def test_simple(self): complexes, reactions = read_pil(""" length a = 6 length a1 = 2 length a2 = 2 length a3 = 2 length b = 24 length b1 = 8 length b2 = 8 length b3 = 8 length c = 24 length c1 = 8 length c2 = 8 length c3 = 8 I = a b c C = b( c( + ) ) a* J = a( b c + b( c( + ) ) ) D = a( b( c( + ) ) ) cI = a1 a2 a3 b1 b2 b3 c1 c2 c3 cC = b1( b2( b3( c1( c2( c3( + ) ) ) ) ) ) a3* a2* a1* cJ = a1( a2( a3( b1 b2 b3 c1 c2 c3 + b1( b2( b3( c1( c2( c3( + ) ) ) ) ) ) ) ) ) cD = a1( a2( a3( b1( b2( b3( c1( c2( c3( + ) ) ) ) ) ) ) ) ) """) enum = Enumerator( [complexes['I'], complexes['C'], complexes['J'], complexes['D']], named_complexes=list(complexes.values())) enum.k_fast = 0 enum.k_slow = 0 enum.max_helix = True enum.enumerate() enum2 = Enumerator([ complexes['cI'], complexes['cC'], complexes['cJ'], complexes['cD'] ], named_complexes=list(complexes.values())) enum.k_fast = 0 enum2.k_fast = 0 enum2.k_slow = 0 enum2.max_helix = True enum2.enumerate() self.assertEqual(len(list(enum2.reactions)), len(list(enum.reactions)))
def test_cooperative_binding(self): complexes, reactions = read_pil(""" length a = 5 length x = 10 length y = 10 length b = 5 C = x( y( + b* ) ) a* L = a x R = y b T = x y LC = a( x + x( y( + b* ) ) ) CR = x( y( + y b( + ) ) ) a* LCR = a( x + x( y( + y b( + ) ) ) ) LCF = a( x( + x y( + b* ) ) ) CRF = x( y + y( b( + ) ) ) a* LCRF1 = a( x( + x y( + y b( + ) ) ) ) LCRF2 = a( x + x( y + y( b( + ) ) ) ) LR = a( x( + y( b( + ) ) ) ) """) C = complexes['C'] L = complexes['L'] R = complexes['R'] T = complexes['T'] LC = complexes['LC'] LCF = complexes['LCF'] CR = complexes['CR'] CRF = complexes['CRF'] LCRF1 = complexes['LCRF1'] LR = complexes['LR'] path1 = PepperReaction([L, C], [LC], 'bind21') path1r = PepperReaction([LC], [L, C], 'open') path2 = PepperReaction([LC], [LCF], 'branch-3way') path3 = PepperReaction([R, LCF], [LCRF1], 'bind21') path4 = PepperReaction([LCRF1], [LR, T], 'branch-3way') enum = Enumerator(list(complexes.values())) enum.k_fast = float('inf') enum.k_slow = 0 enum.max_helix = True enum.enumerate() self.assertEqual(len(list(enum.reactions)), 22)
def test_max_helix_01(self): complexes, reactions = read_pil(""" length a = 15 length x = 15 length x1 = 15 length x2 = 15 length y = 15 length y1 = 15 length y2 = 15 length z = 15 length z1 = 15 length z2 = 15 # should be one reaction, is one A1 = x( y z + y( z( + ) ) ) A1_2 = x( y( z( + ) ) ) YZ = y z # should be one reactions, is one B1 = x1( x2( y1 y2 z1 z2 + y1( y2( z1( z2( + ) ) ) ) ) ) B1_2 = x1( x2( y1( y2( z1( z2( + ) ) ) ) ) ) YZ2 = y1 y2 z1 z2 # should be two reactions, is two A2 = x( y z + y( + z( + ) ) ) A2_1 = x( y( z + z( + ) ) ) #A2_2 = x( y( z( + ) ) ) # = A1_2 Y1 = y Z1 = z # should be two reactions, is two B2 = x1( x2( y1 y2 z1 z2 + y1( y2( + z1( z2( + ) ) ) ) ) ) B2_1 = x1( x2( y1( y2( z1 z2 + z1( z2( + ) ) ) ) ) ) Y2 = y1 y2 Z2 = z1 z2 # should be two reactions, is two C = x( y z + y( + a( + ) z( + ) ) ) C1 = x( y( z + a( + ) z( + ) ) ) r1 = a( + ) z """) A1 = complexes['A1'] A1_2 = complexes['A1_2'] YZ = complexes['YZ'] A2 = complexes['A2'] A2_1 = complexes['A2_1'] #A2_2 = complexes['A2_2'] Y1 = complexes['Y1'] Z1 = complexes['Z1'] enum = Enumerator([A1, A2]) enum.k_fast = 0 enum.k_slow = 0 enum.max_helix = True enum.enumerate() path1 = PepperReaction([A1], sorted([A1_2, YZ]), 'branch-3way') path2 = PepperReaction([A2], sorted([A2_1, Y1]), 'branch-3way') path3 = PepperReaction([A2_1], sorted([A1_2, Z1]), 'branch-3way') self.assertEqual(sorted(enum.reactions), sorted([path1, path2, path3])) B1 = complexes['B1'] B1_2 = complexes['B1_2'] YZ2 = complexes['YZ2'] B2 = complexes['B2'] B2_1 = complexes['B2_1'] Y2 = complexes['Y2'] Z2 = complexes['Z2'] enum = Enumerator([B1, B2]) enum.k_fast = 0 enum.k_slow = 0 enum.max_helix = True enum.enumerate() path1 = PepperReaction([B1], sorted([B1_2, YZ2]), 'branch-3way') path2 = PepperReaction([B2], sorted([B2_1, Y2]), 'branch-3way') path3 = PepperReaction([B2_1], sorted([B1_2, Z2]), 'branch-3way') self.assertEqual(sorted(enum.reactions), sorted([path1, path2, path3])) C = complexes['C'] enum = Enumerator([C]) enum.k_fast = 0 enum.k_slow = 0 enum.max_helix = True enum.enumerate() self.assertEqual(len(list(enum.reactions)), 2)