+++ /dev/null
-% 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
--- /dev/null
+% 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);
+
+
+%%%%%%%%%%%%%%%%%%%%%%%% START OF MACROS %%%%%%%%%%%%%%%%%%%%%%%
+BITS12_ZERO_MACRO : BITVECTOR(12);
+BITS12_ONE_MACRO : BITVECTOR(12);
+BITS16_ONE_MACRO : BITVECTOR(16);
+BITS16_TWO_MACRO : BITVECTOR(16);
+
+HIGH_ENERGY_MACRO : BITVECTOR(16);
+LOW_ENERGY_MACRO : BITVECTOR(16);
+
+FACE_LEN1_MACRO : BITVECTOR(4);
+FACE_LEN2_MACRO : BITVECTOR(4);
+RUNG_LEN_MACRO : BITVECTOR(4);
+HELIX_LEN_MACRO : BITVECTOR(4);
+COIL_LEN_LOW_MACRO : BITVECTOR(8);
+COIL_LEN_HIGH_MACRO : BITVECTOR(8);
+
+LAST_ARRAYINDEX_MACRO : BITVECTOR(12);
+STARTCOIL_HIGHINDEX_MACRO : BITVECTOR(12);
+COIL12_HIGHINDEX_MACRO : BITVECTOR(12);
+COIL23_HIGHINDEX_MACRO : BITVECTOR(12);
+COIL34_HIGHINDEX_MACRO : BITVECTOR(12);
+ENDCOIL_HIGHINDEX_MACRO : BITVECTOR(12);
+
+ASSERT (BITS12_ZERO_MACRO = 0hex000);
+ASSERT (BITS12_ONE_MACRO = 0hex001);
+ASSERT (BITS16_ONE_MACRO = 0hex0001);
+ASSERT (BITS16_TWO_MACRO = 0hex0002);
+
+ASSERT (HIGH_ENERGY_MACRO = 0hex0001);
+ASSERT (LOW_ENERGY_MACRO = 0hex0000);
+
+ASSERT (FACE_LEN1_MACRO = 0hex1);
+ASSERT (FACE_LEN2_MACRO = 0hex2);
+ASSERT (RUNG_LEN_MACRO = 0hex3);
+ASSERT (HELIX_LEN_MACRO = 0hex9);
+ASSERT (COIL_LEN_LOW_MACRO = 0hex00);
+ASSERT (COIL_LEN_HIGH_MACRO = 0hex20);
+
+ASSERT (LAST_ARRAYINDEX_MACRO = 0hex063);
+ASSERT (STARTCOIL_HIGHINDEX_MACRO = 0hex010);
+ASSERT (COIL12_HIGHINDEX_MACRO = 0hex00A);
+ASSERT (COIL23_HIGHINDEX_MACRO = 0hex00A);
+ASSERT (COIL34_HIGHINDEX_MACRO = 0hex00A);
+ASSERT (ENDCOIL_HIGHINDEX_MACRO = 0hex020);
+
+%%%%%%%%%%%%%%%%%%%%%%%% END OF MACROS %%%%%%%%%%%%%%%%%%%%%%
+
+
+%%%%%%%%%%%%%% START OF AMINO ACID ENERGY ARRAY %%%%%%%%%%%%%
+aminoacid_energies : ARRAY BITVECTOR(12) OF BITVECTOR(16);
+ASSERT (aminoacid_energies[0hex000] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex001] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex002] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex003] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex004] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex005] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex006] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex007] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex008] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex009] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex00A] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex00B] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex00C] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex00D] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex00E] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex00F] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex010] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex011] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex012] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex013] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex014] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex015] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex016] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex017] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex018] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex019] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex01A] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex01B] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex01C] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex01D] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex01E] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex01F] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex020] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex021] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex022] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex023] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex024] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex025] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex026] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex027] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex028] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex029] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex02A] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex02B] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex02C] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex02D] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex02E] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex02F] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex030] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex031] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex032] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex033] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex034] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex035] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex036] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex037] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex038] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex039] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex03A] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex03B] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex03C] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex03D] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex03E] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex03F] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex040] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex041] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex042] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex043] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex044] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex045] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex046] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex047] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex048] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex049] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex04A] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex04B] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex04C] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex04D] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex04E] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex04F] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex050] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex051] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex052] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex053] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex054] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex055] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex056] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex057] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex058] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex059] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex05A] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex05B] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex05C] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex05D] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex05E] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex05F] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex060] = LOW_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex061] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex062] = HIGH_ENERGY_MACRO);
+ASSERT (aminoacid_energies[0hex063] = LOW_ENERGY_MACRO);
+%%%%%%%%%%%%%% END OF AMINO ACID ENERGY ARRAY %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%% START OF RUNG LENGTH CONSTRAINTS %%%%%%%%%%%%%%%%%%%%%%%%
+
+ASSERT (alpha1_inner1_length = FACE_LEN1_MACRO OR alpha1_inner1_length = FACE_LEN2_MACRO);
+ASSERT (alpha1_outer1_length = FACE_LEN1_MACRO OR alpha1_outer1_length = FACE_LEN2_MACRO);
+ASSERT (alpha1_inner2_length = FACE_LEN1_MACRO OR alpha1_inner2_length = FACE_LEN2_MACRO);
+ASSERT (alpha1_outer2_length = FACE_LEN1_MACRO OR alpha1_outer2_length = FACE_LEN2_MACRO);
+ASSERT (alpha1_inner3_length = FACE_LEN1_MACRO OR alpha1_inner3_length = FACE_LEN2_MACRO);
+ASSERT (alpha1_outer3_length = FACE_LEN1_MACRO OR alpha1_outer3_length = FACE_LEN2_MACRO);
+
+ASSERT (alpha2_inner1_length = FACE_LEN1_MACRO OR alpha2_inner1_length = FACE_LEN2_MACRO);
+ASSERT (alpha2_outer1_length = FACE_LEN1_MACRO OR alpha2_outer1_length = FACE_LEN2_MACRO);
+ASSERT (alpha2_inner2_length = FACE_LEN1_MACRO OR alpha2_inner2_length = FACE_LEN2_MACRO);
+ASSERT (alpha2_outer2_length = FACE_LEN1_MACRO OR alpha2_outer2_length = FACE_LEN2_MACRO);
+ASSERT (alpha2_inner3_length = FACE_LEN1_MACRO OR alpha2_inner3_length = FACE_LEN2_MACRO);
+ASSERT (alpha2_outer3_length = FACE_LEN1_MACRO OR alpha2_outer3_length = FACE_LEN2_MACRO);
+
+ASSERT (alpha3_inner1_length = FACE_LEN1_MACRO OR alpha3_inner1_length = FACE_LEN2_MACRO);
+ASSERT (alpha3_outer1_length = FACE_LEN1_MACRO OR alpha3_outer1_length = FACE_LEN2_MACRO);
+ASSERT (alpha3_inner2_length = FACE_LEN1_MACRO OR alpha3_inner2_length = FACE_LEN2_MACRO);
+ASSERT (alpha3_outer2_length = FACE_LEN1_MACRO OR alpha3_outer2_length = FACE_LEN2_MACRO);
+ASSERT (alpha3_inner3_length = FACE_LEN1_MACRO OR alpha3_inner3_length = FACE_LEN2_MACRO);
+ASSERT (alpha3_outer3_length = FACE_LEN1_MACRO OR alpha3_outer3_length = FACE_LEN2_MACRO);
+
+ASSERT (alpha4_inner1_length = FACE_LEN1_MACRO OR alpha4_inner1_length = FACE_LEN2_MACRO);
+ASSERT (alpha4_outer1_length = FACE_LEN1_MACRO OR alpha4_outer1_length = FACE_LEN2_MACRO);
+ASSERT (alpha4_inner2_length = FACE_LEN1_MACRO OR alpha4_inner2_length = FACE_LEN2_MACRO);
+ASSERT (alpha4_outer2_length = FACE_LEN1_MACRO OR alpha4_outer2_length = FACE_LEN2_MACRO);
+ASSERT (alpha4_inner3_length = FACE_LEN1_MACRO OR alpha4_inner3_length = FACE_LEN2_MACRO);
+ASSERT (alpha4_outer3_length = FACE_LEN1_MACRO OR alpha4_outer3_length = FACE_LEN2_MACRO);
+
+
+ASSERT (BVPLUS(4, alpha1_inner1_length, alpha1_outer1_length, alpha1_inner2_length,
+ alpha1_outer2_length, alpha1_inner3_length, alpha1_outer3_length) = HELIX_LEN_MACRO);
+ASSERT (BVPLUS(4, alpha2_inner1_length, alpha2_outer1_length, alpha2_inner2_length,
+ alpha2_outer2_length, alpha2_inner3_length, alpha2_outer3_length) = HELIX_LEN_MACRO);
+ASSERT (BVPLUS(4, alpha3_inner1_length, alpha3_outer1_length, alpha3_inner2_length,
+ alpha3_outer2_length, alpha3_inner3_length, alpha3_outer3_length) = HELIX_LEN_MACRO);
+ASSERT (BVPLUS(4, alpha4_inner1_length, alpha4_outer1_length, alpha4_inner2_length,
+ alpha4_outer2_length, alpha4_inner3_length, alpha4_outer3_length) = HELIX_LEN_MACRO);
+
+
+ASSERT (BVPLUS(4, alpha1_inner1_length, alpha1_outer1_length) = RUNG_LEN_MACRO);
+ASSERT (BVPLUS(4, alpha1_inner2_length, alpha1_outer2_length) = RUNG_LEN_MACRO);
