Move predict_top_k_ms2deepscore as well

Author: niekdejonge

…evelopment/predict_top_k_ms2deepscore.py …ce_methods/predict_top_k_ms2deepscore.pyms2query/ms2query_development/predict_top_k_ms2deepscore.py renamed to ms2query/ms2query_development/reference_methods/predict_top_k_ms2deepscore.py ms2query/ms2query_development/predict_top_k_ms2deepscore.py renamed to ms2query/ms2query_development/reference_methods/predict_top_k_ms2deepscore.py

@@ -1 +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. 
+All files here are not important to core functionality and in fact not used for running the final version of MS2Query. However MS2DeepSCoresForTopInChikeys and predict_top-k_ms2deepscore are core to the benchmarking and experimenting 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. 

ms2query/ms2query_development/reference_methods/readme.md

@@ -488,7 +488,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from ms2query.ms2query_development.predict_top_k_ms2deepscore import select_inchikeys_with_highest_ms2deepscore\n",
+    "from ms2query.ms2query_development.reference_methods.predict_top_k_ms2deepscore import select_inchikeys_with_highest_ms2deepscore\n",
     "\n",
     "inchikeys_with_highest_ms2deepscores = select_inchikeys_with_highest_ms2deepscore(\n",
     "        pos_val_spectra, pos_train_spectra, nr_of_inchikeys_to_select=1, batch_size=1000,)\n"
@@ -2632,7 +2632,7 @@
    "source": [
     "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.reference_methods.predict_top_k_ms2deepscore import select_inchikeys_with_highest_ms2deepscore\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",
@@ -2714,7 +2714,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from ms2query.ms2query_development.predict_top_k_ms2deepscore import predict_top_k_ms2deepscores\n",
+    "from ms2query.ms2query_development.reference_methods.predict_top_k_ms2deepscore import predict_top_k_ms2deepscores\n",
     "\n",
     "indexes, ms2deepscores = predict_top_k_ms2deepscores(neg_train_spectra.embeddings, neg_val_spectra.embeddings)\n",
     "neg_predicted_inchikeys_ms2deepscore = [neg_train_spectra.spectra[int(index)].get(\"inchikey\")[:14] for index in indexes]\n",

ms2query/notebooks/develop_and_compare_ms2query_2.ipynb

@@ -1,5 +1,5 @@
 from ms2query.ms2query_development.AnnotatedSpectrumSet import AnnotatedSpectrumSet
-from ms2query.ms2query_development.MS2DeepScoresForTopInChikeys import (
+from ms2query.ms2query_development.reference_methods.MS2DeepScoresForTopInChikeys import (
     calculate_MS2DeepScoresForTopKInChikeys_from_spectra,
 )
 from tests.helper_functions import create_test_spectra, ms2deepscore_model