-classes ("compound") |
---|
| 491 | :properties |
---|
| 492 | (("abstract" :value "no")) |
---|
| 493 | :icon "icons/struct/ubiquitinLigase") |
---|
| 494 | |
---|
| 495 | (define-module |
---|
[6969] | 496 | :class "adapter" |
---|
[5872] | 497 | :super-classes ("compound") |
---|
[7565] | 498 | :properties |
---|
| 499 | (("abstract" :value "no")) |
---|
[6969] | 500 | :icon "icons/struct/adapter") |
---|
[5872] | 501 | |
---|
| 502 | (define-module |
---|
[6969] | 503 | :class "transfactor" |
---|
[5872] | 504 | :super-classes ("compound") |
---|
[7565] | 505 | :properties |
---|
| 506 | (("abstract" :value "no")) |
---|
[6969] | 507 | :icon "icons/struct/transfactor") |
---|
[5872] | 508 | |
---|
| 509 | (define-module |
---|
[6969] | 510 | :class "gtpase" |
---|
[5872] | 511 | :super-classes ("compound") |
---|
[7565] | 512 | :properties |
---|
| 513 | (("abstract" :value "no")) |
---|
[6969] | 514 | :icon "icons/struct/gpro") |
---|
[5872] | 515 | |
---|
| 516 | (define-module |
---|
[7488] | 517 | :class "gprotein" |
---|
| 518 | :super-classes ("compound") |
---|
[7565] | 519 | :properties |
---|
| 520 | (("abstract" :value "no")) |
---|
[6969] | 521 | :icon "icons/struct/gpro") |
---|
[6061] | 522 | |
---|
[7498] | 523 | (define-module |
---|
| 524 | :class "gef" |
---|
| 525 | :super-classes ("compound") |
---|
[7565] | 526 | :properties |
---|
| 527 | (("abstract" :value "no")) |
---|
[7498] | 528 | :documentation "guanine nucleotide exchange factor" |
---|
| 529 | :icon "icons/struct/gef") |
---|
[6969] | 530 | |
---|
[6061] | 531 | (define-module |
---|
[7498] | 532 | :class "gap" |
---|
| 533 | :super-classes ("compound") |
---|
[7565] | 534 | :properties |
---|
| 535 | (("abstract" :value "no")) |
---|
[7498] | 536 | :documentation "gtpase activating protein" |
---|
| 537 | :icon "icons/struct/gap") |
---|
| 538 | |
---|
| 539 | (define-module |
---|
[6969] | 540 | :class "reservoir" |
---|
[7565] | 541 | :super-classes ("compound") |
---|
| 542 | :properties |
---|
[7566] | 543 | (("abstract" :value "no")) |
---|
| 544 | :icon "icons/struct/reservoir") |
---|
[5872] | 545 | |
---|
[7488] | 546 | (define-module |
---|
| 547 | :class "other" |
---|
[7565] | 548 | :super-classes ("compound") |
---|
| 549 | :properties |
---|
| 550 | (("abstract" :value "no"))) |
---|
[5872] | 551 | |
---|
| 552 | (define-module |
---|
[7565] | 553 | :class "drug" |
---|
| 554 | :super-classes ("compound") |
---|
| 555 | :properties |
---|
| 556 | (("abstract" :value "no")) |
---|
| 557 | :icon "icons/struct/drug") |
---|
| 558 | |
---|
| 559 | (define-module |
---|
[8015] | 560 | :class "external-stimulus" |
---|
| 561 | :super-classes ("compound") |
---|
| 562 | :properties |
---|
| 563 | (("abstract" :value "no")) |
---|
| 564 | :icon "icons/struct/externalStimulus") |
---|
| 565 | |
---|
| 566 | (define-module |
---|
| 567 | :class "phenotype" |
---|
| 568 | :super-classes ("compound") |
---|
| 569 | :properties |
---|
| 570 | (("abstract" :value "no")) |