+ASSERT (BVPLUS(4, alpha1_inner3_length, alpha1_outer3_length) = RUNG_LEN_MACRO);
+
+ASSERT (BVPLUS(4, alpha2_inner1_length, alpha2_outer1_length) = RUNG_LEN_MACRO);
+ASSERT (BVPLUS(4, alpha2_inner2_length, alpha2_outer2_length) = RUNG_LEN_MACRO);
+ASSERT (BVPLUS(4, alpha2_inner3_length, alpha2_outer3_length) = RUNG_LEN_MACRO);
+
+ASSERT (BVPLUS(4, alpha3_inner1_length, alpha3_outer1_length) = RUNG_LEN_MACRO);
+ASSERT (BVPLUS(4, alpha3_inner2_length, alpha3_outer2_length) = RUNG_LEN_MACRO);
+ASSERT (BVPLUS(4, alpha3_inner3_length, alpha3_outer3_length) = RUNG_LEN_MACRO);
+
+ASSERT (BVPLUS(4, alpha4_inner1_length, alpha4_outer1_length) = RUNG_LEN_MACRO);
+ASSERT (BVPLUS(4, alpha4_inner2_length, alpha4_outer2_length) = RUNG_LEN_MACRO);
+ASSERT (BVPLUS(4, alpha4_inner3_length, alpha4_outer3_length) = RUNG_LEN_MACRO);
+
+%%%%%%%%%%%%%%%%%%%%%%%%%% END OF RUNG LENGTH CONSTRAINTS %%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%% END OF COIL LENGTH CONSTRAINTS %%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+ASSERT (BVLT(COIL_LEN_LOW_MACRO,start_coil_length) AND BVLT(start_coil_length, COIL_LEN_HIGH_MACRO));
+ASSERT (BVLT(COIL_LEN_LOW_MACRO,coil_12_length) AND BVLT(coil_12_length, COIL_LEN_HIGH_MACRO));
+ASSERT (BVLT(COIL_LEN_LOW_MACRO,coil_23_length) AND BVLT(coil_23_length, COIL_LEN_HIGH_MACRO));
+ASSERT (BVLT(COIL_LEN_LOW_MACRO,coil_34_length) AND BVLT(coil_34_length, COIL_LEN_HIGH_MACRO));
+ASSERT (BVLT(COIL_LEN_LOW_MACRO,end_coil_length) AND BVLT(end_coil_length, COIL_LEN_HIGH_MACRO));
+
+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,BITS12_ONE_MACRO));
+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,LAST_ARRAYINDEX_MACRO,alpha4_inner1_index));
+
+%%%%%%%%%%%%%%%%%%%%%%%%%% END OF COIL LENGTH CONSTRAINTS %%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%% START OF CHAINING %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ASSERT (BVLE(BITS12_ZERO_MACRO,start_coil_index) AND BVLE(start_coil_index,STARTCOIL_HIGHINDEX_MACRO));
+ASSERT (alpha1_inner1_length = FACE_LEN1_MACRO => alpha1_inner1_index = BVPLUS(12,start_coil_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha1_inner1_length = FACE_LEN2_MACRO => alpha1_inner1_index = BVPLUS(12,start_coil_index,0hex00@FACE_LEN2_MACRO));
+ASSERT (alpha1_outer1_length = FACE_LEN1_MACRO => alpha1_outer1_index = BVPLUS(12,alpha1_inner1_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha1_outer1_length = FACE_LEN2_MACRO => alpha1_outer1_index = BVPLUS(12,alpha1_inner1_index,0hex00@FACE_LEN2_MACRO));
+ASSERT (alpha1_inner2_length = FACE_LEN1_MACRO => alpha1_inner2_index = BVPLUS(12,alpha1_outer1_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha1_inner2_length = FACE_LEN2_MACRO => alpha1_inner2_index = BVPLUS(12,alpha1_outer1_index,0hex00@FACE_LEN2_MACRO));
+ASSERT (alpha1_outer2_length = FACE_LEN1_MACRO => alpha1_outer2_index = BVPLUS(12,alpha1_inner2_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha1_outer2_length = FACE_LEN2_MACRO => alpha1_outer2_index = BVPLUS(12,alpha1_inner2_index,0hex00@FACE_LEN2_MACRO));
+ASSERT (alpha1_inner3_length = FACE_LEN1_MACRO => alpha1_inner3_index = BVPLUS(12,alpha1_outer2_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha1_inner3_length = FACE_LEN2_MACRO => alpha1_inner3_index = BVPLUS(12,alpha1_outer2_index,0hex00@FACE_LEN2_MACRO));
+ASSERT (alpha1_outer3_length = FACE_LEN1_MACRO => alpha1_outer3_index = BVPLUS(12,alpha1_inner3_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha1_outer3_length = FACE_LEN2_MACRO => alpha1_outer3_index = BVPLUS(12,alpha1_inner3_index,0hex00@FACE_LEN2_MACRO));
+
