Mercurial > repos > pablocarb > synbiodesign
annotate Selenzyme_query.ipynb @ 1:b0b7deebb71e draft
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author | pablocarb |
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date | Mon, 29 Apr 2019 10:53:09 -0400 |
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1 { |
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2 "cells": [ |
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4 "cell_type": "code", |
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5 "execution_count": 1, |
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6 "metadata": {}, |
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7 "outputs": [], |
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8 "source": [ |
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9 "import json\n", |
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10 "import os\n", |
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11 "import sys\n", |
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12 "import time\n", |
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13 "import signal\n", |
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14 "import datetime\n", |
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15 "import logging\n", |
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16 "import copy\n", |
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17 "import requests" |
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18 ] |
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19 }, |
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20 { |
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21 "cell_type": "code", |
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22 "execution_count": 15, |
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23 "metadata": {}, |
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24 "outputs": [], |
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25 "source": [ |
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26 "smarts = \"O=C([O-])CCC(=O)C(=O)[O-].NC(CC(=O)[O-])C(=O)O>>O=C([O-])CC(=O)C(=O)[O-].NC(CCC(=O)[O-])C(=O)O\"\n", |
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27 "targets = 2\n", |
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28 "noMSA = False" |
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29 ] |
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30 }, |
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31 { |
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32 "cell_type": "markdown", |
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33 "metadata": {}, |
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34 "source": [ |
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35 "Request with smarts string" |
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36 ] |
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37 }, |
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38 { |
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39 "cell_type": "code", |
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40 "execution_count": 16, |
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41 "metadata": {}, |
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42 "outputs": [], |
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43 "source": [ |
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44 "all_request_data = {'smarts': smarts, \"targets\": targets, \"noMSA\": noMSA}\n" |
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45 ] |
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46 }, |
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47 { |
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48 "cell_type": "code", |
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49 "execution_count": 18, |
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50 "metadata": {}, |
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51 "outputs": [], |
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52 "source": [ |
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53 "url = 'http://selenzyme.synbiochem.co.uk/REST'\n", |
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54 "url = 'http://localhost:5000/REST'\n", |
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55 "r = requests.post( os.path.join(url, 'Query') , json=all_request_data )\n", |
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56 "res = json.loads( r.content.decode('utf-8') )\n", |
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57 "assert res['data'] is not None\n", |
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58 "val = json.loads( res['data'] )\n", |
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59 "assert 'Seq. ID' in val and len(val['Seq. ID'])>0" |
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60 ] |
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61 }, |
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62 { |
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63 "cell_type": "code", |
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64 "execution_count": 19, |
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65 "metadata": {}, |
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66 "outputs": [ |
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67 { |
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68 "data": { |
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69 "text/plain": [ |
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70 "{'app': 'Selenzy',\n", |
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71 " 'author': 'Synbiochem',\n", |