---|
| 571 | :icon "icons/struct/phenotype") |
---|
| 572 | |
---|
| 573 | |
---|
| 574 | (define-module |
---|
[6969] | 575 | :class "boundary" |
---|
[6590] | 576 | :super-classes ("gate")) |
---|
[6482] | 577 | |
---|
[6969] | 578 | |
---|
[6590] | 579 | (define-module |
---|
| 580 | :class "source" |
---|
| 581 | :super-classes ("boundary") |
---|
[7565] | 582 | :properties |
---|
| 583 | (("abstract" :value "no")) |
---|
[6969] | 584 | :icon "icons/struct/input" |
---|
| 585 | :terminals |
---|
| 586 | (("output" |
---|
| 587 | :is-a "term-struct-output" |
---|
| 588 | :geometry-side "bottom" |
---|
[8713] | 589 | :geometry-position "0.5"))) |
---|
[6482] | 590 | |
---|
[6969] | 591 | |
---|
[6590] | 592 | (define-module |
---|
| 593 | :class "drain" |
---|
| 594 | :super-classes ("boundary") |
---|
[7565] | 595 | :properties |
---|
| 596 | (("abstract" :value "no")) |
---|
[6590] | 597 | :icon "icons/struct/output" |
---|
[6969] | 598 | :terminals |
---|
| 599 | (("input" |
---|
| 600 | :is-a "term-struct-input" |
---|
| 601 | :geometry-side "top" |
---|
[8713] | 602 | :geometry-position "0.5"))) |
---|
[6482] | 603 | |
---|
[3864] | 604 | (define-module |
---|
| 605 | :class "not" |
---|
[5872] | 606 | :super-classes ("struct-library") |
---|
[8727] | 607 | :properties |
---|
| 608 | (("abstract" |
---|
| 609 | :value "no")) |
---|
[5872] | 610 | :icon "icons/struct/not" |
---|
[6969] | 611 | :terminals |
---|
| 612 | (("input" |
---|
| 613 | :is-a "term-struct-input" |
---|
| 614 | :geometry-side "top" |
---|
| 615 | :geometry-position "0.5") |
---|
| 616 | ("output" |
---|
| 617 | :is-a "term-struct-output" |
---|
| 618 | :geometry-side "bottom" |
---|
| 619 | :geometry-position "0.5"))) |
---|
[3864] | 620 | |
---|
[3935] | 621 | (define-module |
---|
[5872] | 622 | :class "or" |
---|
[6061] | 623 | :super-classes ("gate") |
---|
[6969] | 624 | :icon "icons/struct/or") |
---|
[4102] | 625 | |
---|
[5872] | 626 | (define-module |
---|
| 627 | :class "or-2" |
---|
[7565] | 628 | :super-classes ("or" "gate-2") |
---|
| 629 | :properties |
---|
| 630 | (("abstract" :value "no")) |
---|
[5872] | 631 | :terminals |
---|
| 632 | (("input1" |
---|
[7565] | 633 | :is-eq-to "activ.input1") |
---|
[5872] | 634 | ("input2" |
---|
[7565] | 635 | :is-eq-to "activ2.input1") |
---|
[5872] | 636 | ("output" |
---|
[7565] | 637 | :is-eq-to "struct_adapter.output")) |
---|
[5872] | 638 | :modules |
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| 639 | (("activ" |
---|
| 640 | :is-a "activ" |
---|
| 641 | :geometry-x "71" |
---|
| 642 | :geometry-y "81") |
---|
| 643 | ("activ2" |
---|
| 644 | :is-a "activ" |
---|
| 645 | :geometry-x "202" |
---|
| 646 | :geometry-y "84") |
---|
| 647 | ("struct_adapter" |
---|
[6616] | 648 | :is-a "struct-adapter-gate" |
---|
[5872] | 649 | :geometry-x "124" |
---|
| 650 | :geometry-y "176")) |
---|
| 651 | :links |
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| 652 | (("struct_adapterinput_activ2output" |
