{ "engine": "bio-suite repeat-motif-compare (Repetitive Protein Motif Scanner + Candle-Core Ridge Regressor)", "benchmark_id": "TOOL-BENCHMARK-21-REPEAT-MOTIF-VS-SCIPY", "validation_set_id": "VAL-SET-010-REPEAT-MOTIF-BIOMECHANICS-12COHORT", "external_reference": "SciPy v1.18.1 (scipy.linalg.solve) + NumPy v2.5.4 + Arakawa et al. (2022) Spider Silkome Reference Data", "total_cohorts": 12, "dev_cohorts": 6, "reserve_cohorts": 6, "dev_mean_toughness_diff_vs_scipy": 0.0, "reserve_mean_toughness_diff_vs_scipy": 0.0, "dev_mean_tensile_diff_vs_scipy": 0.0, "reserve_mean_tensile_diff_vs_scipy": 0.0, "native_vs_scipy_toughness_r": 1.0, "native_vs_scipy_tensile_r": 1.0, "empirical_toughness_r": 0.9668, "empirical_tensile_r": 0.9979, "regime_concordance_pct": 100.0, "total_native_ms": 0.247, "total_scipy_ms": 210.7591, "speedup_factor": 853.2757, "cohorts": [ { "cohort_id": "DEV-01", "split": "Development", "name": "Caerostris darwini (Darwin's Bark Spider) MaSp1/MaSp2/MaSp3 Dragline Consensus", "organism": "Caerostris darwini", "accession": "PRD23988.1", "protein_class": "Orb-Weaver Dragline Spidroin (MaSp1/MaSp2/MaSp3 + SpiCE)", "seq_len_aa": 120, "poly_ala_block_count": 3, "mean_poly_ala_block_len": 8.0, "crystal_beta_sheet_fraction": 0.2, "gpgxx_elastic_spiral_density": 0.6667, "ggx_amorphous_helix_density": 0.3, "shannon_entropy_bits": 2.1012, "gen1_clamped_placeholder_error_mj_m3": 9.0, "measured_tensile_gpa": 1.65, "native_pred_tensile_gpa": 1.6706, "scipy_pred_tensile_gpa": 1.6706, "abs_diff_tensile_vs_scipy": 0.0, "measured_toughness_mj_m3": 354.0, "native_pred_toughness_mj_m3": 325.2804, "scipy_pred_toughness_mj_m3": 325.2804, "abs_diff_toughness_vs_scipy": 0.0, "regime_classification": "Repetitive Elastomeric Lattice Validated (Ala Len = 8.00 aa, GPGXX = 66.7%, Toughness = 325.3 MJ/m3)", "concordant_with_scipy": true, "native_runtime_ms": 0.0206, "scipy_runtime_ms": 17.5633 }, { "cohort_id": "DEV-02", "split": "Development", "name": "Trichonephila clavipes (Golden Silk Orb-Weaver) MaSp1/MaSp2 Major Ampullate", "organism": "Trichonephila clavipes", "accession": "P19837.3", "protein_class": "Orb-Weaver Major Ampullate Spidroin (MaSp1/MaSp2)", "seq_len_aa": 113, "poly_ala_block_count": 3, "mean_poly_ala_block_len": 7.0, "crystal_beta_sheet_fraction": 0.1858, "gpgxx_elastic_spiral_density": 0.4425, "ggx_amorphous_helix_density": 0.3451, "shannon_entropy_bits": 2.181, "gen1_clamped_placeholder_error_mj_m3": 163.0, "measured_tensile_gpa": 1.28, "native_pred_tensile_gpa": 1.2211, "scipy_pred_tensile_gpa": 1.2211, "abs_diff_tensile_vs_scipy": 0.0, "measured_toughness_mj_m3": 182.0, "native_pred_toughness_mj_m3": 199.9688, "scipy_pred_toughness_mj_m3": 199.9688, "abs_diff_toughness_vs_scipy": 0.0, "regime_classification": "Repetitive Elastomeric Lattice Validated (Ala Len = 7.00 aa, GPGXX = 44.2%, Toughness = 200.0 MJ/m3)", "concordant_with_scipy": true, "native_runtime_ms": 0.0206, "scipy_runtime_ms": 17.5633 }, { "cohort_id": "DEV-03", "split": "Development", "name": "Araneus diadematus (Cross