Merge pull request #1 from bioasp/port-to-clasp-3.0.1

use pyasp-1.3

CHANGES.txt

@@ -1,3 +1,7 @@
+1.4
+----------
+use pyasp-1.3
+
 1.0 (unreleased)
 ----------------
 Initial release

setup.py

@@ -33,7 +33,7 @@ def run(self):
 
 setup(cmdclass={'install': install},
       name='meneco',
-      version='1.3.2',
+      version='1.4',
       url='http://pypi.python.org/pypi/meneco/',
       license='GPLv3+',
       description='Metabolic Network Completion. Compute minimal completions to your draft net with reactions from a repair net.',
@@ -45,6 +45,6 @@ def run(self):
       package_data = {'__meneco__' : ['encodings/*.lp']},
       scripts = ['meneco.py'],
       install_requires=[
-        "pyasp >= 1.2.1"
+        "pyasp == 1.3"
       ]
-)
+)

src/encodings/card_min_completions_all_targets.lp

@@ -109,9 +109,6 @@
 
 % optimizations
 
-  ireaction(R) :- ireaction(R,N).
-
-%#maximize [ xreaction(R)  : ireaction(R) : not reaction(R,N) : draft(N) : value(R,C) = C].
 #minimize [ not false= 0, xreaction(R,N)  : ireaction(R,N) ].
 
 #hide.

src/encodings/completions_all_targets.lp

@@ -8,6 +8,7 @@
 
 % find minimal set of xreactions such that xscope contains targets in pscope
 
+
 % what is producible by the original network
 
   dscope(M) :- seed(M).
@@ -28,7 +29,6 @@
   pscope(M) :- reactant(M,R,N), reaction(R,N), reversible(R),
                pscope(M2) : product(M2,R,N).
 
-
 % what are the interesting reactions
 % ireactions reactions are now defined in ireactions.lp
 
@@ -46,7 +46,6 @@
   oreaction(R,N) :- reaction(R,N), not draft(N), xscope(M) : reactant(M,R,N).
   oreaction(R,N) :- xscope(M) : product(M,R,N), reaction(R,N), reversible(R), not draft(N).
 
-
   :- xreaction(R,N), not oreaction(R,N).
 
 

src/encodings/ireactions.lp

@@ -11,7 +11,12 @@
 
 % what is producible by the original network
 
-  dreaction(R) :- reaction(R,N), draft(N).
+  samenames(R,N1,N2) :- reaction(R,N1),draft(N1),N1!=N2,reaction(R,N2).
+  samereactants(R) :- samenames(R,N1,N2), reactant(M2,R,N1): reactant(M2,R,N2).
+  sameproducts(R) :- samenames(R,N1,N2), products(M2,R,N1): products(M2,R,N2).
+  same(R):- samenames(R,N1,N2), samereactants(R), sameproducts(R), reversible(R,N1), reversible(R,N2).
+  same(R):- samenames(R,N1,N2), samereactants(R), sameproducts(R), not reversible(R,N1), not reversible(R,N2).
+
 
   dscope(M) :- seed(M).
 
@@ -51,7 +56,7 @@
   bireaction(R,N) :- binteresting(M), reactant(M,R,N), product(M2,R,N), not dscope(M2), reaction(R,N).
   bireaction(R,N) :- binteresting(M), product(M,R,N), reactant(M2,R,N), not dscope(M2), reaction(R,N), reversible(R).
 
- ireaction(R,N) :- iireaction(R,N), bireaction(R,N), not dreaction(R).
+ ireaction(R,N) :- iireaction(R,N), bireaction(R,N), not same(R).
 %  ireaction(R,N) :- iireaction(R,N), bireaction(R,N), not draft(N).
 
