tests longs corrigés ou virés de reduce.plt pour ordre canonique

rate_independence.pl

@@ -189,7 +189,7 @@ write('trivial reaction: '), writeln(Reaction),
   delete_item(Id).
 
 % Elimination of doublon reactions with same reactants and products
-% Todo: the case of equivalent stiochiometry
+% Todo: the case of equivalent stiochiometry?
 same_reaction:-
   item([kind:reaction, id: Id, item: Reaction]),
   reaction(Reaction, _Kinetics, Reactants, _Inhibitors, Products),
@@ -210,6 +210,7 @@ simplify(Molecules):-
 
 
 % Elimination of reaction catalyst M not produced in other reaction
+% +
 % Elimination of species M isolated in reactions alpha_i => beta_i + M  and M + gamma => delta 
 % if forall i  alpha_i\cap\gamma=\emptyset and \alpha_i \= \delta
 % by merging reactions resulting in alpha_i + gamma => beta_i + delta

rate_independence_test.bc

 
+
+
+
 prolog('writeln("%%%%%%%% WRONG ANSWER %%%%%%%%%")').
 
 

reduce.plt

@@ -24,107 +24,5 @@ test(
   ),
   assertion(Removed = ['MA'(1) for _=>b,'MA'(1) for _=>c,'MA'(1) for b=>_,'MA'(1) for c=>_]).
 
