/* 

  DNA in Picat.

  Port of nprolog example dna.pl
  https://github.com/sasagawa888/nprolog/blob/master/example/dna.pl
 

  This model was created by Hakan Kjellerstrand, hakank@gmail.com
  See also my Picat page: http://www.hakank.org/picat/

*/

import v3_utils.

main => go.

% Here are examples from the program.

go ?=>
  assert($trans(off)),
  data(X),rna_amino(X,Y),
  println([x=X,y=Y]),
  fail,
  
  nl.
go => true.

go2 ?=>
  assert($trans(off)),
  rna_amino(X,[begin,arg,asn,val,end]),
  println(x=X),
  fail,
  nl.
go2 => true.


go3 ?=>
  assert($trans(off)),
  dna_rna([t,t,g,c,g,a,t],X),
  println(x=X),
  fail,
  nl.
go3 => true.

go4 ?=>
  assert($trans(off)),
  make_dna([arg,asn,val],X),
  println(x=X),
  fail,
  nl.
go4 => true.


% hakank: The code below is from
% https://github.com/sasagawa888/nprolog/blob/master/example/dna.pl

%?-data(X),rna_amino(X,Y).
%X   = [a,u,g,c,g,c,a,a,u,g,u,g,u,a,a],
%Y   = [begin,arg,asn,val,end]
%yes

%?-rna_amino(X,[begin,arg,asn,val,end]).
%X   = [a,u,g,c,g,u,a,a,u,g,u,u,u,a,a]
%yes
 

%?-dna_rna([t,t,g,c,g,a,t],X).
%X   = [a,a,c,g,c,u,a]
%yes
 

%?- make_dna([arg,asn,val],X).
%X   = [[g,c],[c,g],[a,t],[t,a],[t,a],[a,t],[c,g],[a,t],[a,t]]
%yes


%Convert DNA code to amino acid name.
%test data
data([a,u,g,c,g,c,a,a,u,g,u,g,u,a,a]).

% hakank: trans/1 must be asserted from the program.
% global variable that indicates whether the conversion is in progress.
% Necessary for judging begin or met (methionine).
% trans(off).

%Convert RNA sequence to amino acid name. Inverse conversion is also possible.
rna_amino([],[]) :-
    abolish($trans/1),
    assert($trans(off)).

rna_amino([A,B,C|Xs],[Z|Zs]) :-
    dnaward([A,B,C],Z),
    bp.trans(on),
    rna_amino(Xs,Zs).

rna_amino([A,B,C|Xs],[Z|Zs]) :-
    dnaward([A,B,C],Z),
    abolish($trans/1),
    assert($trans(on)),
    rna_amino(Xs,Zs).

%RNA and its corresponding amino acid name
dnaward([u,u,u],phe).
dnaward([u,u,c],ala).
dnaward([u,u,a],leu).
dnaward([u,u,g],leu).
dnaward([c,u,u],leu).
dnaward([c,u,c],leu).
dnaward([c,u,a],leu).
dnaward([c,u,g],leu).
dnaward([a,u,u],ile).
dnaward([a,u,c],ile).
dnaward([a,u,a],ile).
dnaward([a,u,g],met) :- bp.trans(on).
dnaward([a,u,g],begin).
dnaward([g,u,u],val).
dnaward([g,u,c],val).
dnaward([g,u,a],val).
dnaward([g,u,g],val).
dnaward([u,c,u],ser).
dnaward([u,c,c],ser).
dnaward([u,c,a],ser).
dnaward([u,c,g],ser).
dnaward([c,c,u],pro).
dnaward([c,c,c],pro).
dnaward([c,c,a],pro).
dnaward([c,c,g],pro).
dnaward([a,c,u],thr).
dnaward([a,c,c],thr).
dnaward([a,c,a],thr).
dnaward([a,c,g],thr).
dnaward([g,c,u],ala).
dnaward([g,c,c],ala).
dnaward([g,c,a],ala).
dnaward([g,c,g],ala).
dnaward([u,a,u],tyr).
dnaward([u,a,c],thr).
dnaward([u,a,a],end).
dnaward([u,a,g],end).
dnaward([c,a,u],his).
dnaward([c,a,c],his).
dnaward([c,a,a],gln).
dnaward([c,a,g],gln).
dnaward([a,a,u],asn).
dnaward([a,a,c],asn).
dnaward([a,a,a],lys).
dnaward([a,a,g],lys).
dnaward([g,a,u],asp).
dnaward([g,a,c],asp).
dnaward([g,a,a],glu).
dnaward([g,a,g],glu).
dnaward([u,g,u],cys).
dnaward([u,g,c],cys).
dnaward([u,g,a],end).
dnaward([u,g,g],trp).
dnaward([c,g,u],arg).
dnaward([c,g,c],arg).
dnaward([c,g,a],arg).
dnaward([c,g,g],arg).
dnaward([a,g,u],ser).
dnaward([a,g,c],ser).
dnaward([a,g,a],arg).
dnaward([a,g,g],arg).
dnaward([g,g,u],gly).
dnaward([g,g,c],gly).
dnaward([g,g,a],gly).
dnaward([g,g,g],gly).

%Convert DNA sequence (divided into one) to RNA sequence, reverse conversion possible
dna_rna([],[]).
dna_rna([X|Xs],[Z|Zs]) :-
    copy_rule(X,Z),
    dna_rna(Xs,Zs).

copy_rule(a,u).
copy_rule(t,a).
copy_rule(g,c).
copy_rule(c,g).

%A pair of DNA strings is generated from one DNA string.
make_dna_pair([],[]).
make_dna_pair([X|Xs],[Z|Zs]) :-
    pair_rule(X,Z),
    make_dna_pair(Xs,Zs).

pair_rule(a,t).
pair_rule(t,a).
pair_rule(g,c).
pair_rule(c,g).

%Attach two DNA strands into one double helix
conjugate_dna([],[],[]).
conjugate_dna([X|Xs],[Y|Ys],[[X,Y]|Zs]) :-
    conjugate_dna(Xs,Ys,Zs).

%Generate double helix DNA sequence from amino acid name.
make_dna(X,Z) :-
    rna_amino(Z1,X),
    dna_rna(X1,Z1),
    make_dna_pair(X1,X2),
    conjugate_dna(X1,X2,Z).