 %  iscope(M) :- seed(M).

src/query.py

@@ -43,7 +43,8 @@ def get_mapping_ireaction(termset):
     #print revdict
     #quit()
     return dict, revdict
-
+
+
 def map_reaction_ids(termset, dict):
     mapped = TermSet()
     for a in termset:
@@ -95,8 +96,7 @@ def unmap_reaction_ids(termset, revdict):
 
     return unmapped
 
-
-
+
 def get_unproducible(draft, seeds, targets):
     draft_f = draft.to_file()
     seed_f =  seeds.to_file()
@@ -109,6 +109,7 @@ def get_unproducible(draft, seeds, targets):
     os.unlink(target_f)
     return models[0]
 
+
 def compute_ireactions(instance):
     instance_f = instance.to_file()
     prg = [ ireaction_prg, instance_f]
@@ -128,17 +129,17 @@ def get_minimal_completion_size(draft, repairnet, seeds, targets):
     instance_f= instance.to_file()
     #prg = [minimal_completion_prg, heuristic_prg, instance_f]
     #co="--heu=domain"
-    #solver = GringoHClaspOpt(clasp_options=co)
+    #solver = GringoHClasp(clasp_options=co)
     prg = [minimal_completion_prg, instance_f]
 
-    solver = GringoUnClasp()
+    co="--opt-strategy=5"
+    solver = GringoClasp(clasp_options=co)
 
     optimum = solver.run(prg,collapseTerms=True, collapseAtoms=False)
     os.unlink(instance_f)
     return optimum
 
 
-
 def get_intersection_of_optimal_completions(draft, repairnet, seeds, targets, optimum):
     draftfact = String2TermSet('draft("draft")')
     ubfact = String2TermSet('ub('+str(optimum)+')')
@@ -153,8 +154,8 @@ def get_intersection_of_optimal_completions(draft, repairnet, seeds, targets, op
     #print revdict
     #exit()
     prg = [minimal_completion_wb_prg , instance_f ]
-    #options='-t 2 --enum-mode cautious --opt-all='+str(optimum)
-    options='--configuration jumpy --enum-mode cautious --opt-all='+str(optimum)
+    options='--configuration jumpy --enum-mode cautious --opt-mode=optN'
+
     solver = GringoClasp(clasp_options=options)
     models = solver.run(prg,nmodels=0,collapseTerms=True, collapseAtoms=False)
 
@@ -174,8 +175,8 @@ def get_union_of_optimal_completions(draft, repairnet, seeds, targets, optimum):
     instance = map_reaction_ids(instance.union(ireactions), dict)
 
     prg = [minimal_completion_wb_prg , instance.to_file() ]
-    #options='-t 2 --enum-mode brave --opt-all='+str(optimum)
-    options='--configuration jumpy --enum-mode brave --opt-all='+str(optimum)
+    options='--configuration jumpy --enum-mode brave --opt-mode=optN'
+
     solver = GringoClasp(clasp_options=options)
     models = solver.run(prg,nmodels=0,collapseTerms=True, collapseAtoms=False)
     os.unlink(prg[1])
@@ -195,7 +196,7 @@ def get_optimal_completions(draft, repairnet, seeds, targets, optimum, nmodels=0
     instance = map_reaction_ids(instance.union(ireactions), dict)    
 
     prg = [minimal_completion_wb_prg , instance.to_file() ]
-    options='--configuration jumpy --opt-all='+str(optimum)
+    options='--configuration jumpy --opt-mode=optN'    
     solver = GringoClasp(clasp_options=options)
     models = solver.run(prg,nmodels,collapseTerms=True, collapseAtoms=False)
     os.unlink(prg[1])
@@ -215,7 +216,8 @@ def get_intersection_of_completions(draft, repairnet, seeds, targets):
     instance_f = instance.to_file()
 
     prg = [completion_prg, instance_f]
-    options='--enum-mode cautious --opt-ignore '
+    options='--enum-mode cautious --opt-mode=ignore '
+
     solver = GringoClasp(clasp_options=options)
     models = solver.run(prg,nmodels=0,collapseTerms=True, collapseAtoms=False)
     os.unlink(instance_f)