.. This file is GENERATED by scripts/gen_descriptor_table.py -- do not edit it. Every descriptor, with its units ================================ All 164 descriptors ``tcren features --all`` emits, in catalogue order, with what each is invariant under and what it is measured in. The *receptor* column says whether the TCR enters the definition: a column marked **no** is computed from the peptide and its allele alone, so every structure of one epitope on one allele shares its value whatever the receptor, and it carries cohort identity rather than interface physics. Units are what a transform has to respect. A ``count`` is variance-stabilized by a square root, a ``fraction`` by the arcsine -- the classical angular transformation -- and an unbounded continuous quantity by neither. placement (31) -------------- Where the receptor sits on the groove and how it leans. Every column is a length, an angle or a direction cosine, so the family is geometric throughout. .. list-table:: :header-rows: 1 :widths: 18 14 10 8 50 * - descriptor - invariance - units - receptor - definition * - ``pitch`` - geometric - deg - yes - Incident angle of the TCR out of the groove plane. **Banned as a feature**: it reproduces no clean geometric angle yet out-discriminates every one of them, which is AlphaFold-confidence contamination rather than geometry. * - ``crossing`` - geometric - deg - yes - Crossing (scanning) angle between the Valpha->Vbeta axis projected into the groove plane and the groove long axis. * - ``crossing_signed`` - geometric - deg - yes - The same angle on [-180, 180); its sign is the docking polarity, canonical or reversed. * - ``dock_d`` - geometric - A - yes - MHC-stub to TCR-stub rigid-body separation. * - ``dock_torsion`` - geometric - rad - yes - Rigid-body dihedral of the TCR about the MHC stub; the docking twist. Circular, wraps at +-pi. * - ``dock_tcr_uy`` - geometric - cosine - yes - y component of the TCR stub unit vector in the MHC frame. * - ``dock_tcr_uz`` - geometric - cosine - yes - z component of the TCR stub unit vector; how high the receptor body rides over the groove. * - ``dock_mhc_uy`` - geometric - cosine - yes - y component of the MHC stub unit vector. * - ``dock_mhc_uz`` - geometric - cosine - yes - z component of the MHC stub unit vector. * - ``height`` - geometric - A - yes - Elevation of the CDR Calpha centroid above the groove plane. * - ``shift_u`` - geometric - A - yes - In-plane displacement of that centroid from the peptide centroid along the groove long axis. * - ``shift_w`` - geometric - A - yes - The same along the groove short axis. * - ``offset`` - geometric - A - yes - Length of the in-plane displacement; lateral shift whatever its direction. * - ``cdr3a_reach`` - geometric - A - yes - Distance from the loop's Calpha centroid to the peptide Calpha centroid; how far CDR3alpha reaches. * - ``cdr3a_ou`` - geometric - cosine - yes - Where CDR3alpha sits over the groove, along the long axis u. * - ``cdr3a_ow`` - geometric - cosine - yes - Where CDR3alpha sits over the groove, along the short axis w. * - ``cdr3a_on`` - geometric - cosine - yes - Where CDR3alpha sits over the groove, along the groove normal n. * - ``cdr3a_au`` - geometric - cosine - yes - Orientation of CDR3alpha's N->C axis against the groove long axis u. * - ``cdr3a_aw`` - geometric - cosine - yes - Orientation of CDR3alpha's N->C axis against the groove short axis w. * - ``cdr3a_an`` - geometric - cosine - yes - Orientation of CDR3alpha's N->C axis against the groove normal n. * - ``cdr3a_topep`` - geometric - A - yes - Minimum Calpha-Calpha distance from CDR3alpha to the peptide; its engagement depth. * - ``cdr3a_ext`` - geometric - A - yes - End-to-end extension of CDR3alpha, the Calpha_N to Calpha_C distance. * - ``cdr3b_reach`` - geometric - A - yes - Distance from the loop's Calpha centroid to the peptide Calpha centroid; how far CDR3beta reaches. * - ``cdr3b_ou`` - geometric - cosine - yes - Where CDR3beta sits over the groove, along the long axis u. * - ``cdr3b_ow`` - geometric - cosine - yes - Where CDR3beta sits over the groove, along the short axis w. * - ``cdr3b_on`` - geometric - cosine - yes - Where CDR3beta sits over the groove, along the groove normal