+ASSERT (BVLE(BVPLUS(12,BITS12_ONE_MACRO,alpha1_outer3_index),coil_12_index) AND BVLE(coil_12_index, BVPLUS(12,alpha1_outer3_index,COIL12_HIGHINDEX_MACRO)));
+ASSERT (alpha2_outer3_length = FACE_LEN1_MACRO => alpha2_outer3_index = BVPLUS(12,coil_12_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha2_outer3_length = FACE_LEN2_MACRO => alpha2_outer3_index = BVPLUS(12,coil_12_index,0hex00@FACE_LEN2_MACRO));
+ASSERT (alpha2_inner3_length = FACE_LEN1_MACRO => alpha2_inner3_index = BVPLUS(12,alpha2_outer3_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha2_inner3_length = FACE_LEN2_MACRO => alpha2_inner3_index = BVPLUS(12,alpha2_outer3_index,0hex00@FACE_LEN2_MACRO));
+ASSERT (alpha2_outer2_length = FACE_LEN1_MACRO => alpha2_outer2_index = BVPLUS(12,alpha2_inner3_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha2_outer2_length = FACE_LEN2_MACRO => alpha2_outer2_index = BVPLUS(12,alpha2_inner3_index,0hex00@FACE_LEN2_MACRO));
+ASSERT (alpha2_inner2_length = FACE_LEN1_MACRO => alpha2_inner2_index = BVPLUS(12,alpha2_outer2_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha2_inner2_length = FACE_LEN2_MACRO => alpha2_inner2_index = BVPLUS(12,alpha2_outer2_index,0hex00@FACE_LEN2_MACRO));
+ASSERT (alpha2_outer1_length = FACE_LEN1_MACRO => alpha2_outer1_index = BVPLUS(12,alpha2_inner2_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha2_outer1_length = FACE_LEN2_MACRO => alpha2_outer1_index = BVPLUS(12,alpha2_inner2_index,0hex00@FACE_LEN2_MACRO));
+ASSERT (alpha2_inner1_length = FACE_LEN1_MACRO => alpha2_inner1_index = BVPLUS(12,alpha2_outer1_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha2_inner1_length = FACE_LEN2_MACRO => alpha2_inner1_index = BVPLUS(12,alpha2_outer1_index,0hex00@FACE_LEN2_MACRO));
+
+ASSERT (BVLE(BVPLUS(12,BITS12_ONE_MACRO,alpha2_inner1_index),coil_23_index) AND BVLE(coil_23_index, BVPLUS(12,alpha2_inner1_index,COIL23_HIGHINDEX_MACRO)));
+ASSERT (alpha3_inner1_length = FACE_LEN1_MACRO => alpha3_inner1_index = BVPLUS(12,coil_23_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha3_inner1_length = FACE_LEN2_MACRO => alpha3_inner1_index = BVPLUS(12,coil_23_index,0hex00@FACE_LEN2_MACRO));
+ASSERT (alpha3_outer1_length = FACE_LEN1_MACRO => alpha3_outer1_index = BVPLUS(12,alpha3_inner1_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha3_outer1_length = FACE_LEN2_MACRO => alpha3_outer1_index = BVPLUS(12,alpha3_inner1_index,0hex00@FACE_LEN2_MACRO));
+ASSERT (alpha3_inner2_length = FACE_LEN1_MACRO => alpha3_inner2_index = BVPLUS(12,alpha3_outer1_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha3_inner2_length = FACE_LEN2_MACRO => alpha3_inner2_index = BVPLUS(12,alpha3_outer1_index,0hex00@FACE_LEN2_MACRO));
+ASSERT (alpha3_outer2_length = FACE_LEN1_MACRO => alpha3_outer2_index = BVPLUS(12,alpha3_inner2_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha3_outer2_length = FACE_LEN2_MACRO => alpha3_outer2_index = BVPLUS(12,alpha3_inner2_index,0hex00@FACE_LEN2_MACRO));
+ASSERT (alpha3_inner3_length = FACE_LEN1_MACRO => alpha3_inner3_index = BVPLUS(12,alpha3_outer2_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha3_inner3_length = FACE_LEN2_MACRO => alpha3_inner3_index = BVPLUS(12,alpha3_outer2_index,0hex00@FACE_LEN2_MACRO));
+ASSERT (alpha3_outer3_length = FACE_LEN1_MACRO => alpha3_outer3_index = BVPLUS(12,alpha3_inner3_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha3_outer3_length = FACE_LEN2_MACRO => alpha3_outer3_index = BVPLUS(12,alpha3_inner3_index,0hex00@FACE_LEN2_MACRO));
+
+ASSERT (BVLE(BVPLUS(12,BITS12_ONE_MACRO,alpha3_outer3_index),coil_34_index) AND BVLE(coil_34_index, BVPLUS(12,alpha3_outer3_index,COIL34_HIGHINDEX_MACRO)));
