v0.13.3 - fix cleavage inhibitor 'restrict' parameter

CHANGELOG.md

@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.13.3]
+### Fixed
+- Bug in `database.enzyme.restrict` parameter, where `null` values were being overriden with "P" (causing Trypsin/P to behave like Trypsin)
+
 ## [v0.13.2]
 ### Changed
 - Subtle change to TMT integration tolerance, and selection of which ion to quantify (most intense). As a result, TMT integration should be more in agreement (if not 100% so) with ProteomeDiscover/FragPipe/etc

crates/sage-cli/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "sage-cli"
-version = "0.13.2"
+version = "0.13.3"
 authors = ["Michael Lazear <michaellazear92@gmail.com"]
 edition = "2021"
 rust-version = "1.62"

crates/sage/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "sage-core"
-version = "0.13.2"
+version = "0.13.3"
 authors = ["Michael Lazear <michaellazear92@gmail.com"]
 edition = "2021"
 rust-version = "1.62"

crates/sage/src/database.rs

@@ -46,7 +46,7 @@ impl From<EnzymeBuilder> for EnzymeParameters {
             max_len: en.max_len.unwrap_or(50),
             enyzme: Enzyme::new(
                 &en.cleave_at.unwrap_or_else(|| "KR".into()),
-                en.restrict.or(Some('P')),
+                en.restrict,
                 en.c_terminal.unwrap_or(true),
             ),
         }
@@ -628,4 +628,23 @@ mod test {
             vec!["sp|AAAAA".to_string().into()]
         );
     }
+
+    #[test]
+    fn deserialize_enzyme_builder() -> Result<(), serde_json::Error> {
+        let a: EnzymeBuilder = serde_json::from_value(serde_json::json!({
+            "cleave_at": "KR",
+        }))?;
+        let b: EnzymeBuilder = serde_json::from_value(serde_json::json!({
+            "cleave_at": "KR",
+            "restrict": "P",
+        }))?;
+
+        let a: EnzymeParameters = a.into();
+        let b: EnzymeParameters = b.into();
+
+        assert_eq!(a.enyzme.and_then(|e| e.skip_suffix), None);
+        assert_eq!(b.enyzme.and_then(|e| e.skip_suffix), Some('P'));
+
+        Ok(())
+    }
 }

crates/sage/src/enzyme.rs

@@ -88,7 +88,7 @@ pub struct EnzymeParameters {
 
 pub struct Enzyme {
     // Skip cleaving if the site is followed matching this AA
-    skip_suffix: Option<char>,
+    pub(crate) skip_suffix: Option<char>,
     // Regex for matching cleavage sites
     regex: Regex,
     // Cleave at c-terminal?