n. * - ``cdr3b_au`` - geometric - cosine - yes - Orientation of CDR3beta's N->C axis against the groove long axis u. * - ``cdr3b_aw`` - geometric - cosine - yes - Orientation of CDR3beta's N->C axis against the groove short axis w. * - ``cdr3b_an`` - geometric - cosine - yes - Orientation of CDR3beta's N->C axis against the groove normal n. * - ``cdr3b_topep`` - geometric - A - yes - Minimum Calpha-Calpha distance from CDR3beta to the peptide; its engagement depth. * - ``cdr3b_ext`` - geometric - A - yes - End-to-end extension of CDR3beta, the Calpha_N to Calpha_C distance. interface (26) -------------- How much contact there is and of what chemical kind. Two continuous quantities -- buried surface and clash depth -- and counts for the rest. .. list-table:: :header-rows: 1 :widths: 18 14 10 8 50 * - descriptor - invariance - units - receptor - definition * - ``burial`` - geometric - A^2 - yes - Interface buried surface, SASA(TCR) + SASA(pMHC) - SASA(complex), by Shrake-Rupley. * - ``extent`` - compositional - count - yes - Distinct TCR residues contacting the pMHC over both receptor interfaces. * - ``chain_balance`` - compositional - fraction - yes - min(a,b)/(a+b) over TCR:peptide contacts by chain; 0.5 when both chains engage equally, 0 when only one does. * - ``n_contacts_tp`` - compositional - count - yes - TCR-peptide residue-residue contacts. * - ``n_contacts_tm`` - compositional - count - yes - TCR-MHC residue-residue contacts. * - ``n_pep_contacted`` - compositional - count - yes - Distinct peptide residues the TCR contacts. * - ``n_hbond`` - compositional - count - yes - Polar N/O atom pairs within 3.5 A across TCR:peptide. * - ``ct_tp_salt_bridge`` - compositional - count - yes - Cationic-N / anionic-O pairs within 4 A across TCR:peptide. * - ``ct_tp_aromatic`` - compositional - count - yes - Ring-atom pairs between aromatic residues across TCR:peptide. * - ``ct_tp_hydrophobic`` - compositional - count - yes - Apolar C-C pairs between apolar residues across TCR:peptide. * - ``ct_tp_other`` - compositional - count - yes - Remaining classified TCR:peptide contacts. * - ``ct_tm_salt_bridge`` - compositional - count - yes - Salt bridges across TCR:MHC. * - ``ct_tm_hydrogen_bond`` - compositional - count - yes - Hydrogen bonds across TCR:MHC. * - ``ct_tm_aromatic`` - compositional - count - yes - Aromatic contacts across TCR:MHC. * - ``ct_tm_hydrophobic`` - compositional - count - yes - Hydrophobic contacts across TCR:MHC. * - ``ct_tm_other`` - compositional - count - yes - Remaining classified TCR:MHC contacts. * - ``cdr3_dominance`` - compositional - fraction - yes - CDR3(alpha+beta) share of all CDR TCR:peptide contacts. * - ``cdr3_ab_imbalance`` - compositional - fraction - yes - abs(CDR3a - CDR3b) / (CDR3a + CDR3b); how one-sided the CDR3 engagement is. * - ``chain_cdr_imbalance`` - compositional - fraction - yes - abs(a - b) / (a + b) over all CDR contacts; the chain-level mirror of chain_balance. * - ``n_clashes`` - compositional - count - yes - Peptide-partner heavy-atom pairs overlapping by more than 0.4 A on Bondi radii. * - ``clash_score`` - geometric - A - yes - Summed overlap depth of those clashing pairs; the steric burden of a forced pose. * - ``mhc_class_bin`` - categorical - class I / II - **no** - Which class of MHC presents the peptide: 0 for class I, 1 for class II. Class I and class II grooves differ in shape and in how they hold a peptide, so this conditions the other descriptors rather than being scored beside them; a coefficient fitted across both classes without it is fitted to a mixture. * - ``n_loop_contacts`` - compositional - count - yes - Contacts the six-CDR-loop partition sees; framework contacts are outside it by construction. * - ``n_pep_contacts`` - compositional - count - yes - Of those loop contacts, the ones reaching the peptide. * - ``n_mhc_contacts`` - compositional - count - yes - Of those loop contacts, the ones reaching the MHC. * - ``n_pep_int`` - compositional - count - **no** - Intra-peptide residue contacts, at 5 A with a sequence separation of at least three. topology (70) ------------- The footprint: its connectivity, its composition over labelled cells, and how the receptor's contacts spread along the