{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Example of using mmtfPyspark to find water interactions\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Imports and variables" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "scrolled": true }, "outputs": [], "source": [ "from pyspark import SparkConf, SparkContext\n", "from pyspark.sql.functions import col\n", "from mmtfPyspark.io import mmtfReader\n", "from mmtfPyspark.interactions import InteractionFilter, GroupInteractionExtractor, ExcludedLigandSets\n", "from mmtfPyspark.filters import ContainsLProteinChain, Resolution\n", "import matplotlib.pyplot as plt\n", "import pandas as pd\n", "import py3Dmol\n", "import time\n", "\n", " \n", "# Create variables \n", "APP_NAME = \"MMTF_Spark\" \n", "path = \"../../resources/mmtf_full_sample/\"\n", "\n", "# Configure Spark \n", "conf = SparkConf().setAppName(APP_NAME).setMaster(\"local[*]\") \n", "sc = SparkContext(conf=conf) " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Define Variables" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "# input parameters\n", "resolution = 2.0\n", "minInteractions = 2\n", "maxInteractions = 4\n", "distanceCutoff = 3.0\n", "bFactorCutoff = 1.645\n", "includeWaters = True" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Read PDB and filter by resolution and only include proteins" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "pdb = mmtfReader.read_sequence_file(path, sc)\n", "pdb = pdb.filter(Resolution(minResolution=0.0, maxResolution=2.0))\\\n", " .filter(ContainsLProteinChain(exclusive=True))" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Setup criteria for metal interactions" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [], "source": [ "interactions_filter = InteractionFilter()\n", "interactions_filter.set_distance_cutoff(3.0)\n", "interactions_filter.set_normalized_b_factor_cutoff(1.645)\n", "interactions_filter.set_min_interactions(2)\n", "interactions_filter.set_max_interactions(4)\n", "interactions_filter.set_query_groups(True, [\"HOH\"])\n", "interactions_filter.set_query_elements(True, \"O\") # Only use water oxygen\n", "interactions_filter.set_target_elements(True, [\"O\", \"N\", \"S\"])" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Exclude \"uninteresting\" ligands " ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [], "source": [ "prohibitedGroups = ExcludedLigandSets.ALL_GROUPS\n", "if not includeWaters:\n", " prohibitedGroups.add(\"HOH\")\n", "interactions_filter.set_prohibited_target_groups(prohibitedGroups)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Calculate interactions" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [], "source": [ "data = GroupInteractionExtractor().get_interactions(structures=pdb, interactionFilter=interactions_filter)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Define Filter Bridging Water Interactions Function" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [], "source": [ "def filter_bridging_water_interactions(data, maxInteractions):\n", " if maxInteractions == 2:\n", " data = data.filter((col(\"type1\") == \"LGO\") | \\\n", " (col(\"type2\") == \"LGO\"))\n", " data = data.filter((col(\"type1\") == \"PRO\") | \\\n", " (col(\"type2\") == \"PRO\"))\n", " elif maxInteractions == 3:\n", " data = data.filter((col(\"type1\") == \"LGO\") | \\\n", " (col(\"type2\") == \"LGO\") | \\\n", " (col(\"type3\") == \"LGO\"))\n", " data = data.filter((col(\"type1\") == \"PRO\") | \\\n", " (col(\"type2\") == \"PRO\") | \\\n", " (col(\"type3\") == \"PRO\"))\n", " elif maxInteractions == 4:\n", " data = data.filter((col(\"type1\") == \"LGO\") | \\\n", " (col(\"type2\") == \"LGO\") | \\\n", " (col(\"type3\") == \"LGO\") | \\\n", " (col(\"type4\") == \"LGO\"))\n", " data = data.filter((col(\"type1\") == \"PRO\") | \\\n", " (col(\"type2\") == \"PRO\") | \\\n", " (col(\"type3\") == \"PRO\") | \\\n", " (col(\"type4\") == \"PRO\"))\n", " else:\n", " raise ValueError(\"maxInteractions > 4 are not supported yet\")\n", " return data" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Keep only interactions with at least one organic ligand and one protein interaction" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Hits(all): 25050\n" ] }, { "data": { "text/html": [ "
\n", " | pdbId | \n", "polyChains | \n", "q3 | \n", "q4 | \n", "q5 | \n", "q6 | \n", "atom0 | \n", "element0 | \n", "group0 | \n", "groupNum0 | \n", "... | \n", "type4 | \n", "chain4 | \n", "nbFactor4 | \n", "distance4 | \n", "angle1-2 | \n", "angle1-3 | \n", "angle1-4 | \n", "angle2-3 | \n", "angle2-4 | \n", "angle3-4 | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "5VNX | \n", "2 | \n", "0.917888 | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "802 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "1.808243 | \n", "2.442852 | \n", "2.032056 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
1 | \n", "5VNX | \n", "2 | \n", "0.923362 | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "720 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "1.999510 | \n", "2.444744 | \n", "1.837754 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
2 | \n", "5VNX | \n", "1 | \n", "0.981236 | \n", "0.859927 | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "832 | \n", "... | \n", "WAT | \n", "A | \n", "0.107415 | \n", "2.835226 | \n", "2.201767 | \n", "1.899949 | \n", "1.955327 | \n", "1.868961 | \n", "1.987020 | \n", "1.355446 | \n", "
3 | \n", "5VNX | \n", "2 | \n", "0.913232 | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "753 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "2.480631 | \n", "1.956003 | \n", "1.844749 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
4 | \n", "4X9D | \n", "1 | \n", "NaN | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "233 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "1.821897 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
5 | \n", "5H9N | \n", "1 | \n", "0.997502 | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "341 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "2.036827 | \n", "2.099268 | \n", "2.143945 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
6 | \n", "5H9N | \n", "1 | \n", "0.694474 | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "349 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "2.397284 | \n", "1.392314 | \n", "2.267734 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
7 | \n", "5LCA | \n", "1 | \n", "0.920665 | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "621 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "1.736914 | \n", "2.296526 | \n", "2.103182 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
8 | \n", "5LCA | \n", "3 | \n", "0.957595 | \n", "0.839895 | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "633 | \n", "... | \n", "PRO | \n", "A | \n", "-0.677593 | \n", "2.874640 | \n", "1.989787 | \n", "2.061019 | \n", "1.597358 | \n", "1.819018 | \n", "2.430154 | \n", "1.556288 | \n", "
9 | \n", "5LCF | \n", "3 | \n", "0.977555 | \n", "0.801750 | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "634 | \n", "... | \n", "PRO | \n", "A | \n", "-0.090881 | \n", "2.792826 | \n", "2.465741 | \n", "1.989851 | \n", "1.971329 | \n", "1.450782 | \n", "1.566221 | \n", "1.943373 | \n", "
10 | \n", "5LCF | \n", "1 | \n", "0.916752 | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "665 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "2.078905 | \n", "1.759737 | \n", "2.373434 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
11 | \n", "5LCH | \n", "3 | \n", "0.971902 | \n", "0.788855 | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "648 | \n", "... | \n", "LGO | \n", "A | \n", "0.079471 | \n", "2.683238 | \n", "2.009260 | \n", "1.608932 | \n", "1.911190 | \n", "2.478863 | \n", "1.954119 | \n", "1.394372 | \n", "
12 | \n", "5LE1 | \n", "3 | \n", "0.933710 | \n", "0.769073 | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "649 | \n", "... | \n", "PRO | \n", "A | \n", "0.597268 | \n", "2.743888 | \n", "2.396844 | \n", "2.197642 | \n", "1.976304 | \n", "1.412055 | \n", "1.552328 | \n", "1.759869 | \n", "
13 | \n", "5MMN | \n", "3 | \n", "0.805579 | \n", "0.840680 | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "424 | \n", "... | \n", "PRO | \n", "A | \n", "-0.191379 | \n", "2.660059 | \n", "1.835154 | \n", "1.547962 | \n", "2.337603 | \n", "1.530142 | \n", "2.067027 | \n", "1.857040 | \n", "
14 | \n", "5MMN | \n", "2 | \n", "0.857262 | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "473 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "1.892428 | \n", "1.890819 | \n", "1.644718 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
15 | \n", "5MMO | \n", "3 | \n", "0.794642 | \n", "0.836989 | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "417 | \n", "... | \n", "PRO | \n", "A | \n", "-0.385945 | \n", "2.628243 | \n", "1.841165 | \n", "1.538125 | \n", "2.314125 | \n", "1.529892 | \n", "2.101835 | \n", "1.814811 | \n", "
16 | \n", "5MMO | \n", "2 | \n", "0.817830 | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "462 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "1.919041 | \n", "1.823202 | \n", "1.590212 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
17 | \n", "5MMO | \n", "1 | \n", "NaN | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "472 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "2.270356 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
18 | \n", "5N49 | \n", "1 | \n", "0.923594 | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "810 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "2.150182 | \n", "1.716559 | \n", "2.009910 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
19 | \n", "5UEW | \n", "1 | \n", "0.911381 | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "611 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "1.717024 | \n", "2.102965 | \n", "1.905225 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
20 | \n", "5UEW | \n", "1 | \n", "0.904136 | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "602 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "1.691051 | \n", "1.944444 | \n", "2.179145 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
21 | \n", "5UEZ | \n", "1 | \n", "0.939357 | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "607 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "1.965640 | \n", "1.787436 | \n", "2.223777 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
22 | \n", "5UEZ | \n", "1 | \n", "0.895376 | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "642 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "1.716711 | \n", "2.391761 | \n", "2.165344 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
23 | \n", "3U96 | \n", "2 | \n", "0.886328 | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "481 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "2.144969 | \n", "1.817851 | \n", "1.708172 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
24 | \n", "3U98 | \n", "1 | \n", "NaN | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "1043 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "2.333080 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
25 | \n", "3U9H | \n", "1 | \n", "0.850342 | \n", "0.863505 | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "226 | \n", "... | \n", "PRO | \n", "A | \n", "0.032156 | \n", "2.768258 | \n", "2.431111 | \n", "1.714931 | \n", "1.655102 | \n", "1.811743 | \n", "2.035461 | \n", "1.652409 | \n", "
26 | \n", "3U9N | \n", "1 | \n", "0.966877 | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "435 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "2.094525 | \n", "1.839143 | \n", "2.156703 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