Orb-Weaver) ADF-3 / MaSp2 Viscoelastic Dragline", "organism": "Araneus diadematus", "accession": "Q16987.1", "protein_class": "Araneid Major Ampullate Spidroin (ADF-3/MaSp2)", "seq_len_aa": 106, "poly_ala_block_count": 3, "mean_poly_ala_block_len": 7.0, "crystal_beta_sheet_fraction": 0.1981, "gpgxx_elastic_spiral_density": 0.5189, "ggx_amorphous_helix_density": 0.3113, "shannon_entropy_bits": 2.1485, "gen1_clamped_placeholder_error_mj_m3": 131.0, "measured_tensile_gpa": 1.34, "native_pred_tensile_gpa": 1.345, "scipy_pred_tensile_gpa": 1.345, "abs_diff_tensile_vs_scipy": 0.0, "measured_toughness_mj_m3": 214.0, "native_pred_toughness_mj_m3": 242.7909, "scipy_pred_toughness_mj_m3": 242.7909, "abs_diff_toughness_vs_scipy": 0.0, "regime_classification": "Repetitive Elastomeric Lattice Validated (Ala Len = 7.00 aa, GPGXX = 51.9%, Toughness = 242.8 MJ/m3)", "concordant_with_scipy": true, "native_runtime_ms": 0.0206, "scipy_runtime_ms": 17.5633 }, { "cohort_id": "DEV-04", "split": "Development", "name": "Trichonephila clavipes Flagelliform (Flag) Capture Spiral Elastomer", "organism": "Trichonephila clavipes", "accession": "AF027973.1", "protein_class": "Flagelliform Capture-Spiral Spidroin (Flag)", "seq_len_aa": 103, "poly_ala_block_count": 0, "mean_poly_ala_block_len": 0.0, "crystal_beta_sheet_fraction": 0.0, "gpgxx_elastic_spiral_density": 0.9223, "ggx_amorphous_helix_density": 0.5534, "shannon_entropy_bits": 1.836, "gen1_clamped_placeholder_error_mj_m3": 195.0, "measured_tensile_gpa": 0.52, "native_pred_tensile_gpa": 0.5291, "scipy_pred_tensile_gpa": 0.5291, "abs_diff_tensile_vs_scipy": 0.0, "measured_toughness_mj_m3": 150.0, "native_pred_toughness_mj_m3": 144.901, "scipy_pred_toughness_mj_m3": 144.901, "abs_diff_toughness_vs_scipy": 0.0, "regime_classification": "Repetitive Elastomeric Lattice Validated (Ala Len = 0.00 aa, GPGXX = 92.2%, Toughness = 144.9 MJ/m3)", "concordant_with_scipy": true, "native_runtime_ms": 0.0206, "scipy_runtime_ms": 17.5633 }, { "cohort_id": "DEV-05", "split": "Development", "name": "Bombyx mori (Domestic Silkworm) Fibroin Heavy Chain Crystalline Core", "organism": "Bombyx mori", "accession": "NP_001106733.1", "protein_class": "Lepidopteran Crystalline Beta-Sheet Fibroin (Fib-H)", "seq_len_aa": 96, "poly_ala_block_count": 9, "mean_poly_ala_block_len": 6.0, "crystal_beta_sheet_fraction": 0.5625, "gpgxx_elastic_spiral_density": 0.0, "ggx_amorphous_helix_density": 0.1875, "shannon_entropy_bits": 1.7259, "gen1_clamped_placeholder_error_mj_m3": 273.0, "measured_tensile_gpa": 0.62, "native_pred_tensile_gpa": 0.6553, "scipy_pred_tensile_gpa": 0.6553, "abs_diff_tensile_vs_scipy": 0.0, "measured_toughness_mj_m3": 72.0, "native_pred_toughness_mj_m3": 55.7303, "scipy_pred_toughness_mj_m3": 55.7303, "abs_diff_toughness_vs_scipy": 0.0, "regime_classification": "Repetitive Elastomeric Lattice Validated (Ala Len = 6.00 aa, GPGXX = 0.0%, Toughness = 55.7 MJ/m3)", "concordant_with_scipy": true, "native_runtime_ms": 0.0206, "scipy_runtime_ms": 17.5633 }, { "cohort_id": "DEV-06", "split": "Development", "name": "Human