+ASSERT (alpha4_outer3_length = FACE_LEN1_MACRO => alpha4_outer3_index = BVPLUS(12,coil_34_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha4_outer3_length = FACE_LEN2_MACRO => alpha4_outer3_index = BVPLUS(12,coil_34_index,0hex00@FACE_LEN2_MACRO));
+ASSERT (alpha4_inner3_length = FACE_LEN1_MACRO => alpha4_inner3_index = BVPLUS(12,alpha4_outer3_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha4_inner3_length = FACE_LEN2_MACRO => alpha4_inner3_index = BVPLUS(12,alpha4_outer3_index,0hex00@FACE_LEN2_MACRO));
+ASSERT (alpha4_outer2_length = FACE_LEN1_MACRO => alpha4_outer2_index = BVPLUS(12,alpha4_inner3_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha4_outer2_length = FACE_LEN2_MACRO => alpha4_outer2_index = BVPLUS(12,alpha4_inner3_index,0hex00@FACE_LEN2_MACRO));
+ASSERT (alpha4_inner2_length = FACE_LEN1_MACRO => alpha4_inner2_index = BVPLUS(12,alpha4_outer2_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha4_inner2_length = FACE_LEN2_MACRO => alpha4_inner2_index = BVPLUS(12,alpha4_outer2_index,0hex00@FACE_LEN2_MACRO));
+ASSERT (alpha4_outer1_length = FACE_LEN1_MACRO => alpha4_outer1_index = BVPLUS(12,alpha4_inner2_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha4_outer1_length = FACE_LEN2_MACRO => alpha4_outer1_index = BVPLUS(12,alpha4_inner2_index,0hex00@FACE_LEN2_MACRO));
+ASSERT (alpha4_inner1_length = FACE_LEN1_MACRO => alpha4_inner1_index = BVPLUS(12,alpha4_outer1_index,0hex00@FACE_LEN1_MACRO));
+ASSERT (alpha4_inner1_length = FACE_LEN2_MACRO => alpha4_inner1_index = BVPLUS(12,alpha4_outer1_index,0hex00@FACE_LEN2_MACRO));
+
+ASSERT (BVLE(BVPLUS(12,BITS12_ONE_MACRO,alpha4_inner1_index),end_coil_index) AND BVLE(end_coil_index, BVPLUS(12,alpha4_inner1_index,ENDCOIL_HIGHINDEX_MACRO)));
+%%%%%%%%%%%%%%%%%%%%%%%%%% END OF CHAINING %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%% START OF ENERGY COMPUTATION ALPHA1 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+ASSERT (alpha1_inner1_length = FACE_LEN1_MACRO => alpha1_inner1_energy = aminoacid_energies[alpha1_inner1_index]);
+ASSERT (alpha1_inner1_length = FACE_LEN2_MACRO => alpha1_inner1_energy = BVPLUS(16,aminoacid_energies[alpha1_inner1_index],
+ aminoacid_energies[BVSUB(12,alpha1_inner1_index,BITS12_ONE_MACRO)]));
+
+ASSERT (alpha1_outer1_length = FACE_LEN1_MACRO => alpha1_outer1_energy = BVSUB(16,BITS16_ONE_MACRO,aminoacid_energies[alpha1_outer1_index]));
+ASSERT (alpha1_outer1_length = FACE_LEN2_MACRO => alpha1_outer1_energy = BVSUB(16,BITS16_TWO_MACRO,BVPLUS(16,aminoacid_energies[alpha1_outer1_index],
+ aminoacid_energies[BVSUB(12,alpha1_outer1_index,BITS12_ONE_MACRO)])));
+
+
+ASSERT (alpha1_inner2_length = FACE_LEN1_MACRO => alpha1_inner2_energy = aminoacid_energies[alpha1_inner2_index]);
+ASSERT (alpha1_inner2_length = FACE_LEN2_MACRO => alpha1_inner2_energy = BVPLUS(16,aminoacid_energies[alpha1_inner2_index],
+ aminoacid_energies[BVSUB(12,alpha1_inner2_index,BITS12_ONE_MACRO)]));
+
+
+ASSERT (alpha1_outer2_length = FACE_LEN1_MACRO => alpha1_outer2_energy = BVSUB(16,BITS16_ONE_MACRO,aminoacid_energies[alpha1_outer2_index]));
+ASSERT (alpha1_outer2_length = FACE_LEN2_MACRO => alpha1_outer2_energy = BVSUB(16,BITS16_TWO_MACRO,BVPLUS(16,aminoacid_energies[alpha1_outer2_index],
+ aminoacid_energies[BVSUB(12,alpha1_outer2_index,BITS12_ONE_MACRO)])));
+
+ASSERT (alpha1_inner3_length = FACE_LEN1_MACRO => alpha1_inner3_energy = aminoacid_energies[alpha1_inner3_index]);
+ASSERT (alpha1_inner3_length = FACE_LEN2_MACRO => alpha1_inner3_energy = BVPLUS(16,aminoacid_energies[alpha1_inner3_index],
+ aminoacid_energies[BVSUB(12,alpha1_inner3_index,BITS12_ONE_MACRO)]));
+
+
