SAT - Tissue cell separation
============================

Description
-----------

Well-known problem SAT, solved with tissue P systems with cell separation.

Model in P-Lingua
-----------------

The corresponding P-Lingua file is the following::

        @model<TSCS>
        
        def main()
        {
                let m= 3; 
                let n= 4; 
                
                call init_membrane_structure();
                call init_first_alphabet(m,n);
                call init_second_alphabet(m,n);
                call init_environment(m,n);
                call init_multisets();
                call init_rules(m,n);
                call define_input();
        }
        
        
        def define_input()
        {
        /* DEFINIR AQUI LA DE ENTRADA DEL SISTEMA P */
        /* ESCRIBIR DIFERENTES FUNCIONES PARA DIFERENTES ENTRADAS */
        @ms(3) +=nx{1,1},x{2,1},x{3,1},x{1,2},nx{2,2},nx{3,2},x{1,3},nx{2,3},x{3,3}, x{1,4},x{2,4},x{3,4};
        
        }
        
        
        def init_membrane_structure()
        {
                @mu = [ [ ]'1 [ ]'2 [ ]'3 ]'0;
        }
        
        
        def init_first_alphabet(m,n)
        {
                @ms1 += A{i},B{i} : 1<=i<=n+1;
                @ms1 += a{i},b{i},T{i},F{i},y{i},v{i},w{i} : 1<=i<=n;
                @ms1 += c{i},t{i},f{i},s{i},z{i} : 1<= i <= n-1;
                @ms1 += E{j} : 1<= j <= m+1;
                @ms1 += alpha{i} : 0<= i <= 3*n+2*m+1;
                @ms1 += beta{i} : 0<= i <= 3*n + 2*m +2;
                @ms1 += q{i,j},r{i,j},u{i,j} : 1<=i<=n-1,1<=j<=n-1;
                @ms1 += x{i,j},nx{i,j},e{i,j},ne{i,j} : 1<=i<=n,1<=j<=m;
                @ms1 += d{i,j,k},nd{i,j,k} : 1 <=i<=n,1<=j<=m,1<=k<=n;
                @ms1 += q{0},S,yes,no;
        
        }
        
        def init_second_alphabet(m,n)
        {
                @ms2 += Ap{i},Bp{i} : 1<=i<=n+1;
                @ms2 += ap{i},bp{i},Tp{i},Fp{i} : 1<=i<=n;
        }
        
        def init_environment(m,n)
        {
                @ms(0) += S;
                @ms(0) += A{i},B{i},Ap{i},Bp{i} : 2<=i<=n+1;
                @ms(0) += T{i},F{i},Fp{i},y{i},w{i} : 1<=i<=n;
                @ms(0) += a{i},ap{i},b{i},bp{i},v{i} : 2<=i<=n;
                @ms(0) += Tp{i},c{i},t{i},f{i},s{i},z{i} : 1<=i<=n-1;
                @ms(0) += E{j} : 1<=j<=m+1;
                @ms(0) += alpha{i} : 1<= i <= 3*n+2*m+1;
                @ms(0) += beta{i} : 1<=i<=3*n+2*m+2;
                @ms(0) += q{i,j},r{i,j},u{i,j} : 1<=i<=n-1,2<=j<=n-1;
                @ms(0) += r{1,1}; 
                @ms(0) += u{1,1}; 
                @ms(0) += e{i,j},ne{i,j} : 1<=i<=n,1<=j<=m;
                @ms(0) += d{i,j,k},nd{i,j,k} : 1<=i<=n,1<=k<=n,1<=j<=m;
        }
        
