From 5206acd43b2480db385984276630bdfcfe2dc79b Mon Sep 17 00:00:00 2001 From: vijay_ganesh Date: Wed, 12 Aug 2009 16:08:32 +0000 Subject: [PATCH] git-svn-id: https://stp-fast-prover.svn.sourceforge.net/svnroot/stp-fast-prover/trunk/stp@115 e59a4935-1847-0410-ae03-e826735625c1 --- liblinks.sh | 2 - src/AST/ToSAT.cpp | 11 +- .../4-alpha-helices-3-rungs-fewerbits.cvc | 473 ++++++++++++++++++ 3 files changed, 479 insertions(+), 7 deletions(-) create mode 100644 tests/bio-tests/4-alpha-helices-3-rungs-fewerbits.cvc diff --git a/liblinks.sh b/liblinks.sh index b6f3c35..2966385 100755 --- a/liblinks.sh +++ b/liblinks.sh @@ -2,8 +2,6 @@ # You can use this script to symbolically link the requested libraries. # You can then compile STP using: # make STATIC=true -# or -# make -f Makefile.smt STATIC=true # if you want to use the SMT-LIB parser ln -s `g++ -print-file-name=libstdc++.a` ln -s `g++ -print-file-name=libc.a` diff --git a/src/AST/ToSAT.cpp b/src/AST/ToSAT.cpp index 8d6b542..06f6e76 100644 --- a/src/AST/ToSAT.cpp +++ b/src/AST/ToSAT.cpp @@ -1221,7 +1221,7 @@ int BeevMgr::TopLevelSATAux(const ASTNode& inputasserts) } FatalError("TopLevelSATAux: reached the end without proper conclusion:" - "either a divide by zero in the input or a bug in STP"); + "either a divide by zero in the input or a bug in STP"); //bogus return to make the compiler shut up return 2; } //End of TopLevelSAT @@ -1242,8 +1242,7 @@ int BeevMgr::TopLevelSATAux(const ASTNode& inputasserts) // This is not the most obvious way to do it, and I don't know how it // compares with other approaches (e.g., one false axiom at a time or // all the false axioms each time). -int BeevMgr::SATBased_ArrayReadRefinement(MINISAT::Solver& newS, const ASTNode& q, const ASTNode& orig_input) -{ +int BeevMgr::SATBased_ArrayReadRefinement(MINISAT::Solver& newS, const ASTNode& q, const ASTNode& orig_input) { //printf("doing array read refinement\n"); if (!arrayread_refinement) FatalError("SATBased_ArrayReadRefinement: Control should not reach here"); @@ -1279,7 +1278,8 @@ int BeevMgr::SATBased_ArrayReadRefinement(MINISAT::Solver& newS, const ASTNode& //get the variable corresponding to the array_read1 ASTNode arrsym1 = _arrayread_symbol[arr_read1]; if (!(SYMBOL == arrsym1.GetKind() || BVCONST == arrsym1.GetKind())) - FatalError("TopLevelSAT: refinementloop:term arrsym1 corresponding to READ must be a var", arrsym1); + FatalError("TopLevelSAT: refinementloop:" + "term arrsym1 corresponding to READ must be a var", arrsym1); //we have nonconst index here. create Leibnitz axiom for it //w.r.t every index in listOfIndices @@ -1300,7 +1300,7 @@ int BeevMgr::SATBased_ArrayReadRefinement(MINISAT::Solver& newS, const ASTNode& ASTNode arrsym2 = _arrayread_symbol[arr_read2]; if (!(SYMBOL == arrsym2.GetKind() || BVCONST == arrsym2.GetKind())) FatalError("TopLevelSAT: refinement loop:" - "term arrsym2 corresponding to READ must be a var", arrsym2); + "term arrsym2 corresponding to READ must be a var", arrsym2); ASTNode eqOfReads = CreateSimplifiedEQ(arrsym1, arrsym2); //construct appropriate Leibnitz axiom @@ -1328,6 +1328,7 @@ int BeevMgr::SATBased_ArrayReadRefinement(MINISAT::Solver& newS, const ASTNode& } } } + //ASTNode RemainingAxioms = RemainingAxiomsVec[0]; ASTNode RemainingAxioms = (RemainingAxiomsVec.size() > 1) ? CreateNode(AND, RemainingAxiomsVec) : RemainingAxiomsVec[0]; ASTNodeStats("adding remaining readaxioms to SAT: ", RemainingAxioms); return CallSAT_ResultCheck(newS, RemainingAxioms, orig_input); diff --git a/tests/bio-tests/4-alpha-helices-3-rungs-fewerbits.cvc b/tests/bio-tests/4-alpha-helices-3-rungs-fewerbits.cvc new file mode 100644 index 0000000..5af3867 --- /dev/null +++ b/tests/bio-tests/4-alpha-helices-3-rungs-fewerbits.cvc @@ -0,0 +1,473 @@ +% 4 alpha helices. Each helix with 6 amino acid (residues), and 4 +% faces (two inner and two outer). Each face has 1 or 2 residues +% The problem is encoded with two bit bit-vector variable per face. + + +%%% ALPHA1 Helix variables +alpha1_inner1_length, alpha1_outer1_length, alpha1_inner2_length, alpha1_outer2_length, alpha1_inner3_length, alpha1_outer3_length : BITVECTOR(4); +alpha1_inner1_index, alpha1_outer1_index, alpha1_inner2_index, alpha1_outer2_index, alpha1_inner3_index, alpha1_outer3_index : BITVECTOR(12); +alpha1_inner1_energy, alpha1_outer1_energy, alpha1_inner2_energy, alpha1_outer2_energy, alpha1_inner3_energy, alpha1_outer3_energy : BITVECTOR(16); + + +%%% ALPHA2 Helix variables +alpha2_inner1_length, alpha2_outer1_length, alpha2_inner2_length, alpha2_outer2_length, alpha2_inner3_length, alpha2_outer3_length : BITVECTOR(4); +alpha2_inner1_index, alpha2_outer1_index, alpha2_inner2_index, alpha2_outer2_index, alpha2_inner3_index, alpha2_outer3_index : BITVECTOR(12); +alpha2_inner1_energy, alpha2_outer1_energy, alpha2_inner2_energy, alpha2_outer2_energy, alpha2_inner3_energy, alpha2_outer3_energy : BITVECTOR(16); + + +%%% ALPHA3 Helix variables +alpha3_inner1_length, alpha3_outer1_length, alpha3_inner2_length, alpha3_outer2_length, alpha3_inner3_length, alpha3_outer3_length : BITVECTOR(4); +alpha3_inner1_index, alpha3_outer1_index, alpha3_inner2_index, alpha3_outer2_index, alpha3_inner3_index, alpha3_outer3_index : BITVECTOR(12); +alpha3_inner1_energy, alpha3_outer1_energy, alpha3_inner2_energy, alpha3_outer2_energy, alpha3_inner3_energy, alpha3_outer3_energy : BITVECTOR(16); + + +%%% ALPHA4 Helix variables +alpha4_inner1_length, alpha4_outer1_length, alpha4_inner2_length, alpha4_outer2_length, alpha4_inner3_length, alpha4_outer3_length : BITVECTOR(4); +alpha4_inner1_index, alpha4_outer1_index, alpha4_inner2_index, alpha4_outer2_index, alpha4_inner3_index, alpha4_outer3_index : BITVECTOR(12); +alpha4_inner1_energy, alpha4_outer1_energy, alpha4_inner2_energy, alpha4_outer2_energy, alpha4_inner3_energy, alpha4_outer3_energy : BITVECTOR(16); + +start_coil_length, coil_12_length, coil_23_length, coil_34_length, end_coil_length : BITVECTOR(8); +start_coil_index, coil_12_index, coil_23_index, coil_34_index, end_coil_index : BITVECTOR(12); +start_coil_energy, coil_12_energy, coil_23_energy, coil_34_energy, end_coil_energy : BITVECTOR(16); + +contact_energy12_zero, contact_energy12_one, contact_energy12_two : BITVECTOR(16); +contact_energy23_zero, contact_energy23_one, contact_energy23_two : BITVECTOR(16); +contact_energy34_zero, contact_energy34_one, contact_energy34_two : BITVECTOR(16); +contact_energy41_zero, contact_energy41_one, contact_energy41_two : BITVECTOR(16); + +outer_energy : BITVECTOR(16); +inner_energy : BITVECTOR(16); +bits16_one : BITVECTOR(16); +bits16_two : BITVECTOR(16); +high_energy : BITVECTOR(16); +low_energy : BITVECTOR(16); + +rung_length_limit : BITVECTOR(4); +COIL_LEN_LOW_LIMIT : BITVECTOR(8); +COIL_LEN_HIGH_LIMIT : BITVECTOR(8); + + +%%%%%%%%%%%%%%%%%%%%%%%% START OF MACROS %%%%%%%%%%%%%%%%%%%%%%% +ASSERT (bits16_one = 0hex0001); +ASSERT (bits16_two = 0hex0002); +ASSERT (high_energy = 0hex0001); +ASSERT (low_energy = 0hex0000); +ASSERT (COIL_LEN_LOW_LIMIT = 0hex00); +ASSERT (COIL_LEN_HIGH_LIMIT = 0hex20); +%%%%%%%%%%%%%%%%%%%%%%%% END OF MACROS %%%%%%%%%%%%%%%%%%%%%%%% + + +%%%%%%%%%%%%%% START OF AMINO ACID ENERGY ARRAY %%%%%%%%%%%%% +aminoacid_energies : ARRAY BITVECTOR(12) OF BITVECTOR(16); +ASSERT (aminoacid_energies[0hex000] = high_energy); +ASSERT (aminoacid_energies[0hex001] = high_energy); +ASSERT (aminoacid_energies[0hex002] = low_energy); +ASSERT (aminoacid_energies[0hex003] = high_energy); +ASSERT (aminoacid_energies[0hex004] = low_energy); +ASSERT (aminoacid_energies[0hex005] = high_energy); +ASSERT (aminoacid_energies[0hex006] = low_energy); +ASSERT (aminoacid_energies[0hex007] = high_energy); +ASSERT (aminoacid_energies[0hex008] = low_energy); +ASSERT (aminoacid_energies[0hex009] = high_energy); +ASSERT (aminoacid_energies[0hex00A] = low_energy); +ASSERT (aminoacid_energies[0hex00B] = high_energy); +ASSERT (aminoacid_energies[0hex00C] = low_energy); +ASSERT (aminoacid_energies[0hex00D] = high_energy); +ASSERT (aminoacid_energies[0hex00E] = high_energy); +ASSERT (aminoacid_energies[0hex00F] = high_energy); +ASSERT (aminoacid_energies[0hex010] = high_energy); +ASSERT (aminoacid_energies[0hex011] = low_energy); +ASSERT (aminoacid_energies[0hex012] = high_energy); +ASSERT (aminoacid_energies[0hex013] = high_energy); +ASSERT (aminoacid_energies[0hex014] = low_energy); +ASSERT (aminoacid_energies[0hex015] = high_energy); +ASSERT (aminoacid_energies[0hex016] = low_energy); +ASSERT (aminoacid_energies[0hex017] = high_energy); +ASSERT (aminoacid_energies[0hex018] = low_energy); +ASSERT (aminoacid_energies[0hex019] = high_energy); +ASSERT (aminoacid_energies[0hex01A] = low_energy); +ASSERT (aminoacid_energies[0hex01B] = high_energy); +ASSERT (aminoacid_energies[0hex01C] = high_energy); +ASSERT (aminoacid_energies[0hex01D] = high_energy); +ASSERT (aminoacid_energies[0hex01E] = high_energy); +ASSERT (aminoacid_energies[0hex01F] = high_energy); +ASSERT (aminoacid_energies[0hex020] = high_energy); +ASSERT (aminoacid_energies[0hex021] = low_energy); +ASSERT (aminoacid_energies[0hex022] = high_energy); +ASSERT (aminoacid_energies[0hex023] = low_energy); +ASSERT (aminoacid_energies[0hex024] = high_energy); +ASSERT (aminoacid_energies[0hex025] = low_energy); +ASSERT (aminoacid_energies[0hex026] = high_energy); +ASSERT (aminoacid_energies[0hex027] = low_energy); +ASSERT (aminoacid_energies[0hex028] = high_energy); +ASSERT (aminoacid_energies[0hex029] = high_energy); +ASSERT (aminoacid_energies[0hex02A] = low_energy); +ASSERT (aminoacid_energies[0hex02B] = high_energy); +ASSERT (aminoacid_energies[0hex02C] = low_energy); +ASSERT (aminoacid_energies[0hex02D] = low_energy); +ASSERT (aminoacid_energies[0hex02E] = high_energy); +ASSERT (aminoacid_energies[0hex02F] = high_energy); +ASSERT (aminoacid_energies[0hex030] = low_energy); +ASSERT (aminoacid_energies[0hex031] = high_energy); +ASSERT (aminoacid_energies[0hex032] = low_energy); +ASSERT (aminoacid_energies[0hex033] = high_energy); +ASSERT (aminoacid_energies[0hex034] = low_energy); +ASSERT (aminoacid_energies[0hex035] = high_energy); +ASSERT (aminoacid_energies[0hex036] = low_energy); +ASSERT (aminoacid_energies[0hex037] = high_energy); +ASSERT (aminoacid_energies[0hex038] = low_energy); +ASSERT (aminoacid_energies[0hex039] = high_energy); +ASSERT (aminoacid_energies[0hex03A] = high_energy); +ASSERT (aminoacid_energies[0hex03B] = low_energy); +ASSERT (aminoacid_energies[0hex03C] = high_energy); +ASSERT (aminoacid_energies[0hex03D] = low_energy); +ASSERT (aminoacid_energies[0hex03E] = high_energy); +ASSERT (aminoacid_energies[0hex03F] = low_energy); +ASSERT (aminoacid_energies[0hex040] = high_energy); +ASSERT (aminoacid_energies[0hex041] = low_energy); +ASSERT (aminoacid_energies[0hex042] = high_energy); +ASSERT (aminoacid_energies[0hex043] = low_energy); +ASSERT (aminoacid_energies[0hex044] = high_energy); +ASSERT (aminoacid_energies[0hex045] = low_energy); +ASSERT (aminoacid_energies[0hex046] = high_energy); +ASSERT (aminoacid_energies[0hex047] = low_energy); +ASSERT (aminoacid_energies[0hex048] = high_energy); +ASSERT (aminoacid_energies[0hex049] = low_energy); +ASSERT (aminoacid_energies[0hex04A] = high_energy); +ASSERT (aminoacid_energies[0hex04B] = high_energy); +ASSERT (aminoacid_energies[0hex04C] = high_energy); +ASSERT (aminoacid_energies[0hex04D] = high_energy); +ASSERT (aminoacid_energies[0hex04E] = high_energy); +ASSERT (aminoacid_energies[0hex04F] = high_energy); +ASSERT (aminoacid_energies[0hex050] = high_energy); +ASSERT (aminoacid_energies[0hex051] = low_energy); +ASSERT (aminoacid_energies[0hex052] = high_energy); +ASSERT (aminoacid_energies[0hex053] = low_energy); +ASSERT (aminoacid_energies[0hex054] = high_energy); +ASSERT (aminoacid_energies[0hex055] = low_energy); +ASSERT (aminoacid_energies[0hex056] = high_energy); +ASSERT (aminoacid_energies[0hex057] = low_energy); +ASSERT (aminoacid_energies[0hex058] = high_energy); +ASSERT (aminoacid_energies[0hex059] = high_energy); +ASSERT (aminoacid_energies[0hex05A] = high_energy); +ASSERT (aminoacid_energies[0hex05B] = low_energy); +ASSERT (aminoacid_energies[0hex05C] = high_energy); +ASSERT (aminoacid_energies[0hex05D] = low_energy); +ASSERT (aminoacid_energies[0hex05E] = high_energy); +ASSERT (aminoacid_energies[0hex05F] = high_energy); +ASSERT (aminoacid_energies[0hex060] = low_energy); +ASSERT (aminoacid_energies[0hex061] = high_energy); +ASSERT (aminoacid_energies[0hex062] = high_energy); +ASSERT (aminoacid_energies[0hex063] = low_energy); + +%%%%%%%%%%%%%% END OF AMINO ACID ENERGY ARRAY %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + + +%%%%%%%%%%%%%%%%%%%%%%%%%% START OF RUNG LENGTH CONSTRAINTS %%%%%%%%%%%%%%%%%%%%%%%% + +ASSERT (alpha1_inner1_length = 0hex1 OR alpha1_inner1_length = 0hex2); +ASSERT (alpha1_outer1_length = 0hex1 OR alpha1_outer1_length = 0hex2); +ASSERT (alpha1_inner2_length = 0hex1 OR alpha1_inner2_length = 0hex2); +ASSERT (alpha1_outer2_length = 0hex1 OR alpha1_outer2_length = 0hex2); +ASSERT (alpha1_inner3_length = 0hex1 OR alpha1_inner3_length = 0hex2); +ASSERT (alpha1_outer3_length = 0hex1 OR alpha1_outer3_length = 0hex2); + +ASSERT (alpha2_inner1_length = 0hex1 OR alpha2_inner1_length = 0hex2); +ASSERT (alpha2_outer1_length = 0hex1 OR alpha2_outer1_length = 0hex2); +ASSERT (alpha2_inner2_length = 0hex1 OR alpha2_inner2_length = 0hex2); +ASSERT (alpha2_outer2_length = 0hex1 OR alpha2_outer2_length = 0hex2); +ASSERT (alpha2_inner3_length = 0hex1 OR alpha2_inner3_length = 0hex2); +ASSERT (alpha2_outer3_length = 0hex1 OR alpha2_outer3_length = 0hex2); + +ASSERT (alpha3_inner1_length = 0hex1 OR alpha3_inner1_length = 0hex2); +ASSERT (alpha3_outer1_length = 0hex1 OR alpha3_outer1_length = 0hex2); +ASSERT (alpha3_inner2_length = 0hex1 OR alpha3_inner2_length = 0hex2); +ASSERT (alpha3_outer2_length = 0hex1 OR alpha3_outer2_length = 0hex2); +ASSERT (alpha3_inner3_length = 0hex1 OR alpha3_inner3_length = 0hex2); +ASSERT (alpha3_outer3_length = 0hex1 OR alpha3_outer3_length = 0hex2); + +ASSERT (alpha4_inner1_length = 0hex1 OR alpha4_inner1_length = 0hex2); +ASSERT (alpha4_outer1_length = 0hex1 OR alpha4_outer1_length = 0hex2); +ASSERT (alpha4_inner2_length = 0hex1 OR alpha4_inner2_length = 0hex2); +ASSERT (alpha4_outer2_length = 0hex1 OR alpha4_outer2_length = 0hex2); +ASSERT (alpha4_inner3_length = 0hex1 OR alpha4_inner3_length = 0hex2); +ASSERT (alpha4_outer3_length = 0hex1 OR alpha4_outer3_length = 0hex2); + + +ASSERT (BVPLUS(4, alpha1_inner1_length, alpha1_outer1_length, alpha1_inner2_length, + alpha1_outer2_length, alpha1_inner3_length, alpha1_outer3_length) = 0hex9); +ASSERT (BVPLUS(4, alpha2_inner1_length, alpha2_outer1_length, alpha2_inner2_length, + alpha2_outer2_length, alpha2_inner3_length, alpha2_outer3_length) = 0hex9); +ASSERT (BVPLUS(4, alpha3_inner1_length, alpha3_outer1_length, alpha3_inner2_length, + alpha3_outer2_length, alpha3_inner3_length, alpha3_outer3_length) = 0hex9); +ASSERT (BVPLUS(4, alpha4_inner1_length, alpha4_outer1_length, alpha4_inner2_length, + alpha4_outer2_length, alpha4_inner3_length, alpha4_outer3_length) = 0hex9); + + +ASSERT (BVPLUS(4, alpha1_inner1_length, alpha1_outer1_length) = 0hex3); +ASSERT (BVPLUS(4, alpha1_inner2_length, alpha1_outer2_length) = 0hex3); +ASSERT (BVPLUS(4, alpha1_inner3_length, alpha1_outer3_length) = 0hex3); + +ASSERT (BVPLUS(4, alpha2_inner1_length, alpha2_outer1_length) = 0hex3); +ASSERT (BVPLUS(4, alpha2_inner2_length, alpha2_outer2_length) = 0hex3); +ASSERT (BVPLUS(4, alpha2_inner3_length, alpha2_outer3_length) = 0hex3); + +ASSERT (BVPLUS(4, alpha3_inner1_length, alpha3_outer1_length) = 0hex3); +ASSERT (BVPLUS(4, alpha3_inner2_length, alpha3_outer2_length) = 0hex3); +ASSERT (BVPLUS(4, alpha3_inner3_length, alpha3_outer3_length) = 0hex3); + +ASSERT (BVPLUS(4, alpha4_inner1_length, alpha4_outer1_length) = 0hex3); +ASSERT (BVPLUS(4, alpha4_inner2_length, alpha4_outer2_length) = 0hex3); +ASSERT (BVPLUS(4, alpha4_inner3_length, alpha4_outer3_length) = 0hex3); + +%%%%%%%%%%%%%%%%%%%%%%%%%% END OF RUNG LENGTH CONSTRAINTS %%%%%%%%%%%%%%%%%%%%%%%%%%%% + +%%%%%%%%%%%%%%%%%%%%%%%%%% END OF COIL LENGTH CONSTRAINTS %%%%%%%%%%%%%%%%%%%%%%%%%%%% + +ASSERT (BVLT(COIL_LEN_LOW_LIMIT,start_coil_length) AND BVLT(start_coil_length, COIL_LEN_HIGH_LIMIT)); +ASSERT (BVLT(COIL_LEN_LOW_LIMIT,coil_12_length) AND BVLT(coil_12_length, COIL_LEN_HIGH_LIMIT)); +ASSERT (BVLT(COIL_LEN_LOW_LIMIT,coil_23_length) AND BVLT(coil_23_length, COIL_LEN_HIGH_LIMIT)); +ASSERT (BVLT(COIL_LEN_LOW_LIMIT,coil_34_length) AND BVLT(coil_34_length, COIL_LEN_HIGH_LIMIT)); +ASSERT (BVLT(COIL_LEN_LOW_LIMIT,end_coil_length) AND BVLT(end_coil_length, COIL_LEN_HIGH_LIMIT)); + +ASSERT (0hex64 = BVPLUS(8,start_coil_length,coil_12_length,coil_23_length,coil_34_length,end_coil_length, + 0hex0@alpha1_inner1_length, 0hex0@alpha1_outer1_length, 0hex0@alpha1_inner2_length, + 0hex0@alpha1_outer2_length, 0hex0@alpha1_inner3_length, 