diff --git a/results/protein_fold_analysis.txt b/results/protein_fold_analysis.txt deleted file mode 100644 index e3a5c37..0000000 --- a/results/protein_fold_analysis.txt +++ /dev/null @@ -1,202 +0,0 @@ -====================================================================== - PROTEIN FOLDING FRACTAL ECHO ANALYZER -====================================================================== - Source: D:\Resonance_Engine\sweep_results\em_direct_sweep_20260327_080716.csv - Points: 375 - Coherence: 0.737800 to 0.852700 - Mean=0.750005 Std=0.026647 - -====================================================================== - TEST 1: BASIN COUNTING (Ramachandran has 4-5 basins) -====================================================================== - om=0.5: 9 distinct, 1 basins - om=0.6: 10 distinct, 1 basins - om=0.7: 5 distinct, 1 basins - om=0.8: 7 distinct, 2 basins - om=0.9: 5 distinct, 1 basins - om=1.0: 6 distinct, 2 basins - om=1.1: 6 distinct, 1 basins - om=1.2: 6 distinct, 1 basins - om=1.3: 7 distinct, 1 basins - om=1.4: 7 distinct, 2 basins - om=1.5: 8 distinct, 2 basins - om=1.6: 7 distinct, 2 basins - om=1.7: 8 distinct, 2 basins - om=1.8: 7 distinct, 2 basins - om=1.9: 3 distinct, 1 basins - - Slices with 3-6 basins: 0/15 - -====================================================================== - TEST 2: FORBIDDEN FRACTION (Ramachandran ~35% allowed) -====================================================================== - Top 35% threshold: 0.739500 - Allowed fraction: 44.3% - Ramachandran target: 35% - Difference: 9.3% - PASS - -====================================================================== - TEST 3: FUNNEL TOPOLOGY (proteins have positive skewness) -====================================================================== - 0.7378-0.7493: 318 ######################################## - 0.7493-0.7608: 0 - 0.7608-0.7723: 0 - 0.7723-0.7838: 0 - 0.7838-0.7953: 24 ### - 0.7953-0.8067: 3 - 0.8067-0.8182: 1 - 0.8182-0.8297: 26 ### - 0.8297-0.8412: 0 - 0.8412-0.8527: 3 - - Skewness: +2.1874 - >>> FUNNEL DETECTED - -====================================================================== - TEST 4: AMINO ACID CLASS MAPPING (5 classes expected) -====================================================================== - om=0.5: range=0.002100 -> beta_branched - om=0.6: range=0.001800 -> pre_proline - om=0.7: range=0.001300 -> pre_proline - om=0.8: range=0.001500 -> pre_proline - om=0.9: range=0.002200 -> beta_branched - om=1.0: range=0.001700 -> pre_proline - om=1.1: range=0.001400 -> pre_proline - om=1.2: range=0.001100 -> pre_proline - om=1.3: range=0.001700 -> pre_proline - om=1.4: range=0.001800 -> pre_proline - om=1.5: range=0.002000 -> beta_branched - om=1.6: range=0.001700 -> pre_proline - om=1.7: range=0.114900 -> glycine - om=1.8: range=0.018900 -> general - om=1.9: range=0.011800 -> general - - Classes found: 4/5 = ['beta_branched', 'general', 'glycine', 'pre_proline'] - -====================================================================== - TEST 5: LEVINTHAL COMPRESSION -====================================================================== - Combinations: 375 - Distinct modes: 39 - Compression: 9.6:1 - -====================================================================== - TEST 6: HIERARCHICAL STRUCTURE -====================================================================== - CATH: 4 classes -> 41 arch -> 1393 topo - Lattice: 15 classes -> 39 topo - -====================================================================== - VERDICT -====================================================================== - Basin count (3-6) FAIL - Forbidden fraction (25-45%) PASS - Funnel topology PASS - Amino acid classes (3+/5) PASS - Levinthal compression (>2:1) PASS - Hierarchical structure PASS - - PASSED: 5/6 - STRONG EVIDENCE: Fractal echo extends to protein