+ASSERT (alpha1_outer3_length = FACE_LEN1_MACRO => alpha1_outer3_energy = BVSUB(16,BITS16_ONE_MACRO,aminoacid_energies[alpha1_outer3_index]));
+ASSERT (alpha1_outer3_length = FACE_LEN2_MACRO => alpha1_outer3_energy = BVSUB(16,BITS16_TWO_MACRO, BVPLUS(16,aminoacid_energies[alpha1_outer3_index],
+ aminoacid_energies[BVSUB(12,alpha1_outer3_index,BITS12_ONE_MACRO)])));
+
+%%%%%%%%%%%%%%%%%%%%%%%%%% END OF ENERGY COMPUTATION ALPHA1 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%% START OF ENERGY COMPUTATION ALPHA2 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+ASSERT (alpha2_inner1_length = FACE_LEN1_MACRO => alpha2_inner1_energy = aminoacid_energies[alpha2_inner1_index]);
+ASSERT (alpha2_inner1_length = FACE_LEN2_MACRO => alpha2_inner1_energy = BVPLUS(16,aminoacid_energies[alpha2_inner1_index],
+ aminoacid_energies[BVSUB(12,alpha2_inner1_index,BITS12_ONE_MACRO)]));
+
+ASSERT (alpha2_outer1_length = FACE_LEN1_MACRO => alpha2_outer1_energy = BVSUB(16,BITS16_ONE_MACRO,aminoacid_energies[alpha2_outer1_index]));
+ASSERT (alpha2_outer1_length = FACE_LEN2_MACRO => alpha2_outer1_energy = BVSUB(16,BITS16_TWO_MACRO,BVPLUS(16,aminoacid_energies[alpha2_outer1_index],
+ aminoacid_energies[BVSUB(12,alpha2_outer1_index,BITS12_ONE_MACRO)])));
+
+
+ASSERT (alpha2_inner2_length = FACE_LEN1_MACRO => alpha2_inner2_energy = aminoacid_energies[alpha2_inner2_index]);
+ASSERT (alpha2_inner2_length = FACE_LEN2_MACRO => alpha2_inner2_energy = BVPLUS(16,aminoacid_energies[alpha2_inner2_index],
+ aminoacid_energies[BVSUB(12,alpha2_inner2_index,BITS12_ONE_MACRO)]));
+
+
+ASSERT (alpha2_outer2_length = FACE_LEN1_MACRO => alpha2_outer2_energy = BVSUB(16,BITS16_ONE_MACRO,aminoacid_energies[alpha2_outer2_index]));
+ASSERT (alpha2_outer2_length = FACE_LEN2_MACRO => alpha2_outer2_energy = BVSUB(16,BITS16_TWO_MACRO,BVPLUS(16,aminoacid_energies[alpha2_outer2_index],
+ aminoacid_energies[BVSUB(12,alpha2_outer2_index,BITS12_ONE_MACRO)])));
+
+ASSERT (alpha2_inner3_length = FACE_LEN1_MACRO => alpha2_inner3_energy = aminoacid_energies[alpha2_inner3_index]);
+ASSERT (alpha2_inner3_length = FACE_LEN2_MACRO => alpha2_inner3_energy = BVPLUS(16,aminoacid_energies[alpha2_inner3_index],
+ aminoacid_energies[BVSUB(12,alpha2_inner3_index,BITS12_ONE_MACRO)]));
+
+
+ASSERT (alpha2_outer3_length = FACE_LEN1_MACRO => alpha2_outer3_energy = BVSUB(16,BITS16_ONE_MACRO,aminoacid_energies[alpha2_outer3_index]));
+ASSERT (alpha2_outer3_length = FACE_LEN2_MACRO => alpha2_outer3_energy = BVSUB(16,BITS16_TWO_MACRO, BVPLUS(16,aminoacid_energies[alpha2_outer3_index],
+ aminoacid_energies[BVSUB(12,alpha2_outer3_index,BITS12_ONE_MACRO)])));
+
+%%%%%%%%%%%%%%%%%%%%%%%%%% END OF ENERGY COMPUTATION ALPHA2 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%% START OF ENERGY COMPUTATION ALPHA3 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+ASSERT (alpha3_inner1_length = FACE_LEN1_MACRO => alpha3_inner1_energy = aminoacid_energies[alpha3_inner1_index]);
+ASSERT (alpha3_inner1_length = FACE_LEN2_MACRO => alpha3_inner1_energy = BVPLUS(16,aminoacid_energies[alpha3_inner1_index],
+ aminoacid_energies[BVSUB(12,alpha3_inner1_index,BITS12_ONE_MACRO)]));
+
+ASSERT (alpha3_outer1_length = FACE_LEN1_MACRO => alpha3_outer1_energy = BVSUB(16,BITS16_ONE_MACRO,aminoacid_energies[alpha3_outer1_index]));
+ASSERT (alpha3_outer1_length = FACE_LEN2_MACRO => alpha3_outer1_energy = BVSUB(16,BITS16_TWO_MACRO,BVPLUS(16,aminoacid_energies[alpha3_outer1_index],
+ aminoacid_energies[BVSUB(12,alpha3_outer1_index,BITS12_ONE_MACRO)])));
+
+
+ASSERT (alpha3_inner2_length = FACE_LEN1_MACRO => alpha3_inner2_energy = aminoacid_energies[alpha3_inner2_index]);
