:-doc('Function to rewrite a graph with reduced patterns (for example MichaelisMenten patterns).').

:-doc('This section describes commands to rewrite a reaction graph by reducing some specified patterns (for example Michaelis-Menten patterns). The idea behind this function is to use graph rewriting before searching SEPIs. It is also possible to expand reduced Michaelis-Menten patterns, in order to exhibit the intermediary step of reversible complexation substrate-enzyme.').

:-initial(option(michaelis_menten:yes)).

...

...

@@ -42,16 +42,16 @@ yesnomaybe(maybe).

pattern_reduction(Input_file):-

biocham_command,

type(Input_file,input_file),

doc('Function to rewrite a graph with reduced patterns (for example michaelis menten patterns).'),

option(michaelis_menten,yesno,MM_complete,'specifies if reducing michaelis menten patterns'),

option(r_1,yesnomaybe,MM_R_1,'michaelis menten with R-1 reaction'),

option(r_2,yesnomaybe,MM_R_2,'michaelis menten with R-2 reaction'),

option(ep,yesnomaybe,MM_EP,'michaelis menten with EP specie'),

option(hill_reaction,yesno,Hill,'specifies if reducing hill patterns'),

option(partial_hill_reaction,yesno,Part_Hill,'specifies if reducing partial hill patterns'),

option(double_michaelis_menten,yesno,Double_MM,'specifies if reducing double michaelis menten'),

option(enzyme,yesno,MM_E,'michaelis menten reduced reaction with enzyme'),

option(michaelis_menten_expansion,yesno,MM_expansion,'expansion of michaelis menten patterns'),

doc('The patterns to be searched into the input graph are specified by the options. For a pattern, being found into a graph means that there is a subgraph isomorphism from the graph to the pattern and that only the vertices sent to the image vertices enzyme, substrate, product can have edges with other vertices in the graph (for example it constrains the complex not to intervene in any other reaction). In the output graph (written in a new file .bc), all occurrences of these patterns are reduced to the one-reaction Michaelis-Menten pattern, with a double-arrow from the enzyme. The michaelis_menten_expansion option has the opposite effect to expand reduced Michaelis-Menten patterns'),

option(michaelis_menten,yesno,MM_complete,'specifies if reducing Michaelis Menten patterns'),

option(r_1,yesnomaybe,MM_R_1,'R-1 reaction (from the commplex ES to enzyme E and substrate S) in the searched Michaelis-Menten pattern'),

option(r_2,yesnomaybe,MM_R_2,'R-2 reaction (from the product P and enzyme E to the complex EP or ES) in the searched Michaelis-Menten pattern'),

option(ep,yesnomaybe,MM_EP,'irreversible reaction from the complex ES to the complex EP in the searched Michaelis-Menten pattern'),

option(hill_reaction,yesno,Hill,'specifies if reducing Hill patterns'),

option(partial_hill_reaction,yesno,Part_Hill,'specifies if reducing partial Hill patterns'),

option(double_michaelis_menten,yesno,Double_MM,'specifies if reducing double Michaelis-Menten'),

option(enzyme,yesno,MM_E,'specifies if the reduced Michaelis-Menten pattern (that will appear in the output graph) is with enzyme or no'),

option(michaelis_menten_expansion,yesno,MM_expansion,'expansion of Michaelis-Menten patterns (form the reduced form with enzyme to form with complex ES and reaction R-1'),