Vendored data

The static tables shipped inside the package.

mhcmatch.data.aa_tables module

The vendored amino-acid property tables. Their values are not reproduced here — they are plain dict[str, float] and large; The amino-acid property basis states what their principal components are.

Amino-acid property tables, vendored (generated – do not edit by hand).

Regenerate with bench/immuno/vendor_aa_tables.py in the 2026-mhcmatch-benchmark repo.

Provenance

DESCRIPTORS, HYDROPHOBICITY

peptides 0.5.0 (althonos/peptides.py), GPL-3.0-or-later, peptides/tables/__init__.py. 17 descriptor families, 102 components total.

PROPERTY_PC1, PROPERTY_PC2

the first two principal components of the 20 x 142 amino-acid property matrix – the DESCRIPTORS / HYDROPHOBICITY tables in this module, column-standardized over the 20 residues, SVD. Derived/computed and label-free, so identical under every refit; the sign convention is that each component’s largest-magnitude residue score is positive. Regenerate with python bench/ipred/pca.py in the 2026-mhcmatch-benchmark repo. These vectors were first vendored inside ipred_mhc1.json (residue_scores); that artifact has since been removed and they are self-contained here, which is why the basis outlived it.

MJ_PARTITION

tcren 2.8.0 src/tcren/data/MJ1985_partition_energies.csv = AAindex MIYS850101 (Miyazawa & Jernigan 1985 effective contact/transfer energies). Larger = more hydrophobic. Re-fetch: https://www.genome.jp/dbget-bin/www_bget?aaindex:MIYS850101

All tables are dict[str, float] over the standard 20 residues, so a caller may pass any of them wherever a residue->value scale is expected. Non-standard residues (B, J, O, U, X, Z) are absent by construction – callers must decide how to handle them rather than silently scoring them as 0.