+ASSERT (alpha3_inner2_length = FACE_LEN2_MACRO => alpha3_inner2_energy = BVPLUS(16,aminoacid_energies[alpha3_inner2_index],
+ aminoacid_energies[BVSUB(12,alpha3_inner2_index,BITS12_ONE_MACRO)]));
+
+
+ASSERT (alpha3_outer2_length = FACE_LEN1_MACRO => alpha3_outer2_energy = BVSUB(16,BITS16_ONE_MACRO,aminoacid_energies[alpha3_outer2_index]));
+ASSERT (alpha3_outer2_length = FACE_LEN2_MACRO => alpha3_outer2_energy = BVSUB(16,BITS16_TWO_MACRO,BVPLUS(16,aminoacid_energies[alpha3_outer2_index],
+ aminoacid_energies[BVSUB(12,alpha3_outer2_index,BITS12_ONE_MACRO)])));
+
+ASSERT (alpha3_inner3_length = FACE_LEN1_MACRO => alpha3_inner3_energy = aminoacid_energies[alpha3_inner3_index]);
+ASSERT (alpha3_inner3_length = FACE_LEN2_MACRO => alpha3_inner3_energy = BVPLUS(16,aminoacid_energies[alpha3_inner3_index],
+ aminoacid_energies[BVSUB(12,alpha3_inner3_index,BITS12_ONE_MACRO)]));
+
+
+ASSERT (alpha3_outer3_length = FACE_LEN1_MACRO => alpha3_outer3_energy = BVSUB(16,BITS16_ONE_MACRO,aminoacid_energies[alpha3_outer3_index]));
+ASSERT (alpha3_outer3_length = FACE_LEN2_MACRO => alpha3_outer3_energy = BVSUB(16,BITS16_TWO_MACRO, BVPLUS(16,aminoacid_energies[alpha3_outer3_index],
+ aminoacid_energies[BVSUB(12,alpha3_outer3_index,BITS12_ONE_MACRO)])));
+
+%%%%%%%%%%%%%%%%%%%%%%%%%% END OF ENERGY COMPUTATION ALPHA3 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%% START OF ENERGY COMPUTATION ALPHA4 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+ASSERT (alpha4_inner1_length = FACE_LEN1_MACRO => alpha4_inner1_energy = aminoacid_energies[alpha4_inner1_index]);
+ASSERT (alpha4_inner1_length = FACE_LEN2_MACRO => alpha4_inner1_energy = BVPLUS(16,aminoacid_energies[alpha4_inner1_index],
+ aminoacid_energies[BVSUB(12,alpha4_inner1_index,BITS12_ONE_MACRO)]));
+
+ASSERT (alpha4_outer1_length = FACE_LEN1_MACRO => alpha4_outer1_energy = BVSUB(16,BITS16_ONE_MACRO,aminoacid_energies[alpha4_outer1_index]));
+ASSERT (alpha4_outer1_length = FACE_LEN2_MACRO => alpha4_outer1_energy = BVSUB(16,BITS16_TWO_MACRO,BVPLUS(16,aminoacid_energies[alpha4_outer1_index],
+ aminoacid_energies[BVSUB(12,alpha4_outer1_index,BITS12_ONE_MACRO)])));
+
+
+ASSERT (alpha4_inner2_length = FACE_LEN1_MACRO => alpha4_inner2_energy = aminoacid_energies[alpha4_inner2_index]);
+ASSERT (alpha4_inner2_length = FACE_LEN2_MACRO => alpha4_inner2_energy = BVPLUS(16,aminoacid_energies[alpha4_inner2_index],
+ aminoacid_energies[BVSUB(12,alpha4_inner2_index,BITS12_ONE_MACRO)]));
+
+
+ASSERT (alpha4_outer2_length = FACE_LEN1_MACRO => alpha4_outer2_energy = BVSUB(16,BITS16_ONE_MACRO,aminoacid_energies[alpha4_outer2_index]));
+ASSERT (alpha4_outer2_length = FACE_LEN2_MACRO => alpha4_outer2_energy = BVSUB(16,BITS16_TWO_MACRO,BVPLUS(16,aminoacid_energies[alpha4_outer2_index],
+ aminoacid_energies[BVSUB(12,alpha4_outer2_index,BITS12_ONE_MACRO)])));
+
+ASSERT (alpha4_inner3_length = FACE_LEN1_MACRO => alpha4_inner3_energy = aminoacid_energies[alpha4_inner3_index]);
+ASSERT (alpha4_inner3_length = FACE_LEN2_MACRO => alpha4_inner3_energy = BVPLUS(16,aminoacid_energies[alpha4_inner3_index],
+ aminoacid_energies[BVSUB(12,alpha4_inner3_index,BITS12_ONE_MACRO)]));
+
+
+ASSERT (alpha4_outer3_length = FACE_LEN1_MACRO => alpha4_outer3_energy = BVSUB(16,BITS16_ONE_MACRO,aminoacid_energies[alpha4_outer3_index]));
+ASSERT (alpha4_outer3_length = FACE_LEN2_MACRO => alpha4_outer3_energy = BVSUB(16,BITS16_TWO_MACRO, BVPLUS(16,aminoacid_energies[alpha4_outer3_index],
+ aminoacid_energies[BVSUB(12,alpha4_outer3_index,BITS12_ONE_MACRO)])));
+
+%%%%%%%%%%%%%%%%%%%%%%%%%% 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, 0hex0010));
+QUERY FALSE;
\ No newline at end of file
projects / francis / stp.git / commitdiff