Support Chothia Martin and Aho

BENCHMARKS.toml

@@ -1,5 +1,5 @@
-last_updated = "2026-03-17"
-execution_time_secs = 0.6
+last_updated = "2026-07-20"
+execution_time_secs = 1.3
 
 [imgt.A]
 total_sequences = 865
@@ -60,3 +60,57 @@ total_sequences = 371
 perfect_sequences = 369
 perfect_pct = 99.46
 overall_accuracy = 99.99
+
+[martin.H]
+total_sequences = 2461
+perfect_sequences = 2451
+perfect_pct = 99.59
+overall_accuracy = 99.98
+
+[martin.K]
+total_sequences = 1469
+perfect_sequences = 1462
+perfect_pct = 99.52
+overall_accuracy = 99.98
+
+[martin.L]
+total_sequences = 383
+perfect_sequences = 380
+perfect_pct = 99.22
+overall_accuracy = 99.98
+
+[chothia.H]
+total_sequences = 2451
+perfect_sequences = 2448
+perfect_pct = 99.88
+overall_accuracy = 99.99
+
+[chothia.K]
+total_sequences = 1485
+perfect_sequences = 1481
+perfect_pct = 99.73
+overall_accuracy = 99.98
+
+[chothia.L]
+total_sequences = 371
+perfect_sequences = 367
+perfect_pct = 98.92
+overall_accuracy = 99.98
+
+[aho.H]
+total_sequences = 2461
+perfect_sequences = 2451
+perfect_pct = 99.59
+overall_accuracy = 99.87
+
+[aho.K]
+total_sequences = 1491
+perfect_sequences = 1474
+perfect_pct = 98.86
+overall_accuracy = 99.98
+
+[aho.L]
+total_sequences = 381
+perfect_sequences = 378
+perfect_pct = 99.21
+overall_accuracy = 99.99

resources/consensus/IGH.csv

@@ -8,7 +8,6 @@ position,consensus_aas,frequencies,occupancy,region
 7,S|P,0.911|0.057,1.000,FR1
 8,G,0.968,1.000,FR1
 9,P|G|A,0.347|0.312|0.278,1.000,FR1
-10,-,1.000,0.000,FR1
 11,G|E,0.499|0.421,1.000,FR1
 12,L|V,0.822|0.138,1.000,FR1
 13,V|K,0.754|0.135,1.000,FR1
@@ -71,7 +70,6 @@ position,consensus_aas,frequencies,occupancy,region
 70,S|K|A,0.467|0.375|0.063,1.000,FR3
 71,F|V|L,0.447|0.298|0.223,1.000,FR3
 72,K|Q,0.785|0.123,1.000,FR3
-73,-,1.000,0.000,FR3
 74,G|S|D,0.630|0.244|0.083,1.000,FR3
 75,R|K,0.653|0.309,1.000,FR3
 76,F|A|V|L,0.372|0.298|0.163|0.112,1.000,FR3

resources/consensus/IGK.csv

@@ -71,7 +71,6 @@ position,consensus_aas,frequencies,occupancy,region
 70,G,0.966,1.000,FR3
 71,V|I,0.828|0.152,1.000,FR3
 72,P,0.957,1.000,FR3
-73,-,1.000,0.000,FR3
 74,S|D|A,0.364|0.336|0.252,1.000,FR3
 75,R,0.972,1.000,FR3
 76,F,1.000,1.000,FR3

resources/consensus/IGL.csv

@@ -8,7 +8,6 @@ position,consensus_aas,frequencies,occupancy,region
 7,P|E,0.776|0.134,1.000,FR1
 8,P|S|A|H,0.657|0.134|0.060|0.060,1.000,FR1
 9,S|A,0.896|0.075,1.000,FR1
-10,-,1.000,0.000,FR1
 11,V|L|A,0.597|0.194|0.119,1.000,FR1
 12,S|T,0.896|0.104,1.000,FR1
 13,V|G|A|E,0.358|0.299|0.209|0.060,1.000,FR1
@@ -71,7 +70,6 @@ position,consensus_aas,frequencies,occupancy,region
 70,G|W,0.940|0.060,1.000,FR3
 71,V|I|T,0.552|0.388|0.060,1.000,FR3
 72,P|S,0.851|0.149,1.000,FR3
-73,-,1.000,0.000,FR3
 74,D|E|S|A|N,0.418|0.269|0.149|0.082|0.060,1.000,FR3
 75,R,0.940,1.000,FR3
 76,F,0.970,1.000,FR3

resources/consensus/README.md

@@ -1,6 +1,6 @@
 # Consensus Files
 
-Generated by `scripts/generate_consensus.py` in the [immunum-scripts](https://github.com/thijsvanloef/immunum-scripts) repo.
+Generated by `scripts/generate_consensus.py`.
 
