{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Read Local MMTF Full Demo\n", "\n", "Simple example reading PDB entries from local Hadoop Sequence Files\n", "\n", "## Imports" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "from pyspark import SparkConf, SparkContext\n", "from mmtfPyspark.io import mmtfReader\n", "from mmtfPyspark.structureViewer import view_structure" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Configure Spark" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "conf = SparkConf().setMaster(\"local[*]\") \\\n", " .setAppName(\"ReadLocalMMTFFull\")\n", "sc = SparkContext(conf = conf)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Read in local Hadoop Sequence Files and count number of entries" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "number of pdb entries read : 4394\n" ] } ], "source": [ "path = \"../../resources/mmtf_full_sample/\"\n", "\n", "pdb = mmtfReader.read_sequence_file(path, sc)\n", "\n", "count = pdb.count()\n", "\n", "print(f'number of pdb entries read : {count}')" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "## Visualize Structures" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "data": { "application/vnd.jupyter.widget-view+json": { "model_id": "e9b59b5e39f44f7e9cfb2bc39b76dde9", "version_major": 2, "version_minor": 0 }, "text/html": [ "
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