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72 " 'data': '{\"Score\":{\"1\":163.7,\"2\":155.9},\"Seq. ID\":{\"1\":\"Q68XV9\",\"2\":\"P85951\"},\"Description\":{\"1\":\"Aspartate aminotransferase\",\"2\":\"Aspartate aminotransferase 2 (Fragments)\"},\"Organism Source\":{\"1\":\"Rickettsia typhi (strain ATCC VR-144 \\\\/ Wilmington) \",\"2\":\"Pseudotsuga menziesii PE=1 SV=1\"},\"Tax. distance\":{\"1\":15,\"2\":23},\"Rxn. ID\":{\"1\":\"MNXR32641\",\"2\":\"MNXR32641\"},\"EC Number\":{\"1\":\"2.6.1.1\",\"2\":\"2.6.1.1\"},\"Uniprot protein evidence\":{\"1\":3,\"2\":1},\"Consv. Score\":{\"1\":79.0,\"2\":79.0},\"Rxn Sim.\":{\"1\":1.0,\"2\":1.0},\"Direction Used\":{\"1\":1,\"2\":1},\"Direction Preferred\":{\"1\":0,\"2\":0},\"% helices\":{\"1\":42.6,\"2\":27.8},\"% sheets\":{\"1\":24.8,\"2\":72.2},\"% turns\":{\"1\":19.6,\"2\":5.6},\"% coils\":{\"1\":17.2,\"2\":83.3},\"Mol. Weight\":{\"1\":44337.23,\"2\":3587.11},\"Isoelec. Point\":{\"1\":8.3119,\"2\":10.4338},\"Polar %\":{\"1\":45.113,\"2\":41.176},\"Query\":{\"1\":\"O=C([O-])CCC(=O)C(=O)[O-].NC(CC(=O)[O-])C(=O)O>>O=C([O-])CC(=O)C(=O)[O-].NC(CCC(=O)[O-])C(=O)O\",\"2\":\"O=C([O-])CCC(=O)C(=O)[O-].NC(CC(=O)[O-])C(=O)O>>O=C([O-])CC(=O)C(=O)[O-].NC(CCC(=O)[O-])C(=O)O\"},\"Hit\":{\"1\":\"O=C([O-])CC(=O)C(=O)[O-].NC(CCC(=O)[O-])C(=O)O>>O=C([O-])CCC(=O)C(=O)[O-].NC(CC(=O)[O-])C(=O)O\",\"2\":\"O=C([O-])CC(=O)C(=O)[O-].NC(CCC(=O)[O-])C(=O)O>>O=C([O-])CCC(=O)C(=O)[O-].NC(CC(=O)[O-])C(=O)O\"}}',\n", |
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73 " 'version': '1.0'}" |
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74 ] |
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75 }, |
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76 "execution_count": 19, |
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77 "metadata": {}, |
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78 "output_type": "execute_result" |
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79 } |
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80 ], |
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81 "source": [ |
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82 "res" |
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83 ] |
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84 }, |
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85 { |
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86 "cell_type": "code", |
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87 "execution_count": 5, |
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88 "metadata": {}, |
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89 "outputs": [ |
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90 { |
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91 "name": "stdout", |
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92 "output_type": "stream", |
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93 "text": [ |
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94 "{'Score': {'1': 136.7, '2': 125.9}, 'Seq. ID': {'1': 'P39643', '2': 'E9L7A5'}, 'Description': {'1': 'Probable aspartate aminotransferase', '2': 'Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase'}, 'Organism Source': {'1': 'Bacillus subtilis (strain 168) ', '2': 'Petunia hybrida PE=1 SV=1'}, 'Tax. distance': {'1': 18, '2': 29}, 'Rxn. ID': {'1': 'MNXR32641', '2': 'MNXR32641'}, 'EC Number': {'1': '2.6.1.1', '2': '2.6.1.1'}, 'Uniprot protein evidence': {'1': 3, '2': 1}, 'Consv. Score': {'1': 55.0, '2': 55.0}, 'Rxn Sim.': {'1': 1.0, '2': 1.0}, 'Direction Used': {'1': 1, '2': 1}, 'Direction Preferred': {'1': 0, '2': 0}, '% helices': {'1': 51.4, '2': 31.3}, '% sheets': {'1': 16.2, '2': 29.4}, '% turns': {'1': 13.8, '2': 18.6}, '% coils': {'1': 22.7, '2': 24.2}, 'Mol. Weight': {'1': 44702.91, '2': 51743.31}, 'Isoelec. Point': {'1': 5.4491, '2': 8.6228}, 'Polar %': {'1': 42.105, '2': 43.841}, 'Query': {'1': 'O=C([O-])CCC(=O)C(=O)[O-].NC(CC(=O)[O-])C(=O)O>>O=C([O-])CC(=O)C(=O)[O-].NC(CCC(=O)[O-])C(=O)O', '2': 'O=C([O-])CCC(=O)C(=O)[O-].NC(CC(=O)[O-])C(=O)O>>O=C([O-])CC(=O)C(=O)[O-].NC(CCC(=O)[O-])C(=O)O'}, 'Hit': {'1': 'O=C([O-])CC(=O)C(=O)[O-].NC(CCC(=O)[O-])C(=O)O>>O=C([O-])CCC(=O)C(=O)[O-].NC(CC(=O)[O-])C(=O)O', '2': 'O=C([O-])CC(=O)C(=O)[O-].NC(CCC(=O)[O-])C(=O)O>>O=C([O-])CCC(=O)C(=O)[O-].NC(CC(=O)[O-])C(=O)O'}}\n" |
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95 ] |
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96 } |
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97 ], |
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98 "source": [ |
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99 "print(val)" |
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100 ] |
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101 }, |
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102 { |
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103 "cell_type": "markdown", |
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104 "metadata": {}, |
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105 "source": [ |
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106 "Request with reaction DB and reaction ID following indications on http://selenzyme.synbiochem.co.uk/" |
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107 ] |
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108 }, |
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109 { |
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110 "cell_type": "code", |
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111 "execution_count": 6, |
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112 "metadata": {}, |
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113 "outputs": [], |
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114 "source": [ |
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115 "all_request_data = {\"db\": \"mnx\", \"rxnid\": \"MNXR141534\", \"targets\": targets, \"noMSA\": noMSA}" |
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116 ] |
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117 }, |
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118 { |
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119 "cell_type": "code", |