Lysozyme C (LYZ) Globular Non-Repetitive Negative Control (0-Beaker Gate)", "organism": "Homo sapiens", "accession": "NP_000230.1", "protein_class": "0🧪 Non-Repetitive Globular Enzyme Control", "seq_len_aa": 130, "poly_ala_block_count": 0, "mean_poly_ala_block_len": 0.0, "crystal_beta_sheet_fraction": 0.0, "gpgxx_elastic_spiral_density": 0.0, "ggx_amorphous_helix_density": 0.0, "shannon_entropy_bits": 4.0829, "gen1_clamped_placeholder_error_mj_m3": 342.5, "measured_tensile_gpa": 0.02, "native_pred_tensile_gpa": 0.0088, "scipy_pred_tensile_gpa": 0.0088, "abs_diff_tensile_vs_scipy": 0.0, "measured_toughness_mj_m3": 2.5, "native_pred_toughness_mj_m3": 5.8285, "scipy_pred_toughness_mj_m3": 5.8285, "abs_diff_toughness_vs_scipy": 0.0, "regime_classification": "0-Beaker Non-Repetitive / Disrupted-Block Control Rejected (Ala Blocks = 0, Toughness = 5.8 MJ/m3)", "concordant_with_scipy": true, "native_runtime_ms": 0.0206, "scipy_runtime_ms": 17.5633 }, { "cohort_id": "RES-01", "split": "Reserve", "name": "Caerostris extrusa (Bark Spider Sister Clade) MaSp1/MaSp2/MaSp3 Dragline", "organism": "Caerostris extrusa", "accession": "PRD24102.1", "protein_class": "Bark Spider Dragline Spidroin (MaSp1/MaSp2/MaSp3 + SpiCE)", "seq_len_aa": 105, "poly_ala_block_count": 3, "mean_poly_ala_block_len": 8.0, "crystal_beta_sheet_fraction": 0.2286, "gpgxx_elastic_spiral_density": 0.619, "ggx_amorphous_helix_density": 0.3429, "shannon_entropy_bits": 2.0783, "gen1_clamped_placeholder_error_mj_m3": 27.0, "measured_tensile_gpa": 1.54, "native_pred_tensile_gpa": 1.6109, "scipy_pred_tensile_gpa": 1.6109, "abs_diff_tensile_vs_scipy": 0.0, "measured_toughness_mj_m3": 318.0, "native_pred_toughness_mj_m3": 298.5344, "scipy_pred_toughness_mj_m3": 298.5344, "abs_diff_toughness_vs_scipy": 0.0, "regime_classification": "Repetitive Elastomeric Lattice Validated (Ala Len = 8.00 aa, GPGXX = 61.9%, Toughness = 298.5 MJ/m3)", "concordant_with_scipy": true, "native_runtime_ms": 0.0206, "scipy_runtime_ms": 17.5633 }, { "cohort_id": "RES-02", "split": "Reserve", "name": "Araneus ventricosus (Orb-Weaver) MaSp2/MaSp3 Composite Dragline", "organism": "Araneus ventricosus", "accession": "GBN88412.1", "protein_class": "Araneid Major Ampullate Spidroin (MaSp2/MaSp3)", "seq_len_aa": 101, "poly_ala_block_count": 3, "mean_poly_ala_block_len": 7.0, "crystal_beta_sheet_fraction": 0.2079, "gpgxx_elastic_spiral_density": 0.495, "ggx_amorphous_helix_density": 0.3267, "shannon_entropy_bits": 2.1275, "gen1_clamped_placeholder_error_mj_m3": 147.0, "measured_tensile_gpa": 1.31, "native_pred_tensile_gpa": 1.3003, "scipy_pred_tensile_gpa": 1.3003, "abs_diff_tensile_vs_scipy": 0.0, "measured_toughness_mj_m3": 198.0, "native_pred_toughness_mj_m3": 227.2759, "scipy_pred_toughness_mj_m3": 227.2759, "abs_diff_toughness_vs_scipy": 0.0, "regime_classification": "Repetitive Elastomeric Lattice Validated (Ala Len = 7.00 aa, GPGXX = 49.5%, Toughness = 227.3 MJ/m3)", "concordant_with_scipy": true, "native_runtime_ms": 0.0206, "scipy_runtime_ms": 17.5633 }, { "cohort_id": "RES-03", "split": "Reserve", "name": "Latrodectus hesperus (Western Black Widow) MaSp1/MaSp2 Cobweb Dragline", "organism": "Latrodectus hesperus", "accession": "ABR68856.1", "protein_class": "Theridiid Major Ampullate Spidroin (MaSp1/MaSp2)", "seq_len_aa": 101, "poly_ala_block_count": 3, "mean_poly_ala_block_len": 7.0, "crystal_beta_sheet_fraction": 0.2079, "gpgxx_elastic_spiral_density": 0.297, "ggx_amorphous_helix_density": 0.3861, "shannon_entropy_bits": 2.1627, "gen1_clamped_placeholder_error_mj_m3": 187.0, "measured_tensile_gpa": 1.18, "native_pred_tensile_gpa": 1.1212, "scipy_pred_tensile_gpa": 1.1212, "abs_diff_tensile_vs_scipy": 0.0, "measured_toughness_mj_m3": 158.0, "native_pred_toughness_mj_m3": 151.7652, "scipy_pred_toughness_mj_m3": 151.7652, "abs_diff_toughness_vs_scipy": 0.0, "regime_classification": "Repetitive Elastomeric Lattice Validated (Ala Len = 7.00 aa, GPGXX = 29.7%, Toughness = 151.8 MJ/m3)", "concordant_with_scipy": true, "native_runtime_ms": 0.0206, "scipy_runtime_ms": 17.5633 }, { "cohort_id": "RES-04", "split": "Reserve", "name": "Argiope aurantia (Yellow Garden Orb-Weaver) MaSp2 Dragline", "organism": "Argiope aurantia", "accession": "AF350266.1", "protein_class": "Orb-Weaver Major Ampullate Spidroin (MaSp2)", "seq_len_aa": 102, "poly_ala_block_count": 3, "mean_poly_ala_block_len": 7.0, "crystal_beta_sheet_fraction": 0.2059, "gpgxx_elastic_spiral_density": 0.5392, "ggx_amorphous_helix_density": 0.2647, "shannon_entropy_bits": 2.2344, "gen1_clamped_placeholder_error_mj_m3": 151.0, "measured_tensile_gpa": 1.29, "native_pred_tensile_gpa": 1.2734, "scipy_pred_tensile_gpa": 1.2734, "abs_diff_tensile_vs_scipy": 0.0, "measured_toughness_mj_m3": 194.0, "native_pred_toughness_mj_m3": 238.2324, "scipy_pred_toughness_mj_m3": 238.2324, "abs_diff_toughness_vs_scipy": 0.0, "regime_classification": "Repetitive Elastomeric Lattice Validated (Ala Len = 7.00 aa, GPGXX = 53.9%, Toughness = 238.2 MJ/m3)", "concordant_with_scipy": true, "native_runtime_ms": 0.0206, "scipy_runtime_ms": 17.5633 }, { "cohort_id": "RES-05", "split": "Reserve", "name": "Latrodectus hesperus Tubuliform (TuSp1) Egg-Case Crystalline Spidroin", "organism": "Latrodectus hesperus", "accession": "AY953070.1", "protein_class": "Tubuliform Egg-Case Spidroin (TuSp1)", "seq_len_aa": 97, "poly_ala_block_count": 4, "mean_poly_ala_block_len": 6.0, "crystal_beta_sheet_fraction": 0.2474, "gpgxx_elastic_spiral_density": 0.0, "ggx_amorphous_helix_density": 0.433, "shannon_entropy_bits": 2.0234, "gen1_clamped_placeholder_error_mj_m3": 249.0, "measured_tensile_gpa": 0.78, "native_pred_tensile_gpa": 0.7621, "scipy_pred_tensile_gpa": 0.7621, "abs_diff_tensile_vs_scipy": 0.0, "measured_toughness_mj_m3": 96.0, "native_pred_toughness_mj_m3": 35.8401, "scipy_pred_toughness_mj_m3": 35.8401, "abs_diff_toughness_vs_scipy": 0.0, "regime_classification": "Repetitive Elastomeric Lattice Validated (Ala Len = 6.00 aa, GPGXX = 0.0%, Toughness = 35.8 MJ/m3)", "concordant_with_scipy": true, "native_runtime_ms": 0.0206, "scipy_runtime_ms": 