mhcmatch.data.aa_tables.DESCRIPTORS: dict[str, dict[str, dict[str, float]]] = {'ATCHLEY': {'AF1': {'A': -0.59145974, 'C': -1.34267179, 'D': 1.05015062, 'E': 1.35733226, 'F': -1.00610084, 'G': -0.38387987, 'H': 0.33616543, 'I': -1.23936304, 'K': 1.83146558, 'L': -1.01895162, 'M': -0.66312569, 'N': 0.94535614, 'P': 0.18862522, 'Q': 0.93056541, 'R': 1.53754853, 'S': -0.22788299, 'T': -0.03181782, 'V': -1.33661279, 'W': -0.59533918, 'Y': 0.25999617}, 'AF2': {'A': -1.30209266, 'C': 0.465423, 'D': 0.30242411, 'E': -1.45275578, 'F': -0.59046634, 'G': 1.65201497, 'H': -0.4166278, 'I': -0.54652238, 'K': -0.56109831, 'L': -0.98693471, 'M': -1.52353917, 'N': 0.82846219, 'P': 2.08084151, 'Q': -0.17926549, 'R': -0.05472897, 'S': 1.39869991, 'T': 0.32571153, 'V': -0.27854634, 'W': 0.0090776, 'Y': 0.82992312}, 'AF3': {'A': -0.7330651, 'C': -0.8620345, 'D': -3.6559147, 'E': 1.476661, 'F': 1.8909687, 'G': 1.3301017, 'H': -1.673369, 'I': 2.1314349, 'K': 0.5332237, 'L': -1.5046185, 'M': 2.2194787, 'N': 1.2991286, 'P': -1.6283286, 'Q': -3.0048731, 'R': 1.5021086, 'S': -4.7596375, 'T': 2.2134612, 'V': -0.5440132, 'W': 0.6719274, 'Y': 3.0973596}, 'AF4': {'A': 1.5703918, 'C': -1.0200786, 'D': -0.2590236, 'E': 0.1129444, 'F': -0.3966186, 'G': 1.0449765, 'H': -1.4738898, 'I': 0.3931618, 'K': -0.2771101, 'L': 1.2658296, 'M': -1.0047207, 'N': -0.1688162, 'P': 0.4207004, 'Q': -0.502591, 'R': 0.4403185, 'S': 0.6701745, 'T': 0.9078985, 'V': 1.2419935, 'W': -2.1275244, 'Y': -0.8380164}, 'AF5': {'A': -0.14550842, 'C': -0.25516894, 'D': -3.24176791, 'E': -0.83715681, 'F': 0.41194139, 'G': 2.06385566, 'H': -0.07772917, 'I': 0.81630366, 'K': 1.64762794, 'L': -0.91181195, 'M': 1.21181214, 'N': 0.93339498, 'P': -1.39177378, 'Q': -1.85303476, 'R': 2.89744417, 'S': -2.64747356, 'T': 1.31337035, 'V': -1.26225362, 'W': -0.18358096, 'Y': 1.51150958}}, 'BLOSUM': {'BLOSUM1': {'A': 0.08, 'C': -1.08, 'D': 1.55, 'E': 1.48, 'F': -1.62, 'G': 0.85, 'H': 0.72, 'I': -1.46, 'K': 1.14, 'L': -1.41, 'M': -0.96, 'N': 1.51, 'P': 0.88, 'Q': 1.09, 'R': 1.01, 'S': 0.84, 'T': 0.19, 'V': -1.13, 'W': -1.58, 'Y': -1.14}, 'BLOSUM10': {'A': 0.33, 'C': -0.1, 'D': -0.28, 'E': 0.3, 'F': -1.29, 'G': 0.24, 'H': 0.99, 'I': 0.21, 'K': -0.85, 'L': -0.02, 'M': 0.36, 'N': -0.14, 'P': -0.3, 'Q': 0.67, 'R': -0.52, 'S': -0.13, 'T': 0.06, 'V': 0.61, 'W': 0.5, 'Y': -0.25}, 'BLOSUM2': {'A': -0.92, 'C': -1.11, 'D': 0.01, 'E': 0.23, 'F': 1.01, 'G': 0.17, 'H': 1.55, 'I': -1.13, 'K': -0.04, 'L': -0.86, 'M': -0.59, 'N': 0.22, 'P': -0.68, 'Q': 0.3, 'R': 0.19, 'S': -0.45, 'T': -0.73, 'V': -1.23, 'W': 2.28, 'Y': 1.74}, 'BLOSUM3': {'A': 0.53, 'C': 1.56, 'D': 0.32, 'E': -0.67, 'F': -0.31, 'G': 1.73, 'H': -0.8, 'I': -0.76, 'K': -0.8, 'L': -0.88, 'M': -0.97, 'N': -0.05, 'P': 0.38, 'Q': -0.87, 'R': -0.86, 'S': 0.42, 'T': 0.18, 'V': -0.63, 'W': 1.17, 'Y': -0.58}, 'BLOSUM4': {'A': 0.0, 'C': 0.81, 'D': 0.49, 'E': -0.36, 'F': 0.62, 'G': 0.09, 'H': 1.55, 'I': 0.38, 'K': -0.85, 'L': -0.17, 'M': -0.53, 'N': 1.01, 'P': -0.87, 'Q': -0.72, 'R': -0.61, 'S': 0.32, 'T': -0.01, 'V': 0.06, 'W': -1.61, 'Y': 0.75}, 'BLOSUM5': {'A': 0.24, 'C': 1.83, 'D': -0.99, 'E': -0.28, 'F': -0.55, 'G': -0.55, 'H': 0.35, 'I': -0.6, 'K': 0.82, 'L': 0.03, 'M': 0.24, 'N': 0.12, 'P': -1.24, 'Q': 0.5, 'R': 1.28, 'S': 0.2, 'T': 0.02, 'V': -0.6, 'W': 0.12, 'Y': -0.12}, 'BLOSUM6': {'A': 0.19, 'C': -1.05, 'D': 0.01, 'E': -0.08, 'F': 0.29, 'G': 1.19, 'H': -0.79, 'I': 0.28, 'K': 0.1, 'L': 0.34, 'M': 0.37, 'N': 0.83, 'P': -2.02, 'Q': -0.08, 'R': 0.2, 'S': 0.54, 'T': 0.38, 'V': 0.16, 'W': 0.24, 'Y': -0.48}, 'BLOSUM7': {'A': 0.66, 'C': -0.74, 'D': -1.62, 'E': -1.01, 'F': -0.02, 'G': 1.21, 'H': 0.66, 'I': -0.13, 'K': 0.21, 'L': 0.11, 'M': 0.06, 'N': -0.03, 'P': 0.85, 'Q': -0.44, 'R': 0.66, 'S': 0.01, 'T': -0.3, 'V': 0.01, 'W': -0.54, 'Y': 0.24}, 'BLOSUM8': {'A': -0.05, 'C': 0.38, 'D': 0.53, 'E': 0.36, 'F': 0.1, 'G': 0.87, 'H': -0.08, 'I': 0.2, 'K': 0.13, 'L': 0.15, 'M': 0.21, 'N': -0.57, 'P': -0.35, 'Q': 0.2, 'R': 0.18, 'S': -0.8, 'T': -1.96, 'V': 0.02, 'W': -0.4, 'Y': -0.25}, 'BLOSUM9': {'A': 1.36, 'C': -0.12, 'D': -0.15, 'E': 0.77, 'F': 0.43, 'G': 0.01, 'H': -0.19, 'I': -0.22, 'K': 0.18, 'L': -0.44, 'M': -0.56, 'N': -1.2, 'P': -0.42, 'Q': 0.38, 'R': -0.22, 'S': 0.62, 'T': 0.15, 'V': 0.25, 'W': -0.35, 'Y': 0.71}}, 'CRUCIANI': {'PP1': {'A': -0.96, 'C': -0.55, 'D': 1.0, 'E': 0.94, 'F': -0.85, 'G': -0.88, 'H': 0.67, 'I': -0.94, 'K': 0.6, 'L': -0.9, 'M': -0.82, 'N': 0.82, 'P': -0.81, 'Q': 0.78, 'R': 0.8, 'S': 0.41, 'T': 0.4, 'V': -1.0, 'W': 0.06, 'Y': 0.31}, 'PP2': {'A': -0.76, 'C': -0.47, 'D': -0.89, 'E': -0.54, 'F': 0.48, 'G': -1.0, 