---|
| 653 | :terminals ("struct_adapter.input" "activ2.output" "activ.output") |
---|
| 654 | :nodes (("136" "112")) |
---|
[8013] | 655 | :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil)))) |
---|
| 656 | :parameters( |
---|
| 657 | ("activ.ignore_in_export" |
---|
| 658 | :value "parent.ignore_in_export") |
---|
| 659 | ("activ2.ignore_in_export" |
---|
| 660 | :value "parent.ignore_in_export") |
---|
| 661 | ("struct_adapter.ignore_in_export" |
---|
| 662 | :value "parent.ignore_in_export"))) |
---|
[4102] | 663 | |
---|
[5872] | 664 | (define-module |
---|
| 665 | :class "or-3" |
---|
[7565] | 666 | :super-classes ("or" "gate-3") |
---|
| 667 | :properties |
---|
| 668 | (("abstract" :value "no")) |
---|
[5872] | 669 | :geometry-width "438" |
---|
| 670 | :geometry-height "300" |
---|
| 671 | :terminals |
---|
| 672 | (("input1" |
---|
[7565] | 673 | :is-eq-to "activ.input1") |
---|
[5872] | 674 | ("input2" |
---|
[7565] | 675 | :is-eq-to "activ2.input1") |
---|
[5872] | 676 | ("input3" |
---|
[7565] | 677 | :is-eq-to "activ0.input1") |
---|
[5872] | 678 | ("output" |
---|
[7565] | 679 | :is-eq-to "struct_adapter.output")) |
---|
[5872] | 680 | :modules |
---|
| 681 | (("activ" |
---|
| 682 | :is-a "activ" |
---|
| 683 | :geometry-x "71" |
---|
| 684 | :geometry-y "81") |
---|
| 685 | ("activ0" |
---|
| 686 | :is-a "activ" |
---|
| 687 | :geometry-x "290" |
---|
| 688 | :geometry-y "85") |
---|
| 689 | ("activ2" |
---|
| 690 | :is-a "activ" |
---|
| 691 | :geometry-x "202" |
---|
| 692 | :geometry-y "84") |
---|
| 693 | ("struct_adapter" |
---|
[6616] | 694 | :is-a "struct-adapter-gate" |
---|
[5872] | 695 | :geometry-x "124" |
---|
| 696 | :geometry-y "176")) |
---|
| 697 | :links |
---|
| 698 | (("struct_adapterinput_activ2output" |
---|
| 699 | :terminals ("struct_adapter.input" "activ2.output" "activ.output" |
---|
| 700 | "activ0.output") |
---|
| 701 | :nodes (("136" "112")) |
---|
[8013] | 702 | :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil)))) |
---|
| 703 | :parameters( |
---|
| 704 | ("activ.ignore_in_export" |
---|
| 705 | :value "parent.ignore_in_export") |
---|
| 706 | ("activ0.ignore_in_export" |
---|
| 707 | :value "parent.ignore_in_export") |
---|
| 708 | ("activ2.ignore_in_export" |
---|
| 709 | :value "parent.ignore_in_export") |
---|
| 710 | ("struct_adapter.ignore_in_export" |
---|
| 711 | :value "parent.ignore_in_export"))) |
---|
[5872] | 712 | |
---|
| 713 | |
---|
| 714 | (define-module |
---|
| 715 | :class "or-4" |
---|
[7565] | 716 | :super-classes ("or" "gate-4") |
---|
| 717 | :properties |
---|
| 718 | (("abstract" :value "no")) |
---|
[5872] | 719 | :geometry-width "407" |
---|
| 720 | :geometry-height "300" |
---|
| 721 | :terminals |
---|
| 722 | (("input1" |
---|
[7565] | 723 | :is-eq-to "activ.input1") |
---|
[5872] | 724 | ("input2" |
---|
[7565] | 725 | :is-eq-to "activ2.input1") |
---|
[5872] | 726 | ("input3" |
---|
[7565] | 727 | :is-eq-to "activ0.input1") |