 ## How they're generated
 

src/annotator.rs

@@ -127,11 +127,17 @@ impl Annotator {
             return Err(Error::InvalidChain("chains cannot be empty".to_string()));
         }
 
-        // Validate: Kabat only supported for antibody chains
-        if scheme == Scheme::Kabat && chains.iter().any(|c| TCR_CHAINS.contains(c)) {
-            return Err(Error::InvalidScheme(
-                "Kabat scheme only supported for antibody chains (IGH, IGK, IGL)".to_string(),
-            ));
+        // Validate: Kabat, Chothia, Martin and AHo are only supported for antibody chains.
+        // (AHo is defined for TCR chains too, but immunum does not ship TCR AHo rules yet.)
+        if matches!(
+            scheme,
+            Scheme::Kabat | Scheme::Chothia | Scheme::Martin | Scheme::Aho
+        ) && chains.iter().any(|c| TCR_CHAINS.contains(c))
+        {
+            return Err(Error::InvalidScheme(format!(
+                "{} scheme only supported for antibody chains (IGH, IGK, IGL)",
+                scheme
+            )));
         }
 
         let mut matrices = Vec::new();
@@ -157,7 +163,22 @@ impl Annotator {
 
         // Apply numbering only to the aligned subregion of the query
         let aligned_positions = &alignment.positions[alignment.query_start..=alignment.query_end];
-        let positions = apply_numbering(aligned_positions, self.scheme, chain);
+        let mut positions = apply_numbering(aligned_positions, self.scheme, chain);
+        let mut query_end = alignment.query_end;
+
+        // AHo light chains carry one extra C-terminal position (149) beyond the IMGT-numbered
+        // region: IMGT ends light chains at 127 -> AHo 148, so the 149 residue has no IMGT
+        // state and is appended here when a residue follows, matching ANARCI's number_aho tail
+        // rule. Heavy chains populate IMGT 128 -> AHo 149 directly and need no append.
+        if self.scheme == Scheme::Aho
+            && matches!(chain, Chain::IGK | Chain::IGL)
+            && positions.last() == Some(&Position::new(148))
+            && query_end + 1 < sequence.len()
+        {
+            positions.push(Position::new(149));
+            query_end += 1;
+        }
+
         let confidence = if alignment.max_confidence_score > 0.0 {
             (alignment.confidence_score / alignment.max_confidence_score).clamp(0.0, 1.0)
         } else {
@@ -179,7 +200,7 @@ impl Annotator {
             cons_end: alignment.cons_end as usize,
             confidence,
             query_start: alignment.query_start,
-            query_end: alignment.query_end,
+            query_end,
         })
     }
 

src/bin/benchmark.rs

@@ -18,6 +18,12 @@ struct BenchmarkReport {
     imgt: BTreeMap<String, ChainEntry>,
     #[serde(default)]
     kabat: BTreeMap<String, ChainEntry>,
+    #[serde(default)]
+    martin: BTreeMap<String, ChainEntry>,
+    #[serde(default)]
+    chothia: BTreeMap<String, ChainEntry>,
+    #[serde(default)]
+    aho: BTreeMap<String, ChainEntry>,
 }
 
 #[derive(Debug, Serialize, Deserialize, Clone)]
@@ -66,8 +72,29 @@ fn main() {
         (Chain::IGL, "fixtures/validation/ab_L_kabat.csv"),
     ];
 
+    let martin_chains = vec![
+        (Chain::IGH, "fixtures/validation/ab_H_martin.csv"),
+        (Chain::IGK, "fixtures/validation/ab_K_martin.csv"),
+        (Chain::IGL, "fixtures/validation/ab_L_martin.csv"),
+    ];
+
+    let chothia_chains = vec![
+        (Chain::IGH, "fixtures/validation/ab_H_chothia.csv"),
+        (Chain::IGK, "fixtures/validation/ab_K_chothia.csv"),
+        (Chain::IGL, "fixtures/validation/ab_L_chothia.csv"),
+    ];
+
+    let aho_chains = vec![
+        (Chain::IGH, "fixtures/validation/ab_H_aho.csv"),
+        (Chain::IGK, "fixtures/validation/ab_K_aho.csv"),
+        (Chain::IGL, "fixtures/validation/ab_L_aho.csv"),
+    ];
+
     let imgt_metrics = collect_metrics(&imgt_chains, Scheme::IMGT);
     let kabat_metrics = collect_metrics(&kabat_chains, Scheme::Kabat);
+    let martin_metrics = collect_metrics(&martin_chains, Scheme::Martin);
+    let chothia_metrics = collect_metrics(&chothia_chains, Scheme::Chothia);
+    let aho_metrics = collect_metrics(&aho_chains, Scheme::Aho);
 
     let end_time = Local::now();
     let elapsed = end_time.signed_duration_since(start_time);
@@ -78,11 +105,25 @@ fn main() {
         execution_time_secs: round2(elapsed_secs),
         imgt: metrics_to_map(&imgt_metrics),
         kabat: metrics_to_map(&kabat_metrics),
+        martin: metrics_to_map(&martin_metrics),
+        chothia: metrics_to_map(&chothia_metrics),
+        aho: metrics_to_map(&aho_metrics),
     };
 
