From 600cea0d2f099fb0df4a1078547bdb07cf2138d8 Mon Sep 17 00:00:00 2001
From: Sean Colby <seanmcolby@gmail.com>
Date: Fri, 11 Oct 2024 14:45:28 -0700
Subject: [PATCH] Update CoreMS configuration to version 2.* compliance

---
 configuration/corems.toml | 35 +++++++++++++++++++----------------
 1 file changed, 19 insertions(+), 16 deletions(-)

diff --git a/configuration/corems.toml b/configuration/corems.toml
index a3629cb..0c6d1ed 100644
--- a/configuration/corems.toml
+++ b/configuration/corems.toml
@@ -1,24 +1,26 @@
 [MolecularSearch]
-url_database: "sqlite:///db/MetabRef_Library_EILowRes_20240816.db"
-ri_search_range = 35
+url_database = "sqlite:///db/MetabRef_Library_EILowRes_20240816.db"
+ri_search_range = 35.0
 rt_search_range = 1.0
 correlation_threshold = 0.5
 score_threshold = 0.0
 ri_spacing = 200.0
 ri_std = 3.0
-ri_calibration_compound_names = ['Methyl Caprylate', 
-                                 'Methyl Caprate', 
-                                 'Methyl Pelargonate', 
-                                 'Methyl Laurate', 
-                                 'Methyl Myristate', 
-                                 'Methyl Palmitate', 
-                                 'Methyl Stearate', 
-                                 'Methyl Eicosanoate', 
-                                 'Methyl Docosanoate', 
-                                 'Methyl Linocerate', 
-                                 'Methyl Hexacosanoate', 
-                                 'Methyl Octacosanoate', 
-                                 'Methyl Triacontanoate']
+ri_calibration_compound_names = [
+    "Methyl Caprylate",
+    "Methyl Caprate",
+    "Methyl Pelargonate",
+    "Methyl Laurate",
+    "Methyl Myristate", 
+    "Methyl Palmitate", 
+    "Methyl Stearate", 
+    "Methyl Eicosanoate", 
+    "Methyl Docosanoate", 
+    "Methyl Linocerate", 
+    "Methyl Hexacosanoate", 
+    "Methyl Octacosanoate", 
+    "Methyl Triacontanoate",
+]
 exploratory_mode = false
 score_methods = [ "highest_sim_score", "highest_ss",]
 output_score_method = "All"
@@ -29,12 +31,13 @@ implemented_smooth_method = [ "savgol", "hanning", "blackman", "bartlett", "flat
 smooth_window = 5
 smooth_method = "savgol"
 savgol_pol_order = 2
+peak_derivative_threshold = 0.0005
 peak_height_max_percent = 10.0
 peak_max_prominence_percent = 1.0
 min_peak_datapoints = 5.0
 max_peak_width = 0.1
 noise_threshold_method = "manual_relative_abundance"
-implemented_noise_threshold_methods = [ "auto_relative_abundance", "manual_relative_abundance", "second_derivative",]
+noise_threshold_methods_implemented = [ "auto_relative_abundance", "manual_relative_abundance", "second_derivative",]
 std_noise_threshold = 3
 peak_height_min_percent = 0.1
 peak_min_prominence_percent = 0.1