folding -====================================================================== - PROTEIN FOLDING FRACTAL ECHO ANALYZER -====================================================================== - Source: D:\Resonance_Engine\sweep_results\em_direct_sweep_20260327_145447.csv - Points: 375 - Coherence: 0.737000 to 0.739300 - Mean=0.738280 Std=0.000571 - -====================================================================== - TEST 1: BASIN COUNTING (Ramachandran has 4-5 basins) -====================================================================== - om=0.5: 6 distinct, 2 basins - om=0.6: 3 distinct, 1 basins - om=0.7: 8 distinct, 2 basins - om=0.8: 8 distinct, 2 basins - om=0.9: 8 distinct, 1 basins - om=1.0: 3 distinct, 1 basins - om=1.1: 10 distinct, 2 basins - om=1.2: 5 distinct, 2 basins - om=1.3: 10 distinct, 1 basins - om=1.4: 4 distinct, 1 basins - om=1.5: 11 distinct, 3 basins <<< - om=1.6: 8 distinct, 1 basins - om=1.7: 11 distinct, 1 basins - om=1.8: 8 distinct, 2 basins - om=1.9: 2 distinct, 1 basins - - Slices with 3-6 basins: 1/15 - -====================================================================== - TEST 2: FORBIDDEN FRACTION (Ramachandran ~35% allowed) -====================================================================== - Top 35% threshold: 0.738500 - Allowed fraction: 40.0% - Ramachandran target: 35% - Difference: 5.0% - PASS - -====================================================================== - TEST 3: FUNNEL TOPOLOGY (proteins have positive skewness) -====================================================================== - 0.7370-0.7372: 15 ######### - 0.7372-0.7375: 8 #### - 0.7375-0.7377: 33 #################### - 0.7377-0.7379: 53 ################################ - 0.7379-0.7381: 66 ######################################## - 0.7381-0.7384: 37 ###################### - 0.7384-0.7386: 50 ############################## - 0.7386-0.7388: 33 #################### - 0.7388-0.7391: 31 ################## - 0.7391-0.7393: 49 ############################# - - Skewness: -0.0718 - >>> FLAT LANDSCAPE - -====================================================================== - TEST 4: AMINO ACID CLASS MAPPING (5 classes expected) -====================================================================== - om=0.5: range=0.000700 -> pre_proline - om=0.6: range=0.001500 -> pre_proline - om=0.7: range=0.001800 -> pre_proline - om=0.8: range=0.000900 -> pre_proline - om=0.9: range=0.001100 -> pre_proline - om=1.0: range=0.000500 -> pre_proline - om=1.1: range=0.001800 -> pre_proline - om=1.2: range=0.000900 -> pre_proline - om=1.3: range=0.001400 -> pre_proline - om=1.4: range=0.001400 -> pre_proline - om=1.5: range=0.002300 -> beta_branched - om=1.6: range=0.001900 -> pre_proline - om=1.7: range=0.002000 -> beta_branched - om=1.8: range=0.001800 -> pre_proline - om=1.9: range=0.000200 -> proline - - Classes found: 3/5 = ['beta_branched', 'pre_proline', 'proline'] - -====================================================================== - TEST 5: LEVINTHAL COMPRESSION -====================================================================== - Combinations: 375 - Distinct modes: 23 - Compression: 16.3:1 - -====================================================================== - TEST 6: HIERARCHICAL STRUCTURE -====================================================================== - CATH: 4 classes -> 41 arch -> 1393 topo - Lattice: 15 classes -> 23 topo - -====================================================================== - VERDICT -====================================================================== - Basin count (3-6) FAIL - Forbidden fraction (25-45%) PASS - Funnel topology FAIL - Amino acid classes (3+/5) PASS - Levinthal compression (>2:1) PASS - Hierarchical structure PASS - - PASSED: 4/6 - STRONG EVIDENCE: Fractal echo extends to protein folding