'H': -0.11, 'I': -0.05, 'K': 0.1, 'L': 0.03, 'M': 0.03, 'N': -0.57, 'P': -0.4, 'Q': -0.3, 'R': 0.63, 'S': -0.82, 'T': -0.64, 'V': -0.43, 'W': 1.0, 'Y': 0.42}, 'PP3': {'A': 0.31, 'C': 0.19, 'D': -1.0, 'E': -0.99, 'F': -0.58, 'G': 0.49, 'H': 0.37, 'I': -0.18, 'K': 1.0, 'L': -0.24, 'M': -0.08, 'N': 0.02, 'P': -0.07, 'Q': -0.38, 'R': 0.99, 'S': 0.57, 'T': 0.37, 'V': -0.14, 'W': -0.47, 'Y': -0.2}}, 'FASGAI': {'F1': {'A': 0.207, 'C': 0.997, 'D': -1.298, 'E': -1.349, 'F': 1.247, 'G': -0.205, 'H': -0.27, 'I': 1.524, 'K': -1.387, 'L': 1.2, 'M': 0.886, 'N': -1.009, 'P': -0.407, 'Q': -0.88, 'R': -1.229, 'S': -0.495, 'T': -0.032, 'V': -1.332, 'W': 0.844, 'Y': 0.329}, 'F2': {'A': 0.821, 'C': 0.021, 'D': -0.444, 'E': 1.388, 'F': 0.293, 'G': -2.219, 'H': 0.461, 'I': 0.536, 'K': 0.572, 'L': 1.128, 'M': 1.346, 'N': -0.939, 'P': -2.038, 'Q': 0.381, 'R': 0.378, 'S': -0.847, 'T': -0.45, 'V': 0.545, 'W': -0.075, 'Y': -0.858}, 'F3': {'A': -1.009, 'C': -1.419, 'D': -0.584, 'E': -0.361, 'F': 1.336, 'G': -1.656, 'H': -0.024, 'I': 0.809, 'K': 0.285, 'L': 0.703, 'M': 0.277, 'N': -0.428, 'P': -0.564, 'Q': -0.044, 'R': 0.516, 'S': -1.079, 'T': -0.61, 'V': 0.029, 'W': 2.069, 'Y': 1.753}, 'F4': {'A': 1.387, 'C': -2.08, 'D': -0.175, 'E': 0.213, 'F': -0.026, 'G': 1.229, 'H': -1.407, 'I': 0.734, 'K': 0.333, 'L': 1.904, 'M': -0.913, 'N': -0.397, 'P': -0.128, 'Q': -0.455, 'R': -0.328, 'S': 0.582, 'T': 0.341, 'V': 1.026, 'W': -1.36, 'Y': -0.479}, 'F5': {'A': 0.063, 'C': -0.799, 'D': -0.259, 'E': 0.424, 'F': 0.012, 'G': -1.115, 'H': 0.001, 'I': -0.196, 'K': -0.169, 'L': 0.536, 'M': 0.007, 'N': -0.539, 'P': 3.847, 'Q': -0.04, 'R': -0.052, 'S': 0.035, 'T': 0.117, 'V': -0.229, 'W': -0.81, 'Y': -0.835}, 'F6': {'A': -0.6, 'C': 0.502, 'D': -1.762, 'E': -1.303, 'F': -0.015, 'G': -1.146, 'H': 0.169, 'I': 0.427, 'K': 1.157, 'L': -0.141, 'M': -0.265, 'N': -0.605, 'P': -1.108, 'Q': 0.405, 'R': 2.728, 'S': -0.068, 'T': 0.577, 'V': 1.038, 'W': -0.38, 'Y': 0.289}}, 'KIDERA': {'KF1': {'A': -1.56, 'C': 0.12, 'D': 0.58, 'E': -1.45, 'F': -0.21, 'G': 1.46, 'H': -0.41, 'I': -0.73, 'K': -0.34, 'L': -1.04, 'M': -1.4, 'N': 1.14, 'P': 2.06, 'Q': -0.47, 'R': 0.22, 'S': 0.81, 'T': 0.26, 'V': -0.74, 'W': 0.3, 'Y': 1.38}, 'KF10': {'A': -0.48, 'C': 1.1, 'D': 0.7, 'E': -0.12, 'F': -0.44, 'G': 0.46, 'H': 1.63, 'I': -1.78, 'K': 0.6, 'L': 0.93, 'M': 0.27, 'N': -1.73, 'P': -0.28, 'Q': -2.33, 'R': 0.93, 'S': -0.23, 'T': 0.19, 'V': 0.65, 'W': -0.6, 'Y': 0.53}, 'KF2': {'A': -1.67, 'C': -0.89, 'D': -0.22, 'E': 0.19, 'F': 0.98, 'G': -1.96, 'H': 0.52, 'I': -0.16, 'K': 0.82, 'L': 0.0, 'M': 0.18, 'N': -0.07, 'P': -0.33, 'Q': 0.24, 'R': 1.27, 'S': -1.08, 'T': -0.7, 'V': -0.71, 'W': 2.1, 'Y': 1.48}, 'KF3': {'A': -0.97, 'C': 0.45, 'D': -1.58, 'E': -1.61, 'F': -0.36, 'G': -0.23, 'H': -0.28, 'I': 1.79, 'K': -0.23, 'L': -0.24, 'M': -0.42, 'N': -0.12, 'P': -1.15, 'Q': 0.07, 'R': 1.37, 'S': 0.16, 'T': 1.21, 'V': 2.04, 'W': -0.72, 'Y': 0.8}, 'KF4': {'A': -0.27, 'C': -1.05, 'D': 0.81, 'E': 1.17, 'F': -1.43, 'G': -0.16, 'H': 0.28, 'I': -0.77, 'K': 1.7, 'L': -1.1, 'M': -0.73, 'N': 0.81, 'P': -0.75, 'Q': 1.1, 'R': 1.87, 'S': 0.42, 'T': 0.63, 'V': -0.4, 'W': -1.57, 'Y': -0.56}, 'KF5': {'A': -0.93, 'C': -0.71, 'D': -0.92, 'E': -1.31, 'F': 0.22, 'G': 0.1, 'H': 1.61, 'I': -0.54, 'K': 1.54, 'L': -0.55, 'M': 2.0, 'N': 0.18, 'P': 0.88, 'Q': 1.1, 'R': -1.7, 'S': -0.21, 'T': -0.1, 'V': 0.5, 'W': -1.16, 'Y': 0.0}, 'KF6': {'A': -0.78, 'C': 2.41, 'D': 0.15, 'E': 0.4, 'F': -0.81, 'G': -0.11, 'H': 1.01, 'I': 0.03, 'K': -1.62, 'L': -2.05, 'M': 1.52, 'N': 0.37, 'P': -0.45, 'Q': 0.59, 'R': 0.46, 'S': -0.43, 'T': 0.21, 'V': -0.81, 'W': 0.57, 'Y': -0.68}, 'KF7': {'A': -0.2, 'C': 1.52, 'D': -1.52, 'E': 0.04, 'F': 0.67, 'G': 1.32, 'H': -1.85, 'I': -0.83, 'K': 1.15, 'L': 0.96, 'M': 0.26, 'N': -0.09, 'P': 0.3, 'Q': 0.84, 'R': 0.92, 'S': -1.89, 'T': 0.24, 'V': -1.07, 'W': -0.48, 'Y': -0.31}, 'KF8': {'A': -0.08, 'C': -0.69, 'D': 0.47, 'E': 0.38, 'F': 1.1, 'G': 2.36, 'H': 0.47, 'I': 0.51, 'K': -0.08, 'L': -0.76, 'M': 0.11, 'N': 1.23, 'P': -2.3, 'Q': -0.71, 'R': -0.39, 'S': -1.15, 'T': -1.15, 'V': 0.06, 'W': -0.4, 'Y': 1.03}, 'KF9': {'A': 0.21, 'C': 1.13, 'D': 0.76, 'E': -0.35, 'F': 1.71, 'G': -1.66, 'H': 1.13, 'I': 0.66, 'K': -0.48, 'L': 0.45, 'M': -1.27, 'N': 1.1, 'P': 0.74, 'Q': -0.03, 'R': 0.23, 'S': -0.97, 'T': -0.56, 'V': -0.46, 'W': -2.3, 'Y': -0.05}}, 'MSWHIM': {'MSWHIM1': {'A': -0.73, 'C': -0.66, 'D': 0.11, 'E': 0.24, 'F': 0.76, 'G': -0.31, 'H': 0.84, 'I': -0.91, 'K': -0.51, 'L': -0.74, 'M': -0.7, 'N': 0.14, 'P': -0.43, 'Q': 0.3, 'R': -0.22, 'S': -0.8, 'T': -0.58, 'V': -1.0, 'W': 1.0, 'Y': 0.97}, 