1# membranecomputing package 2# Matthew Bertucci 10/5/2021 for v0.2 3 4#include:ifthen 5#include:xstring 6 7### Basic notations ### 8\wa 9\ia 10\ls 11\ms 12\im{index%formula} 13\rs{index%formula} 14\ps{index%formula} 15\vE 16\neuron{index%formula} 17\compartment{index%formula} 18\agent{index%formula} 19\degree 20\syn 21\iin 22\iout 23\yes 24\no 25 26### Languages and computability theory ### 27\REG 28\LIN 29\CF 30\CS 31\RE 32\compSet{arg%formula} 33 34### Families of membrane systems ### 35\AM{arg%formula} 36\AM[sup%formula]{arg%formula} 37\AMO{arg%formula} 38\TC[optarg%formula]{arg%formula} 39\TDC{arg%formula} 40\TSC{arg%formula} 41\CC[optarg%formula]{arg%formula} 42\CDC{arg%formula} 43\CSC{arg%formula} 44\TEC[optarg%formula]{arg%formula} 45\TDEC{arg%formula} 46\TSEC{arg%formula} 47\CEC[optarg%formula]{arg%formula} 48\CDEC{arg%formula} 49\CSEC{arg%formula} 50\Pfamily{name%formula}{sup%formula}{sub%formula}{arg%formula} 51 52### Computational complexity theory ### 53\PMC{sub%formula} 54\PMC[sup%formula]{sub%formula} 55\PSPACEMC{sub%formula} 56\PSPACEMC[sup%formula]{sub%formula} 57\EXPMC{sub%formula} 58\EXPMC[sup%formula]{sub%formula} 59\EXPSPACEMC{sub%formula} 60\EXPSPACEMC[sup%formula]{sub%formula} 61\complClass{name%formula}{sup%formula}{sub%formula} 62 63### P systems ### 64\psystem{memb struc}{parameters%keyvals}{sub%formula}{degree} 65\psystem[input option]{memb struc}{parameters%keyvals}{sub%formula}{degree} 66#keyvals:\psystem 67transition 68activemembranes 69symportantiport 70spiking 71kernel 72colony 73#endkeyvals 74\psystemAM 75\rpsystemAM 76\psystemSA 77\rpsystemSA 78\SNpsystem 79\kpsystem 80\rkpsystem 81\pcolony 82\rpcolony 83 84### Rules ### 85\mcrule{parameters%keyvals}{num1}{num2}{rulespecs1%formula}{rulespec2%formula} 86\mcrule[notation]{parameters%keyvals}{num1}{num2}{rulespecs1%formula}{rulespec2%formula} 87#keyvals:\mcrule 88rewriting 89single 90multiple 91paren 92spike 93#endkeyvals 94\rewriting{arg1%formula}{arg2%formula} 95\rewritingT 96\evolution{arg1%formula}{arg2%formula}{sub%formula}{sup%formula} 97\evolutionT 98\evolutionP{arg1%formula}{arg2%formula}{sub%formula}{sup%formula} 99\evolutionPT 100\pevolution{arg1%formula}{arg2%formula}{sub%formula} 101\pevolutionT 102\pevolutionP{arg1%formula}{arg2%formula}{sub%formula} 103\pevolutionPT 104\antiport{arg1%formula}{index1%formula}{arg2%formula}{index2%formula} 105\antiportT 106\symportT 107\antiportP{arg1%formula}{index1%formula}{arg2%formula}{index2%formula} 108\antiportPT 109\symportPT 110\sendin{arg1%formula}{arg2%formula}{sub%formula}{sup1%formula}{sup2%formula} 111\sendinT 112\sendinP{arg1%formula}{arg2%formula}{sub%formula}{sup1%formula}{sup2%formula} 113\sendinPT 114\psendin{arg1%formula}{arg2%formula}{sub%formula} 115\psendinT 116\psendinP{arg1%formula}{arg2%formula}{sub%formula} 117\psendinPT 118\sendout{arg1%formula}{arg2%formula}{sub%formula}{sup1%formula}{sup2%formula} 119\sendoutT 120\sendoutP{arg1%formula}{arg2%formula}{sub%formula}{sup1%formula}{sup2%formula} 121\sendoutPT 