Move MS2DeepScoresForTopInChikeys since not used for core functionality

niekdejonge · niekdejonge · commit 25508a6ea5e0 · 2026-03-24T09:42:23.000+01:00
diff --git a/ms2query/ms2query_development/reference_methods/MS2DeepScoresForTopInChikeys.py b/ms2query/ms2query_development/reference_methods/MS2DeepScoresForTopInChikeys.py
diff --git a/ms2query/ms2query_development/reference_methods/readme.md b/ms2query/ms2query_development/reference_methods/readme.md
@@ -1 +1 @@
-All files here are not important to core functionality and in fact not used, but might be nice to use for future testing. They are currently not yet used in the notebooks. Once they are used there they can probably be removed here.
+All files here are not important to core functionality and in fact not used for running the final version of MS2Query. However MS2DeepSCoresForTopInChikeys is core to the benchmarking in the notebooks. predict_best_possible_match and EvaluateExactMatchSearch are not yet used for the benchmarking, but both should still be done, so this could be used for that. 
diff --git a/ms2query/notebooks/develop_and_compare_ms2query_2.ipynb b/ms2query/notebooks/develop_and_compare_ms2query_2.ipynb
@@ -509,7 +509,7 @@
     }
    ],
    "source": [
-    "from ms2query.ms2query_development.MS2DeepScoresForTopInChikeys import calculate_MS2DeepScoresForTopKInChikeys\n",
+    "from ms2query.ms2query_development.reference_methods.MS2DeepScoresForTopInChikeys import calculate_MS2DeepScoresForTopKInChikeys\n",
     "close_tanimoto_scores = calculate_MS2DeepScoresForTopKInChikeys(pos_train_spectra, pos_val_spectra, top_k_tanimoto_scores, inchikeys_with_highest_ms2deepscores)"
    ]
   },
@@ -2633,7 +2633,7 @@
     "from ms2query.ms2query_development.Fingerprints import Fingerprints\n",
     "from ms2query.ms2query_development.TopKTanimotoScores import TopKTanimotoScores\n",
     "from ms2query.ms2query_development.predict_top_k_ms2deepscore import select_inchikeys_with_highest_ms2deepscore\n",
-    "from ms2query.ms2query_development.MS2DeepScoresForTopInChikeys import calculate_MS2DeepScoresForTopKInChikeys\n",
+    "from ms2query.ms2query_development.reference_methods.MS2DeepScoresForTopInChikeys import calculate_MS2DeepScoresForTopKInChikeys\n",
     "\n",
     "neg_val_fingerprints = Fingerprints.from_spectrum_set(neg_val_spectra, \"daylight\", 4096)\n",
     "neg_train_fingerprints = Fingerprints.from_spectrum_set(neg_train_spectra, \"daylight\", 4096)\n",

Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-All files here are not important to core functionality and in fact not used, but might be nice to use for future testing. They are currently not yet used in the notebooks. Once they are used there they can probably be removed here.`
	`1`	`+All files here are not important to core functionality and in fact not used for running the final version of MS2Query. However MS2DeepSCoresForTopInChikeys is core to the benchmarking in the notebooks. predict_best_possible_match and EvaluateExactMatchSearch are not yet used for the benchmarking, but both should still be done, so this could be used for that.`