'MSWHIM2': {'A': 0.2, 'C': 0.26, 'D': -1.0, 'E': -0.39, 'F': 0.85, 'G': -0.28, 'H': 0.67, 'I': 0.83, 'K': 0.08, 'L': 0.72, 'M': 1.0, 'N': 0.2, 'P': 0.73, 'Q': 1.0, 'R': 0.27, 'S': 0.61, 'T': 0.85, 'V': 0.79, 'W': 0.98, 'Y': 0.66}, 'MSWHIM3': {'A': -0.62, 'C': -0.27, 'D': -0.96, 'E': -0.04, 'F': -0.34, 'G': -0.75, 'H': -0.78, 'I': -0.25, 'K': 0.6, 'L': -0.16, 'M': -0.32, 'N': -0.66, 'P': -0.6, 'Q': -0.3, 'R': 1.0, 'S': -1.0, 'T': -0.89, 'V': -0.58, 'W': -0.47, 'Y': -0.16}}, 'PCP_DESCRIPTORS': {'E1': {'A': 0.008, 'C': -0.132, 'D': 0.303, 'E': 0.221, 'F': -0.329, 'G': 0.218, 'H': 0.023, 'I': -0.353, 'K': 0.243, 'L': -0.267, 'M': -0.239, 'N': 0.255, 'P': 0.173, 'Q': 0.149, 'R': 0.171, 'S': 0.199, 'T': 0.068, 'V': -0.274, 'W': -0.296, 'Y': -0.141}, 'E2': {'A': 0.134, 'C': 0.174, 'D': -0.057, 'E': -0.28, 'F': -0.023, 'G': 0.562, 'H': -0.177, 'I': 0.071, 'K': -0.339, 'L': 0.018, 'M': -0.141, 'N': 0.038, 'P': 0.286, 'Q': -0.184, 'R': -0.361, 'S': 0.238, 'T': 0.147, 'V': 0.136, 'W': -0.186, 'Y': -0.057}, 'E3': {'A': -0.475, 'C': 0.07, 'D': -0.014, 'E': -0.315, 'F': 0.072, 'G': -0.024, 'H': 0.041, 'I': -0.088, 'K': -0.044, 'L': -0.265, 'M': -0.155, 'N': 0.117, 'P': 0.407, 'Q': -0.03, 'R': 0.107, 'S': -0.015, 'T': -0.015, 'V': -0.187, 'W': 0.389, 'Y': 0.425}, 'E4': {'A': -0.039, 'C': 0.565, 'D': 0.225, 'E': 0.157, 'F': -0.002, 'G': 0.018, 'H': 0.28, 'I': -0.195, 'K': -0.325, 'L': -0.274, 'M': 0.321, 'N': 0.118, 'P': -0.215, 'Q': 0.035, 'R': -0.258, 'S': -0.068, 'T': -0.132, 'V': -0.196, 'W': 0.083, 'Y': -0.096}, 'E5': {'A': 0.181, 'C': -0.374, 'D': 0.156, 'E': 0.303, 'F': 0.208, 'G': 0.106, 'H': -0.021, 'I': -0.107, 'K': -0.027, 'L': 0.206, 'M': 0.077, 'N': -0.055, 'P': 0.384, 'Q': -0.112, 'R': -0.364, 'S': -0.196, 'T': -0.274, 'V': -0.299, 'W': 0.297, 'Y': -0.091}}, 'PHYSICAL_DESCRIPTORS': {'PD1': {'A': -2.9, 'C': -1.89, 'D': -0.92, 'E': 0.16, 'F': 2.22, 'G': -4.04, 'H': 0.83, 'I': 0.51, 'K': 0.92, 'L': 0.52, 'M': 0.92, 'N': -0.68, 'P': -1.25, 'Q': 0.36, 'R': 2.41, 'S': -2.36, 'T': -1.19, 'V': -0.65, 'W': 4.28, 'Y': 2.75}, 'PD2': {'A': -1.03, 'C': 0.15, 'D': 1.23, 'E': 1.28, 'F': -1.47, 'G': 0.01, 'H': 1.15, 'I': -1.32, 'K': 1.23, 'L': -1.4, 'M': -1.42, 'N': 0.79, 'P': -0.64, 'Q': 1.09, 'R': 1.31, 'S': 0.38, 'T': 0.28, 'V': -1.27, 'W': -0.18, 'Y': -0.18}}, 'PRIN': {'PRIN1': {'A': -1.0169, 'C': 5.7345, 'D': -10.2708, 'E': -8.8179, 'F': 11.5142, 'G': -4.6415, 'H': -0.9279, 'I': 11.1181, 'K': -8.5038, 'L': 9.3995, 'M': 7.8783, 'N': -8.0017, 'P': -1.3637, 'Q': -7.3957, 'R': -8.4267, 'S': -6.5985, 'T': -4.0894, 'V': 7.695, 'W': 11.919, 'Y': 4.7959}, 'PRIN2': {'A': -7.9863, 'C': -3.3045, 'D': -0.3838, 'E': 1.4271, 'F': 2.657, 'G': -10.7191, 'H': 3.3268, 'I': -1.9529, 'K': 7.2728, 'L': -1.5643, 'M': 0.3062, 'N': 0.3275, 'P': -3.4392, 'Q': 2.5179, 'R': 10.1801, 'S': -5.2529, 'T': -3.3886, 'V': -4.268, 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'V': -2.29, 'W': 2.77, 'Y': 2.45}, 'ProtFP4': {'A': 1.7, 'C': -1.26, 'D': -4.58, 'E': -2.26, 'F': -1.12, 'G': -1.35, 'H': 0.71, 'I': 1.09, 'K': 3.0, 'L': 0.63, 'M': 0.15, 'N': -0.14, 'P': 1.0, 'Q': 0.52, 'R': 2.07, 'S': 1.11, 'T': 1.02, 'V': 1.38, 'W': -2.41, 'Y': -1.27}, 'ProtFP5': {'A': -0.39, 'C': 3.27, 'D': 0.48, 'E': -2.14, 'F': -0.49, 'G': -0.31, 'H': 1.16, 'I': -0.34, 'K': -1.23, 'L': -1.7, 'M': 0.13, 'N': 1.23, 'P': -3.22, 'Q': 0.9, 'R': 1.67, 'S': 0.99, 'T': 1.06, 'V': 0.06, 'W': -1.08, 'Y': -0.06}, 'ProtFP6': {'A': 1.06, 'C': -0.34, 'D': -1.31, 'E': 1.35, 'F': -0.55, 'G': 2.91, 'H': -0.38, 'I': -0.28, 'K': 1.41, 'L': 0.71, 'M': -0.3, 'N': -0.65, 'P': -3.54, 'Q': 0.55, 'R': 0.76, 'S': -1.02, 'T': -1.2, 'V': 0.08, 'W': 1.04, 'Y': -0.29}, 'ProtFP7': {'A': -1.39, 'C': -0.47, 'D': 0.1, 'E': -0.45, 'F': -0.87, 'G': 0.32, 'H': -1.85, 'I': 1.97, 'K': 0.19, 'L': -0.05, 'M': -2.95, 'N': 1.02, 'P': -0.36, 'Q': -0.08, 'R': 0.0, 'S': 0.11, 'T': 0.74, 'V': 1.79, 'W': 0.23, 'Y': 1.99}, 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0.51, 'F': -0.63, 'G': -0.12, 'H': 0.01, 'I': -0.15, 'K': -1.69, 'L': -0.49, 'M': -2.34, 'N': 1.16, 'P': -0.53, 'Q': 0.28, 'R': -1.16, 'S': 0.68, 'T': 1.11, 'V': 0.28, 'W': -0.07, 'Y': 0.07}, 'T4': {'A': 1.04, 'C': 0.8, 'D': -0.4, 'E': -0.58, 'F': -1.27, 'G': 0.75, 'H': -1.81, 'I': 1.4, 'K': 0.41, 'L': 1.45, 'M': 1.64, 'N': -0.22, 'P': -0.36, 'Q': -0.39, 'R': -0.39, 'S': -0.17, 'T': 0.31, 'V': 1.1, 'W': -1.96, 'Y': -1.67}, 'T5': {'A': 2.26, 'C': 0.98, 'D': 1.05, 'E': 0.43, 'F': -0.44, 'G': 3.25, 'H': -0.21, 'I': -0.21, 'K': -0.21, 'L': 0.02, 'M': -0.79, 'N': 0.93, 'P': -0.29, 'Q': 0.33, 'R': -0.06, 'S': 1.58, 'T': 0.95, 'V': 0.48, 'W': -0.54, 