peptide. .. list-table:: :header-rows: 1 :widths: 18 14 10 8 50 * - descriptor - invariance - units - receptor - definition * - ``H_cell`` - compositional - fraction - yes - Normalized Shannon entropy of the contact composition over the twelve cells (six CDR loops x {peptide, MHC}). * - ``D1_cell`` - compositional - count - yes - Hill number of order 1 over the same cells, exp(H); monotone in H_cell. * - ``D2_cell`` - compositional - count - yes - Hill number of order 2, 1/sum(p^2); the effective number of engaged cells, discounting the weakly populated ones. * - ``S_cell`` - compositional - count - yes - Richness: how many of the twelve cells are occupied. * - ``J_cell`` - compositional - fraction - yes - Pielou evenness over the occupied cells. NaN when one cell is occupied. * - ``H_loop`` - compositional - fraction - yes - Normalized entropy over the six CDR loops alone, ignoring which target each contact reaches. * - ``D2_loop`` - compositional - count - yes - Hill number of order 2 over the six loops. * - ``D2_pep24`` - compositional - count - yes - Hill number of order 2 over the twenty-four-cell partition, the peptide split into N-terminal, central and C-terminal bands. * - ``ab_imb`` - compositional - signed fraction - yes - Signed (TRA - TRB)/(TRA + TRB) over CDR-loop contacts; positive is alpha-shifted. * - ``ab_imb_pep`` - compositional - signed fraction - yes - The same restricted to peptide-side contacts. * - ``ab_imb_mhc`` - compositional - signed fraction - yes - The same restricted to MHC-side contacts. * - ``L_canon`` - compositional - log-odds - yes - Canonical-docking log odds-ratio of loop class (germline, CDR3) against target (MHC, peptide), Haldane-Anscombe corrected. High when CDR3 sits on the peptide and the germline loops on the helices. * - ``p_germ_mhc`` - compositional - fraction - yes - Share of germline (CDR1/CDR2) contacts that reach the MHC. * - ``p_cdr3_pep`` - compositional - fraction - yes - Share of CDR3 contacts that reach the peptide. * - ``pep_free_frac`` - compositional - fraction - yes - Share of the peptide the groove leaves for the receptor: mean over positions of n_TCR/(n_TCR + n_MHC). The threshold-free reading of 'peptide without its MHC anchors'. * - ``pep_cov_frac`` - compositional - fraction - yes - Peptide positions the TCR contacts, over peptide length. * - ``pep_cov_even`` - compositional - fraction - yes - Pielou evenness of the accessibility-discounted contact distribution, base ln(peptide length); how evenly the receptor uses the peptide it can reach. * - ``pep_cov_d2n`` - compositional - fraction - yes - Hill number of order 2 of that distribution over peptide length; the effective share of the peptide engaged. * - ``pep_cov_centre`` - compositional - fraction - yes - Contact-weighted mean position on [0, 1] from N- to C-terminus; 0.5 is centred. * - ``pep_cov_spread`` - compositional - fraction - yes - Contact-weighted standard deviation of that position, doubled; approaches 1 when the receptor reaches both termini. * - ``h0_pers_ent`` - geometric - fraction - yes - Normalized entropy of the H0 barcode of the contacted pMHC Calpha cloud. The bar lengths are the minimum spanning tree's edges, so no filtration is chosen. * - ``g_even_tcr`` - topological - fraction - yes - Pielou evenness of the contact degrees of the engaged CDR-loop residues, base the engaged count. 1 when every engaged residue carries the same number of partners. * - ``g_even_pmhc`` - topological - fraction - yes - Pielou evenness of the contact degrees of the engaged pMHC residues, base the engaged count. * - ``g_comp_frac`` - topological - fraction - yes - Connected components of the bipartite contact graph per node; the parameter-free form of the footprint patch count, needing no Calpha radius. * - ``g_alg_conn`` - topological - ratio - yes - Second-smallest eigenvalue of the normalised Laplacian on the largest contact-graph component, in [0, 2]. Near 0 when the footprint is about to fall into two patches. * - ``g_cyclo_frac`` - topological - fraction - yes - Contacts beyond a spanning forest over all contacts, (E - V + C) / E, which is the contact graph's first Betti number made size-free. High when the footprint is interlocked. * - ``g_loop_even`` - compositional - fraction - yes - Pielou evenness over the six CDR loops of the number of distinct pMHC residues each reaches, base 6. Counts partners rather than contacts, so it does not track residue size. * - ``g_loop_overlap`` - compositional - fraction - yes - Mean pairwise Jaccard overlap of the engaged CDR loops' pMHC partner sets. High when the loops crowd onto the same residues instead of partitioning the surface. * - ``g_assort`` - topological - ratio - yes - Degree assortativity of the contact graph: the correlation, over contacts, between the degrees of the two residues involved. * - ``degree_evenness_tp`` - compositional - fraction - yes - Participation ratio of the receptor-side contact degrees across TCR:peptide, in [0, 1]. Low when a few over-reaching side chains hoard the contact budget. * - ``frac_well_coordinated_tp`` - compositional - fraction - yes - Share of contacting receptor residues reaching no more than three peptide residues, the count a crystal side chain typically makes. * - ``m_erank_tp`` - geometric - fraction - yes - Effective rank of the CDR-loop x peptide Calpha proximity kernel over its maximum: how many independent approach modes the interface has. Peptide-length coupled (Spearman -0.547 on 148 class I crystals) because a longer class I peptide bulges. * - ``m_gap_tp`` - geometric - ratio - yes - Second over first singular value of that kernel. Near 0 when the approach is separable into a loop profile times a peptide profile rather than pairing specific residues. * - ``m_erank_tm`` - geometric - fraction - yes - Effective rank fraction of the CDR-loop x MHC-helix kernel. CDR3-length coupled (Spearman -0.437), so it reads how much loop there is to spread over the helices. * - ``m_gap_tm`` - geometric - ratio - yes - Second over first singular value of the CDR-loop x MHC-helix kernel. The least length-coupled column in the catalogue: -0.012 against CDR3 length, +0.027 against peptide length, 99.9 per cent of its variance surviving both. * - ``m_face_tp`` - geometric - A - yes - Mean Calpha-Calpha minus Cbeta-Cbeta distance over the contacting TCR:peptide residue pairs. Positive when side chains lean towards each other, negative when the backbones are the close part and the side chains point away. * - ``m_face_tm`` - geometric - A - yes - Mean Calpha-Calpha minus Cbeta-Cbeta distance over the contacting TCR:MHC residue pairs. * - ``ca_cb_agreement_tp`` - geometric - ratio - yes - Spearman correlation between the Calpha and Cbeta distance maps over the TCR:peptide approach shell. High when the side chains track the backbone, as they do in a crystal. * - ``ca_cb_agreement_tm`` - geometric - ratio - yes - The same rank correlation across the TCR:MHC approach shell. * - ``fp_b0_r7`` - topological - count - yes - Betti-0 of the flag complex on the contacted pMHC Calpha atoms at 7 A: how many disconnected patches the footprint falls into. * - ``fp_b1_r7`` - topological - count - yes - Betti-1 at 7 A: how many holes the footprint encloses. * - ``fp_chi_r7`` - topological - count - yes - Euler characteristic b0 - b1 at 7 A. * - ``fp_b0_frac_r7`` - topological - fraction - yes - Patches per contacted residue at 7 A; the size-free form of Betti-0. * - ``fp_b0_r8`` - topological - count - yes - Betti-0 of the flag complex on the contacted pMHC Calpha atoms at 8 A: how many disconnected patches the footprint falls into. * - ``fp_b1_r8`` - topological - count - yes - Betti-1 at 8 A: how many holes the footprint encloses. * - ``fp_chi_r8`` - topological - count - yes - Euler characteristic b0 - b1 at 8 A. * - ``fp_b0_frac_r8`` - topological - fraction - yes - Patches per contacted residue at 8 A; the size-free form of Betti-0. * - ``sc_shape`` - geometric - ratio - yes - Pearson r between the pMHC and TCR height fields over the shared grid; positive is complementary, the receptor riding up where the groove rises. Lawrence & Colman's Sc is the same idea on a dot surface. * - ``sc_charge`` - compositional - ratio - yes - Pearson r between the two charge fields; NEGATIVE is complementary, plus meeting minus. * - ``sc_phobic`` - compositional - ratio - yes - Pearson r between the two Kyte-Doolittle fields; positive is complementary, apolar