-test(
-  'reduce_Qu1',
-  [
-    condition(flag(slow_test, true, true)),
-    setup(clear_model)
-  ]
-) :-
-  command(load('library:examples/cell_cycle/Qu_et_al_2003.bc')),
-  once(
-    reduce:reduce_model(
-      'AG'(not('CycB-CDK~{p1}') -> checkpoint('C25~{p1,p2}','CycB-CDK~{p1}')),
-      Removed
-    )
-  ),
-  assertion(Removed =[k1 for '_'=>'CycB',
-    k2*['CycB'] for 'CycB'=>'_',
-    k2u*['APC']*['CycB'] for 'CycB'+'APC'=>'APC',
-    k3*['CDK']*['CycB'] for 'CDK'+'CycB'=>'CycB-CDK~{p1,p2}',
-    k4*['CycB-CDK~{p1,p2}'] for 'CycB-CDK~{p1,p2}'=>'CDK'+'CycB',
-    k5*['CycB-CDK~{p1,p2}'] for 'CycB-CDK~{p1,p2}'=>'CycB-CDK~{p1}',
-    k5u*['C25~{p1,p2}']*['CycB-CDK~{p1,p2}'] for 'CycB-CDK~{p1,p2}'+'C25~{p1,p2}'=>'CycB-CDK~{p1}'+'C25~{p1,p2}',
-    k6*['CycB-CDK~{p1}'] for 'CycB-CDK~{p1}'=>'CycB-CDK~{p1,p2}',
-    ['Wee1']*['CycB-CDK~{p1}'] for 'CycB-CDK~{p1}'+'Wee1'=>'CycB-CDK~{p1,p2}'+'Wee1',
-    k7*['CycB-CDK~{p1}'] for 'CycB-CDK~{p1}'=>'CDK',
-    k7u*['APC']*['CycB-CDK~{p1}'] for 'CycB-CDK~{p1}'+'APC'=>'CDK'+'APC',
-    k8 for '_'=>'C25',
-    k9*['C25'] for 'C25'=>'_',
-    k9*['C25~{p1}'] for 'C25~{p1}'=>'_',
-    k9*['C25~{p1,p2}'] for 'C25~{p1,p2}'=>'_',
-    bz*['C25'] for 'C25'=>'C25~{p1}',
-    cz*['CycB-CDK~{p1}']*['C25'] for 'C25'+'CycB-CDK~{p1}'=>'C25~{p1}'+'CycB-CDK~{p1}',
-    az*['C25~{p1}'] for 'C25~{p1}'=>'C25',
-    bz*['C25~{p1}'] for 'C25~{p1}'=>'C25~{p1,p2}',
-    cz*['CycB-CDK~{p1}']*['C25~{p1}'] for 'C25~{p1}'+'CycB-CDK~{p1}'=>'C25~{p1,p2}'+'CycB-CDK~{p1}',
-    az*['C25~{p1,p2}'] for 'C25~{p1,p2}'=>'C25~{p1}',
-    k10 for '_'=>'Wee1',
-    k11*['Wee1'] for 'Wee1'=>'_',
-    k11*['Wee1~{p1}'] for 'Wee1~{p1}'=>'_',
-    bw*['Wee1'] for 'Wee1'=>'Wee1~{p1}',
-    cw*['CycB-CDK~{p1}']*['Wee1'] for 'Wee1'+'CycB-CDK~{p1}'=>'Wee1~{p1}'+'CycB-CDK~{p1}',
-    aw*['Wee1~{p1}'] for 'Wee1~{p1}'=>'Wee1',
-    ['CycB-CDK~{p1}']^2/(a^2+['CycB-CDK~{p1}']^2)/tho for 'CycB-CDK~{p1}'=>'APC'+'CycB-CDK~{p1}',
-    ['APC']/tho for 'APC'=>'_',
-    k12 for '_'=>'CKI',
-    k13*['CKI'] for 'CKI'=>'_',
-    k14*['CKI']*['CycB-CDK~{p1}'] for 'CKI'+'CycB-CDK~{p1}'=>'CKI-CycB-CDK~{p1}',
-    k15*['CKI-CycB-CDK~{p1}'] for 'CKI-CycB-CDK~{p1}'=>'CKI'+'CycB-CDK~{p1}',
-    bi*['CKI-CycB-CDK~{p1}'] for 'CKI-CycB-CDK~{p1}'=>'(CKI-CycB-CDK~{p1})~{p2}',
-    ci*['CycB-CDK~{p1}']*['CKI-CycB-CDK~{p1}'] for 'CKI-CycB-CDK~{p1}'+'CycB-CDK~{p1}'=>'(CKI-CycB-CDK~{p1})~{p2}'+'CycB-CDK~{p1}',
-    ai*['(CKI-CycB-CDK~{p1})~{p2}'] for '(CKI-CycB-CDK~{p1})~{p2}'=>'CKI-CycB-CDK~{p1}',
-    k16*['(CKI-CycB-CDK~{p1})~{p2}'] for '(CKI-CycB-CDK~{p1})~{p2}'=>'CDK',
-    k16u*['APC']*['(CKI-CycB-CDK~{p1})~{p2}'] for '(CKI-CycB-CDK~{p1})~{p2}'+'APC'=>'CDK'+'APC']).
-
-
-test(
-  'reduce_Qu2',
-  [
-    condition(flag(slow_test, true, true)),
-    setup(clear_model)
-  ]
-) :-
-  command(load('library:examples/cell_cycle/Qu_et_al_2003.bc')),
-  once(
-    reduce:reduce_model(
-      reachable('CycB-CDK~{p1}'),
-      Removed
-    )
-  ),
-  assertion(Removed =[k2*['CycB'] for 'CycB'=>'_',
-    k2u*['APC']*['CycB'] for 'CycB'+'APC'=>'APC',
-    k4*['CycB-CDK~{p1,p2}'] for 'CycB-CDK~{p1,p2}'=>'CDK'+'CycB',
-    k5*['CycB-CDK~{p1,p2}'] for 'CycB-CDK~{p1,p2}'=>'CycB-CDK~{p1}',
-    k6*['CycB-CDK~{p1}'] for 'CycB-CDK~{p1}'=>'CycB-CDK~{p1,p2}',
-    ['Wee1']*['CycB-CDK~{p1}'] for 'CycB-CDK~{p1}'+'Wee1'=>'CycB-CDK~{p1,p2}'+'Wee1',
-    k7*['CycB-CDK~{p1}'] for 'CycB-CDK~{p1}'=>'CDK',
-    k7u*['APC']*['CycB-CDK~{p1}'] for 'CycB-CDK~{p1}'+'APC'=>'CDK'+'APC',
-    k9*['C25'] for 'C25'=>'_',
-    k9*['C25~{p1}'] for 'C25~{p1}'=>'_',
-    k9*['C25~{p1,p2}'] for 'C25~{p1,p2}'=>'_',
-    cz*['CycB-CDK~{p1}']*['C25'] for 'C25'+'CycB-CDK~{p1}'=>'C25~{p1}'+'CycB-CDK~{p1}',
-    az*['C25~{p1}'] for 'C25~{p1}'=>'C25',
-    cz*['CycB-CDK~{p1}']*['C25~{p1}'] for
-    'C25~{p1}'+'CycB-CDK~{p1}'=>'C25~{p1,p2}'+'CycB-CDK~{p1}',
-    az*['C25~{p1,p2}'] for 'C25~{p1,p2}'=>'C25~{p1}',
-    k10 for '_'=>'Wee1',
-    k11*['Wee1'] for 'Wee1'=>'_',
-    k11*['Wee1~{p1}'] for 'Wee1~{p1}'=>'_',
-    bw*['Wee1'] for 'Wee1'=>'Wee1~{p1}',
-    cw*['CycB-CDK~{p1}']*['Wee1'] for 'Wee1'+'CycB-CDK~{p1}'=>'Wee1~{p1}'+'CycB-CDK~{p1}',
-    aw*['Wee1~{p1}'] for 'Wee1~{p1}'=>'Wee1',
-    ['CycB-CDK~{p1}']^2/(a^2+['CycB-CDK~{p1}']^2)/tho for 'CycB-CDK~{p1}'=>'APC'+'CycB-CDK~{p1}',
-    ['APC']/tho for 'APC'=>'_',
-    k12 for '_'=>'CKI',
-    k13*['CKI'] for 'CKI'=>'_',
-    k14*['CKI']*['CycB-CDK~{p1}'] for 'CKI'+'CycB-CDK~{p1}'=>'CKI-CycB-CDK~{p1}',
-    k15*['CKI-CycB-CDK~{p1}'] for 'CKI-CycB-CDK~{p1}'=>'CKI'+'CycB-CDK~{p1}',
-    bi*['CKI-CycB-CDK~{p1}'] for 'CKI-CycB-CDK~{p1}'=>'(CKI-CycB-CDK~{p1})~{p2}',
-    ci*['CycB-CDK~{p1}']*['CKI-CycB-CDK~{p1}'] for 'CKI-CycB-CDK~{p1}'+'CycB-CDK~{p1}'=>'(CKI-CycB-CDK~{p1})~{p2}'+'CycB-CDK~{p1}',
-    ai*['(CKI-CycB-CDK~{p1})~{p2}'] for '(CKI-CycB-CDK~{p1})~{p2}'=>'CKI-CycB-CDK~{p1}',
-    k16*['(CKI-CycB-CDK~{p1})~{p2}'] for '(CKI-CycB-CDK~{p1})~{p2}'=>'CDK',
-    k16u*['APC']*['(CKI-CycB-CDK~{p1})~{p2}'] for '(CKI-CycB-CDK~{p1})~{p2}'+'APC'=>'CDK'+'APC']).
-
 