'Y': -0.35}}, 'VHSE': {'VHSE1': {'A': 0.15, 'C': 0.18, 'D': -1.15, 'E': -1.18, 'F': 1.52, 'G': -0.2, 'H': -0.43, 'I': 1.27, 'K': -1.17, 'L': 1.36, 'M': 1.01, 'N': -0.99, 'P': 0.22, 'Q': -0.96, 'R': -1.47, 'S': -0.67, 'T': -0.34, 'V': 0.76, 'W': 1.5, 'Y': 0.61}, 'VHSE2': {'A': -1.11, 'C': -1.67, 'D': 0.67, 'E': 0.4, 'F': 0.61, 'G': -1.53, 'H': -0.25, 'I': -0.14, 'K': 0.7, 'L': 0.07, 'M': -0.53, 'N': 0.0, 'P': -0.17, 'Q': 0.12, 'R': 1.45, 'S': -0.86, 'T': -0.51, 'V': -0.92, 'W': 2.06, 'Y': 1.6}, 'VHSE3': {'A': -1.35, 'C': -0.46, 'D': -0.41, 'E': 0.1, 'F': 0.96, 'G': -2.63, 'H': 0.37, 'I': 0.3, 'K': 0.7, 'L': 0.36, 'M': 0.43, 'N': -0.37, 'P': -0.5, 'Q': 0.18, 'R': 1.24, 'S': -1.07, 'T': -0.55, 'V': -0.17, 'W': 1.79, 'Y': 1.17}, 'VHSE4': {'A': -0.92, 'C': -0.21, 'D': -0.01, 'E': 0.36, 'F': -0.16, 'G': 2.28, 'H': 0.19, 'I': -1.8, 'K': 0.8, 'L': -0.8, 'M': 0.0, 'N': 0.69, 'P': 0.05, 'Q': 0.16, 'R': 1.27, 'S': -0.41, 'T': -1.06, 'V': -1.91, 'W': 0.75, 'Y': 0.73}, 'VHSE5': {'A': 0.02, 'C': 0.0, 'D': -2.68, 'E': -2.16, 'F': 0.25, 'G': -0.53, 'H': 0.51, 'I': 0.3, 'K': 1.64, 'L': 0.22, 'M': 0.23, 'N': -0.55, 'P': -0.01, 'Q': 0.09, 'R': 1.55, 'S': -0.32, 'T': -0.06, 'V': 0.22, 'W': 0.75, 'Y': 0.53}, 'VHSE6': {'A': -0.91, 'C': 1.2, 'D': 1.31, 'E': -0.17, 'F': 0.28, 'G': -1.18, 'H': 1.28, 'I': -1.61, 'K': 0.67, 'L': -1.37, 'M': 0.1, 'N': 0.85, 'P': -1.34, 'Q': 0.42, 'R': 1.47, 'S': 0.27, 'T': -0.01, 'V': -1.4, 'W': -0.13, 'Y': 0.25}, 'VHSE7': {'A': 0.36, 'C': -1.61, 'D': 0.03, 'E': 0.91, 'F': -1.33, 'G': 2.01, 'H': 0.93, 'I': -0.16, 'K': 1.63, 'L': 0.08, 'M': -0.86, 'N': 0.73, 'P': -0.19, 'Q': -0.2, 'R': 1.3, 'S': -0.64, 'T': -0.79, 'V': -0.24, 'W': -1.01, 'Y': -0.96}, 'VHSE8': {'A': -0.48, 'C': -0.19, 'D': 0.56, 'E': 0.02, 'F': -0.2, 'G': -1.34, 'H': 0.65, 'I': -0.13, 'K': 0.13, 'L': -0.62, 'M': -0.68, 'N': -0.8, 'P': 3.56, 'Q': -0.41, 'R': 0.83, 'S': 0.11, 'T': 0.39, 'V': -0.03, 'W': -0.85, 'Y': -0.52}}, 'VSTPV': {'VSTPV1': {'A': -1.54, 'C': -1.22, 'D': -0.8, 'E': -0.55, 'F': -0.11, 'G': -1.76, 'H': -0.31, 'I': -0.78, 'K': -0.5, 'L': -0.78, 'M': -0.7, 'N': -0.79, 'P': -0.94, 'Q': -0.55, 'R': -0.05, 'S': -1.24, 'T': -1.04, 'V': -1.04, 'W': 0.61, 'Y': 0.17}, 'VSTPV2': {'A': -0.21, 'C': 0.12, 'D': -0.22, 'E': 0.3, 'F': -0.2, 'G': 0.21, 'H': -1.16, 'I': 0.14, 'K': 1.26, 'L': 0.63, 'M': 1.43, 'N': -0.16, 'P': -0.99, 'Q': 0.35, 'R': 1.33, 'S': -0.48, 'T': -0.3, 'V': 0.02, 'W': -1.13, 'Y': -0.22}, 'VSTPV3': {'A': 1.23, 'C': 1.26, 'D': 0.07, 'E': -0.06, 'F': -0.63, 'G': 1.16, 'H': 0.02, 'I': 0.8, 'K': 0.11, 'L': 0.64, 'M': 1.07, 'N': 0.14, 'P': 0.06, 'Q': 0.01, 'R': -0.36, 'S': 0.68, 'T': 0.44, 'V': 0.78, 'W': -0.39, 'Y': -0.85}, 'VSTPV4': {'A': -1.38, 'C': 0.41, 'D': -1.34, 'E': -0.81, 'F': 0.18, 'G': -1.39, 'H': 0.35, 'I': 0.61, 'K': 0.64, 'L': 0.24, 'M': 2.19, 'N': -1.22, 'P': 0.28, 'Q': -0.69, 'R': -0.39, 'S': -0.75, 'T': -1.22, 'V': -0.41, 'W': 0.82, 'Y': -0.21}, 'VSTPV5': {'A': -0.27, 'C': 0.39, 'D': 0.76, 'E': 0.85, 'F': -0.02, 'G': 1.31, 'H': 1.58, 'I': -0.32, 'K': 0.7, 'L': -0.75, 'M': -0.02, 'N': 0.68, 'P': -0.9, 'Q': 0.77, 'R': 0.85, 'S': 1.18, 'T': -0.57, 'V': -1.22, 'W': 0.78, 'Y': 0.05}, 'VSTPV6': {'A': -1.01, 'C': 0.56, 'D': 0.17, 'E': 0.37, 'F': -1.0, 'G': -2.22, 'H': 0.23, 'I': 0.29, 'K': -0.19, 'L': 0.09, 'M': 0.98, 'N': 0.33, 'P': -1.48, 'Q': 0.51, 'R': 0.51, 'S': -0.43, 'T': -0.17, 'V': -0.12, 'W': -0.16, 'Y': -0.26}}, 'Z_SCALES': {'Z1': {'A': 0.24, 'C': 0.84, 'D': 3.98, 'E': 3.11, 'F': -4.22, 'G': 2.05, 'H': 2.47, 'I': -3.89, 'K': 2.29, 'L': -4.28, 'M': -2.85, 'N': 3.05, 'P': -1.66, 'Q': 1.75, 'R': 3.52, 'S': 2.39, 'T': 0.75, 'V': -2.59, 'W': -4.36, 'Y': -2.54}, 'Z2': {'A': -2.32, 'C': -1.67, 'D': 0.93, 'E': 0.26, 'F': 1.94, 'G': -4.06, 'H': 1.95, 'I': -1.73, 'K': 0.89, 'L': -1.3, 'M': -0.22, 'N': 1.62, 'P': 0.27, 'Q': 0.5, 'R': 2.5, 'S': -1.07, 'T': -2.18, 'V': -2.64, 'W': 3.94, 'Y': 2.44}, 'Z3': {'A': 0.6, 'C': 3.75, 'D': 1.93, 'E': -0.11, 'F': 1.06, 'G': 0.36, 'H': 0.26, 'I': -1.71, 'K': -2.49, 'L': -1.49, 'M': 0.47, 'N': 1.04, 'P': 1.84, 'Q': -1.44, 'R': -3.5, 'S': 1.15, 'T': -1.12, 'V': -1.54, 'W': 0.59, 'Y': 0.43}, 'Z4': {'A': -0.14, 'C': 0.18, 'D': -2.46, 'E': -3.04, 'F': 0.54, 'G': -0.82, 'H': 3.9, 'I': -0.84, 'K': 1.49, 'L': -0.72, 'M': 1.94, 'N': -1.15, 'P': 0.7, 'Q': -1.34, 'R': 1.99, 'S': -1.39, 'T': -1.46, 'V': -0.85, 'W': 3.44, 'Y': 0.04}, 'Z5': {'A': 1.3, 'C': -2.65, 'D': 0.75, 'E': -0.25, 'F': -0.62, 'G': -0.38, 'H': 0.09, 'I': 0.26, 'K': 0.31, 'L': 0.84, 'M': -0.98, 'N': 1.61, 'P': 2.0, 'Q': 0.66, 'R': -0.17, 'S': 0.67, 'T': -0.4, 'V': -0.02, 'W': -1.59, 'Y': -1.47}}}