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120 "execution_count": 7, |
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121 "metadata": { |
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122 "scrolled": true |
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123 }, |
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124 "outputs": [ |
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125 { |
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126 "ename": "AssertionError", |
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127 "evalue": "", |
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128 "output_type": "error", |
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129 "traceback": [ |
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130 "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", |
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131 "\u001b[0;31mAssertionError\u001b[0m Traceback (most recent call last)", |
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132 "\u001b[0;32m<ipython-input-7-b6f4ae0ef527>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0mr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrequests\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpost\u001b[0m\u001b[0;34m(\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mjoin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0murl\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'Query'\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m,\u001b[0m \u001b[0mjson\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mall_request_data\u001b[0m \u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 3\u001b[0m \u001b[0mres\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mjson\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mloads\u001b[0m\u001b[0;34m(\u001b[0m \u001b[0mr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcontent\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdecode\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'utf-8'\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 4\u001b[0;31m \u001b[0;32massert\u001b[0m \u001b[0mres\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'data'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 5\u001b[0m \u001b[0mval\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mjson\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mloads\u001b[0m\u001b[0;34m(\u001b[0m \u001b[0mres\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'data'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 6\u001b[0m \u001b[0;32massert\u001b[0m \u001b[0;34m'Seq. ID'\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mval\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mval\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'Seq. ID'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m>\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", |
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133 "\u001b[0;31mAssertionError\u001b[0m: " |
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134 ] |
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135 } |
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136 ], |
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137 "source": [ |
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138 "url = 'http://selenzyme.synbiochem.co.uk/REST'\n", |
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139 "r = requests.post( os.path.join(url, 'Query') , json=all_request_data )\n", |
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140 "res = json.loads( r.content.decode('utf-8') )\n", |
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141 "assert res['data'] is not None\n", |
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142 "val = json.loads( res['data'] )\n", |
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143 "assert 'Seq. ID' in val and len(val['Seq. ID'])>0" |
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144 ] |
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145 }, |
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146 { |
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147 "cell_type": "markdown", |
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148 "metadata": {}, |
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149 "source": [ |
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150 "Same reaction with its sabiork id" |
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151 ] |
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152 }, |
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153 { |
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154 "cell_type": "code", |
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155 "execution_count": 8, |
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156 "metadata": {}, |
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157 "outputs": [], |
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158 "source": [ |
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159 "all_request_data = {\"db\": \"sabiork\", \"rxnid\": \"12346\", \"targets\": targets, \"noMSA\": noMSA}" |
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160 ] |
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161 }, |
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162 { |
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163 "cell_type": "code", |
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164 "execution_count": 9, |
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165 "metadata": {}, |
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166 "outputs": [ |
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167 { |
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168 "ename": "AssertionError", |
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169 "evalue": "", |