122\psendout{arg1%formula}{arg2%formula}{sub%formula} 123\psendoutT 124\psendoutP{arg1%formula}{arg2%formula}{sub%formula} 125\psendoutPT 126\dissolution{arg1%formula}{arg2%formula}{sub%formula}{sup%formula} 127\dissolutionT 128\dissolutionP{arg1%formula}{arg2%formula}{sub%formula}{sup%formula} 129\dissolutionPT 130\pdissolution{arg1%formula}{arg2%formula}{sub%formula} 131\pdissolutionT 132\pdissolutionP{arg1%formula}{arg2%formula}{sub%formula} 133\pdissolutionPT 134\division{arg1%formula}{arg2%formula}{arg3%formula}{sub%formula}{sup1%formula}{sup2%formula}{sup3%formula} 135\divisionT 136\divisionP{arg1%formula}{arg2%formula}{arg3%formula}{sub%formula}{sup1%formula}{sup2%formula}{sup3%formula} 137\divisionPT 138\pdivision{arg1%formula}{arg2%formula}{arg3%formula}{sub%formula} 139\pdivisionT 140\pdivisionP{arg1%formula}{arg2%formula}{arg3%formula}{sub%formula} 141\pdivisionPT 142\separation{arg%formula}{sub%formula}{sup1%formula}{sup2%formula}{sup3%formula} 143\separationT 144\separationP{arg%formula}{sub%formula}{sup1%formula}{sup2%formula}{sup3%formula} 145\separationPT 146\pseparation{arg%formula}{sub%formula} 147\pseparationT 148\pseparationP{arg%formula}{sub%formula} 149\pseparationPT 150\creation{arg1%formula}{arg2%formula}{arg3%formula}{sub1%formula}{sub2%formula}{sup1%formula}{sup2%formula}{sup3%formula} 151\creationT 152\creationP{arg1%formula}{arg2%formula}{arg3%formula}{sub1%formula}{sub2%formula}{sup1%formula}{sup2%formula}{sup3%formula} 153\creationPT 154\pcreation{arg1%formula}{arg2%formula}{arg3%formula}{sub1%formula}{sub2%formula} 155\pcreationT 156\pcreationP{arg1%formula}{arg2%formula}{arg3%formula}{sub1%formula}{sub2%formula} 157\pcreationPT 158\spiking{arg1%formula}{arg2%formula}{arg3%formula}{arg4%formula} 159\spikingT 160\forgettingT 161\spikingP{arg1%formula}{arg2%formula}{arg3%formula}{arg4%formula} 162\spikingPT 163\forgettingPT 164\krewriting{arg1%formula}{arg2%formula}{arg3%formula} 165\krewritingT 166\krewritingP{arg1%formula}{arg2%formula}{arg3%formula} 167\krewritingPT 168\linkcreation{arg1%formula}{arg2%formula}{sub1%formula}{sub2%formula}{arg3%formula} 169\linkcreationT 170\linkcreationP{arg1%formula}{arg2%formula}{sub1%formula}{sub2%formula}{arg3%formula} 171\linkcreationPT 172\linkdestruction{arg1%formula}{arg2%formula}{sub1%formula}{sub2%formula}{arg3%formula} 173\linkdestructionT 174\linkdestructionP{arg1%formula}{arg2%formula}{sub1%formula}{sub2%formula}{arg3%formula} 175\linkdestructionPT 176\tissueevolcomm{arg1%formula}{arg2%formula}{arg3%formula}{arg4%formula}{sub1%formula}{sub2%formula} 177\tissueevolcommT 178\tissueevolsympT 179\tissueevolcommP{arg1%formula}{arg2%formula}{arg3%formula}{arg4%formula}{sub1%formula}{sub2%formula} 180\tissueevolcommPT 181\tissueevolsympPT 182\evolcomm{arg1%formula}{arg2%formula}{arg3%formula}{arg4%formula}{sub1%formula}{sub2%formula} 183\evolcommT 184\evolsyminT 185\evolsymoutT 186\evolcommP{arg1%formula}{arg2%formula}{arg3%formula}{arg4%formula}{sub1%formula}{sub2%formula} 187\evolcommPT 188\evolsyminPT 189\evolsymoutPT