Descriptor families -> component name -> residue -> value.

mhcmatch.data.aa_tables.DESCRIPTOR_PREFIX: dict[str, str] = {'ATCHLEY': 'AF', 'BLOSUM': 'BLOSUM', 'CRUCIANI': 'PP', 'FASGAI': 'F', 'KIDERA': 'KF', 'MSWHIM': 'MSWHIM', 'PCP_DESCRIPTORS': 'E', 'PHYSICAL_DESCRIPTORS': 'PD', 'PRIN': 'PRIN', 'PROTFP': 'ProtFP', 'SNEATH': 'SV', 'ST_SCALES': 'ST', 'SVGER': 'SVGER', 'T_SCALES': 'T', 'VHSE': 'VHSE', 'VSTPV': 'VSTPV', 'Z_SCALES': 'Z'}

Family -> the key prefix used by peptides’ descriptors(). Not always the family name: PCP->E, Cruciani->PP, Sneath->SV, Physical->PD, and ProtFP is mixed-case.

mhcmatch.data.aa_tables.HYDROPHOBICITY: dict[str, dict[str, float]] = {'Aboderin': {'A': 5.1, 'C': 0.0, 'D': 0.7, 'E': 1.8, 'F': 9.6, 'G': 4.1, 'H': 1.6, 'I': 9.3, 'K': 1.3, 'L': 10.0, 'M': 8.7, 'N': 0.6, 'P': 4.9, 'Q': 1.4, 'R': 2.0, 'S': 3.1, 'T': 3.5, 'V': 8.5, 'W': 9.2, 'Y': 8.0}, 'AbrahamLeo': {'A': 0.44, 'C': 0.58, 'D': -0.31, 'E': -0.34, 'F': 2.54, 'G': 0.0, 'H': -0.01, 'I': 2.46, 'K': -2.45, 'L': 2.46, 'M': 1.1, 'N': -1.32, 'P': 1.29, 'Q': -0.71, 'R': -2.42, 'S': -0.84, 'T': -0.41, 'V': 1.73, 'W': 2.56, 'Y': 1.63}, 'Argos': {'A': 0.61, 'C': 1.07, 'D': 0.46, 'E': 0.47, 'F': 2.02, 'G': 0.07, 'H': 0.61, 'I': 2.22, 'K': 1.15, 'L': 1.53, 'M': 1.18, 'N': 0.06, 'P': 1.95, 'Q': 0.0, 'R': 0.6, 'S': 0.05, 'T': 0.05, 'V': 1.32, 'W': 2.65, 'Y': 1.88}, 'Barley': {'A': -1.03, 'C': 0.15, 'D': 1.23, 'E': 1.28, 'F': -1.47, 'G': 0.01, 'H': 1.15, 'I': -1.32, 'K': 1.23, 'L': -1.4, 'M': -1.42, 'N': 0.79, 'P': -0.64, 'Q': 1.09, 'R': 1.31, 'S': 0.38, 'T': 0.28, 'V': -1.27, 'W': -0.18, 'Y': -0.18}, 'BlackMould': {'A': 0.616, 'C': 0.68, 'D': 0.028, 'E': 0.043, 'F': 1.0, 'G': 0.501, 'H': 0.165, 'I': 0.943, 'K': 0.283, 'L': 0.943, 'M': 0.738, 'N': 0.236, 'P': 0.711, 'Q': 0.251, 'R': 0.0, 'S': 0.359, 'T': 0.45, 'V': 0.825, 'W': 0.878, 'Y': 0.88}, 'BullBreese': {'A': 0.61, 'C': 0.36, 'D': 0.61, 'E': 0.51, 'F': -1.52, 'G': 0.81, 'H': 0.69, 'I': -1.45, 'K': 0.46, 'L': -1.65, 'M': -0.66, 'N': 0.89, 'P': -0.17, 'Q': 0.97, 'R': 0.69, 'S': 0.42, 'T': 0.29, 'V': -0.75, 'W': -1.2, 'Y': -1.43}, 'Casari': {'A': 0.2, 'C': 1.9, 'D': -1.4, 'E': -1.3, 'F': 1.0, 'G': -0.1, 'H': 0.4, 'I': 1.4, 'K': -1.6, 'L': 0.5, 'M': 0.5, 'N': -0.5, 'P': -1.0, 'Q': -1.1, 'R': -0.7, 'S': -0.7, 'T': -0.4, 'V': 0.7, 'W': 1.6, 'Y': 0.5}, 'Chothia': {'A': 0.38, 'C': 0.5, 'D': 0.15, 'E': 0.18, 'F': 0.5, 'G': 0.36, 'H': 0.17, 'I': 0.6, 'K': 0.03, 'L': 0.45, 'M': 0.4, 'N': 0.12, 'P': 0.18, 'Q': 0.07, 'R': 0.01, 'S': 0.22, 'T': 0.23, 'V': 0.54, 'W': 0.27, 'Y': 0.15}, 'Cid': {'A': 0.02, 'C': 0.77, 'D': -1.04, 'E': -1.14, 'F': 1.35, 'G': -0.8, 'H': 0.26, 'I': 1.81, 'K': -0.41, 'L': 1.14, 'M': 1.0, 'N': -0.77, 'P': -0.09, 'Q': -1.1, 'R': -0.42, 'S': -0.97, 'T': -0.77, 'V': 1.13, 'W': 1.71, 'Y': 1.11}, 'Cowan3.4': {'A': 0.42, 'C': 0.84, 'D': -0.51, 'E': -0.37, 'F': 1.74, 'G': 0.0, 'H': -2.28, 'I': 1.81, 'K': -2.03, 'L': 1.8, 'M': 1.18, 'N': -1.03, 'P': 0.86, 'Q': -0.96, 'R': -1.56, 'S': -0.64, 'T': -0.26, 'V': 1.34, 'W': 1.46, 'Y': 0.51}, 'Cowan7.5': {'A': 0.35, 'C': 0.76, 'D': -2.15, 'E': -1.95, 'F': 1.69, 'G': 0.0, 'H': -0.65, 'I': 1.83, 'K': -1.54, 'L': 1.8, 'M': 1.1, 'N': -0.99, 'P': 0.84, 'Q': -0.93, 'R': -1.5, 'S': -0.63, 'T': -0.27, 'V': 1.32, 'W': 1.35, 'Y': 0.39}, 'Eisenberg': {'A': 0.62, 'C': 0.29, 'D': -0.9, 'E': -0.74, 'F': 1.19, 'G': 0.48, 'H': -0.4, 'I': 1.38, 'K': -1.5, 'L': 1.06, 'M': 0.64, 'N': -0.78, 'P': 0.12, 'Q': -0.85, 'R': -2.53, 'S': -0.18, 'T': -0.05, 'V': 1.08, 'W': 0.81, 'Y': 0.26}, 'Engelman': {'A': -1.6, 'C': -2.0, 'D': 9.2, 'E': 8.2, 'F': -3.7, 'G': -1.0, 'H': 3.0, 'I': -3.1, 'K': 8.8, 'L': -2.8, 'M': -3.4, 'N': 4.8, 'P': 0.2, 'Q': 4.1, 'R': 12.3, 'S': -0.6, 'T': -1.2, 'V': -2.6, 'W': -1.9, 'Y': 0.7}, 'Fasman': {'A': -0.21, 'C': -6.04, 'D': 1.36, 'E': 2.3, 'F': -4.65, 'G': 0.0, 'H': -1.23, 'I': -4.81, 'K': 3.88, 'L': -4.68, 'M': -3.66, 'N': 0.96, 'P': 0.75, 'Q': 1.52, 'R': 2.11, 'S': 1.74, 'T': 0.78, 'V': -3.5, 'W': -3.32, 'Y': -1.01}, 'Fauchere': {'A': 0.31, 'C': 1.54, 'D': -0.77, 'E': -0.64, 'F': 1.79, 'G': 0.0, 'H': 0.13, 'I': 1.8, 'K': -0.99, 'L': 1.7, 'M': 1.23, 'N': -0.6, 'P': 0.72, 'Q': -0.22, 'R': -1.01, 'S': -0.04, 'T': 0.26, 'V': 1.22, 'W': 2.25, 'Y': 0.96}, 'Goldsack': {'A': 0.75, 'C': 1.0, 'D': 0.0, 'E': 0.0, 'F': 2.65, 'G': 0.0, 'H': 0.0, 'I': 2.95, 'K': 1.5, 'L': 2.4, 'M': 1.3, 'N': 0.69, 'P': 2.6, 'Q': 0.59, 'R': 0.75, 'S': 0.0, 'T': 0.45, 'V': 1.7, 'W': 3.0, 'Y': 2.85}, 'Guy': {'A': 0.1, 'C': -1.42, 'D': 0.78, 'E': 0.83, 'F': -2.12, 'G': 0.33, 'H': -0.5, 'I': -1.13, 'K': 1.4, 'L': -1.18, 'M': -1.59, 'N': 0.48, 'P': 0.73, 'Q': 0.95, 'R': 1.91, 'S': 0.52, 'T': 0.07, 'V': -1.27, 'W': -0.51, 'Y': -0.21}, 'HoppWoods': {'A': -0.5, 'C': -1.0, 'D': 3.0, 'E': 3.0, 'F': -2.5, 'G': 0.0, 'H': -0.5, 'I': -1.8, 'K': 3.0, 'L': -1.8, 'M': -1.3, 'N': 0.2, 'P': 0.0, 'Q': 0.2, 'R': 3.0, 'S': 0.3, 'T': -0.4, 'V': -1.5, 'W': -3.4, 'Y': -2.3}, 'Janin': {'A': 0.3, 'C': 0.9, 'D': -0.6, 'E': -0.7, 'F': 0.5, 'G': 0.3, 'H': -0.1, 'I': 0.7, 'K': -1.8, 'L': 0.5, 'M': 0.4, 'N': -0.5, 'P': -0.3, 'Q': -0.7, 'R': -1.4, 'S': -0.1, 'T': -0.2, 'V': 0.6, 'W': 0.3, 'Y': -0.4}, 'Jones': {'A': 0.87, 'C': 1.52, 'D': 0.66, 'E': 0.67, 'F': 2.87, 'G': 0.1, 'H': 0.87, 'I': 3.15, 'K': 1.64, 'L': 2.17, 'M': 1.67, 'N': 0.09, 'P': 2.77, 'Q': 0.0, 'R': 0.85, 'S': 0.07, 'T': 0.07, 'V': 1.87, 'W': 3.77, 'Y': 2.67}, 'Juretic': {'A': 