Merge branch 'main' of github.com:RECETOX/ei_spectra_predictions into…

… main

analysis/Python_scripts/add_zeros_matching.ipynb

@@ -0,0 +1,95 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "import plotly.graph_objs as go\n",
+    "import pandas as pd\n",
+    "import seaborn as sns\n",
+    "import os\n",
+    "from matplotlib import pyplot as plt\n",
+    "from rdkit import Chem"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "query = Chem.SDMolSupplier(\"../../data/simulated_spectra.msp\")\n",
+    "reference = Chem.SDMolSupplier(\"../data/experimental/RECETOX_GC-EI_MS_20201028_norm_matchms.msp\")\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def append_classes(molecules):\n",
+    "    class_names = pd.DataFrame({\n",
+    "        \"molname\" : [m.GetProp(\"NAME\") for m in molecules],\n",
+    "\n",
+    "    })\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 21,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "[15:52:07] ERROR: Cannot convert '35.' to unsigned int on line 4\n",
+      "[15:52:07] ERROR: moving to the beginning of the next molecule\n"
+     ]
+    },
+    {
+     "ename": "AttributeError",
+     "evalue": "'NoneType' object has no attribute 'GetProp'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
+      "\u001b[1;32m/home/wrojas/dev/RECETOX/ei_spectra_predictions/analysis/Python_scripts/add_zeros_matching.ipynb Cell 4\u001b[0m line \u001b[0;36m1\n\u001b[0;32m----> <a href='vscode-notebook-cell://wsl%2Bubuntu-20.04/home/wrojas/dev/RECETOX/ei_spectra_predictions/analysis/Python_scripts/add_zeros_matching.ipynb#X20sdnNjb2RlLXJlbW90ZQ%3D%3D?line=0'>1</a>\u001b[0m merged_top5_same \u001b[39m=\u001b[39m append_classes(query)\n",
+      "\u001b[1;32m/home/wrojas/dev/RECETOX/ei_spectra_predictions/analysis/Python_scripts/add_zeros_matching.ipynb Cell 4\u001b[0m line \u001b[0;36m3\n\u001b[1;32m      <a href='vscode-notebook-cell://wsl%2Bubuntu-20.04/home/wrojas/dev/RECETOX/ei_spectra_predictions/analysis/Python_scripts/add_zeros_matching.ipynb#X20sdnNjb2RlLXJlbW90ZQ%3D%3D?line=0'>1</a>\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39mappend_classes\u001b[39m(molecules):\n\u001b[1;32m      <a href='vscode-notebook-cell://wsl%2Bubuntu-20.04/home/wrojas/dev/RECETOX/ei_spectra_predictions/analysis/Python_scripts/add_zeros_matching.ipynb#X20sdnNjb2RlLXJlbW90ZQ%3D%3D?line=1'>2</a>\u001b[0m     class_names \u001b[39m=\u001b[39m pd\u001b[39m.\u001b[39mDataFrame({\n\u001b[0;32m----> <a href='vscode-notebook-cell://wsl%2Bubuntu-20.04/home/wrojas/dev/RECETOX/ei_spectra_predictions/analysis/Python_scripts/add_zeros_matching.ipynb#X20sdnNjb2RlLXJlbW90ZQ%3D%3D?line=2'>3</a>\u001b[0m         \u001b[39m\"\u001b[39m\u001b[39mmolname\u001b[39m\u001b[39m\"\u001b[39m : [m\u001b[39m.\u001b[39mGetProp(\u001b[39m\"\u001b[39m\u001b[39mNAME\u001b[39m\u001b[39m\"\u001b[39m) \u001b[39mfor\u001b[39;00m m \u001b[39min\u001b[39;00m molecules],\n\u001b[1;32m      <a href='vscode-notebook-cell://wsl%2Bubuntu-20.04/home/wrojas/dev/RECETOX/ei_spectra_predictions/analysis/Python_scripts/add_zeros_matching.ipynb#X20sdnNjb2RlLXJlbW90ZQ%3D%3D?line=3'>4</a>\u001b[0m \n\u001b[1;32m      <a href='vscode-notebook-cell://wsl%2Bubuntu-20.04/home/wrojas/dev/RECETOX/ei_spectra_predictions/analysis/Python_scripts/add_zeros_matching.ipynb#X20sdnNjb2RlLXJlbW90ZQ%3D%3D?line=4'>5</a>\u001b[0m     })\n",
+      "\u001b[1;32m/home/wrojas/dev/RECETOX/ei_spectra_predictions/analysis/Python_scripts/add_zeros_matching.ipynb Cell 4\u001b[0m line \u001b[0;36m3\n\u001b[1;32m      <a href='vscode-notebook-cell://wsl%2Bubuntu-20.04/home/wrojas/dev/RECETOX/ei_spectra_predictions/analysis/Python_scripts/add_zeros_matching.ipynb#X20sdnNjb2RlLXJlbW90ZQ%3D%3D?line=0'>1</a>\u001b[0m \u001b[39mdef\u001b[39;00m \u001b[39mappend_classes\u001b[39m(molecules):\n\u001b[1;32m      <a href='vscode-notebook-cell://wsl%2Bubuntu-20.04/home/wrojas/dev/RECETOX/ei_spectra_predictions/analysis/Python_scripts/add_zeros_matching.ipynb#X20sdnNjb2RlLXJlbW90ZQ%3D%3D?line=1'>2</a>\u001b[0m     class_names \u001b[39m=\u001b[39m pd\u001b[39m.\u001b[39mDataFrame({\n\u001b[0;32m----> <a href='vscode-notebook-cell://wsl%2Bubuntu-20.04/home/wrojas/dev/RECETOX/ei_spectra_predictions/analysis/Python_scripts/add_zeros_matching.ipynb#X20sdnNjb2RlLXJlbW90ZQ%3D%3D?line=2'>3</a>\u001b[0m         \u001b[39m\"\u001b[39m\u001b[39mmolname\u001b[39m\u001b[39m\"\u001b[39m : [m\u001b[39m.\u001b[39;49mGetProp(\u001b[39m\"\u001b[39m\u001b[39mNAME\u001b[39m\u001b[39m\"\u001b[39m) \u001b[39mfor\u001b[39;00m m \u001b[39min\u001b[39;00m molecules],\n\u001b[1;32m      <a href='vscode-notebook-cell://wsl%2Bubuntu-20.04/home/wrojas/dev/RECETOX/ei_spectra_predictions/analysis/Python_scripts/add_zeros_matching.ipynb#X20sdnNjb2RlLXJlbW90ZQ%3D%3D?line=3'>4</a>\u001b[0m \n\u001b[1;32m      <a href='vscode-notebook-cell://wsl%2Bubuntu-20.04/home/wrojas/dev/RECETOX/ei_spectra_predictions/analysis/Python_scripts/add_zeros_matching.ipynb#X20sdnNjb2RlLXJlbW90ZQ%3D%3D?line=4'>5</a>\u001b[0m     })\n",
+      "\u001b[0;31mAttributeError\u001b[0m: 'NoneType' object has no attribute 'GetProp'"
+     ]
+    }
+   ],
+   "source": [
+    "merged_top5_same = append_classes(query)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "base",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.2"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

analysis/Python_scripts/method_comparison_histogram.ipynb

@@ -5373,7 +5373,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.18"
+   "version": "3.10.2"
   }
  },
  "nbformat": 4,