        def init_multisets()
        {
                @ms(1) = A{1},B{1};
                @ms(2) = a{1},ap{1},b{1},bp{1},v{1},q{1,1},alpha{0},yes,no;
                @ms(3) = beta{0};
        }
        def init_rules(m,n)
        {
                /*1*/  [A{i}]'1    <--> [a{i},ap{i}]'2 : 1<=i<=n;
                       [A{n+1}]'1  <--> [E{1}]'2;
                /*2*/  [Ap{i}]'1   <--> [a{i},ap{i}]'2 : 1<=i<=n;
                       [Ap{n+1}]'1 <--> [E{1}]'2;
                /*3*/  [B{i}]'1    <--> [b{i},bp{i}]'2 : 1<=i<=n;
                /*4*/  [Bp{i}]'1   <--> [b{i},bp{i}]'2 : 1<=i<=n;
                /*5*/  [T{i}]'1    <--> [t{i}]'2       : 1<=i<=n-1;
                /*6*/  [Tp{i}]'1   <--> [t{i}]'2       : 1<=i<=n-1;
                /*7*/  [F{i}]'1    <--> [f{i}]'2       : 1<=i<=n-1;
                /*8*/  [Fp{i}]'1   <--> [f{i}]'2       : 1<=i<=n-1;
                /*9*/  [t{i}]'1    <--> [T{i},Tp{i}]'0 : 1<=i<=n-1; 
                /*10*/ [f{i}]'1    <--> [F{i},Fp{i}]'0 : 1<=i<=n-1;
                /*11*/ [b{i}]'1    <--> [B{i+1},S]'0   : 1<=i<=n;
                       [B{n+1}]'1  <--> [#]'0;
                /*12*/ [bp{i}]'1   <--> [Bp{i+1}]'0    : 1<=i<=n;
                       [Bp{n+1}]'1 <--> [#]'0;
                /*13*/ [a{i}]'1    <--> [T{i},A{i+1}]'0 : 1<=i<=n;
                /*14*/ [ap{i}]'1   <--> [Fp{i},Ap{i+1}]'0 : 1<=i<=n;
                /*15*/ [A{i}]'2    <--> [c{i}]'0          : 1<=i<=n-1;
                       [A{i}]'2    <--> [#]'0             : n<=i<=n+1;
                /*16*/ [Ap{i}]'2   <--> [c{i}]'0          : 1<=i<=n-1;
                       [Ap{i}]'2   <--> [#]'0             : n<=i<=n+1;
                /*17*/ [B{i}]'2    <--> [c{i}]'0          : 1<=i<=n-1;
                       [B{n}]'2    <--> [#]'0;
                /*18*/ [Bp{i}]'2   <--> [c{i}]'0          : 1<=i<=n-1;
                       [Bp{n}]'2   <--> [#]'0;
                /*19*/ [c{i}]'2    <--> [b{i+1},bp{i+1}]'0 : 1<=i<=n-1;
                /*20*/ [v{i}]'2    <--> [y{i}*2]'0         : 1<=i<=n;
                /*21*/ [y{i}]'2    <--> [z{i},w{i}]'0      : 1<=i<=n-1;
                       [y{n}]'2    <--> [w{n}]'0;
                /*22*/ [z{i}]'2    <--> [v{i+1}]'0         : 1<=i<=n-1;
                /*23*/ [w{i}]'2    <--> [a{i+1},ap{i+1}]'0  : 1<=i<=n-1;
                       [w{n}]'2    <--> [E{1}]'0;
                /*24*/ [q{1,1}]'2  <--> [r{1,1}]'0;
                /*25*/ [q{i,j}]'2  <--> [r{i,j}*2]'0       : 1<=i<=n-1,2<=j<=n-1;
                /*26*/ [r{i,j}]'2  <--> [s{i},u{i,j}]'0    : 1<=i<=n-1,1<=j<=n-1;
                /*27*/ [s{i}]'2    <--> [t{i},f{i}]'0      : 1<=i<=n-1;
                /*28*/ [u{1,j}]'2  <--> [q{1,j+1},q{2,j+1}]'0 : 1<=j<=n-2;
                /*29*/ [u{i,j}]'2  <--> [q{i+1,j+1}]'0 : 2<=i<=n-2,2<=j<=n-2;
                /*30*/ [u{i,n-1}]'2 <--> [#]'0         : 1<=i<=n-1;
                /*31*/ [T{i}]'2     <--> [#]'0         : 1<=i<=n-1;
                /*32*/ [Tp{i}]'2    <--> [#]'0         : 1<=i<=n-1;
                /*33*/ [F{i}]'2     <--> [#]'0         : 1<=i<=n-1;
                /*34*/ [Fp{i}]'2    <--> [#]'0         : 1<=i<=n-1;
                /*35*/ [S]'1 --> [ ]'1 [ ]'1;
                /*36*/ [alpha{i}]'2 <--> [alpha{i+1}]'0 : 0<=i<=3*n+2*m;
                /*37*/ [beta{i}]'3  <--> [beta{i+1}]'0  : 0<=i<=3*n+2*m+1;
                /*38*/ [x{i,j}]'3   <--> [d{i,j,1}*2]'0 : 1<=i<=n,1<=j<=m;
                       [nx{i,j}]'3  <--> [nd{i,j,1}*2]'0 : 1<=i<=n,1<=j<=m;
                /*39*/ [d{i,j,k}]'3 <--> [d{i,j,k+1}*2]'0 : 1<=i<=n,1<=j<=m,1<=k<=n-1;
                       [nd{i,j,k}]'3 <--> [nd{i,j,k+1}*2]'0 : 1<=i<=n,1<=j<=m,1<=k<=n-1;
                /*40*/ [d{i,j,n}]'3 <--> [e{i,j}]'0 : 1<=i<=n,1<=j<=m;
                       [nd{i,j,n}]'3 <--> [ne{i,j}]'0 : 1<=i<=n, 1<=j<=m;
                /*41*/ [T{i},E{j}]'1 <--> [e{i,j}]'3 : 1<=i<=n,1<=j<=m;
                       [F{i},E{j}]'1 <--> [ne{i,j}]'3 : 1<=i<=n,1<=j<=m;
                       [Tp{i},E{j}]'1 <--> [e{i,j}]'3 : 1<=i<=n,1<=j<=m;
                       [Fp{i},E{j}]'1 <--> [ne{i,j}]'3 : 1<=i<=n,1<=j<=m;
                /*42*/ [e{i,j}]'1 <--> [T{i},E{j+1}]'0 : 1<=i<=n,1<=j<=m-1;
                       [ne{i,j}]'1 <--> [F{i},E{j+1}]'0 : 1<=i<=n,1<=j<=m-1;
                /*43*/ [e{i,m}]'1 <--> [E{m+1}]'0 : 1<=i<=n;
                       [ne{i,m}]'1 <--> [E{m+1}]'0 : 1<=i<=n;
                /*44*/ [T{i}]'3 <--> [#]'0 : 1<=i<=n;
                       [F{i}]'3 <--> [#]'0 : 1<=i<=n;
                       [Tp{i}]'3 <--> [#]'0 : 1<=i<=n;
                       [Fp{i}]'3 <--> [#]'0 : 1<=i<=n;
                /*45*/ [E{j}]'3 <--> [#]'0 : 1<=j<=m;
                /*46*/ [E{m+1}]'1 <--> [yes,alpha{3*n+1+2*m}]'2;
                /*47*/ [yes]'1 <--> [beta{3*n+1+2*m+1}]'3;
                /*48*/ [alpha{3*n+1+2*m}]'2 <--> [beta{3*n+1+2*m+1}]'3;
                /*49*/ [no,beta{3*n+1+2*m+1}]'2 <--> [#]'0;
                /*50*/ [yes]'3 <--> [#]'0;      
                                            
