From cb204a05f612870a06e953510703b0bab067fb06 Mon Sep 17 00:00:00 2001
From: ivan-aksamentov <ivan.aksamentov@gmail.com>
Date: Mon, 3 Oct 2022 18:43:24 +0200
Subject: [PATCH 1/3] feat: calculate composite fitness

---
 packages_rs/nextclade/src/analyze/phenotype.rs | 18 ++++++++++++++++--
 .../nextclade/src/run/nextclade_run_one.rs     | 16 +++++++++++++++-
 2 files changed, 31 insertions(+), 3 deletions(-)

diff --git a/packages_rs/nextclade/src/analyze/phenotype.rs b/packages_rs/nextclade/src/analyze/phenotype.rs
index ad525c328..e6068dc32 100644
--- a/packages_rs/nextclade/src/analyze/phenotype.rs
+++ b/packages_rs/nextclade/src/analyze/phenotype.rs
@@ -28,7 +28,7 @@ pub fn calculate_phenotype(phenotype_data: &PhenotypeData, aa_substitutions: &[A
 }
 
 pub fn get_phenotype_attr_descs(virus_properties: &VirusProperties) -> Vec<PhenotypeAttrDesc> {
-  virus_properties
+  let mut descs = virus_properties
     .phenotype_data
     .as_ref()
     .map_or(vec![], |phenotype_data| {
@@ -40,7 +40,21 @@ pub fn get_phenotype_attr_descs(virus_properties: &VirusProperties) -> Vec<Pheno
           description: ph.description.clone(),
         })
         .collect_vec()
-    })
+    });
+
+  if let Some(phenotype_data) = &virus_properties.phenotype_data {
+    let binding = phenotype_data.iter().find(|&ph| ph.name.contains("binding"));
+    let escape = phenotype_data.iter().find(|&ph| ph.name.contains("escape"));
+    if let (Some(binding), Some(escape)) = (binding, escape) {
+      descs.push(PhenotypeAttrDesc {
+        name: "composite_fitness".to_owned(),
+        name_friendly: "Composite fitness".to_owned(),
+        description: "".to_owned(),
+      });
+    }
+  }
+
+  descs
 }
 
 pub fn get_phenotype_attr_keys(virus_properties: &VirusProperties) -> Vec<String> {
diff --git a/packages_rs/nextclade/src/run/nextclade_run_one.rs b/packages_rs/nextclade/src/run/nextclade_run_one.rs
index 181df9dda..89efaccf7 100644
--- a/packages_rs/nextclade/src/run/nextclade_run_one.rs
+++ b/packages_rs/nextclade/src/run/nextclade_run_one.rs
@@ -155,7 +155,7 @@ pub fn nextclade_run_one(
   let total_covered_nucs = total_aligned_nucs - total_missing - total_non_acgtns;
   let coverage = total_covered_nucs as f64 / ref_seq.len() as f64;
 
-  let phenotype_values = virus_properties.phenotype_data.as_ref().map(|phenotype_data| {
+  let mut phenotype_values = virus_properties.phenotype_data.as_ref().map(|phenotype_data| {
     phenotype_data
       .iter()
       .filter_map(|phenotype_data| {
@@ -183,6 +183,20 @@ pub fn nextclade_run_one(
       .collect_vec()
   });
 
+  if let Some(ref mut phenotype_values) = phenotype_values {
+    let binding = phenotype_values.iter().find(|ph| ph.name.contains("binding"));
+    let escape = phenotype_values.iter().find(|ph| ph.name.contains("escape"));
+    if let (Some(binding), Some(escape)) = (binding, escape) {
+      phenotype_values.push(PhenotypeValue {
+        name: "composite_fitness".to_owned(),
+        name_friendly: "Composite fitness".to_owned(),
+        description: "".to_owned(),
+        gene: binding.gene.clone(),
+        value: 1.2 * escape.value + 0.5 * binding.value,
+      });
+    }
+  }
+
   let qc = qc_run(
     &private_nuc_mutations,
     &nucleotide_composition,

From 6018ac1bd73a745657695de69b57af79c6f2863d Mon Sep 17 00:00:00 2001
From: Cornelius Roemer <cornelius.roemer@gmail.com>
Date: Thu, 3 Nov 2022 01:36:14 +0100
Subject: [PATCH 2/3] Reduce weight of affinity to 0.15, of RBD score to 1.0

---
 packages_rs/nextclade/src/run/nextclade_run_one.rs | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/packages_rs/nextclade/src/run/nextclade_run_one.rs b/packages_rs/nextclade/src/run/nextclade_run_one.rs
index 89efaccf7..89b6fb747 100644
--- a/packages_rs/nextclade/src/run/nextclade_run_one.rs
+++ b/packages_rs/nextclade/src/run/nextclade_run_one.rs
@@ -175,8 +175,6 @@ pub fn nextclade_run_one(
         Some(PhenotypeValue {
           name: name.clone(),
           gene: gene.clone(),
-          name_friendly: name_friendly.clone(),
-          description: description.clone(),
           value: phenotype,
         })
       })
@@ -192,7 +190,7 @@ pub fn nextclade_run_one(
         name_friendly: "Composite fitness".to_owned(),
         description: "".to_owned(),
         gene: binding.gene.clone(),
-        value: 1.2 * escape.value + 0.5 * binding.value,
+        value: 1.0 * escape.value + 0.15 * binding.value,
       });
     }
   }

From 8dfe7a74e90740d450579eaf792e6a4a1e31d5f0 Mon Sep 17 00:00:00 2001
From: Cornelius Roemer <cornelius.roemer@gmail.com>
Date: Thu, 3 Nov 2022 02:10:27 +0100
Subject: [PATCH 3/3] Add name_friendly back

---
 packages_rs/nextclade/src/run/nextclade_run_one.rs | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/packages_rs/nextclade/src/run/nextclade_run_one.rs b/packages_rs/nextclade/src/run/nextclade_run_one.rs
index 89b6fb747..b85a545c2 100644
--- a/packages_rs/nextclade/src/run/nextclade_run_one.rs
+++ b/packages_rs/nextclade/src/run/nextclade_run_one.rs
@@ -175,6 +175,8 @@ pub fn nextclade_run_one(
         Some(PhenotypeValue {
           name: name.clone(),
           gene: gene.clone(),
+          name_friendly: name_friendly.clone(),
+          description: description.clone(),
           value: phenotype,
         })
       })