---|
[5872] | 728 | ("input4" |
---|
[7565] | 729 | :is-eq-to "activ1.input1") |
---|
[5872] | 730 | ("output" |
---|
[7565] | 731 | :is-eq-to "struct_adapter.output")) |
---|
[5872] | 732 | :modules |
---|
| 733 | (("activ" |
---|
| 734 | :is-a "activ" |
---|
| 735 | :geometry-x "55" |
---|
| 736 | :geometry-y "129") |
---|
| 737 | ("activ0" |
---|
| 738 | :is-a "activ" |
---|
| 739 | :geometry-x "250" |
---|
| 740 | :geometry-y "77") |
---|
| 741 | ("activ1" |
---|
| 742 | :is-a "activ" |
---|
| 743 | :geometry-x "330" |
---|
| 744 | :geometry-y "127") |
---|
| 745 | ("activ2" |
---|
| 746 | :is-a "activ" |
---|
| 747 | :geometry-x "122" |
---|
| 748 | :geometry-y "76") |
---|
| 749 | ("struct_adapter" |
---|
[6616] | 750 | :is-a "struct-adapter-gate" |
---|
[5872] | 751 | :geometry-x "172" |
---|
| 752 | :geometry-y "176")) |
---|
| 753 | :links |
---|
| 754 | (("struct_adapterinput_activ2output" |
---|
| 755 | :terminals ("struct_adapter.input" "activ2.output" "activ.output" |
---|
| 756 | "activ0.output" "activ1.output") |
---|
| 757 | :nodes (("174" "104")) |
---|
| 758 | :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil) |
---|
[8013] | 759 | ("4" "-1" nil)))) |
---|
| 760 | :parameters( |
---|
| 761 | ("activ.ignore_in_export" |
---|
| 762 | :value "parent.ignore_in_export") |
---|
| 763 | ("activ0.ignore_in_export" |
---|
| 764 | :value "parent.ignore_in_export") |
---|
| 765 | ("activ1.ignore_in_export" |
---|
| 766 | :value "parent.ignore_in_export") |
---|
| 767 | ("activ2.ignore_in_export" |
---|
| 768 | :value "parent.ignore_in_export") |
---|
| 769 | ("struct_adapter.ignore_in_export" |
---|
| 770 | :value "parent.ignore_in_export"))) |
---|
[5872] | 771 | |
---|
[6969] | 772 | |
---|
[5872] | 773 | (define-module |
---|
[6482] | 774 | :class "or-5" |
---|
[7565] | 775 | :super-classes ("or" "gate-5") |
---|
| 776 | :properties |
---|
| 777 | (("abstract" :value "no")) |
---|
[6482] | 778 | :geometry-width "407" |
---|
| 779 | :geometry-height "300" |
---|
| 780 | :terminals |
---|
| 781 | (("input1" |
---|
[7565] | 782 | :is-eq-to "activ.input1") |
---|
[6482] | 783 | ("input2" |
---|
[7565] | 784 | :is-eq-to "activ2.input1") |
---|
[6482] | 785 | ("input3" |
---|
[7565] | 786 | :is-eq-to "activ0.input1") |
---|
[6482] | 787 | ("input4" |
---|
[7565] | 788 | :is-eq-to "activ1.input1") |
---|
[6482] | 789 | ("input5" |
---|
[7565] | 790 | :is-eq-to "activ3.input1") |
---|
[6482] | 791 | ("output" |
---|
[7565] | 792 | :is-eq-to "struct_adapter.output")) |
---|
[6482] | 793 | :modules |
---|
| 794 | (("activ" |
---|
| 795 | :is-a "activ" |
---|
| 796 | :geometry-x "55" |
---|
| 797 | :geometry-y "129") |
---|
| 798 | ("activ0" |
---|
| 799 | :is-a "activ" |
---|
| 800 | :geometry-x "250" |
---|
| 801 | :geometry-y "77") |
---|
| 802 | ("activ1" |
---|
| 803 | :is-a "activ" |
---|
| 804 | :geometry-x "330" |
---|
| 805 | :geometry-y "127") |
---|
| 806 | ("activ2" |
---|
| 807 | :is-a "activ" |
---|
| 808 | :geometry-x "122" |