1.1, 'C': 2.5, 'D': -3.6, 'E': -3.2, 'F': 2.8, 'G': -0.64, 'H': -3.2, 'I': 4.5, 'K': -4.11, 'L': 3.8, 'M': 1.9, 'N': -3.5, 'P': -1.9, 'Q': -3.68, 'R': -5.1, 'S': -0.5, 'T': -0.7, 'V': 4.2, 'W': -0.46, 'Y': -1.3}, 'Kidera': {'A': -0.27, 'C': -1.05, 'D': 0.81, 'E': 1.17, 'F': -1.43, 'G': -0.16, 'H': 0.28, 'I': -0.77, 'K': 1.7, 'L': -1.1, 'M': -0.73, 'N': 0.81, 'P': -0.75, 'Q': 1.1, 'R': 1.87, 'S': 0.42, 'T': 0.63, 'V': -0.4, 'W': -1.57, 'Y': -0.56}, 'Kuhn': {'A': 0.78, 'C': 0.55, 'D': 1.35, 'E': 1.45, 'F': 0.47, 'G': 0.68, 'H': 0.99, 'I': 0.47, 'K': 1.1, 'L': 0.56, 'M': 0.66, 'N': 1.2, 'P': 0.69, 'Q': 1.19, 'R': 1.58, 'S': 1.0, 'T': 1.05, 'V': 0.51, 'W': 0.7, 'Y': 1.0}, 'KyteDoolittle': {'A': 1.8, 'C': 2.5, 'D': -3.5, 'E': -3.5, 'F': 2.8, 'G': -0.4, 'H': -3.2, 'I': 4.5, 'K': -3.9, 'L': 3.8, 'M': 1.9, 'N': -3.5, 'P': -1.6, 'Q': -3.5, 'R': -4.5, 'S': -0.8, 'T': -0.7, 'V': 4.2, 'W': -0.9, 'Y': -1.3}, 'Levitt': {'A': -0.5, 'C': -1.0, 'D': 2.5, 'E': 2.5, 'F': -2.5, 'G': 0.0, 'H': -0.5, 'I': -1.8, 'K': 3.0, 'L': -1.8, 'M': -1.3, 'N': 0.2, 'P': -1.4, 'Q': 0.2, 'R': 3.0, 'S': 0.3, 'T': -0.4, 'V': -1.5, 'W': -3.4, 'Y': -2.3}, 'Manavalan': {'A': 12.97, 'C': 14.63, 'D': 10.85, 'E': 11.89, 'F': 14.0, 'G': 12.43, 'H': 12.16, 'I': 15.67, 'K': 11.36, 'L': 14.9, 'M': 14.39, 'N': 11.42, 'P': 11.37, 'Q': 11.76, 'R': 11.72, 'S': 11.23, 'T': 11.69, 'V': 15.71, 'W': 13.93, 'Y': 13.42}, 'Miyazawa': {'A': 5.33, 'C': 7.93, 'D': 3.59, 'E': 3.65, 'F': 9.03, 'G': 4.48, 'H': 5.1, 'I': 8.83, 'K': 2.95, 'L': 8.47, 'M': 8.95, 'N': 3.71, 'P': 3.87, 'Q': 3.87, 'R': 4.18, 'S': 4.09, 'T': 4.49, 'V': 7.63, 'W': 7.66, 'Y': 5.89}, 'Parker': {'A': 2.1, 'C': 1.4, 'D': 10.0, 'E': 7.8, 'F': -9.2, 'G': 5.7, 'H': 2.1, 'I': -8.0, 'K': 5.7, 'L': -9.2, 'M': -4.2, 'N': 7.0, 'P': 2.1, 'Q': 6.0, 'R': 4.2, 'S': 6.5, 'T': 5.2, 'V': -3.7, 'W': -10.0, 'Y': -1.9}, 'Ponnuswamy': {'A': 0.85, 'C': 2.1, 'D': -1.1, 'E': -0.79, 'F': 1.69, 'G': 0.0, 'H': 0.22, 'I': 3.14, 'K': -1.19, 'L': 1.99, 'M': 1.42, 'N': -0.48, 'P': -1.14, 'Q': -0.42, 'R': 0.2, 'S': -0.52, 'T': -0.08, 'V': 2.53, 'W': 1.76, 'Y': 1.37}, 'Prabhakaran': {'A': -6.7, 'C': -8.4, 'D': 38.5, 'E': 34.3, 'F': -15.5, 'G': -4.2, 'H': 12.6, 'I': -13.0, 'K': 36.8, 'L': -11.7, 'M': -14.2, 'N': 20.1, 'P': 0.8, 'Q': 17.2, 'R': 51.5, 'S': -2.5, 'T': -5.0, 'V': -10.9, 'W': -7.9, 'Y': 2.9}, 'Rao': {'A': 1.36, 'C': 1.27, 'D': 0.11, 'E': 0.25, 'F': 1.57, 'G': 1.09, 'H': 0.68, 'I': 1.44, 'K': 0.09, 'L': 1.47, 'M': 1.42, 'N': 0.33, 'P': 0.54, 'Q': 0.33, 'R': 0.15, 'S': 0.97, 'T': 1.08, 'V': 1.37, 'W': 1.0, 'Y': 0.83}, 'Rose': {'A': 0.74, 'C': 0.91, 'D': 0.62, 'E': 0.62, 'F': 0.88, 'G': 0.72, 'H': 0.78, 'I': 0.88, 'K': 0.52, 'L': 0.85, 'M': 0.85, 'N': 0.63, 'P': 0.64, 'Q': 0.62, 'R': 0.64, 'S': 0.66, 'T': 0.7, 'V': 0.86, 'W': 0.85, 'Y': 0.76}, 'Roseman': {'A': 0.39, 'C': 0.25, 'D': -3.81, 'E': -2.91, 'F': 2.27, 'G': 0.0, 'H': -0.64, 'I': 1.82, 'K': -2.77, 'L': 1.82, 'M': 0.96, 'N': -1.91, 'P': 0.99, 'Q': -1.3, 'R': -3.95, 'S': -1.24, 'T': -1.0, 'V': 1.3, 'W': 2.13, 'Y': 1.47}, 'Sweet': {'A': -0.4, 'C': 0.17, 'D': -1.31, 'E': -1.22, 'F': 1.92, 'G': -0.67, 'H': -0.64, 'I': 1.25, 'K': -0.67, 'L': 1.22, 'M': 1.02, 'N': -0.92, 'P': -0.49, 'Q': -0.91, 'R': -0.59, 'S': -0.55, 'T': -0.28, 'V': 0.91, 'W': 0.5, 'Y': 1.67}, 'Tanford': {'A': 0.62, 'C': 0.29, 'D': -0.09, 'E': -0.74, 'F': 1.19, 'G': 0.48, 'H': -0.4, 'I': 1.38, 'K': -1.5, 'L': 1.53, 'M': 0.64, 'N': -0.78, 'P': 0.12, 'Q': -0.85, 'R': -2.53, 'S': -0.18, 'T': -0.05, 'V': 1.8, 'W': 0.81, 'Y': 0.26}, 'Welling': {'A': 1.15, 'C': -1.2, 'D': 0.65, 'E': -0.71, 'F': -1.41, 'G': -1.84, 'H': 3.12, 'I': -2.92, 'K': 2.06, 'L': 0.75, 'M': -3.85, 'N': -0.77, 'P': -0.53, 'Q': -0.11, 'R': 0.58, 'S': -0.26, 'T': -0.45, 'V': -0.13, 'W': -1.14, 'Y': 0.13}, 'Wilson': {'A': -0.3, 'C': 6.3, 'D': -1.4, 'E': 0.0, 'F': 7.5, 'G': 1.2, 'H': -1.3, 'I': 4.3, 'K': -3.6, 'L': 6.6, 'M': 2.5, 'N': -0.2, 'P': 2.2, 'Q': -0.2, 'R': -1.1, 'S': -0.6, 'T': -2.2, 'V': 5.9, 'W': 7.9, 'Y': 7.1}, 'Wolfenden': {'A': 1.94, 'C': -1.24, 'D': -10.95, 'E': -10.2, 'F': -0.76, 'G': 2.39, 'H': -10.27, 'I': 2.15, 'K': -9.52, 'L': 2.28, 'M': -1.48, 'N': -9.68, 'P': 0.0, 'Q': -9.38, 'R': -19.92, 'S': -5.06, 'T': -4.88, 'V': 1.99, 'W': -5.88, 'Y': -6.11}, 'Zimmerman': {'A': 0.83, 'C': 1.48, 'D': 0.64, 'E': 0.65, 'F': 2.75, 'G': 0.1, 'H': 1.1, 'I': 3.07, 'K': 1.6, 'L': 2.52, 'M': 1.4, 'N': 0.09, 'P': 2.7, 'Q': 0.0, 'R': 0.83, 'S': 0.14, 'T': 0.54, 'V': 1.79, 'W': 0.31, 'Y': 2.97}, 'interfaceScale_pH2': {'D': -0.07, 'E': -0.01, 'H': 0.96, 'K': 0.99, 'R': 0.81}, 'interfaceScale_pH8': {'A': 0.17, 'C': -0.24, 'D': 0.13, 'E': 2.02, 'F': -1.13, 'G': 0.01, 'H': 0.17, 'I': -0.31, 'L': -0.56, 'M': -0.23, 'N': 0.42, 'P': 0.45, 'Q': 0.58, 'S': 0.13, 'T': 0.14, 'V': 0.07, 'W': -1.85, 'Y': -0.94}, 'octanolScale_pH2': {'D': 0.43, 'E': 0.11, 'H': 2.33, 'K': 2.8, 'R': 1.81}, 'octanolScale_pH8': {'A': 0.5, 'C': -0.02, 'D': 3.64, 'E': 3.63, 'F': -1.71, 'G': 1.15, 'H': 0.11, 'I': -1.12, 'L': -1.25, 'M': -0.67, 'N': 0.85, 'P': 0.14, 'Q': 0.77, 'S': 0.46, 'T': 0.25, 'V': -0.46, 'W': -2.09, 'Y': -0.71}, 'oiScale_pH2': {'D': 0.5, 'E': 0.12, 'H': 1.37, 'K': 1.81, 'R': 1.0}, 'oiScale_pH8': {'A': 0.33, 'C': 0.22, 'D': 2.41, 'E': 1.61, 'F': -0.58, 'G': 1.14, 'H': -0.06, 'I': -0.81, 'L': -0.69, 'M': -0.44, 'N': 0.43, 'P': -0.31, 'Q': 0.19, 'S': 0.33, 'T': 0.11, 'V': -0.53, 'W': -0.24, 'Y': 0.23}}

