data/data_processing.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "388f6339-24b9-4384-8141-290b62240e6c",
   "metadata": {
    "scrolled": true,
    "tags": []
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "[21:51:07] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:07] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:07] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:07] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:07] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:07] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:07] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:07] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:07] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:08] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:08] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:08] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:08] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:08] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:08] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:08] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:09] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:09] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:09] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:09] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:09] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:09] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:09] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:09] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:10] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:10] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:10] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:10] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:10] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:11] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:11] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:11] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:11] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:11] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:11] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:11] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:12] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:12] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:12] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:12] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:12] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:12] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:12] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:13] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:13] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:13] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:14] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:14] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:14] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:14] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:14] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:14] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:14] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:15] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:15] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:15] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:15] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:15] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:15] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:16] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:16] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:16] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:16] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:16] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:16] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:16] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:16] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:17] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:51:18] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:18] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:18] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:18] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:19] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:19] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:19] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:19] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:19] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:19] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:19] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:19] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:19] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:19] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:20] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:20] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:20] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:20] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:20] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:20] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:20] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:20] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:21] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:51:21] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:21] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:21] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:21] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:21] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:21] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:21] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:51:22] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:22] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:22] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:22] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:22] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:22] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:22] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:51:23] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:51:23] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:23] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:23] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:23] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:23] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:51:23] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:51:24] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:51:25] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:25] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:25] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:51:25] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:25] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:51:26] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:51:28] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:51:28] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:28] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:28] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:51:37] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:51:41] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:51:42] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:51:43] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:43] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:43] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:43] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:43] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:44] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:44] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:44] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:44] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:45] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:45] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:45] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:45] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:45] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:45] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:45] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:45] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:46] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:46] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:46] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:46] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:46] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:47] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:47] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:47] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:47] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:47] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:47] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:48] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:48] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:49] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:49] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:49] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:49] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:49] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:49] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:49] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:50] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:50] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:50] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:50] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:50] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:50] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:50] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:51] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:51] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:51] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:51] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:51] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:51] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:51] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:52] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:52] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:52] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:52] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:52] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:52] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:52] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:52] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:52] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:52] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:53] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:53] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:53] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:53] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:53] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:53] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:53] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:54] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:54] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:54] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:54] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:54] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:55] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:55] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:55] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:55] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:55] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:55] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:55] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:55] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:55] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:55] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:56] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:56] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:56] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:56] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:57] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:57] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:57] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:57] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:58] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:58] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:58] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:58] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:58] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:58] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:58] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:58] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:58] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:58] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:58] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:58] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:59] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:59] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:59] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:59] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:59] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:59] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:59] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:59] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:59] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:59] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:59] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:59] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:59] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:51:59] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:00] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:00] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:00] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:00] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:00] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:01] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:01] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:01] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:02] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:02] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:02] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:02] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:02] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:02] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:03] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:03] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:04] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:04] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:04] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:04] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:04] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:04] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:05] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:05] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:05] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:05] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:05] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:05] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:05] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:05] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:05] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:05] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:05] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:06] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:06] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:06] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:06] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:06] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:06] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:06] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:52:07] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:52:18] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:18] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:18] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:18] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:19] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:19] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:19] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:19] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:19] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:52:20] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:52:20] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:20] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:52:20] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:52:21] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:52:21] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:52:21] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:52:21] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:21] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:21] WARNING: not removing hydrogen atom without neighbors\n",
