spec gpac.pl

gpac.pl

@@ -31,6 +31,7 @@ Rq: The distinction between pivp_string and pivp_list is not always obvious.
   [
     %Commands
     compile_from_expression/3,
+    compile_from_pivp/2,
     compile_from_pivp/3,
     %Grammar
     polynomial/1,
@@ -49,7 +50,11 @@ Rq: The distinction between pivp_string and pivp_list is not always obvious.
 :- use_module(reaction_rules).
 :- use_module(util).
 
-:- doc('The Turing completeness of continuous CRNs \\cite{FLBP17cmsb} states that any computable function over the reals can be computed by a CRN over a finite set of molecular species. Biocham uses the proof of that result to compile any computable real function presented as the solution of a polynomial differential equation system into a finite CRN. The restriction to reactions with at most two reactants is an option.').
+:- doc('The Turing completeness of continuous CRNs \\cite{FLBP17cmsb} states that any computable function over the reals can be computed by a CRN over a finite set of molecular species. Biocham uses the proof of that result to compile any computable real function presented as the solution of a polynomial differential equation system into a finite CRN.').
+
+:- doc('The restriction to reactions with at most two reactants is an option.').
+
+:- doc('The lazy introduction of molecular species for negative real values is another option.').
 
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -236,26 +241,53 @@ monomial(X) :-
   name(X).
 
 
+%! compile_from_pivp(+PIVP_string, +Output)
+%
+% biocham command
+%
+% Creates a biochemical reaction network that computes the projection of multivariate function f(t) on one variable Output,
+% where f(t) is the solution of the PIVP.
+%
+% Typical usage will be:
+% ==
+% :- compile_from_pivp( ((1,(d(y)/dt=z)); (0,(d(z)/dt= (-1*y)))), y).
+% ==
+
+compile_from_pivp(PIVP, Output) :-
+  biocham_command,
+  type(PIVP, pivp),
+  type(Output, name),
+  doc('
+    compiles a PIVP into a CRN (with initial concentration values) that computes the projection on one variable Output as a function of time, of the multivariate function f(t) solution of the PIVP.
+  '),
+  option(
+    binomial_reduction,
+    yesno,
+    _Reduction,
+    'Determine if the binomial reduction has to be performed'
+  ),
+  compile_from_pivp(PIVP, time, Output).
+
+
 %! compile_from_pivp(+PIVP_string, +Input , +Output)
 %
 % biocham command
 %
-% Creates a biochemical reaction network such that Output = f(Input)
-% where f is the solution of the PIVP.
+% Creates a biochemical reaction network that computes the projection of multivariate function f(Input) on one variable Output,
+% where f(t) is the solution of the PIVP, and Input is a time value
 %
 % Typical usage will be:
 % ==
-% :- compile_from_pivp( ((1,(d(y)/dt=z)); (0,(d(z)/dt= (-1*y)))),time,output).
+% :- compile_from_pivp( ((1,(d(y)/dt=z)); (0,(d(z)/dt= (-1*y)))), 4, y).
 % ==
 
 compile_from_pivp(PIVP, Input, Output) :-
   biocham_command,
   type(PIVP, pivp),
-  type(Input, name),
+  type(Input, name), % FF   type(Input, expr),
   type(Output, name),
   doc('
-    compiles a PIVP into biochemical reactions. Use \'time\' as input
-    to get output f(t), or use any other input x to get f(x) as output.
+  compiles a PIVP into a CRN (with initial concentration values)  that computes the value of variable Output at time Input, of the multivariate function f(t) solution of the PIVP.
   '),
   option(
     binomial_reduction,