PrologPnet = DynamicDeclarations Netname Constants Metabolites Reactions

Netname = model('MODELNAME').

Constants = Constant Constants | Constant

Constant = IntConstant | DoubleConstant | ValueSet

ValueSet = valueset('NAME' = ListOfValues).
IntConstant = int('NAME' = ListOfValues ) .
DoubleConstant = double('NAME' = ListOfValues ) .

ListOfValues = [ ListOfValues1 ]

ListOfValues1 = Val : ListOfValues1 | Val

Val = INTEGER | DOUBLE

Metabolites = MetaboliteHeading MetabolitesAndValues

MetaboliteHeading = m(X):-m1(X=_).

MetabolitesAndValues = Metabolite Metabolites | Metabolite

Metabolite = m1('NAME'='VALUE').

Reactions = Reaction Reactions | Reaction

Reaction = r('NAME',ListOfMetabolites, RateDeclaration ).

ListOfMetabolites = [ ListOfMetabolites1 ]

ListOfMetabolites1 = MetaboliteAndArc , ListOfMetabolites | MetaboliteAndArc 

MetaboliteAndArc = 'NAME' Sign Value

Sign = + | -

Value = INTEGER


++++

%ANDL file example


spn  [ma1]
{
constants:
  valuesets[Main:V_Set_1:V_Set_2:V_Set_3]
marking:
  int n_A = [5:50:500:1000];
  int n_B = [1:10:100:0];
  int n_E = [1:10:100:1000];
parameter:
  double k1 = [100:1000:10000:100000];
  double k2 = [4:40:400:4000];
  double k3 = [1:10:100:1000];
  double sf = [1:.1:.01:.001];

places:
   M_A = 100;
   M_AE = 0;
   M_B = n_B;
   M_E = 100;

transitions:
  R_1
    : 
    : [M_AE + 1] & [M_A - 1] & [M_E - 1]
    : E*A*k1
    ;
  R_2
    : 
    : [M_A + 1] & [M_E + 1] & [M_AE - 1]
    : AE*k2
    ;
  R_3
    : 
    : [M_B + 1] & [M_E + 1] & [M_AE - 1]
    : AE*k3
    ;

}

++++

% Prolog file example


:-dynamic(model/1).
:-dynamic(modelname/1).
:-dynamic(m1/1).
:-dynamic(r/2).
:-dynamic(int/1).

model('ma1').


int('n_A'='[5:50:500:1000]').
int('n_B'='[1:10:100:0]').
int('n_E'='[1:10:100:1000]').

m(X):-m1(X=_).
m1('M_A'='100').
m1('M_AE'='0').
m1('M_B'='n_B').
m1('M_E'='100').

r('R_1',['M_AE' + 1 , 'M_A' - 1 , 'M_E' - 1], 'E*A*k1').
r('R_2',['M_A' + 1 , 'M_E' + 1 , 'M_AE' - 1], 'AE*k2').
r('R_3',['M_B' + 1 , 'M_E' + 1 , 'M_AE' - 1], 'AE*k3').