PeP input file syntax reference¶

Basic template¶

The basic template of a Numerical P system in PeP is:

num_ps = {
    H = {m1, m2};

    structure = [m1 [m2 ]m2 ]m1;

    m1 = {
        var = {x_1}; # variables that are part of this membrane
        pr = {2*x_1 + 1 -> 1|x_2};
        var0 = (0);
    };

    ...
}

where:

num_ps: the name of the P system

H: a list of membrane names

structure: describes the structure of the system. In this instance, membrane m2 is contained by m1

m1 = { ... }: the definition of membrane m1. Note the name of the membrane is the same as the one defined in H

var = {x_1}: a comma separated list of P objects that are part of this membrane

pr = {2*x_1 + 1 -> 1|x_2}: the definition of a program. A single program is allowed per membrane, for a non-enzymatic Numerical P System

The pr keyword is the same for all programs.

The right arrow -> is used to separate the production function (left-side) from the distribution function (right-side)

var0 = (0): a comma separated list of initial P object valuea, specified in the same order as that used for var

comments start with #

code blocks are delimited using { } and are used for

num_ps

H

m1

var

pr

lists of numeric constants are delimited using ( ) and are used mainly for var0

Note that the three suspension dots ... do not have any syntactical meaning.

Enzymatic Numerical P System¶

An Enzymatic Numerical P System preserves all of the syntax elements of a Numerical P System and introduces several small modifications.

The basic template of an Enzymatic Numerical P system in PeP is:

num_ps = {

    ...

    m3 = {
        var = {x_1_1, x_2_1, x_3_1}; # variables
        E = {e_1_1, e_2_1}; # enzymes
        pr = {2*x_1_1 + x_2_1 [e_1_1 -> ] 1|x_2_1 + 1|x_3_1 + 1|x_1_2};
        pr = {x_2_1 + 3*x_3_1 [e_1_1 -> ] 1|x_2_1 + 2|x_1_2};
        pr = {x_1_1 + 4*x_3_1 [e_2_1 -> ] 1|x_1_1 + 2|x_2_1};
        var0 = (2, 3, 4); # initial values for variables x_1_1, x_2_1, x_3_1
        E0  = (4, 1); # initial values for enzymes e_1_1, e_2_1
    };

    ...
}

Compared to a normal Numerical P System, an Enzymatic Numerical P System introduces the following changes:

E = {e_1_1}: a comma separated list of P objects that are the enzymes of this membrane

E0 = (0): a comma separated list of initial enzyme P object valuea, specified in the same order as that used for E

in what regards programs (pr)

multiple program definitions (pr) are allowed

within the definition of a program, the -> is replaced with [e_1_1 -> ] where e_1_1 is the name of an enzyme P object that conditions the execution of this program. Note that within an Enzymatic Numerical P System, there can be membranes that do not use enzymes.