---|
| 809 | :geometry-y "76") |
---|
| 810 | ("activ3" |
---|
| 811 | :is-a "activ" |
---|
| 812 | :geometry-x "165" |
---|
| 813 | :geometry-y "62") |
---|
| 814 | ("struct_adapter" |
---|
[6616] | 815 | :is-a "struct-adapter-gate" |
---|
[6482] | 816 | :geometry-x "172" |
---|
| 817 | :geometry-y "176")) |
---|
| 818 | :links |
---|
| 819 | (("struct_adapterinput_activ2output" |
---|
| 820 | :terminals ("struct_adapter.input" "activ2.output" "activ.output" |
---|
| 821 | "activ0.output" "activ1.output" "activ3.output") |
---|
| 822 | :nodes (("174" "104")) |
---|
| 823 | :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil) |
---|
[8013] | 824 | ("4" "-1" nil) ("5" "-1" nil)))) |
---|
| 825 | :parameters( |
---|
| 826 | ("activ.ignore_in_export" |
---|
| 827 | :value "parent.ignore_in_export") |
---|
| 828 | ("activ0.ignore_in_export" |
---|
| 829 | :value "parent.ignore_in_export") |
---|
| 830 | ("activ1.ignore_in_export" |
---|
| 831 | :value "parent.ignore_in_export") |
---|
| 832 | ("activ2.ignore_in_export" |
---|
| 833 | :value "parent.ignore_in_export") |
---|
| 834 | ("activ3.ignore_in_export" |
---|
| 835 | :value "parent.ignore_in_export") |
---|
| 836 | ("struct_adapter.ignore_in_export" |
---|
| 837 | :value "parent.ignore_in_export"))) |
---|
[6482] | 838 | |
---|
| 839 | |
---|
| 840 | (define-module |
---|
[5872] | 841 | :class "somehow" |
---|
[6061] | 842 | :super-classes ("gate") |
---|
[8449] | 843 | :documentation " classes to represent incomplete truth tables") |
---|
[6061] | 844 | |
---|
| 845 | |
---|
[5872] | 846 | (define-module |
---|
[6061] | 847 | :class "somehow-2" |
---|
[6969] | 848 | :super-classes ("gate-2" "somehow") |
---|
[7565] | 849 | :properties |
---|
| 850 | (("abstract" :value "no")) |
---|
[6969] | 851 | :icon "icons/struct/somehow") |
---|
[5872] | 852 | |
---|
| 853 | (define-module |
---|
[6061] | 854 | :class "somehow-3" |
---|
[6969] | 855 | :super-classes ("gate-3" "somehow") |
---|
[7565] | 856 | :properties |
---|
| 857 | (("abstract" :value "no")) |
---|
[6969] | 858 | :icon "icons/struct/somehow") |
---|
[5872] | 859 | |
---|
| 860 | (define-module |
---|
[6969] | 861 | :class "somehow-4" |
---|
| 862 | :super-classes ("gate-4" "somehow") |
---|
[7565] | 863 | :properties |
---|
| 864 | (("abstract" :value "no")) |
---|
[6969] | 865 | :icon "icons/struct/somehow") |
---|
[5872] | 866 | |
---|
| 867 | (define-module |
---|
[6969] | 868 | :class "somehow-5" |
---|
| 869 | :super-classes ("gate-5" "somehow") |
---|
[7565] | 870 | :properties |
---|
| 871 | (("abstract" :value "no")) |
---|
[6969] | 872 | :icon "icons/struct/somehow") |
---|
[5872] | 873 | |
---|
[6969] | 874 | (define-module |
---|
[7078] | 875 | :class "struct-model" |
---|
| 876 | :super-classes ("module") |
---|
[8688] | 877 | :documentation "superclass that must be used as a marker for all structural network modules opened in the visual editor") |
---|
[6969] | 878 | |
---|
| 879 | |
---|
[8278] | 880 | |
---|