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