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170 "output_type": "error", |
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171 "traceback": [ |
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172 "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", |
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173 "\u001b[0;31mAssertionError\u001b[0m Traceback (most recent call last)", |
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174 "\u001b[0;32m<ipython-input-9-b6f4ae0ef527>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0mr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrequests\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpost\u001b[0m\u001b[0;34m(\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mjoin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0murl\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'Query'\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m,\u001b[0m \u001b[0mjson\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mall_request_data\u001b[0m \u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 3\u001b[0m \u001b[0mres\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mjson\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mloads\u001b[0m\u001b[0;34m(\u001b[0m \u001b[0mr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcontent\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdecode\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'utf-8'\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 4\u001b[0;31m \u001b[0;32massert\u001b[0m \u001b[0mres\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'data'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 5\u001b[0m \u001b[0mval\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mjson\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mloads\u001b[0m\u001b[0;34m(\u001b[0m \u001b[0mres\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'data'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 6\u001b[0m \u001b[0;32massert\u001b[0m \u001b[0;34m'Seq. ID'\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mval\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mval\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'Seq. ID'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m>\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", |
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175 "\u001b[0;31mAssertionError\u001b[0m: " |
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176 ] |
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177 } |
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178 ], |
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179 "source": [ |
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180 "url = 'http://selenzyme.synbiochem.co.uk/REST'\n", |
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181 "r = requests.post( os.path.join(url, 'Query') , json=all_request_data )\n", |
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182 "res = json.loads( r.content.decode('utf-8') )\n", |
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183 "assert res['data'] is not None\n", |
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184 "val = json.loads( res['data'] )\n", |
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185 "assert 'Seq. ID' in val and len(val['Seq. ID'])>0" |
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186 ] |
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187 }, |
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188 { |
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189 "cell_type": "markdown", |
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190 "metadata": {}, |
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191 "source": [ |
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192 "same reaction with its EC number" |
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193 ] |
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194 }, |
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195 { |
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196 "cell_type": "code", |
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197 "execution_count": 73, |
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198 "metadata": {}, |
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199 "outputs": [], |
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200 "source": [ |
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201 "all_request_data = {\"db\": \"ec\", \"rxnid\": \"3.2.1.2\", \"targets\": targets, \"noMSA\": noMSA}" |
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202 ] |
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203 }, |
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204 { |
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205 "cell_type": "code", |
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206 "execution_count": 74, |
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207 "metadata": { |
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208 "scrolled": true |
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209 }, |
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210 "outputs": [], |
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211 "source": [ |
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212 "url = 'http://selenzyme.synbiochem.co.uk/REST'\n", |
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213 "r = requests.post( os.path.join(url, 'Query') , json=all_request_data )\n", |
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214 "res = json.loads( r.content.decode('utf-8') )\n", |
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215 "assert res['data'] is not None\n", |
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216 "val = json.loads( res['data'] )\n", |
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217 "assert 'Seq. ID' in val and len(val['Seq. ID'])>0" |
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218 ] |
