First pass at SepTop analysis notebook

Author: hannahbaumann

openmm_septop/septop_analysis.ipynb

@@ -0,0 +1,124 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "7fbf1482-25ca-427b-a881-af88a983461c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "import glob\n",
+    "import json\n",
+    "import csv\n",
+    "from gufe.tokenization import JSON_HANDLER"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "ac321210-9974-46e1-ab85-e1a2f0eaa721",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def load_results(f):\n",
+    "    # path to deserialized results\n",
+    "    with open(f, \"r\") as fd:\n",
+    "        result = json.load(fd, cls=JSON_HANDLER.decoder)\n",
+    "    return result"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "d6ea9187-6a47-4438-9e2b-2a06c9c7c657",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def extract(results_0, results_1, results_2, output):\n",
+    "    files_0 = glob.glob(f\"{results_0}/*.json\")\n",
+    "    files_1 = glob.glob(f\"{results_1}/*.json\")\n",
+    "    files_2 = glob.glob(f\"{results_2}/*.json\")\n",
+    "    with open(output, 'w', newline='') as csvfile:\n",
+    "        writer = csv.writer(\n",
+    "            csvfile,\n",
+    "            delimiter=\"\\t\",\n",
+    "            lineterminator=\"\\n\",  # to exactly reproduce previous, prefer \"\\r\\n\"\n",
+    "        )\n",
+    "        writer.writerow([\"ligand\", \"DG(i->j) (kcal/mol)\",\n",
+    "                         \"uncertainty (kcal/mol)\"])\n",
+    "        for file in files_0:\n",
+    "            json_0 = load_results(file)\n",
+    "            dg_0 = json_0[\"estimate\"].magnitude\n",
+    "            try:\n",
+    "                file_1 = f\"{results_1}/{file.split(\"/\")[-1]}\"\n",
+    "                file_2 = f\"{results_2}/{file.split(\"/\")[-1]}\"\n",
+    "                json_1 = load_results(file_1)\n",
+    "                json_2 = load_results(file_2)\n",
+    "                dg_1 = json_1[\"estimate\"].magnitude\n",
+    "                dg_2 = json_2[\"estimate\"].magnitude\n",
+    "                dgs = [dg_0, dg_1, dg_2]\n",
+    "                dg = np.mean(dgs)\n",
+    "                dg_error = np.std(dgs)\n",
+    "                writer.writerow([file.split('/')[-1].split('.')[0], round(dg, 2), round(dg_error, 2)])\n",
+    "            except FileNotFoundError:\n",
+    "                continue"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6d553fd5-3f4a-4a2d-ad7d-542b31b4f9fa",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/hannahbaumann/miniforge3/envs/septop/lib/python3.12/site-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.\n",
+      "\n",
+      "Due to the on going maintenance burden of keeping command line application\n",
+      "wrappers up to date, we have decided to deprecate and eventually remove these\n",
+      "modules.\n",
+      "\n",
+      "We instead now recommend building your command line and invoking it directly\n",
+      "with the subprocess module.\n",
+      "  warnings.warn(\n"
+     ]
+    }
+   ],
+   "source": [
+    "extract('results_0', 'results_1', 'results_2', 'ddg.tsv')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9cb87ef5-eca0-42bd-9265-e8b4d3d9f7a0",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "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": "3.12.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}