Named hydrophobicity scales. KyteDoolittle is the Chowell 2015 axis.

mhcmatch.data.aa_tables.MJ_PARTITION: dict[str, float] = {'A': 2.36, 'C': 3.36, 'D': 1.67, 'E': 1.74, 'F': 4.37, 'G': 2.06, 'H': 2.41, 'I': 4.17, 'K': 1.23, 'L': 3.93, 'M': 4.22, 'N': 1.7, 'P': 1.89, 'Q': 1.75, 'R': 1.92, 'S': 1.81, 'T': 2.04, 'V': 3.49, 'W': 3.82, 'Y': 2.91}

Miyazawa-Jernigan 1985 effective partition energy (AAindex MIYS850101).

mhcmatch.data.aa_tables.PROPERTY_PC1: dict[str, float] = {'A': 1.254672, 'C': 4.346936, 'D': -9.365844, 'E': -8.183104, 'F': 10.105378, 'G': -2.007487, 'H': -3.394648, 'I': 10.300859, 'K': -8.199014, 'L': 8.838052, 'M': 6.67471, 'N': -6.953567, 'P': 1.207809, 'Q': -6.791976, 'R': -9.794956, 'S': -4.572944, 'T': -2.095019, 'V': 7.332347, 'W': 7.60184, 'Y': 3.695956}

PC1 of the amino-acid property matrix – the axis the phys block of mhcmatch.complement projects onto, and the one the retired ipred summed over the peptide. Vendored here rather than read back out of a fitted artifact, which is why the basis outlived the one that first carried it (ipred_mhc1.json, since removed).

mhcmatch.data.aa_tables.PROPERTY_PC2: dict[str, float] = {'A': 8.232053, 'C': 3.587121, 'D': 1.335676, 'E': -0.966133, 'F': -4.624916, 'G': 10.096848, 'H': -4.382562, 'I': 1.268831, 'K': -4.476004, 'L': 1.227076, 'M': -1.45099, 'N': 0.716177, 'P': 2.330299, 'Q': -1.677639, 'R': -7.23446, 'S': 4.800281, 'T': 4.067635, 'V': 4.421173, 'W': -9.811313, 'Y': -7.459154}

PC2 of the same matrix, the second component of the same two-component basis.

mhcmatch.data.contact_profile module

Per-position TCR-contact profile (generated – do not edit by hand).

Regenerate with bench/immuno/build_contact_profile.py in the 2026-mhcmatch-benchmark repo. Source: tcren’s contacts_2026.csv – 8,062 TCR<->peptide residue contacts over 370 crystal structures, joined to orient_metadata.json for MHC class and to markup_2026.csv for peptide length.

PROFILE[(cls, length)] is (fractions, n_structures, n_contacts); fractions sum to 1 over the peptide. POOLED_RELATIVE[cls] is the class profile in relative position, used to interpolate lengths with fewer than 10 structures.

Validation: the class-I 9-mer profile rank-correlates with Calis 2013 Table 2’s label-derived KL position importances at Spearman rho = 0.943 (P3-P8, n=6) – structure and immunogenicity labels agreeing as independent lines of evidence.