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219 }, |
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220 { |
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221 "cell_type": "code", |
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222 "execution_count": 75, |
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223 "metadata": {}, |
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224 "outputs": [ |
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225 { |
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226 "data": { |
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227 "text/plain": [ |
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228 "{'app': 'Selenzy',\n", |
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229 " 'author': 'Synbiochem',\n", |
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230 " 'data': '{\"Score\":{\"1\":134.6,\"2\":121.9},\"Seq. ID\":{\"1\":\"Q9HHC8\",\"2\":\"O23553\"},\"Description\":{\"1\":\"Cyclomaltodextrinase\",\"2\":\"Beta-amylase 3; chloroplastic\"},\"Organism Source\":{\"1\":\"Thermococcus sp. B1001 \",\"2\":\"Arabidopsis thaliana \"},\"Tax. distance\":{\"1\":16,\"2\":29},\"Rxn. ID\":{\"1\":\"MNXR87651\",\"2\":\"MNXR87683\"},\"EC Number\":{\"1\":\"3.2.1\",\"2\":\"3.2.1.2\"},\"Uniprot protein evidence\":{\"1\":4,\"2\":1},\"Consv. Score\":{\"1\":51.0,\"2\":51.0},\"Rxn Sim.\":{\"1\":1.0,\"2\":1.0},\"Direction Used\":{\"1\":-1,\"2\":-1},\"Direction Preferred\":{\"1\":-1,\"2\":-1},\"% helices\":{\"1\":45.7,\"2\":33.8},\"% sheets\":{\"1\":20.7,\"2\":17.9},\"% turns\":{\"1\":18.5,\"2\":24.6},\"% coils\":{\"1\":17.7,\"2\":26.7},\"Mol. Weight\":{\"1\":78842.79,\"2\":61353.16},\"Isoelec. Point\":{\"1\":9.1162,\"2\":7.0599},\"Polar %\":{\"1\":45.455,\"2\":47.993},\"Query\":{\"1\":\"O.[*]OC1C(CO)OC(OC2C(CO)OC(O)C(O)C2O)C(O)C1O>>OCC1OC(OC2C(CO)OC(O)C(O)C2O)C(O)C(O)C1O\",\"2\":\"O.[*]OC1C(CO)OC(OC2C(CO)OC(O)C(O)C2O)C(O)C1O>>OCC1OC(OC2C(CO)OC(O)C(O)C2O)C(O)C(O)C1O\"},\"Hit\":{\"1\":\"O.[*]OC1C(CO)OC(OC2C(CO)OC(OC3C(CO)OC(O)C(O)C3O)C(O)C2O)C(O)C1O>>OCC1OC(OC2C(CO)OC(O)C(O)C2O)C(O)C(O)C1O.OCC1OC(O)C(O)C(O)C1O\",\"2\":\"O.[*]OC1C(CO)OC(OC2C(CO)OC(O)C(O)C2O)C(O)C1O>>OCC1OC(OC2C(CO)OC(O)C(O)C2O)C(O)C(O)C1O.[*]OC1C(CO)OC(OC2C(CO)OC(O)C(O)C2O)C(O)C1O\"}}',\n", |
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231 " 'version': '1.0'}" |
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232 ] |
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233 }, |
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234 "execution_count": 75, |
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235 "metadata": {}, |
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236 "output_type": "execute_result" |
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237 } |
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238 ], |
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239 "source": [ |
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240 "res" |
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241 ] |
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242 }, |
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243 { |
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244 "cell_type": "code", |
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245 "execution_count": null, |
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246 "metadata": {}, |
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247 "outputs": [], |
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248 "source": [] |
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249 }, |
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250 { |
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251 "cell_type": "code", |
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252 "execution_count": null, |
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253 "metadata": {}, |
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254 "outputs": [], |
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255 "source": [] |
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256 } |
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257 ], |
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258 "metadata": { |
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259 "anaconda-cloud": {}, |
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260 "kernelspec": { |
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261 "display_name": "Python 3", |
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262 "language": "python", |
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263 "name": "python3" |
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264 }, |
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265 "language_info": { |
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266 "codemirror_mode": { |
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267 "name": "ipython", |
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268 "version": 3 |
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269 }, |
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270 "file_extension": ".py", |
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271 "mimetype": "text/x-python", |
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272 "name": "python", |
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273 "nbconvert_exporter": "python", |
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274 "pygments_lexer": "ipython3", |
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275 "version": "3.6.6" |
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276 } |
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277 }, |
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278 "nbformat": 4, |
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279 "nbformat_minor": 2 |
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280 } |