     // Print comparison to terminal
     print_comparison(&imgt_metrics, "IMGT", previous.as_ref().map(|p| &p.imgt));
     print_comparison(&kabat_metrics, "Kabat", previous.as_ref().map(|p| &p.kabat));
+    print_comparison(
+        &martin_metrics,
+        "Martin",
+        previous.as_ref().map(|p| &p.martin),
+    );
+    print_comparison(
+        &chothia_metrics,
+        "Chothia",
+        previous.as_ref().map(|p| &p.chothia),
+    );
+    print_comparison(&aho_metrics, "AHo", previous.as_ref().map(|p| &p.aho));
 
     // Write TOML
     let toml_str = toml::to_string_pretty(&report).expect("Failed to serialize TOML");

src/bin/debug_validation.rs

@@ -14,7 +14,7 @@ fn print_usage() {
     eprintln!();
     eprintln!("Arguments:");
     eprintln!("  CHAIN    Chain type (TRA, TRB, TRG, TRD, IGH, IGK, IGL)");
-    eprintln!("  SCHEME   Optional: Numbering scheme (imgt, kabat). Default: imgt");
+    eprintln!("  SCHEME   Optional: Numbering scheme (imgt, kabat, chothia, martin, aho). Default: imgt");
     eprintln!("  HEADER   Optional: Specific sequence header to debug");
     eprintln!("           If not provided, shows all sequences with imperfect alignment");
     eprintln!();
@@ -167,6 +167,9 @@ fn main() {
         match args[2].to_lowercase().as_str() {
             "imgt" => (Scheme::IMGT, 3),
             "kabat" => (Scheme::Kabat, 3),
+            "chothia" => (Scheme::Chothia, 3),
+            "martin" => (Scheme::Martin, 3),
+            "aho" => (Scheme::Aho, 3),
             _ => (Scheme::IMGT, 2), // Not a scheme, treat as header
         }
     } else {
@@ -185,8 +188,18 @@ fn main() {
         (Chain::IGH, Scheme::Kabat) => "fixtures/validation/ab_H_kabat.csv",
         (Chain::IGK, Scheme::Kabat) => "fixtures/validation/ab_K_kabat.csv",
         (Chain::IGL, Scheme::Kabat) => "fixtures/validation/ab_L_kabat.csv",
-        (chain, Scheme::Kabat) => {
-            eprintln!("Error: Kabat scheme not supported for chain {}", chain);
+        (Chain::IGH, Scheme::Chothia) => "fixtures/validation/ab_H_chothia.csv",
+        (Chain::IGK, Scheme::Chothia) => "fixtures/validation/ab_K_chothia.csv",
+        (Chain::IGL, Scheme::Chothia) => "fixtures/validation/ab_L_chothia.csv",
+        (Chain::IGH, Scheme::Martin) => "fixtures/validation/ab_H_martin.csv",
+        (Chain::IGK, Scheme::Martin) => "fixtures/validation/ab_K_martin.csv",
+        (Chain::IGL, Scheme::Martin) => "fixtures/validation/ab_L_martin.csv",
+        (Chain::IGH, Scheme::Aho) => "fixtures/validation/ab_H_aho.csv",
+        (Chain::IGK, Scheme::Aho) => "fixtures/validation/ab_K_aho.csv",
+        (Chain::IGL, Scheme::Aho) => "fixtures/validation/ab_L_aho.csv",
+        // note: TCR AHo fixtures are not available (tools lack TCR AHo support)
+        (chain, scheme) => {
+            eprintln!("Error: {} scheme not supported for chain {}", scheme, chain);
             process::exit(1);
         }
     };

src/lib.rs

@@ -68,8 +68,11 @@ pub mod io;
 #[cfg(not(target_arch = "wasm32"))]
 pub mod validation;
 