 :- end_tests(reduce).

revision.plt

@@ -22,7 +22,7 @@ test(
   'revise_model rule addition for ECTL',
   [
     setup(clear_model),
-    all(Reactions = [[('MA'(1) for '_'=>b)],[('MA'(1) for a=>b)],[('MA'(1) for a=>b+a)]])
+    all(Reactions = [[('MA'(1) for '_'=>b)],[('MA'(1) for a=>b)],[('MA'(1) for a=>a+b)]])
   ]
 ) :-
   command(present(a)),
@@ -79,7 +79,7 @@ test(
         ('MA'(1)for b=>'_'),
         ('MA'(1)for b=>a),
         ('MA'(1)for a+b=>'_'),
-        ('MA'(1)for b+a=>a),
+        ('MA'(1)for a+b=>a),
         ('MA'(1)for a+b=>b)]
       )
     ])
@@ -125,7 +125,7 @@ test(
       Removed
     )
   ),
-  assertion(Added = ['MA'(1) for c+a=>a,'MA'(1) for a+b=>b,'MA'(1) for b+c=>c]),
+  assertion(Added = ['MA'(1) for a+c=>a,'MA'(1) for a+b=>b,'MA'(1) for b+c=>c]),
   assertion(Removed = ['MA'(1) for a=>_,'MA'(1) for b=>_,'MA'(1) for c=>_]).
 
 test(