0hex0@alpha1_outer3_length, + 0hex0@alpha2_inner1_length, 0hex0@alpha2_outer1_length, 0hex0@alpha2_inner2_length, + 0hex0@alpha2_outer2_length, 0hex0@alpha2_inner3_length, 0hex0@alpha2_outer3_length, + 0hex0@alpha3_inner1_length, 0hex0@alpha3_outer1_length, 0hex0@alpha3_inner2_length, + 0hex0@alpha3_outer2_length, 0hex0@alpha3_inner3_length, 0hex0@alpha3_outer3_length, + 0hex0@alpha4_inner1_length, 0hex0@alpha4_outer1_length, 0hex0@alpha4_inner2_length, + 0hex0@alpha4_outer2_length, 0hex0@alpha4_inner3_length, 0hex0@alpha4_outer3_length)); + +ASSERT (0hex0@start_coil_length = BVPLUS(12,start_coil_index,0hex001)); +ASSERT (0hex0@coil_12_length = BVSUB(12,coil_12_index,alpha1_outer3_index)); +ASSERT (0hex0@coil_23_length = BVSUB(12,coil_23_index,alpha2_inner1_index)); +ASSERT (0hex0@coil_34_length = BVSUB(12,coil_34_index,alpha3_outer3_index)); +ASSERT (0hex0@end_coil_length = BVSUB(12,0hex063,alpha4_inner1_index)); + +%%%%%%%%%%%%%%%%%%%%%%%%%% END OF COIL LENGTH CONSTRAINTS %%%%%%%%%%%%%%%%%%%%%%%%%%%% + + +%%%%%%%%%%%%%%%%%%%%%%%%%% START OF CHAINING %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +ASSERT (BVLE(0hex000,start_coil_index) AND BVLE(start_coil_index,0hex010)); +ASSERT (alpha1_inner1_length = 0hex1 => alpha1_inner1_index = BVPLUS(12,start_coil_index,0hex001)); +ASSERT (alpha1_inner1_length = 0hex2 => alpha1_inner1_index = BVPLUS(12,start_coil_index,0hex002)); +ASSERT (alpha1_outer1_length = 0hex1 => alpha1_outer1_index = BVPLUS(12,alpha1_inner1_index,0hex001)); +ASSERT (alpha1_outer1_length = 0hex2 => alpha1_outer1_index = BVPLUS(12,alpha1_inner1_index,0hex002)); +ASSERT (alpha1_inner2_length = 0hex1 => alpha1_inner2_index = BVPLUS(12,alpha1_outer1_index,0hex001)); +ASSERT (alpha1_inner2_length = 0hex2 => alpha1_inner2_index = BVPLUS(12,alpha1_outer1_index,0hex002)); +ASSERT (alpha1_outer2_length = 0hex1 => alpha1_outer2_index = BVPLUS(12,alpha1_inner2_index,0hex001)); +ASSERT (alpha1_outer2_length = 0hex2 => alpha1_outer2_index = BVPLUS(12,alpha1_inner2_index,0hex002)); +ASSERT (alpha1_inner3_length = 0hex1 => alpha1_inner3_index = BVPLUS(12,alpha1_outer2_index,0hex001)); +ASSERT (alpha1_inner3_length = 0hex2 => alpha1_inner3_index = BVPLUS(12,alpha1_outer2_index,0hex002)); +ASSERT (alpha1_outer3_length = 0hex1 => alpha1_outer3_index = BVPLUS(12,alpha1_inner3_index,0hex001)); +ASSERT (alpha1_outer3_length = 0hex2 => alpha1_outer3_index = BVPLUS(12,alpha1_inner3_index,0hex002)); + +ASSERT (BVLE(BVPLUS(12,0hex001,alpha1_outer3_index),coil_12_index) AND BVLE(coil_12_index, BVPLUS(12,alpha1_outer3_index,0hex00A))); +ASSERT (alpha2_outer3_length = 0hex1 => alpha2_outer3_index = BVPLUS(12,coil_12_index,0hex001)); +ASSERT (alpha2_outer3_length = 0hex2 => alpha2_outer3_index = BVPLUS(12,coil_12_index,0hex002)); +ASSERT (alpha2_inner3_length = 0hex1 => alpha2_inner3_index = BVPLUS(12,alpha2_outer3_index,0hex001)); +ASSERT (alpha2_inner3_length = 0hex2 => alpha2_inner3_index = BVPLUS(12,alpha2_outer3_index,0hex002)); +ASSERT (alpha2_outer2_length = 0hex1 => alpha2_outer2_index = BVPLUS(12,alpha2_inner3_index,0hex001)); +ASSERT (alpha2_outer2_length = 0hex2 => alpha2_outer2_index = BVPLUS(12,alpha2_inner3_index,0hex002)); +ASSERT (alpha2_inner2_length = 0hex1 => alpha2_inner2_index = BVPLUS(12,alpha2_outer2_index,0hex001)); +ASSERT (alpha2_inner2_length = 0hex2 => alpha2_inner2_index = BVPLUS(12,alpha2_outer2_index,0hex002)); +ASSERT (alpha2_outer1_length = 0hex1 => alpha2_outer1_index = BVPLUS(12,alpha2_inner2_index,0hex001)); +ASSERT (alpha2_outer1_length = 0hex2 => alpha2_outer1_index = BVPLUS(12,alpha2_inner2_index,0hex002)); +ASSERT (alpha2_inner1_length = 0hex1 => alpha2_inner1_index = BVPLUS(12,alpha2_outer1_index,0hex001)); +ASSERT (alpha2_inner1_length = 0hex2 => alpha2_inner1_index = BVPLUS(12,alpha2_outer1_index,0hex002)); + +ASSERT (BVLE(BVPLUS(12,0hex001,alpha2_inner1_index),coil_23_index) AND BVLE(coil_23_index, BVPLUS(12,alpha2_inner1_index,0hex00A))); +ASSERT (alpha3_inner1_length = 0hex1 => alpha3_inner1_index = BVPLUS(12,coil_23_index,0hex001)); +ASSERT (alpha3_inner1_length = 0hex2 => alpha3_inner1_index = BVPLUS(12,coil_23_index,0hex002)); +ASSERT (alpha3_outer1_length = 0hex1 => alpha3_outer1_index = BVPLUS(12,alpha3_inner1_index,0hex001)); +ASSERT (alpha3_outer1_length = 0hex2 => alpha3_outer1_index = BVPLUS(12,alpha3_inner1_index,0hex002)); +ASSERT (alpha3_inner2_length = 0hex1 => alpha3_inner2_index = BVPLUS(12,alpha3_outer1_index,0hex001)); +ASSERT (alpha3_inner2_length = 0hex2 => alpha3_inner2_index = BVPLUS(12,alpha3_outer1_index,0hex002)); +ASSERT (alpha3_outer2_length = 0hex1 => alpha3_outer2_index = BVPLUS(12,alpha3_inner2_index,0hex001)); +ASSERT (alpha3_outer2_length = 0hex2 => alpha3_outer2_index = BVPLUS(12,alpha3_inner2_index,0hex002)); +ASSERT (alpha3_inner3_length = 0hex1 => alpha3_inner3_index = BVPLUS(12,alpha3_outer2_index,0hex001)); +ASSERT (alpha3_inner3_length = 0hex2 => alpha3_inner3_index = BVPLUS(12,alpha3_outer2_index,0hex002)); +ASSERT (alpha3_outer3_length = 0hex1 => alpha3_outer3_index = BVPLUS(12,alpha3_inner3_index,0hex001)); +ASSERT (alpha3_outer3_length = 0hex2 => alpha3_outer3_index = BVPLUS(12,alpha3_inner3_index,0hex002)); + +ASSERT (BVLE(BVPLUS(12,0hex001,alpha3_outer3_index),coil_34_index) AND BVLE(coil_34_index, BVPLUS(12,alpha3_outer3_index,0hex00A))); +ASSERT (alpha4_outer3_length = 0hex1 => alpha4_outer3_index = BVPLUS(12,coil_34_index,0hex001)); +ASSERT (alpha4_outer3_length = 0hex2 => alpha4_outer3_index = BVPLUS(12,coil_34_index,0hex002)); +ASSERT (alpha4_inner3_length = 0hex1 => alpha4_inner3_index = BVPLUS(12,alpha4_outer3_index,0hex001)); +ASSERT (alpha4_inner3_length = 0hex2 => alpha4_inner3_index = BVPLUS(12,alpha4_outer3_index,0hex002)); +ASSERT (alpha4_outer2_length = 0hex1 => alpha4_outer2_index = BVPLUS(12,alpha4_inner3_index,0hex001)); +ASSERT (alpha4_outer2_length = 0hex2 => alpha4_outer2_index = BVPLUS(12,alpha4_inner3_index,0hex002)); +ASSERT (alpha4_inner2_length = 0hex1 => alpha4_inner2_index = BVPLUS(12,alpha4_outer2_index,0hex001)); +ASSERT (alpha4_inner2_length = 0hex2 => alpha4_inner2_index = BVPLUS(12,alpha4_outer2_index,0hex002)); +ASSERT (alpha4_outer1_length = 0hex1 => alpha4_outer1_index = BVPLUS(12,alpha4_inner2_index,0hex001)); +ASSERT (alpha4_outer1_length = 0hex2 => alpha4_outer1_index = BVPLUS(12,alpha4_inner2_index,0hex002)); +ASSERT (alpha4_inner1_length = 0hex1 => alpha4_inner1_index = BVPLUS(12,alpha4_outer1_index,0hex001)); +ASSERT (alpha4_inner1_length = 0hex2 => alpha4_inner1_index = BVPLUS(12,alpha4_outer1_index,0hex002)); + +ASSERT (BVLE(BVPLUS(12,0hex001,alpha4_inner1_index),end_coil_index) AND BVLE(end_coil_index, BVPLUS(12,alpha4_inner1_index,0hex020))); +%%%%%%%%%%%%%%%%%%%%%%%%%% END OF CHAINING %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + + +%%%%%%%%%%%%%%%%%%%%%%%%%% START OF ENERGY COMPUTATION ALPHA1 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +ASSERT (alpha1_inner1_length = 0hex1 => alpha1_inner1_energy = aminoacid_energies[alpha1_inner1_index]); +ASSERT (alpha1_inner1_length = 0hex2 => alpha1_inner1_energy = BVPLUS(16,aminoacid_energies[alpha1_inner1_index], + aminoacid_energies[BVSUB(12,alpha1_inner1_index,0hex001)])); + +ASSERT (alpha1_outer1_length = 0hex1 => alpha1_outer1_energy = BVSUB(16,bits16_one,aminoacid_energies[alpha1_outer1_index])); +ASSERT (alpha1_outer1_length = 0hex2 => alpha1_outer1_energy = BVSUB(16,bits16_two,BVPLUS(16,aminoacid_energies[alpha1_outer1_index], + aminoacid_energies[BVSUB(12,alpha1_outer1_index,0hex001)]))); + + +ASSERT (alpha1_inner2_length = 0hex1 => alpha1_inner2_energy = aminoacid_energies[alpha1_inner2_index]); +ASSERT (alpha1_inner2_length = 0hex2 => alpha1_inner2_energy = BVPLUS(16,aminoacid_energies[alpha1_inner2_index], + aminoacid_energies[BVSUB(12,alpha1_inner2_index,0hex001)])); + + +ASSERT (alpha1_outer2_length = 0hex1 => alpha1_outer2_energy = BVSUB(16,bits16_one,aminoacid_energies[alpha1_outer2_index])); +ASSERT (alpha1_outer2_length = 0hex2 => alpha1_outer2_energy = BVSUB(16,bits16_two,BVPLUS(16,aminoacid_energies[alpha1_outer2_index], + aminoacid_energies[BVSUB(12,alpha1_outer2_index,0hex001)]))); + +ASSERT (alpha1_inner3_length = 0hex1 => alpha1_inner3_energy = aminoacid_energies[alpha1_inner3_index]); +ASSERT (alpha1_inner3_length = 0hex2 => alpha1_inner3_energy = BVPLUS(16,aminoacid_energies[alpha1_inner3_index], + aminoacid_energies[BVSUB(12,alpha1_inner3_index,0hex001)])); + + +ASSERT (alpha1_outer3_length = 0hex1 => alpha1_outer3_energy = BVSUB(16,bits16_one,aminoacid_energies[alpha1_outer3_index])); +ASSERT (alpha1_outer3_length = 0hex2 => alpha1_outer3_energy = BVSUB(16,bits16_two, BVPLUS(16,aminoacid_energies[alpha1_outer3_index], + aminoacid_energies[BVSUB(12,alpha1_outer3_index,0hex001)]))); + +%%%%%%%%%%%%%%%%%%%%%%%%%% END OF ENERGY COMPUTATION ALPHA1 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + + +%%%%%%%%%%%%%%%%%%%%%%%%%% START OF ENERGY COMPUTATION ALPHA2 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +ASSERT (alpha2_inner1_length = 0hex1 => alpha2_inner1_energy = aminoacid_energies[alpha2_inner1_index]); +ASSERT (alpha2_inner1_length = 0hex2 => alpha2_inner1_energy = BVPLUS(16,aminoacid_energies[alpha2_inner1_index], + aminoacid_energies[BVSUB(12,alpha2_inner1_index,0hex001)])); + +ASSERT (alpha2_outer1_length = 0hex1 => alpha2_outer1_energy = BVSUB(16,bits16_one,aminoacid_energies[alpha2_outer1_index])); +ASSERT (alpha2_outer1_length = 0hex2 => alpha2_outer1_energy = BVSUB(16,bits16_two,BVPLUS(16,aminoacid_energies[alpha2_outer1_index], + aminoacid_energies[BVSUB(12,alpha2_outer1_index,0hex001)]))); + + +ASSERT (alpha2_inner2_length = 0hex1 => alpha2_inner2_energy = aminoacid_energies[alpha2_inner2_index]); +ASSERT (alpha2_inner2_length = 0hex2 => alpha2_inner2_energy = BVPLUS(16,aminoacid_energies[alpha2_inner2_index], + aminoacid_energies[BVSUB(12,alpha2_inner2_index,0hex001)])); + + +ASSERT (alpha2_outer2_length = 0hex1 => alpha2_outer2_energy = BVSUB(16,bits16_one,aminoacid_energies[alpha2_outer2_index])); +ASSERT (alpha2_outer2_length = 0hex2 => alpha2_outer2_energy = BVSUB(16,bits16_two,BVPLUS(16,aminoacid_energies[alpha2_outer2_index], + aminoacid_energies[BVSUB(12,alpha2_outer2_index,0hex001)]))); + +ASSERT (alpha2_inner3_length = 0hex1 => alpha2_inner3_energy = aminoacid_energies[alpha2_inner3_index]); +ASSERT (alpha2_inner3_length = 0hex2 => alpha2_inner3_energy = BVPLUS(16,aminoacid_energies[alpha2_inner3_index], + aminoacid_energies[BVSUB(12,alpha2_inner3_index,0hex001)])); + + +ASSERT (alpha2_outer3_length = 0hex1 => alpha2_outer3_energy = BVSUB(16,bits16_one,aminoacid_energies[alpha2_outer3_index])); +ASSERT (alpha2_outer3_length = 0hex2 => alpha2_outer3_energy = BVSUB(16,bits16_two, BVPLUS(16,aminoacid_energies[alpha2_outer3_index], + aminoacid_energies[BVSUB(12,alpha2_outer3_index,0hex001)]))); + +%%%%%%%%%%%%%%%%%%%%%%%%%% END OF ENERGY COMPUTATION ALPHA2 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + + +%%%%%%%%%%%%%%%%%%%%%%%%%% START OF ENERGY COMPUTATION ALPHA3 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +ASSERT (alpha3_inner1_length = 0hex1 => alpha3_inner1_energy = aminoacid_energies[alpha3_inner1_index]); +ASSERT (alpha3_inner1_length = 0hex2 => alpha3_inner1_energy = BVPLUS(16,aminoacid_energies[alpha3_inner1_index], + aminoacid_energies[BVSUB(12,alpha3_inner1_index,0hex001)])); + +ASSERT (alpha3_outer1_length = 0hex1 => alpha3_outer1_energy = BVSUB(16,bits16_one,aminoacid_energies[alpha3_outer1_index])); +ASSERT (alpha3_outer1_length = 0hex2 => alpha3_outer1_energy = BVSUB(16,bits16_two,BVPLUS(16,aminoacid_energies[alpha3_outer1_index], + aminoacid_energies[BVSUB(12,alpha3_outer1_index,0hex001)]))); + + +ASSERT (alpha3_inner2_length = 0hex1 => alpha3_inner2_energy = aminoacid_energies[alpha3_inner2_index]); +ASSERT (alpha3_inner2_length = 0hex2 => alpha3_inner2_energy = BVPLUS(16,aminoacid_energies[alpha3_inner2_index], + aminoacid_energies[BVSUB(12,alpha3_inner2_index,0hex001)])); + + +ASSERT (alpha3_outer2_length = 0hex1 => alpha3_outer2_energy = BVSUB(16,bits16_one,aminoacid_energies[alpha3_outer2_index])); +ASSERT (alpha3_outer2_length = 0hex2 => alpha3_outer2_energy = BVSUB(16,bits16_two,BVPLUS(16,aminoacid_energies[alpha3_outer2_index], + aminoacid_energies[BVSUB(12,alpha3_outer2_index,0hex001)]))); + +ASSERT (alpha3_inner3_length = 0hex1 => alpha3_inner3_energy = aminoacid_energies[alpha3_inner3_index]); +ASSERT (alpha3_inner3_length = 0hex2 => alpha3_inner3_energy = BVPLUS(16,aminoacid_energies[alpha3_inner3_index], + aminoacid_energies[BVSUB(12,alpha3_inner3_index,0hex001)])); + + +ASSERT (alpha3_outer3_length = 0hex1 => alpha3_outer3_energy = BVSUB(16,bits16_one,aminoacid_energies[alpha3_outer3_index])); +ASSERT (alpha3_outer3_length = 0hex2 => alpha3_outer3_energy = BVSUB(16,bits16_two, BVPLUS(16,aminoacid_energies[alpha3_outer3_index], + aminoacid_energies[BVSUB(12,alpha3_outer3_index,0hex001)]))); + +%%%%%%%%%%%%%%%%%%%%%%%%%% END OF ENERGY COMPUTATION ALPHA3 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + + +%%%%%%%%%%%%%%%%%%%%%%%%%% START OF ENERGY COMPUTATION ALPHA4 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +ASSERT (alpha4_inner1_length = 0hex1 => alpha4_inner1_energy = aminoacid_energies[alpha4_inner1_index]); +ASSERT (alpha4_inner1_length = 0hex2 => alpha4_inner1_energy = BVPLUS(16,aminoacid_energies[alpha4_inner1_index], + aminoacid_energies[BVSUB(12,alpha4_inner1_index,0hex001)])); + +ASSERT (alpha4_outer1_length = 0hex1 => alpha4_outer1_energy = BVSUB(16,bits16_one,aminoacid_energies[alpha4_outer1_index])); +ASSERT (alpha4_outer1_length = 0hex2 => alpha4_outer1_energy = BVSUB(16,bits16_two,BVPLUS(16,aminoacid_energies[alpha4_outer1_index], + aminoacid_energies[BVSUB(12,alpha4_outer1_index,0hex001)]))); + + +ASSERT (alpha4_inner2_length = 0hex1 => alpha4_inner2_energy = aminoacid_energies[alpha4_inner2_index]); +ASSERT (alpha4_inner2_length = 0hex2 => alpha4_inner2_energy = BVPLUS(16,aminoacid_energies[alpha4_inner2_index], + aminoacid_energies[BVSUB(12,alpha4_inner2_index,0hex001)])); + + +ASSERT (alpha4_outer2_length = 0hex1 => alpha4_outer2_energy = BVSUB(16,bits16_one,aminoacid_energies[alpha4_outer2_index])); +ASSERT (alpha4_outer2_length = 0hex2 => alpha4_outer2_energy = BVSUB(16,bits16_two,BVPLUS(16,aminoacid_energies[alpha4_outer2_index], + aminoacid_energies[BVSUB(12,alpha4_outer2_index,0hex001)]))); + +ASSERT (alpha4_inner3_length = 0hex1 => alpha4_inner3_energy = aminoacid_energies[alpha4_inner3_index]); +ASSERT (alpha4_inner3_length = 0hex2 => alpha4_inner3_energy = BVPLUS(16,aminoacid_energies[alpha4_inner3_index], + aminoacid_energies[BVSUB(12,alpha4_inner3_index,0hex001)])); + + +ASSERT (alpha4_outer3_length = 0hex1 => alpha4_outer3_energy = BVSUB(16,bits16_one,aminoacid_energies[alpha4_outer3_index])); +ASSERT (alpha4_outer3_length = 0hex2 => alpha4_outer3_energy = BVSUB(16,bits16_two, BVPLUS(16,aminoacid_energies[alpha4_outer3_index], + aminoacid_energies[BVSUB(12,alpha4_outer3_index,0hex001)]))); + +%%%%%%%%%%%%%%%%%%%%%%%%%% END OF ENERGY COMPUTATION ALPHA4 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +ASSERT (contact_energy12_zero = BVPLUS(16, alpha1_inner1_energy, alpha2_inner1_energy)); +ASSERT (contact_energy12_one = BVPLUS(16, alpha1_inner2_energy, alpha2_inner2_energy)); +ASSERT (contact_energy12_two = BVPLUS(16, alpha1_inner3_energy, alpha2_inner3_energy)); + + +ASSERT (contact_energy23_zero = BVPLUS(16, alpha2_inner1_energy, alpha3_inner1_energy)); +ASSERT (contact_energy23_one = BVPLUS(16, alpha2_inner2_energy, alpha3_inner2_energy)); +ASSERT (contact_energy23_two = BVPLUS(16, alpha2_inner3_energy, alpha3_inner3_energy)); + + +ASSERT (contact_energy34_zero = BVPLUS(16, alpha3_inner1_energy, alpha4_inner1_energy)); +ASSERT (contact_energy34_one = BVPLUS(16, alpha3_inner2_energy, alpha4_inner2_energy)); +ASSERT (contact_energy34_two = BVPLUS(16, alpha3_inner3_energy, alpha4_inner3_energy)); + +ASSERT (contact_energy41_zero = BVPLUS(16, alpha4_inner1_energy, alpha1_inner1_energy)); +ASSERT (contact_energy41_one = BVPLUS(16, alpha4_inner2_energy, alpha1_inner2_energy)); +ASSERT (contact_energy41_two = BVPLUS(16, alpha4_inner3_energy, alpha1_inner3_energy)); + +ASSERT (outer_energy = BVPLUS(16, alpha1_outer1_energy, alpha1_outer2_energy, alpha1_outer3_energy, + alpha2_outer1_energy, alpha2_outer2_energy, alpha2_outer3_energy, + alpha3_outer1_energy, alpha3_outer2_energy, alpha3_outer3_energy, + alpha4_outer1_energy, alpha4_outer2_energy, alpha4_outer3_energy)); + + +ASSERT (inner_energy = BVPLUS(16, contact_energy12_zero, contact_energy12_one, contact_energy12_two, + contact_energy23_zero, contact_energy23_one, contact_energy23_two, + contact_energy34_zero, contact_energy34_one, contact_energy34_two, + contact_energy41_zero, contact_energy41_one, contact_energy41_two)); + + +% final query +ASSERT (BVGE(inner_energy, 0hex00F0)); +QUERY FALSE; \ No newline at end of file -- 2.47.3