17.5633 }, { "cohort_id": "RES-06", "split": "Reserve", "name": "Compositionally Shuffled Disrupted Poly-Ala Decoy (0-Beaker Gate)", "organism": "Synthetic Shuffled Spidroin Decoy", "accession": "SIM-SHUFFLED-RES06", "protein_class": "0🧪 Compositionally Shuffled Block-Disrupted Control", "seq_len_aa": 102, "poly_ala_block_count": 0, "mean_poly_ala_block_len": 0.0, "crystal_beta_sheet_fraction": 0.0, "gpgxx_elastic_spiral_density": 0.0, "ggx_amorphous_helix_density": 0.0, "shannon_entropy_bits": 1.9328, "gen1_clamped_placeholder_error_mj_m3": 341.0, "measured_tensile_gpa": 0.04, "native_pred_tensile_gpa": 0.0088, "scipy_pred_tensile_gpa": 0.0088, "abs_diff_tensile_vs_scipy": 0.0, "measured_toughness_mj_m3": 4.0, "native_pred_toughness_mj_m3": 5.8285, "scipy_pred_toughness_mj_m3": 5.8285, "abs_diff_toughness_vs_scipy": 0.0, "regime_classification": "0-Beaker Non-Repetitive / Disrupted-Block Control Rejected (Ala Blocks = 0, Toughness = 5.8 MJ/m3)", "concordant_with_scipy": true, "native_runtime_ms": 0.0206, "scipy_runtime_ms": 17.5633 } ], "ascii_summary_table": "========================================================================================================================================================\n TOOL BENCHMARK #21: Native Repetitive Protein Motif Scanner & Candle-Core Regressor vs. Live SciPy v1.18.1 (linalg.solve)\n========================================================================================================================================================\nCohort Split AlaBlk MeanAla GPGXX% GGX% Meas GPa Nat GPa SciPy GPa Meas Tough Nat Tough SciPy Tough |ΔTough| Match\n--------------------------------------------------------------------------------------------------------------------------------------------------------\nDEV-01 Development 3 8.00 66.7% 30.0% 1.65 1.6706 1.6706 354.0 325.28 325.28 0.0000 YES (100%)\nDEV-02 Development 3 7.00 44.2% 34.5% 1.28 1.2211 1.2211 182.0 199.97 199.97 0.0000 YES (100%)\nDEV-03 Development 3 7.00 51.9% 31.1% 1.34 1.3450 1.3450 214.0 242.79 242.79 0.0000 YES (100%)\nDEV-04 Development 0 0.00 92.2% 55.3% 0.52 0.5291 0.5291 150.0 144.90 144.90 0.0000 YES (100%)\nDEV-05 Development 9 6.00 0.0% 18.8% 0.62 0.6553 0.6553 72.0 55.73 55.73 0.0000 YES (100%)\nDEV-06 Development 0 0.00 0.0% 0.0% 0.02 0.0088 0.0088 2.5 5.83 5.83 0.0000 YES (100%)\nRES-01 Reserve 3 8.00 61.9% 34.3% 1.54 1.6109 1.6109 318.0 298.53 298.53 0.0000 YES (100%)\nRES-02 Reserve 3 7.00 49.5% 32.7% 1.31 1.3003 1.3003 198.0 227.28 227.28 0.0000 YES (100%)\nRES-03 Reserve 3 7.00 29.7% 38.6% 1.18 1.1212 1.1212 158.0 151.77 151.77 0.0000 YES (100%)\nRES-04 Reserve 3 7.00 53.9% 26.5% 1.29 1.2734 1.2734 194.0 238.23 238.23 0.0000 YES (100%)\nRES-05 Reserve 4 6.00 0.0% 43.3% 0.78 0.7621 0.7621 96.0 35.84 35.84 0.0000 YES (100%)\nRES-06 Reserve 0 0.00 0.0% 0.0% 0.04 0.0088 0.0088 4.0 5.83 5.83 0.0000 YES (100%)\n--------------------------------------------------------------------------------------------------------------------------------------------------------\n" }