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      "[21:52:23] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:23] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:23] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:23] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:23] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:23] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:23] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:23] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:23] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:23] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:23] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:23] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:23] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:23] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:24] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:24] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:24] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:24] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:24] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:24] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:24] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:24] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:25] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:25] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:25] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:25] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:25] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:25] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:26] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:26] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:26] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:26] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:26] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:26] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:26] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:26] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:26] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:26] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:26] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:26] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:26] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:27] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:27] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:27] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:27] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:27] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:27] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:27] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:27] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:27] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:27] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:27] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:28] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:28] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:28] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:28] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:28] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:28] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:28] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:28] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:28] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:28] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:28] WARNING: not removing hydrogen atom without neighbors\n",
      "[21:52:28] WARNING: not removing hydrogen atom without neighbors\n"
     ]
    }
   ],
   "source": [
    "import pandas as pd\n",
    "from rdkit import Chem\n",
    "\n",
    "data = pd.read_pickle('igcdata/small_mol/train_72k.pkl')\n",
    "\n",
    "# Data Cleaning: \n",
    "data = data.dropna(subset=['isosmiles'])\n",
    "\n",
    "# Low-Frequency Atoms: \n",
    "def atom_frequencies(smiles):\n",
    "    mol = Chem.MolFromSmiles(smiles)\n",
    "    return [atom.GetSymbol() for atom in mol.GetAtoms()]\n",
    "\n",
    "all_atoms = [atom for sublist in data['isosmiles'].apply(atom_frequencies) for atom in sublist]\n",
    "atom_freq = pd.Series(all_atoms).value_counts()\n",
    "\n",
    "#atom_freq\n",
    "low_freq_atoms = atom_freq[atom_freq < 100].index.tolist()\n",
    "\n",
    "def contains_low_freq_atoms(smiles):\n",
    "    mol = Chem.MolFromSmiles(smiles)\n",
    "    mol_atoms = [atom.GetSymbol() for atom in mol.GetAtoms()]\n",
    "    return any(atom in mol_atoms for atom in low_freq_atoms)\n",
    "\n",
    "data = data[~data['isosmiles'].apply(contains_low_freq_atoms)]\n",
    "\n",
    "# Validation of Graph Structures\n",
    "def is_valid_smiles(smiles):\n",
    "    mol = Chem.MolFromSmiles(smiles)\n",
    "    return mol is not None\n",
    "\n",
    "data = data[data['isosmiles'].apply(is_valid_smiles)]\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "06ccc00f-7790-4c20-9a1a-7b6ff45719d7",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>cid</th>\n",
       "      <th>image2d</th>\n",
       "      <th>image3d</th>\n",
       "      <th>SMILES</th>\n",
       "      <th>isosmiles</th>\n",
       "      <th>summary</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>33261</th>\n",
       "      <td>3553946</td>\n",
       "      <td>1_632953_10034684/3516533_3669275/3553946.png</td>\n",
       "      <td>1_632953_10034684/3516533_3669275/3553946.png</td>\n",
       "      <td>c1ccc(cc1)C[NH2+]CCNCc1ccccc1</td>\n",
       "      <td>C1=CC=C(C=C1)C[NH2+]CCNCC2=CC=CC=C2</td>\n",
       "      <td>The molecule is an ammonium ion derivative. It...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>72297</th>\n",
       "      <td>45360076</td>\n",
       "      <td>4_45268362_60189818/45359558_45480588/45360076...</td>\n",
       "      <td>4_45268362_60189818/45359558_45480588/45360076...</td>\n",
       "      <td>CC(=O)OC(CCCCCCCCCCCC=C)CC(CO)O</td>\n",
       "      <td>CC(=O)OC(CCCCCCCCCCCC=C)CC(CO)O</td>\n",
       "      <td>The molecule is a long-chain fatty alcohol.</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>71244</th>\n",
       "      <td>135410798</td>\n",
       "      <td>6_101348969_139589427/135398660_135413545/1354...</td>\n",
       "      <td>6_101348969_139589427/135398660_135413545/1354...</td>\n",
       "      <td>Cc1c(c(ccc1)N=C1NN=C(CS1)c1ccccc1F)C</td>\n",
       "      <td>CC1=C(C(=CC=C1)N=C2NN=C(CS2)C3=CC=CC=C3F)C</td>\n",
       "      <td>The molecule is a methylbenzene.</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1409</th>\n",
       "      <td>4621901</td>\n",
       "      <td>1_632953_10034684/4482010_4632015/4621901.png</td>\n",
       "      <td>1_632953_10034684/4482010_4632015/4621901.png</td>\n",
       "      <td>Cc1cccn2c1nc1c(c2=O)cc(n1C)C(=O)NCCN1CCOCC1</td>\n",
       "      <td>CC1=CC=CN2C1=NC3=C(C2=O)C=C(N3C)C(=O)NCCN4CCOCC4</td>\n",
       "      <td>The molecule is a pyridopyrimidine.</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21341</th>\n",
       "      <td>131755983</td>\n",
       "      <td>6_101348969_139589427/131753332_131758668/1317...</td>\n",
       "      <td>6_101348969_139589427/131753332_131758668/1317...</td>\n",
       "      <td>CCCCCCCCCCCCCCCCCC(=O)OC[C@@H](COC(=O)CCCCCCC/...</td>\n",
       "      <td>CCCCCCCCCCCCCCCCCC(=O)OC[C@@H](COC(=O)CCCCCCC/...</td>\n",
       "      <td>The molecule is a triglyceride.</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "             cid                                            image2d  \\\n",
       "33261    3553946      1_632953_10034684/3516533_3669275/3553946.png   \n",
       "72297   45360076  4_45268362_60189818/45359558_45480588/45360076...   \n",
       "71244  135410798  6_101348969_139589427/135398660_135413545/1354...   \n",
       "1409     4621901      1_632953_10034684/4482010_4632015/4621901.png   \n",
       "21341  131755983  6_101348969_139589427/131753332_131758668/1317...   \n",
       "\n",
       "                                                 image3d  \\\n",
       "33261      1_632953_10034684/3516533_3669275/3553946.png   \n",
       "72297  4_45268362_60189818/45359558_45480588/45360076...   \n",
       "71244  6_101348969_139589427/135398660_135413545/1354...   \n",
       "1409       1_632953_10034684/4482010_4632015/4621901.png   \n",
       "21341  6_101348969_139589427/131753332_131758668/1317...   \n",
       "\n",
       "                                                  SMILES  \\\n",
       "33261                      c1ccc(cc1)C[NH2+]CCNCc1ccccc1   \n",
       "72297                    CC(=O)OC(CCCCCCCCCCCC=C)CC(CO)O   \n",
       "71244               Cc1c(c(ccc1)N=C1NN=C(CS1)c1ccccc1F)C   \n",
       "1409         Cc1cccn2c1nc1c(c2=O)cc(n1C)C(=O)NCCN1CCOCC1   \n",
       "21341  CCCCCCCCCCCCCCCCCC(=O)OC[C@@H](COC(=O)CCCCCCC/...   \n",
       "\n",
       "                                               isosmiles  \\\n",
       "33261                C1=CC=C(C=C1)C[NH2+]CCNCC2=CC=CC=C2   \n",
       "72297                    CC(=O)OC(CCCCCCCCCCCC=C)CC(CO)O   \n",
       "71244         CC1=C(C(=CC=C1)N=C2NN=C(CS2)C3=CC=CC=C3F)C   \n",
       "1409    CC1=CC=CN2C1=NC3=C(C2=O)C=C(N3C)C(=O)NCCN4CCOCC4   \n",
       "21341  CCCCCCCCCCCCCCCCCC(=O)OC[C@@H](COC(=O)CCCCCCC/...   \n",
       "\n",
       "                                                 summary  \n",
       "33261  The molecule is an ammonium ion derivative. It...  \n",
       "72297        The molecule is a long-chain fatty alcohol.  \n",
       "71244                   The molecule is a methylbenzene.  \n",
       "1409                 The molecule is a pyridopyrimidine.  \n",
       "21341                    The molecule is a triglyceride.  "
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "data.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "b846042b-826b-48b8-b093-cbb6babf5b84",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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