+pub use numbering::aho;
+pub use numbering::chothia;
 pub use numbering::imgt;
 pub use numbering::kabat;
+pub use numbering::martin;
 
 pub use alignment::{align, Alignment};
 pub use annotator::{Annotator, NumberingResult, SegmentResult, DEFAULT_MIN_CONFIDENCE};

src/main.rs

@@ -24,7 +24,7 @@ struct NumberArgs {
     input: Option<String>,
     /// Output file path (default: stdout)
     output: Option<String>,
-    /// Numbering scheme: imgt (i), kabat (k)
+    /// Numbering scheme: imgt (i), kabat (k), chothia (c), martin (m), aho (a)
     #[arg(short, long, default_value = "imgt")]
     scheme: String,
     /// Chain filter: h,k,l,a,b,g,d or groups: ig, tcr, all

src/numbering.rs

@@ -1,32 +1,29 @@
+pub mod aho;
+pub mod chothia;
 pub mod imgt;
 pub mod kabat;
+pub mod martin;
 
 use std::collections::HashMap;
 
+use crate::aho::{AHO_HEAVY_RULES, AHO_KAPPA_RULES, AHO_LAMBDA_RULES, AHO_REGIONS};
 use crate::alignment::AlignedPosition;
-use crate::imgt::IMGT_RULES;
-use crate::kabat::{KABAT_HEAVY_RULES, KABAT_LIGHT_RULES};
+use crate::chothia::{CHOTHIA_HEAVY_RULES, CHOTHIA_LIGHT_RULES, CHOTHIA_REGIONS};
+use crate::imgt::{IMGT_REGIONS, IMGT_RULES};
+use crate::kabat::{KABAT_HEAVY_RULES, KABAT_LIGHT_RULES, KABAT_REGIONS};
+use crate::martin::{MARTIN_HEAVY_RULES, MARTIN_LIGHT_RULES, MARTIN_REGIONS};
 use crate::types::{Chain, Insertion, NumberingRule, Position, Region, Scheme};
 
 /// Get the region for a position number under the given scheme, or None if outside numbered range
 pub fn region_for_position(pos: u8, scheme: Scheme) -> Option<Region> {
-    match (scheme, pos) {
-        (Scheme::IMGT, 1..=26) => Some(Region::FR1),
-        (Scheme::IMGT, 27..=38) => Some(Region::CDR1),
-        (Scheme::IMGT, 39..=55) => Some(Region::FR2),
-        (Scheme::IMGT, 56..=65) => Some(Region::CDR2),
-        (Scheme::IMGT, 66..=104) => Some(Region::FR3),
-        (Scheme::IMGT, 105..=117) => Some(Region::CDR3),
-        (Scheme::IMGT, 118..=128) => Some(Region::FR4),
-        (Scheme::Kabat, 1..=25) => Some(Region::FR1),
-        (Scheme::Kabat, 26..=35) => Some(Region::CDR1),
-        (Scheme::Kabat, 36..=50) => Some(Region::FR2),
-        (Scheme::Kabat, 51..=57) => Some(Region::CDR2),
-        (Scheme::Kabat, 58..=92) => Some(Region::FR3),
-        (Scheme::Kabat, 93..=100) => Some(Region::CDR3),
-        (Scheme::Kabat, 101..=113) => Some(Region::FR4),
-        _ => None,
-    }
+    let regions = match scheme {
+        Scheme::IMGT => IMGT_REGIONS,
+        Scheme::Kabat => KABAT_REGIONS,
+        Scheme::Chothia => CHOTHIA_REGIONS,
+        Scheme::Martin => MARTIN_REGIONS,
+        Scheme::Aho => AHO_REGIONS,
+    };
+    regions.region(pos)
 }
 
 /// Segment a numbered sequence into its constituent regions
@@ -66,6 +63,13 @@ pub fn apply_numbering(
         (Scheme::IMGT, _) => IMGT_RULES,
         (Scheme::Kabat, Chain::IGH) => KABAT_HEAVY_RULES,
         (Scheme::Kabat, Chain::IGK) | (Scheme::Kabat, Chain::IGL) => KABAT_LIGHT_RULES,
+        (Scheme::Chothia, Chain::IGH) => CHOTHIA_HEAVY_RULES,
+        (Scheme::Chothia, Chain::IGK) | (Scheme::Chothia, Chain::IGL) => CHOTHIA_LIGHT_RULES,
+        (Scheme::Martin, Chain::IGH) => MARTIN_HEAVY_RULES,
+        (Scheme::Martin, Chain::IGK) | (Scheme::Martin, Chain::IGL) => MARTIN_LIGHT_RULES,
+        (Scheme::Aho, Chain::IGH) => AHO_HEAVY_RULES,
+        (Scheme::Aho, Chain::IGK) => AHO_KAPPA_RULES,
+        (Scheme::Aho, Chain::IGL) => AHO_LAMBDA_RULES,
         _ => unreachable!("invalid scheme/chain combination should be prevented by Annotator"),
     };
     number_by_rules(&consensus_positions, rules)