27 | \n", "3U9N | \n", "1 | \n", "NaN | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "498 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "1.831271 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
28 | \n", "3UAG | \n", "3 | \n", "0.803613 | \n", "0.563889 | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "501 | \n", "... | \n", "PRO | \n", "A | \n", "-0.554693 | \n", "2.793061 | \n", "1.127710 | \n", "2.601418 | \n", "1.737904 | \n", "1.548108 | \n", "2.379534 | \n", "1.935428 | \n", "
29 | \n", "3UAG | \n", "2 | \n", "0.860623 | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "502 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "2.273910 | \n", "1.625290 | \n", "1.923401 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
30 | \n", "3UAG | \n", "2 | \n", "0.123106 | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "600 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "1.360162 | \n", "2.408705 | \n", "1.063054 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
31 | \n", "3UAG | \n", "1 | \n", "0.203524 | \n", "0.364127 | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "837 | \n", "... | \n", "LGO | \n", "A | \n", "-0.562174 | \n", "2.777843 | \n", "1.462554 | \n", "2.436885 | \n", "2.061869 | \n", "2.259292 | \n", "2.534806 | \n", "0.862076 | \n", "
32 | \n", "3UAL | \n", "1 | \n", "NaN | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "258 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "2.087371 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
33 | \n", "3UAL | \n", "1 | \n", "0.888170 | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "293 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "2.161019 | \n", "1.666536 | \n", "2.305244 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
34 | \n", "3UAZ | \n", "1 | \n", "0.921715 | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "262 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "2.290687 | \n", "2.221030 | \n", "1.754788 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
35 | \n", "3UB6 | \n", "1 | \n", "0.899168 | \n", "0.672460 | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "407 | \n", "... | \n", "PRO | \n", "A | \n", "-0.475994 | \n", "2.863447 | \n", "1.311276 | \n", "1.740830 | \n", "2.432327 | \n", "2.251388 | \n", "1.456739 | \n", "2.101638 | \n", "
36 | \n", "3UB6 | \n", "1 | \n", "0.901412 | \n", "0.670772 | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "403 | \n", "... | \n", "PRO | \n", "B | \n", "-0.653865 | \n", "2.873985 | \n", "1.741537 | \n", "1.311803 | \n", "2.421566 | \n", "2.262811 | \n", "2.109684 | \n", "1.452782 | \n", "
37 | \n", "3UB7 | \n", "1 | \n", "0.896540 | \n", "0.692493 | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "407 | \n", "... | \n", "PRO | \n", "A | \n", "-0.405171 | \n", "2.855674 | \n", "1.329261 | \n", "1.740892 | \n", "2.445819 | \n", "2.226469 | \n", "1.484874 | \n", "2.083471 | \n", "
38 | \n", "3UB7 | \n", "1 | \n", "0.897268 | \n", "0.685547 | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "407 | \n", "... | \n", "PRO | \n", "B | \n", "-0.610487 | \n", "2.902715 | \n", "1.739871 | \n", "1.330280 | \n", "2.440397 | \n", "2.233240 | \n", "2.092597 | \n", "1.465206 | \n", "
39 | \n", "3UBD | \n", "1 | \n", "NaN | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "530 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "2.258912 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
40 | \n", "3UBW | \n", "1 | \n", "0.713606 | \n", "0.820527 | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "307 | \n", "... | \n", "WAT | \n", "A | \n", "-0.608621 | \n", "2.584318 | \n", "2.006831 | \n", "1.449188 | \n", "1.849012 | \n", "2.064086 | \n", "1.650956 | \n", "2.424514 | \n", "
41 | \n", "3UBW | \n", "1 | \n", "NaN | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "365 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "2.160672 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
42 | \n", "3UD5 | \n", "1 | \n", "NaN | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "242 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "1.420573 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
43 | \n", "3UDE | \n", "1 | \n", "NaN | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "221 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "1.464474 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
44 | \n", "3UDH | \n", "1 | \n", "NaN | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "843 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "2.213616 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
45 | \n", "3UDP | \n", "1 | \n", "NaN | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "821 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "2.270605 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
46 | \n", "3UDR | \n", "1 | \n", "NaN | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "684 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "2.133965 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
47 | \n", "3UDV | \n", "1 | \n", "NaN | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "263 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "2.302813 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
48 | \n", "3UDY | \n", "1 | \n", "NaN | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "654 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "1.924380 | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
49 | \n", "3UEQ | \n", "2 | \n", "0.860294 | \n", "NaN | \n", "None | \n", "None | \n", "O | \n", "O | \n", "HOH | \n", "808 | \n", "... | \n", "None | \n", "None | \n", "NaN | \n", "0.000000 | \n", "1.664870 | \n", "2.468495 | \n", "2.081199 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
50 rows × 51 columns
\n", "