        }



Files
-----

.. container:: boldlink

    * The example does not need input data from any user nor speficic interesting outputs, so it can be run from the `general app  <https://github.com/luivalcab/MeCoSim-public-models/blob/master/001%20-%20General/ConfigFile_General.xls>`_ yet available and pre-loaded in MeCoSim.
    * `Model file <http://www.p-lingua.org/wiki/images/2/2a/Sat_tissue_separation.pli>`_, P-Lingua file with the code above.
    * As in the case of the app, no scenario file with specific input is needed, so the general dummy `scenario file <https://github.com/luivalcab/MeCoSim-public-models/blob/master/001%20-%20General/example1.ec2>`_ can also be used.
    
Adapting a problem to MeCoSim philosophy
----------------------------------------

.. container:: boldlink

    * `Custom application <https://github.com/luivalcab/MeCoSim-public-models/blob/master/008%20-%20SAT%20Tissue/Parameterized/SAT_TSCS_ConfigFile.xls>`_, defining the needed input and output tables for SAT problem solved with tissue P systems with cell separation.
    * `Model file <https://github.com/luivalcab/MeCoSim-public-models/blob/master/008%20-%20SAT%20Tissue/Parameterized/tscs_mecosim.pli>`_, P-Lingua file with the parametrized file specifying the family of P systems for solving the partition problem. The custom interface enable the user to introduce the data corresponding to each different scenario.
    * `Scenario file <https://github.com/luivalcab/MeCoSim-public-models/blob/master/008%20-%20SAT%20Tissue/Parameterized/tscs_Custom_alt2_4_5.ec2>`_, for a specific instance of the problem (that is, a specific P system and SAT formula).

Now the values for *m* and *n* come from the data introduced by the user (not therefore hardcoded in the file) in the input tables, and the same happens with the formula after entering it from SAT plugin and convert into the input table format. The custom app defines the mechanism to convert those data in the params for P-Lingua (m, n, nvals, and variable{i}, clause{i}, val{i}, valn{i} for each i from 1 to nvals)::

        @model<TSCS>
        
        ...
        
        def define_input()
        {
            @ms(3) += nx{variable{i},clause{i}}*valn{i},x{variable{i},clause{i}}*val{i} : 1<=i<=nvals;
        }