meeting apolar. * - ``sc_charge_prod`` - compositional - ratio - yes - Mean per-cell product of the two charge fields. * - ``sc_phobic_prod`` - compositional - ratio - yes - Mean per-cell product of the two hydropathy fields. * - ``sc_gap_mean`` - geometric - A - yes - Mean of h(TCR) - h(pMHC) over retained cells. Negative on a real interface: the median cell interdigitates. * - ``sc_gap_sd`` - geometric - A - yes - Spread of the same gap. High when the receptor rests on a few high points rather than meshing. * - ``sc_gap_vol`` - geometric - A^3 - yes - Void volume, the gap integrated over the contact plane where it is positive. * - ``sc_interlock`` - geometric - A^3 - yes - Interdigitated volume, the gap integrated where it is negative. The larger of the two on a real interface. * - ``sc_gap_index`` - geometric - A - yes - Void volume over retained contact area; the intensive form of the gap-volume channel. * - ``sc_interlock_frac`` - geometric - fraction - yes - Share of retained cells whose gap is negative; the per-structure form of the corpus 71% interdigitation. * - ``sc_gap_depth`` - geometric - A - yes - Mean depth over the interlocked cells alone: how far the receptor reaches in where it does. * - ``sc_gap_height`` - geometric - A - yes - Mean standoff over the void cells alone: how high it stands where it does not mesh. * - ``sc_gap_asym`` - geometric - signed fraction - yes - (void - interlock) / (void + interlock); -1 for a face that only interlocks, +1 for one that only stands off. * - ``sc_dh`` - geometric - A - yes - Mean absolute per-cell height difference between the two faces. * - ``sc_dcharge`` - compositional - ratio - yes - Mean absolute per-cell charge difference between the two faces. * - ``sc_dphobic`` - compositional - ratio - yes - Mean absolute per-cell hydropathy difference between the two faces. * - ``sc_cells`` - geometric - count - yes - Grid cells entering the comparison; bookkeeping, so a low complementarity can be told from a thin one. * - ``sc_coverage`` - geometric - fraction - yes - Retained cells as a share of the occupied pMHC cells in the window; bookkeeping. * - ``co_pep`` - compositional - ratio - yes - Contact order on the peptide: mean sequence separation of the peptide residues one CDR loop reaches, averaged over loops and divided by the peptide's span. * - ``co_mhc`` - compositional - ratio - yes - Contact order on the MHC helices, by the same construction. * - ``partcoef_tcr`` - compositional - fraction - yes - Mean over engaged TCR residues of 1 - sum_s (k_s/k)^2 with the modules peptide and MHC; 0 when every residue reads one target only. * - ``partcoef_pmhc`` - compositional - fraction - yes - The same over engaged pMHC residues with the six CDR loops as modules. energetics (15) --------------- Statistical-potential interface sums and their poly-alanine references. Lower is more favourable. .. list-table:: :header-rows: 1 :widths: 18 14 10 8 50 * - descriptor - invariance - units - receptor - definition * - ``Phi_tcr_pep`` - energetic - log-odds - yes - Phi over TCR-peptide contacts under TCRen2, summed over all TCR regions. Lower is more favourable. * - ``Phi_tcr_mhc`` - energetic - log-odds - yes - Phi over TCR-MHC contacts under Miyazawa-Jernigan. * - ``Phi_cdr12`` - energetic - log-odds - yes - The CDR1 + CDR2 part of the TCR:peptide energy, both chains. * - ``Phi_cdr3a`` - energetic - log-odds - yes - The CDR3alpha part of the TCR:peptide energy. * - ``Phi_cdr3b`` - energetic - log-odds - yes - The CDR3beta part of the TCR:peptide energy. * - ``dPhi_tcr_pep`` - energetic - log-odds - yes - Poly-alanine reference delta of the TCR:peptide energy; the pose-geometry baseline removed. * - ``dPhi_pep_soft`` - energetic - log-odds - yes - Smoothed reference delta, peptide direction: the peptide's energy minus the free energy of the residue background at each peptide position, receptor frozen. * - ``varPhi_pep_soft`` - energetic - log-odds^2 - yes - Variance of the local field under the background, peptide direction: how sharply each peptide position's energy responds to residue identity, summed over positions. NOT a ddG -- it is a second cumulant, not a difference of differences. * - ``dPhi_tcr_soft`` - energetic - log-odds - yes - Smoothed reference delta, receptor direction: the receptor's energy minus the free energy of the residue background at each contacted TCR position, peptide frozen. * - ``varPhi_tcr_soft`` - energetic - log-odds^2 - yes - Variance of the local field under the background, receptor direction, summed over contacted TCR positions. * - ``dPhi_tra_soft`` - energetic - log-odds - yes - The alpha-chain part of the receptor-direction smoothed reference delta. * - ``dPhi_trb_soft`` - energetic - log-odds - yes - The beta-chain part of the receptor-direction smoothed reference delta. * - ``Phi_pep_mhc`` - energetic - log-odds - **no** - Phi over peptide-MHC contacts under Miyazawa-Jernigan. Computed without the receptor. * - ``dPhi_pep_mhc`` - energetic - log-odds - **no** - The same reference across peptide:MHC. Computed without the receptor. * - ``Phi_pep_int`` - energetic - log-odds - **no** - The peptide's own intra-chain contact energy. Computed without the receptor. potts (5) --------- The same interface read against the partition function of the coupled contact model rather than against a poly-alanine interface. .. list-table:: :header-rows: 1 :widths: 18 14 10 8 50 * - descriptor - invariance - units - receptor - definition * - ``neg_energy`` - energetic - kT - yes - -E of the observed contact map under the coupled Potts model; higher is more native-like. Exactly log_z + log_lik. * - ``log_z`` - energetic - kT - yes - Log partition function over every contact map the geometry admits; the interface's capacity. * - ``log_lik`` - energetic - kT - yes - Log probability of the observed contact map; its typicality. * - ``psi`` - energetic - kT/site - yes - log_lik per available site, so interfaces of different size compare. * - ``n_contacts`` - energetic - count - yes - Available residue pairs that engaged. Distinct from the footprint's loop tally. kinetics (17) ------------- The contact map as a network of breakable springs. No potential enters: these are geometry and multiplicity, which is why they carry evidence the energies cannot. .. list-table:: :header-rows: 1 :widths: 18 14 10 8 50 * - descriptor - invariance - units - receptor - definition * - ``exp_lost`` - geometric - count - yes - Expected TCR:peptide contacts lost under a 1 A isotropic shift. * - ``mean_margin`` - geometric - A - yes - Mean contact margin, cutoff minus minimum heavy-atom distance. * - ``frac_robust`` - compositional - fraction - yes - Share of TCR:peptide contacts with at least 1 A of margin. * - ``K_tens`` - geometric - N/m - yes - Tensile stiffness along the docking axis. * - ``K_shear`` - geometric - N/m - yes - In-plane stiffness, S_tot minus K_tens. * - ``aniso`` - geometric - ratio - yes - K_shear / K_tens; how much stiffer the interface is along the pull than across it. * - ``lam_max`` - geometric - N/m - yes - Largest eigenvalue of the stiffness tensor. * - ``lam_min`` - geometric - N/m - yes - Smallest eigenvalue of the stiffness tensor. * - ``n_spring`` - compositional - count - yes - Springs in the interface network; every other kinetics column is NaN below three. * - ``S_tot`` - geometric - N/m - yes - Trace of the stiffness tensor; total interface stiffness. * - ``rupture_force`` - geometric - N - yes - Peak resisting force under steered separation along the weaker axis. * - ``rupture_work`` - geometric - J - yes - Force integrated to full separation; the off-rate proxy, and a geometry-only quantity no potential enters. * - ``couple_pep`` - compositional - count - yes - Peptide residues contacting both the MHC and the TCR. * - ``couple_mhc`` - compositional - count - yes - MHC residues contacting both the peptide and the TCR. * - ``couple_tcr`` - compositional - count - yes - TCR residues in the Valpha-Vbeta interface that also contact the pMHC. * - ``couple_total`` - compositional - count - yes - Sum of the three coupling counts. * - ``n_interface`` - compositional - count - yes - Interface residue count; the size denominator for the coupling counts. flagged descriptors (33) ------------------------ Descriptors that need a second look before they are used, from ``tcren.recognition.STATUS``. A name absent from this table has no known defect; presence is **not** a reason to drop the column, only to know what it is. ``suspicious`` means the quantity is not measuring what its family name suggests -- it reads the generator, or is fixed by an exact identity over other columns, or identifies the cohort rather than the complex. ``stalled`` means it is defined but does not move on the corpus. .. list-table:: :header-rows: 1 :widths: 20 12 68 * - descriptor - flag - why * - ``pitch`` - suspicious - reads the generator's confidence rather than the interface: it is docking_angles' incident_angle, and it out-discriminates every clean docking angle for that reason. Never use it as a feature. * - ``fp_chi_r7`` - suspicious - determined: chi = b0 - b1 at the same radius. * - ``fp_chi_r8`` - suspicious - determined: chi = b0 - b1 at the same radius. * - ``D1_cell`` - suspicious - determined: D1 = 12 ** H_cell. * - ``J_cell`` - suspicious - determined: J = H_cell * ln 12 / ln S_cell. * - ``offset`` - suspicious - determined: offset = hypot(shift_u, shift_w). * - ``n_loop_contacts`` - suspicious - determined: n_pep_contacts + n_mhc_contacts. * - ``neg_energy`` - suspicious - determined: log_z + log_lik. * - ``S_tot`` - suspicious - determined by K_tens and K_shear. * - ``aniso`` - suspicious - determined by K_tens and K_shear. * - ``couple_total`` - suspicious - determined: couple_pep + couple_mhc + couple_tcr. * - ``crossing`` - suspicious - determined: abs(crossing_signed). * - ``sc_gap_index`` - suspicious - determined: (sc_dh + sc_gap_mean) / 2. * - ``dPhi_tcr_soft`` - suspicious - determined: dPhi_tra_soft + dPhi_trb_soft. * - ``n_contacts_tm`` - suspicious - determined: the sum of the five ct_tm_* contact-type tallies. * - ``n_contacts_tp`` - suspicious - determined: ct_tp_salt_bridge + ct_tp_aromatic + ct_tp_hydrophobic + ct_tp_other + n_hbond. * - ``Phi_pep_mhc`` - suspicious - no receptor: constant across every structure of one epitope on one allele, so a receptor-ranking model reading it reaches the cohort label without reading an interface. * - ``dPhi_pep_mhc`` - suspicious - no receptor; see Phi_pep_mhc. * - ``Phi_pep_int`` - suspicious - no receptor; see Phi_pep_mhc. * - ``n_pep_int`` - suspicious - no receptor; see Phi_pep_mhc. * - ``mhc_class_bin`` - suspicious - no receptor: it is the MHC class, I or II. It is also constant on any single-class cohort -- both receptor benchmarks are class I -- so it contributes nothing there and separates the classes everywhere else. * - ``m_erank_tp`` - suspicious - peptide-length coupled: -0.547 / -0.105, 58.3 per cent of variance beyond both lengths. It reads the class I bulge. * - ``m_erank_tm`` - suspicious - CDR3-length coupled: -0.186 / -0.437, 69.4 per cent beyond both. It reads how much loop there is to spread over the helices. * - ``m_gap_tp`` - suspicious - peptide-length coupled: -0.322 / +0.041, 90.8 per cent beyond both. * - ``ca_cb_agreement_tm`` - suspicious - coupled to both lengths: -0.349 / -0.334, 70.5 per cent beyond them -- the most length-loaded column here. * - ``degree_evenness_tp`` - suspicious - peptide-length coupled: -0.450 / -0.006, 88.7 per cent beyond both. It reads the class I bulge. * - ``frac_well_coordinated_tp`` - suspicious - peptide-length coupled: -0.440 / -0.064, 83.4 per cent beyond both; see degree_evenness_tp. * - ``g_even_tcr`` - suspicious - peptide-length coupled: -0.368 / -0.061, 91.0 per cent beyond both. * - ``g_loop_even`` - suspicious - CDR3-length coupled: -0.186 / -0.350, 87.7 per cent beyond both. * - ``g_comp_frac`` - suspicious - CDR3-length coupled: -0.032 / +0.280, 92.7 per cent beyond both. * - ``sc_gap_depth`` - suspicious - peptide-length coupled: +0.366 / +0.124, 71.8 per cent of variance beyond both lengths. A longer class I peptide bulges, and the receptor reaches further in where it does. * - ``co_mhc`` - suspicious - CDR3-length coupled: +0.011 / +0.345, 88.0 per cent beyond both. Contact order divides by the target's span, not the loop's, so a longer loop spreads over more helix. * - ``ct_tp_salt_bridge`` - stalled - only 3 distinct values over 1,707 modelled complexes: a salt bridge across the TCR:peptide interface is rare enough that the count is almost always 0. The TCR:MHC counterpart ct_tm_salt_bridge does move.